def resolve_job_references(io_hash, job_outputs, should_resolve=True):
'''
:param io_hash: an input or output hash in which to resolve any job-based object references possible
:type io_hash: dict
:param job_outputs: a mapping of finished local jobs to their output hashes
:type job_outputs: dict
:param should_resolve: whether it is an error if a job-based object reference in *io_hash* cannot be resolved yet
:type should_resolve: boolean
Modifies *io_hash* in-place.
'''
q = []
for field in io_hash:
if is_job_ref(io_hash[field]):
io_hash[field] = resolve_job_ref(io_hash[field], job_outputs, should_resolve)
elif isinstance(io_hash[field], list) or isinstance(io_hash[field], dict):
q.append(io_hash[field])
while len(q) > 0:
thing = q.pop()
if isinstance(thing, list):
for i in range(len(thing)):
if is_job_ref(thing[i]):
thing[i] = resolve_job_ref(thing[i], job_outputs, should_resolve)
elif isinstance(thing[i], list) or isinstance(thing[i], dict):
q.append(thing[i])
else:
for field in thing:
if is_job_ref(thing[field]):
thing[field] = resolve_job_ref(thing[field], job_outputs, should_resolve)
elif isinstance(thing[field], list) or isinstance(thing[field], dict):
q.append(thing[field])
def has_local_job_refs(io_hash):
'''
:param io_hash: input/output hash
:type io_hash: dict
:returns: boolean indicating whether any job-based object references are found in *io_hash*
'''
q = []
for field in io_hash:
if is_job_ref(io_hash[field]):
if get_job_from_jbor(io_hash[field]).startswith('localjob'):
return True
elif isinstance(io_hash[field], list) or isinstance(io_hash[field], dict):
q.append(io_hash[field])
while len(q) > 0:
thing = q.pop()
if isinstance(thing, list):
for i in range(len(thing)):
if is_job_ref(thing[i]):
if get_job_from_jbor(thing[i]).startswith('localjob'):
return True
elif isinstance(thing[i], list) or isinstance(thing[i], dict):
q.append(thing[i])
else:
for field in thing:
if is_job_ref(thing[field]):
if get_job_from_jbor(thing[field]).startswith('localjob'):
return True
elif isinstance(thing[field], list) or isinstance(thing[field], dict):
q.append(thing[field])
return False
def has_local_job_refs(io_hash):
'''
:param io_hash: input/output hash
:type io_hash: dict
:returns: boolean indicating whether any job-based object references are found in *io_hash*
'''
q = []
for field in io_hash:
if is_job_ref(io_hash[field]):
if get_job_from_jbor(io_hash[field]).startswith('localjob'):
return True
elif isinstance(io_hash[field], list) or isinstance(
io_hash[field], dict):
q.append(io_hash[field])
while len(q) > 0:
thing = q.pop()
if isinstance(thing, list):
for i in range(len(thing)):
if is_job_ref(thing[i]):
if get_job_from_jbor(thing[i]).startswith('localjob'):
return True
elif isinstance(thing[i], list) or isinstance(thing[i], dict):
q.append(thing[i])
else:
for field in thing:
if is_job_ref(thing[field]):
if get_job_from_jbor(thing[field]).startswith('localjob'):
return True
elif isinstance(thing[field], list) or isinstance(
thing[field], dict):
q.append(thing[field])
return False
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_references(io_hash, job_outputs, should_resolve=True):
'''
:param io_hash: an input or output hash in which to resolve any job-based object references possible
:type io_hash: dict
:param job_outputs: a mapping of finished local jobs to their output hashes
:type job_outputs: dict
:param should_resolve: whether it is an error if a job-based object reference in *io_hash* cannot be resolved yet
:type should_resolve: boolean
Modifies *io_hash* in-place.
'''
q = []
for field in io_hash:
if is_job_ref(io_hash[field]):
io_hash[field] = resolve_job_ref(io_hash[field], job_outputs,
should_resolve)
elif isinstance(io_hash[field], list) or isinstance(
io_hash[field], dict):
q.append(io_hash[field])
while len(q) > 0:
thing = q.pop()
if isinstance(thing, list):
for i in range(len(thing)):
if is_job_ref(thing[i]):
thing[i] = resolve_job_ref(thing[i], job_outputs,
should_resolve)
elif isinstance(thing[i], list) or isinstance(thing[i], dict):
q.append(thing[i])
else:
for field in thing:
if is_job_ref(thing[field]):
thing[field] = resolve_job_ref(thing[field], job_outputs,
should_resolve)
elif isinstance(thing[field], list) or isinstance(
thing[field], dict):
q.append(thing[field])
def test_is_job_ref(self):
# Positive results
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": "number"}
self.assertTrue(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": jobref}
self.assertTrue(describe.is_job_ref(jobref))
# Negative results
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": "number", "other": "field"}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": 32}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": jobref}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": "job-B55ZF5kZKQGz1Xxyb5FQ0003"}
self.assertFalse(describe.is_job_ref(jobref))
def test_is_job_ref(self):
# Positive results
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": "number"}
self.assertTrue(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": jobref}
self.assertTrue(describe.is_job_ref(jobref))
# Negative results
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": "number", "other": "field"}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"job": "job-B55ZF5kZKQGz1Xxyb5FQ0003", "field": 32}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": jobref}
self.assertFalse(describe.is_job_ref(jobref))
jobref = {"$dnanexus_link": "job-B55ZF5kZKQGz1Xxyb5FQ0003"}
self.assertFalse(describe.is_job_ref(jobref))
