def resolve_job_ref(jbor, job_outputs={}, should_resolve=True):
'''
:param jbor: a dict that is a valid job-based object reference
:type jbor: dict
:param job_outputs: a dict of finished local jobs to their output hashes
:type job_outputs: :class:`collections.OrderedDict`
:returns: the referenced value if present
:raises: :exc:`Exception` if the job-based object reference cannot be resolved
TODO: Support metadata references
'''
ref_job_id = get_job_from_jbor(jbor)
ref_job_field = get_field_from_jbor(jbor)
if is_localjob_id(ref_job_id):
if job_outputs.get(ref_job_id) is None:
if should_resolve:
raise Exception('Job ' + ref_job_id + ' not found in local finished jobs')
else:
return jbor
if ref_job_field not in job_outputs[ref_job_id]:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id + ' because field "' + ref_job_field + '" was not found in its output')
return job_outputs[ref_job_id][ref_job_field]
else:
dxjob = dxpy.DXJob(ref_job_id)
try:
dxjob.wait_on_done()
except Exception as e:
raise Exception('Could not wait for ' + ref_job_id + ' to finish: ' + str(e))
job_desc = dxjob.describe()
if ref_job_field not in job_desc['output']:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id + ' because field "' + ref_job_field + '" was not found in its output')
return job_desc['output'][ref_job_field]
def test_run_workflow(self):
launched_jobs = self.workflow.run({"0.record": dxpy.dxlink(self.closedrecord)})
self.assertEqual(len(launched_jobs), 2)
job_descs = [dxjob.describe() for dxjob in launched_jobs]
self.assertEqual(job_descs[0]['name'], 'identity-record - workflowname')
self.assertEqual(get_dxlink_ids(job_descs[0]['input']['record'])[0], self.closedrecord.get_id())
self.assertTrue(is_job_ref(job_descs[1]['runInput']['record']))
self.assertEqual(get_job_from_jbor(job_descs[1]['runInput']['record']), job_descs[0]['id'])
self.assertEqual(get_field_from_jbor(job_descs[1]['runInput']['record']), 'record')
launched_jobs[1].wait_on_done()
def resolve_job_ref(jbor, job_outputs={}, should_resolve=True):
'''
:param jbor: a dict that is a valid job-based object reference
:type jbor: dict
:param job_outputs: a dict of finished local jobs to their output hashes
:type job_outputs: :class:`collections.OrderedDict`
:returns: the referenced value if present
:raises: :exc:`Exception` if the job-based object reference cannot be resolved
TODO: Support metadata references
'''
ref_job_id = get_job_from_jbor(jbor)
ref_job_field = get_field_from_jbor(jbor)
ref_job_index = get_index_from_jbor(jbor)
def resolve_from_hash(output_hash):
if ref_job_index is None:
return output_hash[ref_job_field]
else:
return output_hash[ref_job_field][ref_job_index]
if is_localjob_id(ref_job_id):
if job_outputs.get(ref_job_id) is None:
if should_resolve:
raise Exception('Job ' + ref_job_id +
' not found in local finished jobs')
else:
return jbor
if ref_job_field not in job_outputs[ref_job_id]:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id +
' because field "' + ref_job_field +
'" was not found in its output')
return resolve_from_hash(job_outputs[ref_job_id])
else:
dxjob = dxpy.DXJob(ref_job_id)
try:
dxjob.wait_on_done()
except Exception as e:
raise Exception('Could not wait for ' + ref_job_id +
' to finish: ' + str(e))
job_desc = dxjob.describe()
if ref_job_field not in job_desc['output']:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id +
' because field "' + ref_job_field +
'" was not found in its output')
return resolve_from_hash(job_desc['output'])