pyxetabase 4.0.0.dev0__py3-none-any.whl → 4.0.0.dev2__py3-none-any.whl

pyopencga/rest_clients/workflow_client.py

@@ -1,263 +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 Workflow(_ParentRestClient):
-    """
-    This class contains methods for the 'Workflows' webservices
-    PATH: /{apiVersion}/workflows
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Workflow, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def update_acl(self, members, action, data=None, **options):
-        """
-        Update the set of workflow permissions granted for the member.
-        PATH: /{apiVersion}/workflows/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='workflows', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def create(self, data=None, **options):
-        """
-        Create a workflow.
-        PATH: /{apiVersion}/workflows/create
-
-        :param dict data: JSON containing workflow 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        """
-
-        return self._post(category='workflows', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Workflow distinct method.
-        PATH: /{apiVersion}/workflows/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 workflow 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 of workflow 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 of workflow UUIDs up to a
-            maximum of 100.
-        :param str tags: Comma separated list of tags.
-        :param bool draft: Boolean field indicating whether the workflow is a
-            draft or not.
-        :param str internal.registration_user_id: UserId that created the
-            workflow.
-        :param str manager.id: Id of the workflow system (Allowed values:
-            NEXTFLOW).
-        :param str type: Workflow type. Allowed types:
-            [CLINICAL_INTERPRETATION, SECONDARY_ANALYSIS, RESEARCH or OTHER].
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        options['field'] = field
-        return self._get(category='workflows', resource='distinct', **options)
-
-    def import_workflow(self, data=None, **options):
-        """
-        Import a workflow.
-        PATH: /{apiVersion}/workflows/import
-
-        :param dict data: Repository parameters. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._post(category='workflows', resource='import', data=data, **options)
-
-    def run(self, data=None, **options):
-        """
-        Execute a workflow analysis.
-        PATH: /{apiVersion}/workflows/run
-
-        :param dict data: NextFlow run parameters. (REQUIRED)
-        :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_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='workflows', resource='run', data=data, **options)
-
-    def search(self, **options):
-        """
-        Workflow search method.
-        PATH: /{apiVersion}/workflows/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 workflow 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 of workflow 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 of workflow UUIDs up to a
-            maximum of 100.
-        :param str tags: Comma separated list of tags.
-        :param bool draft: Boolean field indicating whether the workflow is a
-            draft or not.
-        :param str internal.registration_user_id: UserId that created the
-            workflow.
-        :param str manager.id: Id of the workflow system (Allowed values:
-            NEXTFLOW).
-        :param str type: Workflow type. Allowed types:
-            [CLINICAL_INTERPRETATION, SECONDARY_ANALYSIS, RESEARCH or OTHER].
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='workflows', resource='search', **options)
-
-    def update(self, workflow_id, data=None, **options):
-        """
-        Update some workflow attributes.
-        PATH: /{apiVersion}/workflows/{workflowId}/update
-
-        :param str workflow_id: Comma separated list workflow IDs or UUIDs 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 bool include_result: Flag indicating to include the created or
-            updated document result in the response.
-        :param dict data: body.
-        """
-
-        return self._post(category='workflows', resource='update', query_id=workflow_id, data=data, **options)
-
-    def acl(self, workflows, **options):
-        """
-        Returns the acl of the workflows. If member is provided, it will only
-            return the acl for the member.
-        PATH: /{apiVersion}/workflows/{workflows}/acl
-
-        :param str workflows: Comma separated list workflow IDs or UUIDs 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='workflows', resource='acl', query_id=workflows, **options)
-
-    def delete(self, workflows, **options):
-        """
-        Delete workflows.
-        PATH: /{apiVersion}/workflows/{workflows}/delete
-
-        :param str workflows: Comma separated list workflow IDs or UUIDs 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.
-        """
-
-        return self._delete(category='workflows', resource='delete', query_id=workflows, **options)
-
-    def info(self, workflows, **options):
-        """
-        Get workflow information.
-        PATH: /{apiVersion}/workflows/{workflows}/info
-
-        :param str workflows: Comma separated list sample IDs or UUIDs 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 workflow versions. 'all'
-            to get all the workflow versions. Not supported if multiple
-            workflow ids are provided.
-        :param bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='workflows', resource='info', query_id=workflows, **options)
-

pyopencga/rest_response.py

@@ -1,220 +0,0 @@
-import sys
-import pandas as pd
-
-from pyopencga.commons import deprecated
-
-
-class RestResponse:
-    def __init__(self, response):
-        self.apiVersion = response.get('apiVersion')
-        self.time = response.get('time')
-        self.events = response.get('events')
-        self.params = response.get('params')
-        self.responses = response.get('responses')
-
-        # TODO: Remove deprecated response in future release. Added for backwards compatibility
-        self.response = response.get('responses')
-
-        # TODO: Remove deprecated result. Added for backwards compatibility
-        for query_result in self.responses:
-            if 'results' in query_result:
-                query_result['result'] = query_result['results']
-
-    @deprecated
-    def first(self):
-        return self.responses[0]
-
-    def get_results(self, response_pos=0):
-        """
-        Return the list of results of the response_pos response.
-        """
-        return self.responses[response_pos]['results']
-
-    def get_result(self, result_pos, response_pos=0):
-        """
-        Return the result 'result_pos' of the response 'response_pos'.
-        """
-        return self.responses[response_pos]['results'][result_pos]
-
-    def get_responses(self):
-        """
-        Return the list of responses
-        """
-        return self.responses
-
-    def get_response(self, response_pos=0):
-        """
-        Return the response_pos response.
-        """
-        return self.responses[response_pos]
-
-    def result_iterator(self, response_pos=None):
-        """
-        Return all results from all responses as an iterator
-        """
-        if response_pos is None:
-            for response in self.responses:
-                for result in response['results']:
-                    yield result
-        else:
-            for result in self.responses[response_pos]['results']:
-                yield result
-
-    @staticmethod
-    def _get_param_value(result, field):
-        items = field.split('.')
-        result2 = result
-        is_list = False
-        for item in items:
-            if item in result2:
-                if isinstance(result2[item], list):
-                    if is_list:
-                        return '.'
-                    is_list = True
-                result2 = result2[item]
-            else:
-                if is_list:
-                    if len(result2) == 0 or isinstance(result2[0][item], list):
-                        return '.'
-                    result2 = [r[item] for r in result2 if item in r]
-                else:
-                    return '.'
-        if is_list:
-            if len(result2) == 0 or isinstance(result2[0], (list, dict)):
-                return '{} items'.format(len(result2))
-            return ','.join(map(str, set(result2)))
-        else:
-            return result2
-
-    def print_results(self, fields=None, response_pos=None, limit=None, separator='\t', title=None,
-                      metadata=True, outfile=None):
-        outfhand = sys.stdout if outfile is None else open(outfile, 'w')
-        if title is not None:
-            outfhand.write(title + '\n' + '-'*(len(title)+5) + '\n')
-        if metadata:
-            for event_type in ['INFO', 'WARNING', 'ERROR']:
-                for event in self.get_response_events(event_type):
-                    msg = '#{}: {}'.format(event['type'], event['description'])
-                    if 'id' in event:
-                        msg += ' ({})'.format(event['id'])
-                    outfhand.write(msg + '\n')
-            outfhand.write('#Time: {}\n'.format(self.time))
-            outfhand.write('#Num matches: {}\n'.format(self.get_num_matches(response_pos)))
-            outfhand.write('#Num results: {}\n'.format(self.get_num_results(response_pos)))
-            outfhand.write('#Num inserted: {}\n'.format(self.get_num_inserted(response_pos)))
-            outfhand.write('#Num updated: {}\n'.format(self.get_num_updated(response_pos)))
-            outfhand.write('#Num deleted: {}\n'.format(self.get_num_deleted(response_pos)))
-
-        responses = [self.get_response(response_pos)] if response_pos is not None else self.get_responses()
-        for response in responses:
-            if fields:
-                fields = fields.split(',')
-            elif 'include' in self.params:
-                fields = self.params['include'].split(',')
-            else:
-                if response['results']:
-                    fields = response['results'][0].keys()
-
-            limit = limit if limit is not None else len(response['results'])
-            if limit:
-                outfhand.write('#{}\n'.format(separator.join(fields)))
-            for result in response['results'][:limit]:
-                values = [self._get_param_value(result, field) for field in fields]
-                outfhand.write(separator.join(map(str, values)) + '\n')
-
-    def to_data_frame(self, response_pos=None):
-        responses = [self.get_response(response_pos)] if response_pos is not None else self.get_responses()
-        return pd.concat([pd.json_normalize(result) for response in responses
-                          for result in response['results']]).reset_index(drop=True)
-
-    def get_response_events(self, event_type=None):
-        """
-        Return response events by name
-        """
-        event_names = ['INFO', 'WARNING', 'ERROR']
-        if event_type is None or self.events is None:
-            return self.events or []
-        elif event_type in event_names:
-            return [event for event in self.events if event['type'] == event_type]
-        else:
-            msg = 'Argument "type" must be one of the following values: "{}"'
-            raise ValueError(msg.format(', '.join(event_names)))
-
-    def get_result_events(self, event_type=None, response_pos=0):
-        """Return result events by name and position"""
-        event_names = ['INFO', 'WARNING', 'ERROR']
-        response = self.responses[response_pos]
-        if event_type is None:
-            return response['events'] \
-                if 'events' in response and response['events'] else []
-        elif event_type in event_names:
-            return [event for event in response['events'] if event['type'] == event_type] \
-                if 'events' in response and response['events'] else []
-        else:
-            msg = 'Argument "type" must be one of the following values: "{}"'
-            raise ValueError(msg.format(', '.join(event_names)))
-
-    def get_num_matches(self, response_pos=None):
-        """
-        Return number of matches
-        """
-        if response_pos is not None:
-            return self.responses[response_pos]['numMatches']
-        else:
-            num_matches = 0
-            for query_result in self.responses:
-                if 'numMatches' in query_result:
-                    num_matches += query_result['numMatches']
-            return num_matches
-
-    def get_num_results(self, response_pos=None):
-        """
-        Return number of results
-        """
-        if response_pos is not None:
-            return self.responses[response_pos]['numResults']
-        else:
-            num_results = 0
-            for query_result in self.responses:
-                if 'numResults' in query_result:
-                    num_results += query_result['numResults']
-            return num_results
-
-    def get_num_inserted(self, response_pos=None):
-        """
-        Return number of inserted
-        """
-        if response_pos is not None:
-            return self.responses[response_pos]['numInserted']
-        else:
-            num_inserted = 0
-            for query_result in self.responses:
-                if 'numInserted' in query_result:
-                    num_inserted += query_result['numInserted']
-            return num_inserted
-
-    def get_num_updated(self, response_pos=None):
-        """
-        Return number of updated
-        """
-        if response_pos is not None:
-            return self.responses[response_pos]['numUpdated']
-        else:
-            num_updated = 0
-            for query_result in self.responses:
-                if 'numUpdated' in query_result:
-                    num_updated += query_result['numUpdated']
-            return num_updated
-
-    def get_num_deleted(self, response_pos=None):
-        """
-        Return number of deleted
-        """
-        if response_pos is not None:
-            return self.responses[response_pos]['numDeleted']
-        else:
-            num_deleted = 0
-            for query_result in self.responses:
-                if 'numDeleted' in query_result:
-                    num_deleted += query_result['numDeleted']
-            return num_deleted

pyopencga/retry.py

@@ -1,57 +0,0 @@
-"""
-This module defines a function to retry execution of a function.
-"""
-import sys
-import time
-
-from pyopencga.exceptions import OpencgaAuthorisationError, OpencgaInvalidToken
-
-
-def retry(func, max_attempts, initial_retry_seconds, max_retry_seconds,
-          login_handler=None, on_retry=None, dont_retry=None):
-    """
-    Attempt a function and retry until success or until running out of
-    allowed attempts.
-    :param func: function to invoke - parameterless
-    :param max_attempts: int: maximum number of attempts allowed
-    :param initial_retry_seconds: initial number of seconds to wait between retries.
-        The wait time is doubled after each failure, until max_retry_seconds is
-        reached.
-    :param max_retry_seconds: int: see initial_retry_seconds
-    :param login_handler: optional; if provided, then if calling func()
-        results in an error because the sessionId is invalid, login_handler()
-        will be called and this failed attempt will not count towards the maximum
-        of attempts
-    :param on_retry: a callback to be called before retrying. Must accept 3 parameters:
-        exception value, exception type, traceback.
-    :param dont_retry: optional; List of strings, if any are present in the exception
-        message don't retry
-    :return: the result of func() if successful, otherwise the last exception raised
-    by calling func.
-    """
-    attempt_number = 1
-    retry_seconds = initial_retry_seconds
-    while True:
-        try:
-            return func()
-        except OpencgaInvalidToken as e:
-
-            if login_handler:
-                login_handler()
-            else:
-                raise e
-        except OpencgaAuthorisationError as e:
-            raise e
-        except Exception as e:
-            if dont_retry and any(string_ in str(e) for string_ in dont_retry):
-                raise e
-            if attempt_number >= max_attempts:  # last attempt failed, propagate error:
-                raise
-            if on_retry:
-                # notify that we are retrying
-                exc_type, exc_val, exc_tb = sys.exc_info()
-                on_retry(exc_type, exc_val, exc_tb)
-
-            time.sleep(retry_seconds)
-            attempt_number += 1
-            retry_seconds = min(retry_seconds * 2, max_retry_seconds)

pyxetabase-4.0.0.dev0.dist-info/RECORD

@@ -1,63 +0,0 @@
-pyopencga/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyopencga/commons.py,sha256=asnM3N7Q6JdgD6hXWmlX875HJizTLAODqs0dl3UYH-E,14307
-pyopencga/exceptions.py,sha256=GmtDcurD3d_fzaa8AEntF4-sZR4Elgg4Iz3z-UUqjYU,274
-pyopencga/opencga_client.py,sha256=gM9UzbjXwHKYRbsz3qmhS8xHuIlr13sn-VEzx6cscxk,14858
-pyopencga/opencga_config.py,sha256=RK23fextK79S5wq4FaQygwuPnE4p4J9GbjY6hJ0Krxc,7009
-pyopencga/rest_response.py,sha256=Gx7utYTsXV-aciFZV4f7M2eNDQg5IlphGK_T8q_PhHE,8634
-pyopencga/retry.py,sha256=_X02bDcJmr9cWH4Bt0YfUPkYborpuStmw5WDDKczwHM,2296
-pyopencga/rest_clients/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyopencga/rest_clients/_parent_rest_clients.py,sha256=6_U1y3fwOCDDlfrdzoigkgbUZke8Msu6dW87CZPwccU,4277
-pyopencga/rest_clients/admin_client.py,sha256=jn34TGFeonEvsC4bEpiw7_kTkH_R47Joo3T3grz8LTs,6926
-pyopencga/rest_clients/alignment_client.py,sha256=qVce3PTZcoYj2HIOwKtHgTp-GNDMnAG6zIWcLDnnWdM,18508
-pyopencga/rest_clients/clinical_analysis_client.py,sha256=e14y-qJznmAIMsIVpdh2ynv5pXx2yjOq7r7Mq_yVSkg,69578
-pyopencga/rest_clients/cohort_client.py,sha256=6HcNiUL3WVsLfRtcitwJuxyraECJ6RExV8GvE2oQhDM,16323
-pyopencga/rest_clients/disease_panel_client.py,sha256=dD5_nzetek5Hk2sSqT1JasdNu8ohkO3yMfdY76jGU8U,18512
-pyopencga/rest_clients/family_client.py,sha256=MC8WHfzycB7WeRqb8FZEt2YLFTNrdSnky-bHwsr-6uY,18585
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