pyxetabase 3.1.1.dev1__py3-none-any.whl → 3.1.2__py3-none-any.whl

pyopencga/rest_clients/job_client.py

@@ -1,415 +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 Job(_ParentRestClient):
-    """
-    This class contains methods for the 'Jobs' webservices
-    PATH: /{apiVersion}/jobs
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Job, 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}/jobs/acl/{members}/update
-
-        :param dict data: JSON containing the parameters to add ACLs.
-            (REQUIRED)
-        :param str action: Action to be performed [ADD, SET, REMOVE or RESET].
-            Allowed values: ['SET ADD REMOVE RESET'] (REQUIRED)
-        :param str members: Comma separated list of user or group ids.
-            (REQUIRED)
-        """
-
-        options['action'] = action
-        return self._post(category='jobs', resource='update', subcategory='acl', second_query_id=members, data=data, **options)
-
-    def aggregation_stats(self, **options):
-        """
-        Fetch catalog job stats.
-        PATH: /{apiVersion}/jobs/aggregationStats
-
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param bool other_studies: Flag indicating the entries being queried
-            can belong to any related study, not just the primary one.
-        :param str id: Comma separated list of job 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 uuid: Comma separated list of job UUIDs up to a maximum of
-            100.
-        :param str tool_id: Tool ID executed by the job. 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 tool_type: Tool type executed by the job [OPERATION,
-            ANALYSIS].
-        :param str user_id: User that created the job.
-        :param str priority: Priority of the job.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param bool visited: Visited status of job.
-        :param str tags: Job tags.
-        :param str input: Comma separated list of file IDs used as input.
-        :param str output: Comma separated list of file IDs used as output.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        :param str field: Field to apply aggregation statistics to (or a list
-            of fields separated by semicolons), e.g.:
-            studies;type;numSamples[0..10]:1;format:sum(size).
-        """
-
-        return self._get(category='jobs', resource='aggregationStats', **options)
-
-    def create(self, data=None, **options):
-        """
-        Register an executed job with POST method.
-        PATH: /{apiVersion}/jobs/create
-
-        :param dict data: job. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._post(category='jobs', resource='create', data=data, **options)
-
-    def distinct(self, field, **options):
-        """
-        Job distinct method.
-        PATH: /{apiVersion}/jobs/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 bool other_studies: Flag indicating the entries being queried
-            can belong to any related study, not just the primary one.
-        :param str id: Comma separated list of job 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 uuid: Comma separated list of job UUIDs up to a maximum of
-            100.
-        :param str type: Job type (NATIVE, WORKFLOW, CUSTOM or WALKER).
-        :param str tool_id: Tool ID executed by the job. 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 tool_type: Tool type executed by the job [OPERATION,
-            ANALYSIS].
-        :param str tool.external_executor.id: Id of the external executor.
-            This field is only applicable for jobs executed by an external
-            executor.
-        :param str parent_id: Job id that generated this job (if any).
-        :param bool 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.
-        :param bool internal.kill_job_requested: Flag indicating that the user
-            requested to kill the job.
-        :param str user_id: User that created the job.
-        :param str priority: Priority of the job.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param bool visited: Visited status of job.
-        :param str tags: Job tags.
-        :param str input: Comma separated list of file IDs used as input.
-        :param str output: Comma separated list of file IDs used as output.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        options['field'] = field
-        return self._get(category='jobs', resource='distinct', **options)
-
-    def retry(self, data=None, **options):
-        """
-        Relaunch a failed job.
-        PATH: /{apiVersion}/jobs/retry
-
-        :param dict data: job. (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 study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._post(category='jobs', resource='retry', data=data, **options)
-
-    def search(self, **options):
-        """
-        Job search method.
-        PATH: /{apiVersion}/jobs/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 bool other_studies: Flag indicating the entries being queried
-            can belong to any related study, not just the primary one.
-        :param str id: Comma separated list of job 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 uuid: Comma separated list of job UUIDs up to a maximum of
-            100.
-        :param str type: Job type (NATIVE, WORKFLOW, CUSTOM or WALKER).
-        :param str tool_id: Tool ID executed by the job. 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 tool_type: Tool type executed by the job [OPERATION,
-            ANALYSIS].
-        :param str tool.external_executor.id: Id of the external executor.
-            This field is only applicable for jobs executed by an external
-            executor.
-        :param str parent_id: Job id that generated this job (if any).
-        :param bool 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.
-        :param bool internal.kill_job_requested: Flag indicating that the user
-            requested to kill the job.
-        :param str user_id: User that created the job.
-        :param str priority: Priority of the job.
-        :param str status: Filter by status.
-        :param str internal_status: Filter by internal status.
-        :param str creation_date: Creation date. Format: yyyyMMddHHmmss.
-            Examples: >2018, 2017-2018, <201805.
-        :param str modification_date: Modification date. Format:
-            yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
-        :param bool visited: Visited status of job.
-        :param str tags: Job tags.
-        :param str input: Comma separated list of file IDs used as input.
-        :param str output: Comma separated list of file IDs used as output.
-        :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 bool deleted: Boolean to retrieve deleted entries.
-        """
-
-        return self._get(category='jobs', resource='search', **options)
-
-    def build_tool(self, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/jobs/tool/build
-
-        :param dict data: body. (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='jobs', resource='build', subcategory='tool', data=data, **options)
-
-    def run_tool(self, data=None, **options):
-        """
-        Execute an analysis from a custom binary.
-        PATH: /{apiVersion}/jobs/tool/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='jobs', resource='run', subcategory='tool', data=data, **options)
-
-    def top(self, **options):
-        """
-        Provide a summary of the running jobs.
-        PATH: /{apiVersion}/jobs/top
-
-        :param int limit: Maximum number of jobs to be returned.
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param str internal_status: Filter by internal status.
-        :param str priority: Priority of the job.
-        :param str user_id: User that created the job.
-        :param str tool_id: Tool ID executed by the job. Also admits basic
-            regular expressions using the operator '~', i.e. '~{perl-regex}'
-            e.g. '~value' for case sensitive, '~/value/i' for case insensitive
-            search.
-        """
-
-        return self._get(category='jobs', resource='top', **options)
-
-    def acl(self, jobs, **options):
-        """
-        Return the acl of the job. If member is provided, it will only return
-            the acl for the member.
-        PATH: /{apiVersion}/jobs/{jobs}/acl
-
-        :param str jobs: Comma separated list of job IDs or UUIDs 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='jobs', resource='acl', query_id=jobs, **options)
-
-    def delete(self, jobs, **options):
-        """
-        Delete existing jobs.
-        PATH: /{apiVersion}/jobs/{jobs}/delete
-
-        :param str jobs: Comma separated list of job ids. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._delete(category='jobs', resource='delete', query_id=jobs, **options)
-
-    def info(self, jobs, **options):
-        """
-        Get job information.
-        PATH: /{apiVersion}/jobs/{jobs}/info
-
-        :param str jobs: Comma separated list of job 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 deleted: Boolean to retrieve deleted jobs.
-        """
-
-        return self._get(category='jobs', resource='info', query_id=jobs, **options)
-
-    def update(self, jobs, data=None, **options):
-        """
-        Update some job attributes.
-        PATH: /{apiVersion}/jobs/{jobs}/update
-
-        :param str jobs: Comma separated list of job 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='jobs', resource='update', query_id=jobs, data=data, **options)
-
-    def kill(self, job, **options):
-        """
-        Send a signal to kill a pending or running job.
-        PATH: /{apiVersion}/jobs/{job}/kill
-
-        :param str job: Job ID or UUID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        """
-
-        return self._post(category='jobs', resource='kill', query_id=job, **options)
-
-    def head_log(self, job, **options):
-        """
-        Show the first lines of a log file (up to a limit).
-        PATH: /{apiVersion}/jobs/{job}/log/head
-
-        :param str job: Job ID or UUID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param int offset: Starting byte from which the file will be read.
-        :param int lines: Maximum number of lines to be returned up to a
-            maximum of 1000.
-        :param str type: Log file to be shown (stdout or stderr).
-        """
-
-        return self._get(category='jobs', resource='head', query_id=job, subcategory='log', **options)
-
-    def tail_log(self, job, **options):
-        """
-        Show the last lines of a log file (up to a limit).
-        PATH: /{apiVersion}/jobs/{job}/log/tail
-
-        :param str job: Job ID or UUID. (REQUIRED)
-        :param str study: Study [[organization@]project:]study where study and
-            project can be either the ID or UUID.
-        :param int lines: Maximum number of lines to be returned up to a
-            maximum of 1000.
-        :param str type: Log file to be shown (stdout or stderr).
-        """
-
-        return self._get(category='jobs', resource='tail', query_id=job, subcategory='log', **options)
-

pyopencga/rest_clients/meta_client.py

@@ -1,85 +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 Meta(_ParentRestClient):
-    """
-    This class contains methods for the 'Meta' webservices
-    PATH: /{apiVersion}/meta
-    """
-
-    def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs):
-        super(Meta, self).__init__(configuration, token, login_handler, *args, **kwargs)
-
-    def about(self, **options):
-        """
-        Returns info about current OpenCGA code.
-        PATH: /{apiVersion}/meta/about
-        """
-
-        return self._get(category='meta', resource='about', **options)
-
-    def api(self, **options):
-        """
-        API.
-        PATH: /{apiVersion}/meta/api
-
-        :param str category: List of categories to get API from.
-        """
-
-        return self._get(category='meta', resource='api', **options)
-
-    def fail(self, **options):
-        """
-        Ping Opencga webservices.
-        PATH: /{apiVersion}/meta/fail
-        """
-
-        return self._get(category='meta', resource='fail', **options)
-
-    def model(self, **options):
-        """
-        Opencga model webservices.
-        PATH: /{apiVersion}/meta/model
-
-        :param str model: Model description.
-        """
-
-        return self._get(category='meta', resource='model', **options)
-
-    def openapi(self, url, **options):
-        """
-        Opencga openapi json.
-        PATH: /{apiVersion}/meta/openapi
-
-        :param str url: Opencga host with environment. (REQUIRED)
-        :param str study: Opencga study to be default in queries.
-        """
-
-        options['url'] = url
-        return self._get(category='meta', resource='openapi', **options)
-
-    def ping(self, **options):
-        """
-        Ping Opencga webservices.
-        PATH: /{apiVersion}/meta/ping
-        """
-
-        return self._get(category='meta', resource='ping', **options)
-
-    def status(self, **options):
-        """
-        Database status.
-        PATH: /{apiVersion}/meta/status
-        """
-
-        return self._get(category='meta', resource='status', **options)
-