pyxetabase 4.0.0.dev56__py3-none-any.whl

pyxetabase/rest_clients/job_client.py

@@ -0,0 +1,416 @@
+"""
+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 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: Container image to be executed and its requirements.
+            (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)
+

pyxetabase/rest_clients/meta_client.py

@@ -0,0 +1,85 @@
+"""
+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 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)
+