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Source code for galaxy.webapps.galaxy.api.jobs

"""
API operations on a jobs.

.. seealso:: :class:`galaxy.model.Jobs`
"""

import logging

from sqlalchemy import or_

from galaxy import (
    exceptions,
    model,
    util,
)
from galaxy.managers import hdas
from galaxy.managers.jobs import (
    JobManager,
    JobSearch,
    summarize_destination_params,
    summarize_job_metrics,
    summarize_job_parameters,
)
from galaxy.web import (
    expose_api,
    expose_api_anonymous,
    require_admin,
)
from galaxy.webapps.base.controller import (
    BaseAPIController,
    UsesVisualizationMixin
)
from galaxy.work.context import WorkRequestContext

log = logging.getLogger(__name__)


[docs]class JobController(BaseAPIController, UsesVisualizationMixin):
[docs] def __init__(self, app): super().__init__(app) self.job_manager = JobManager(app) self.job_search = JobSearch(app) self.hda_manager = hdas.HDAManager(app)
[docs] @expose_api def index(self, trans, **kwd): """ index( trans, state=None, tool_id=None, history_id=None, date_range_min=None, date_range_max=None, user_details=False ) * GET /api/jobs: return jobs for current user !! if user is admin and user_details is True, then return jobs for all galaxy users based on filtering - this is an extended service :type state: string 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: string 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 user_details: boolean :param user_details: if true, and requestor is an admin, will return external job id and user email. :type date_range_min: string '2014-01-01' :param date_range_min: limit the listing of jobs to those updated on or after requested date :type date_range_max: string '2014-12-31' :param date_range_max: limit the listing of jobs to those updated on or before requested date :type history_id: string :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 """ state = kwd.get('state', None) is_admin = trans.user_is_admin user_details = kwd.get('user_details', False) if is_admin: query = trans.sa_session.query(trans.app.model.Job) else: query = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.user == trans.user) def build_and_apply_filters(query, objects, filter_func): if objects is not None: if isinstance(objects, str): query = query.filter(filter_func(objects)) elif isinstance(objects, list): t = [] for obj in objects: t.append(filter_func(obj)) query = query.filter(or_(*t)) return query query = build_and_apply_filters(query, state, lambda s: trans.app.model.Job.state == s) query = build_and_apply_filters(query, kwd.get('tool_id', None), lambda t: trans.app.model.Job.tool_id == t) query = build_and_apply_filters(query, kwd.get('tool_id_like', None), lambda t: trans.app.model.Job.tool_id.like(t)) query = build_and_apply_filters(query, kwd.get('date_range_min', None), lambda dmin: trans.app.model.Job.table.c.update_time >= dmin) query = build_and_apply_filters(query, kwd.get('date_range_max', None), lambda dmax: trans.app.model.Job.table.c.update_time <= dmax) history_id = kwd.get('history_id', None) if history_id is not None: try: decoded_history_id = self.decode_id(history_id) query = query.filter(trans.app.model.Job.history_id == decoded_history_id) except Exception: raise exceptions.ObjectAttributeInvalidException() out = [] if kwd.get('order_by') == 'create_time': order_by = trans.app.model.Job.create_time.desc() else: order_by = trans.app.model.Job.update_time.desc() for job in query.order_by(order_by).all(): job_dict = job.to_dict('collection', system_details=is_admin) j = self.encode_all_ids(trans, job_dict, True) if user_details: j['user_email'] = job.user.email out.append(j) return out
[docs] @expose_api_anonymous def show(self, trans, id, **kwd): """ show( trans, id ) * GET /api/jobs/{id}: return jobs for current user :type id: string :param id: Specific job id :type full: boolean :param full: whether to return extra information :rtype: dictionary :returns: dictionary containing full description of job data """ job = self.__get_job(trans, id) is_admin = trans.user_is_admin job_dict = self.encode_all_ids(trans, job.to_dict('element', system_details=is_admin), True) full_output = util.asbool(kwd.get('full', 'false')) if full_output: job_dict.update(dict( tool_stdout=job.tool_stdout, tool_stderr=job.tool_stderr, job_stdout=job.job_stdout, job_stderr=job.job_stderr, stderr=job.stderr, stdout=job.stdout, job_messages=job.job_messages )) if is_admin: if job.user: job_dict['user_email'] = job.user.email else: job_dict['user_email'] = None job_dict['job_metrics'] = summarize_job_metrics(trans, job) return job_dict
[docs] @expose_api def common_problems(self, trans, id, **kwd): """ * GET /api/jobs/{id}/common_problems check inputs and job for common potential problems to aid in error reporting """ job = self.__get_job(trans, id) seen_ids = set() has_empty_inputs = False has_duplicate_inputs = False for job_input_assoc in job.input_datasets: input_dataset_instance = job_input_assoc.dataset if input_dataset_instance is None: continue if input_dataset_instance.get_total_size() == 0: has_empty_inputs = True input_instance_id = input_dataset_instance.id if input_instance_id in seen_ids: has_duplicate_inputs = True else: seen_ids.add(input_instance_id) # TODO: check percent of failing jobs around a window on job.update_time for handler - report if high. # TODO: check percent of failing jobs around a window on job.update_time for destination_id - report if high. # TODO: sniff inputs (add flag to allow checking files?) return {"has_empty_inputs": has_empty_inputs, "has_duplicate_inputs": has_duplicate_inputs}
[docs] @expose_api def inputs(self, trans, id, **kwd): """ show( trans, id ) * GET /api/jobs/{id}/inputs returns input datasets created by job :type id: string :param id: Encoded job id :rtype: dictionary :returns: dictionary containing input dataset associations """ job = self.__get_job(trans, id) return self.__dictify_associations(trans, job.input_datasets, job.input_library_datasets)
[docs] @expose_api def outputs(self, trans, id, **kwd): """ outputs( trans, id ) * GET /api/jobs/{id}/outputs returns output datasets created by job :type id: string :param id: Encoded job id :rtype: dictionary :returns: dictionary containing output dataset associations """ job = self.__get_job(trans, id) return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
[docs] @expose_api def delete(self, trans, id, **kwd): """ delete( trans, id ) * Delete /api/jobs/{id} cancels specified job :type id: string :param id: Encoded job id :type message: string :param message: Stop message. """ payload = kwd.get("payload") or {} job = self.__get_job(trans, id) message = payload.get("message", None) return self.job_manager.stop(job, message=message)
[docs] @expose_api def resume(self, trans, id, **kwd): """ * PUT /api/jobs/{id}/resume Resumes a paused job :type id: string :param id: Encoded job id :rtype: dictionary :returns: dictionary containing output dataset associations """ job = self.__get_job(trans, id) if not job: raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id) if job.state == job.states.PAUSED: job.resume() else: exceptions.RequestParameterInvalidException("Job with id '%s' is not paused" % (job.tool_id)) return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
[docs] @expose_api_anonymous def metrics(self, trans, **kwd): """ * GET /api/jobs/{job_id}/metrics * GET /api/datasets/{dataset_id}/metrics Return job metrics for specified job. Job accessibility checks are slightly different than dataset checks, so both methods are available. :type job_id: string :param job_id: Encoded job id :type dataset_id: string :param dataset_id: Encoded HDA or LDDA id :type hda_ldda: string :param hda_ldda: hda if dataset_id is an HDA id (default), ldda if it is an ldda id. :rtype: list :returns: list containing job metrics """ job = self.__get_job(trans, **kwd) return summarize_job_metrics(trans, job)
[docs] @require_admin @expose_api def destination_params(self, trans, **kwd): """ * GET /api/jobs/{job_id}/destination_params Return destination parameters for specified job. :type job_id: string :param job_id: Encoded job id :rtype: list :returns: list containing job destination parameters """ job = self.__get_job(trans, **kwd) return summarize_destination_params(trans, job)
[docs] @expose_api_anonymous def parameters_display(self, trans, **kwd): """ * GET /api/jobs/{job_id}/parameters_display * GET /api/datasets/{dataset_id}/parameters_display Resolve parameters as a list for nested display. More client logic here than is ideal but it is hard to reason about tool parameter types on the client relative to the server. Job accessibility checks are slightly different than dataset checks, so both methods are available. This API endpoint is unstable and tied heavily to Galaxy's JS client code, this endpoint will change frequently. :type job_id: string :param job_id: Encoded job id :type dataset_id: string :param dataset_id: Encoded HDA or LDDA id :type hda_ldda: string :param hda_ldda: hda if dataset_id is an HDA id (default), ldda if it is an ldda id. :rtype: list :returns: job parameters for for display """ job = self.__get_job(trans, **kwd) return summarize_job_parameters(trans, job)
[docs] @expose_api_anonymous def build_for_rerun(self, trans, id, **kwd): """ * GET /api/jobs/{id}/build_for_rerun returns a tool input/param template prepopulated with this job's information, suitable for rerunning or rendering parameters of the job. :type id: string :param id: Encoded job id :rtype: dictionary :returns: dictionary containing output dataset associations """ job = self.__get_job(trans, id) if not job: raise exceptions.ObjectNotFound("Could not access job with id '%s'" % id) tool = self.app.toolbox.get_tool(job.tool_id, kwd.get('tool_version') or job.tool_version) if tool is None: raise exceptions.ObjectNotFound("Requested tool not found") if not tool.is_workflow_compatible: raise exceptions.ConfigDoesNotAllowException("Tool '%s' cannot be rerun." % (job.tool_id)) return tool.to_json(trans, {}, job=job)
def __dictify_associations(self, trans, *association_lists): rval = [] for association_list in association_lists: rval.extend(self.__dictify_association(trans, a) for a in association_list) return rval def __dictify_association(self, trans, job_dataset_association): dataset_dict = None dataset = job_dataset_association.dataset if dataset: if isinstance(dataset, model.HistoryDatasetAssociation): dataset_dict = dict(src="hda", id=trans.security.encode_id(dataset.id)) else: dataset_dict = dict(src="ldda", id=trans.security.encode_id(dataset.id)) return dict(name=job_dataset_association.name, dataset=dataset_dict) def __get_job(self, trans, job_id=None, dataset_id=None, **kwd): if job_id is not None: decoded_job_id = self.decode_id(job_id) return self.job_manager.get_accessible_job(trans, decoded_job_id) else: hda_ldda = kwd.get("hda_ldda", "hda") # Following checks dataset accessible dataset_instance = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=dataset_id) return dataset_instance.creating_job
[docs] @expose_api def create(self, trans, payload, **kwd): """ See the create method in tools.py in order to submit a job. """ raise exceptions.NotImplemented('Please POST to /api/tools instead.')
[docs] @expose_api def search(self, trans, payload, **kwd): """ search( trans, payload ) * POST /api/jobs/search: return jobs for current user :type payload: dict :param payload: Dictionary containing description of requested job. This is in the same format as a request to POST /apt/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. """ tool_id = payload.get('tool_id') if tool_id is None: raise exceptions.RequestParameterMissingException("No tool id") tool = trans.app.toolbox.get_tool(tool_id) if tool is None: raise exceptions.ObjectNotFound("Requested tool not found") if 'inputs' not in payload: raise exceptions.RequestParameterMissingException("No inputs defined") inputs = payload.get('inputs', {}) # Find files coming in as multipart file data and add to inputs. for k, v in payload.items(): if k.startswith('files_') or k.startswith('__files_'): inputs[k] = v request_context = WorkRequestContext(app=trans.app, user=trans.user, history=trans.history) all_params, all_errors, _, _ = tool.expand_incoming(trans=trans, incoming=inputs, request_context=request_context) if any(all_errors): return [] params_dump = [tool.params_to_strings(param, self.app, nested=True) for param in all_params] jobs = [] for param_dump, param in zip(params_dump, all_params): job = self.job_search.by_tool_input(trans=trans, tool_id=tool_id, tool_version=tool.version, param=param, param_dump=param_dump, job_state=payload.get('state')) if job: jobs.append(job) return [self.encode_all_ids(trans, single_job.to_dict('element'), True) for single_job in jobs]
[docs] @expose_api_anonymous def error(self, trans, id, payload, **kwd): """ error( trans, id ) * POST /api/jobs/{id}/error submits a bug report via the API. :type id: string :param id: Encoded job id :rtype: dictionary :returns: dictionary containing information regarding where the error report was sent. """ # Get dataset on which this error was triggered dataset_id = payload.get('dataset_id') if not dataset_id: raise exceptions.RequestParameterMissingException('No dataset_id') decoded_dataset_id = self.decode_id(dataset_id) dataset = self.hda_manager.get_accessible(decoded_dataset_id, trans.user) # Get job job = self.__get_job(trans, id) if dataset.creating_job.id != job.id: raise exceptions.RequestParameterInvalidException('dataset_id was not created by job_id') tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version) or None email = payload.get('email') if not email and not trans.anonymous: email = trans.user.email messages = trans.app.error_reports.default_error_plugin.submit_report( dataset=dataset, job=job, tool=tool, user_submission=True, user=trans.user, email=email, message=payload.get('message') ) return {'messages': messages}
[docs] @require_admin @expose_api def show_job_lock(self, trans, **kwd): """ * GET /api/job_lock return boolean indicating if job lock active. """ return {"active": self.app.job_manager.job_lock}
[docs] @require_admin @expose_api def update_job_lock(self, trans, payload, **kwd): """ * PUT /api/job_lock return boolean indicating if job lock active. """ job_lock = payload.get("active") self.app.queue_worker.send_control_task('admin_job_lock', kwargs={'job_lock': job_lock}, get_response=True) return {"active": self.app.job_manager.job_lock}