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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 six import string_types
from sqlalchemy import or_
from galaxy import exceptions
from galaxy import model
from galaxy import util
from galaxy.managers.datasets import DatasetManager
from galaxy.managers.jobs import JobSearch
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import UsesLibraryMixinItems
from galaxy.work.context import WorkRequestContext
log = logging.getLogger(__name__)
[docs]class JobController(BaseAPIController, UsesLibraryMixinItems):
[docs] def __init__(self, app):
super(JobController, self).__init__(app)
self.dataset_manager = DatasetManager(app)
self.job_search = JobSearch(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, string_types):
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(stderr=job.stderr, stdout=job.stdout))
if is_admin:
if job.user:
job_dict['user_email'] = job.user.email
else:
job_dict['user_email'] = None
def metric_to_dict(metric):
metric_name = metric.metric_name
metric_value = metric.metric_value
metric_plugin = metric.plugin
title, value = trans.app.job_metrics.format(metric_plugin, metric_name, metric_value)
return dict(
title=title,
value=value,
plugin=metric_plugin,
name=metric_name,
raw_value=str(metric_value),
)
job_dict['job_metrics'] = [metric_to_dict(metric) for metric in job.metrics]
return job_dict
[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
"""
job = self.__get_job(trans, id)
if not job.finished:
job.mark_deleted(self.app.config.track_jobs_in_database)
trans.sa_session.flush()
self.app.job_manager.stop(job)
return True
else:
return False
[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 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, id):
try:
decoded_job_id = self.decode_id(id)
except Exception:
raise exceptions.MalformedId()
job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
if job is None:
raise exceptions.ObjectNotFound()
belongs_to_user = (job.user == trans.user) if job.user else (job.session_id == trans.get_galaxy_session().id)
if not trans.user_is_admin and not belongs_to_user:
# Check access granted via output datasets.
if not job.output_datasets:
raise exceptions.ItemAccessibilityException("Job has no output datasets.")
for data_assoc in job.output_datasets:
if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
raise exceptions.ItemAccessibilityException("You are not allowed to rerun this job.")
return 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.ObjectAttributeMissingException("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.ObjectAttributeMissingException("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, **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
try:
decoded_dataset_id = self.decode_id(kwd['dataset_id'])
except Exception:
raise exceptions.MalformedId()
dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(decoded_dataset_id)
# Get job
job = self.__get_job(trans, id)
tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version) or None
email = kwd.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=kwd.get('message')
)
return {'messages': messages}