Source code for bioblend.galaxy.jobs

"""
Contains possible interactions with the Galaxy Jobs
"""
from bioblend.galaxy.client import Client


[docs]class JobsClient(Client): def __init__(self, galaxy_instance): self.module = 'jobs' super(JobsClient, self).__init__(galaxy_instance)
[docs] def get_jobs(self): """ Get a list of jobs for current user :type state: str or list :param state: limit listing of jobs to those that match one of the included states. If none, all are returned. Valid Galaxy job states include: 'new', 'upload', 'waiting', 'queued', 'running', 'ok', 'error', 'paused', 'deleted', 'deleted_new' :type tool_id: str or list :param tool_id: limit listing of jobs to those that match one of the included tool_ids. If none, all are returned. :type history_id: str :param history_id: limit listing of jobs to those that match the history_id. If none, all are returned. :rtype: list :returns: list of dictionaries containing summary job information For example:: [{ u'create_time': u'2014-03-01T16:16:48.640550', u'exit_code': 0, u'id': u'ebfb8f50c6abde6d', u'model_class': u'Job', u'state': u'ok', u'tool_id': u'fasta2tab', u'update_time': u'2014-03-01T16:16:50.657399'}, {u'create_time': u'2014-03-01T16:05:34.851246', u'exit_code': 0, u'id': u'1cd8e2f6b131e891', u'model_class': u'Job', u'state': u'ok', u'tool_id': u'upload1', u'update_time': u'2014-03-01T16:05:39.558458'}] """ return Client._get(self)
[docs] def show_job(self, job_id): """ Display information on a single job from current user :type job_id: str :param job_id: Specific job ID :rtype: dict :return: A description of single job For example:: { u'create_time': u'2014-03-01T16:17:29.828624', u'exit_code': 0, u'id': u'a799d38679e985db', u'inputs': { u'input': { u'id': u'ebfb8f50c6abde6d', u'src': u'hda'}}, u'model_class': u'Job', u'outputs': { u'output': { u'id': u'a799d38679e985db', u'src': u'hda'}}, u'params': { u'chromInfo': u'"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"', u'dbkey': u'"?"', u'seq_col': u'"2"', u'title_col': u'["1"]'}, u'state': u'ok', u'tool_id': u'tab2fasta', u'update_time': u'2014-03-01T16:17:31.930728'} """ return Client._get(self, id=job_id)
[docs] def get_state(self, job_id): """ Display the current state for a single job from current user. :type job_id: str :param job_id: Specific job ID :rtype: str :return: State of single job with the following being valid values: `new`, `queued`, `running`, `waiting`, `ok`. In case the state cannot be retrived, an empty string is returned. .. versionadded:: 0.5.3 """ return self.show_job(job_id).get('state', '')
[docs] def search_jobs(self, job_info): """ Return jobs for current user based payload content :type job_info: dict :param job_info: Dictionary containing description of requested job. This is in the same format as a request to POST /api/tools would take to initiate a job :rtype: list :returns: list of dictionaries containing summary job information of the jobs that match the requested job run This method is designed to scan the list of previously run jobs and find records of jobs that had the exact some input parameters and datasets. This can be used to minimize the amount of repeated work, and simply recycle the old results. """ payload = job_info url = self.gi._make_url(self) url = '/'.join([url, "search"]) return Client._post(self, url=url, payload=payload)