def setUp(self):
self._test_data_dir = os.path.join(absltest.get_default_test_srcdir(),
_TESTDATA_PATH)
self._enc = resources_pb2.Encounter()
with open(os.path.join(self._test_data_dir, 'encounter_1.pbtxt')) as f:
text_format.Parse(f.read(), self._enc)
self._bundle = resources_pb2.Bundle()
self._bundle.entry.add().resource.encounter.CopyFrom(self._enc)
self._synthea_enc = resources_pb2.Encounter()
with open(os.path.join(self._test_data_dir,
'encounter_synthea.pbtxt')) as f:
text_format.Parse(f.read(), self._synthea_enc)
self._synthea_bundle = resources_pb2.Bundle()
self._synthea_bundle.entry.add().resource.encounter.CopyFrom(
self._synthea_enc)
def setUp(self):
self._test_data_dir = os.path.join(absltest.get_default_test_srcdir(),
_TESTDATA_PATH)
self._bundle = resources_pb2.Bundle()
with open(os.path.join(self._test_data_dir, 'bundle_1.pbtxt')) as f:
text_format.Parse(f.read(), self._bundle)
enc = self._bundle.entry[0].resource.encounter
patient = self._bundle.entry[1].resource.patient
self._expected_label = label.ComposeLabel(
patient, enc,
label.LOS_RANGE_LABEL,
'above_14',
# 24 hours after admission
datetime.datetime(2009, 2, 14, 23, 31, 30))
def testGetPatient(self):
patient = resources_pb2.Patient()
text_format.Merge(
"""
id: {
value: "Patient/1"
}
birth_date: {
# February 13, 2009 11:31:30 PM
value_us : 1234567890000000
timezone : "America/New_York"
precision: DAY
}
""", patient)
bundle = resources_pb2.Bundle()
bundle.entry.add().resource.patient.CopyFrom(patient)
p = util.GetPatient(bundle)
self.assertEqual(patient, p)
def setUp(self):
self._test_data_dir = os.path.join(absltest.get_default_test_srcdir(),
_TESTDATA_PATH)
enc = resources_pb2.Encounter()
with open(os.path.join(self._test_data_dir, 'encounter_1.pbtxt')) as f:
text_format.Parse(f.read(), enc)
patient = resources_pb2.Patient()
patient.id.value = 'Patient/1'
self._bundle = resources_pb2.Bundle()
self._bundle.entry.add().resource.encounter.CopyFrom(enc)
self._bundle.entry.add().resource.patient.CopyFrom(patient)
self._expected_label = label.ComposeLabel(
patient,
enc,
label.LOS_RANGE_LABEL,
'above_14',
# 24 hours after admission
datetime.datetime(2009, 2, 14, 23, 31, 30))
def _VerifyPipeline(self, for_synthea: bool):
bundle_text_file = 'bundle_1.pbtxt'
if for_synthea:
bundle_text_file = 'bundle_synthea.pbtxt'
bundle = resources_pb2.Bundle()
with open(os.path.join(self._test_data_dir, bundle_text_file)) as f:
text_format.Parse(f.read(), bundle)
enc = bundle.entry[0].resource.encounter
patient = bundle.entry[1].resource.patient
expected_label = label.ComposeLabel(
patient,
enc,
label.LOS_RANGE_LABEL,
'above_14',
# 24 hours after admission
datetime.datetime(2009, 2, 14, 23, 31, 30))
with test_pipeline.TestPipeline() as pipeline:
result = (pipeline
| 'input' >> beam.Create([bundle])
| 'process' >> beam.ParDo(
bundle_to_label.LengthOfStayRangeLabelAt24HoursFn(
for_synthea)))
util.assert_that(result, util.equal_to([expected_label]))
def testKeyBundleByPatientId(self):
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
} } }""", resources_pb2.Bundle())
with test_pipeline.TestPipeline() as p:
result = (p
| "CreateBundles" >> beam.Create([bundle])
| "KeyBundleByPatientId" >> beam.ParDo(
bundle_to_seqex.KeyBundleByPatientIdFn()))
def check_result(got):
try:
self.assertLen(got, 1)
(got_key, got_bundle) = got[0]
self.assertEqual(b"Patient/14", got_key)
self.assertProtoEqual(got_bundle, bundle)
except AssertionError as err:
raise util.BeamAssertException(err)
util.assert_that(result, check_result)
def testSingleTriggerAndStats(self):
event_trigger = text_format.Parse(
"""
event_time { value_us: 1420102800000000 }
""", google_extensions_pb2.EventTrigger())
event_trigger_labels = (event_trigger, list())
event_trigger_labels_list = (event_trigger_labels,)
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
birth_date { value_us: 8640000000000 }
} } }
entry { resource { medication_request {
id { value: "1" }
subject { patient_id { value: "14" } }
contained {
medication {
id { value: "med" }
code { coding {
system { value:
"http://hl7.org/fhir/sid/ndc"
}
code { value: "123" }
} }
}
}
authored_on {
value_us: 1420095600000000 # "2015-01-01T07:00:00+00:00"
}
medication { reference {
medication_id { value: "med" }
} }
} } }
""", resources_pb2.Bundle())
expected_seqex = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1420095600 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "Patient.birthDate"
value { int64_list { value: 8640000 } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 1 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1420102800 } }
} }
feature_lists: {
feature_list {
key: "MedicationRequest.contained.medication.code.ndc"
value { feature { bytes_list { value: "123" } } }
}
feature_list {
key: "MedicationRequest.meta.lastUpdated"
value { feature { int64_list { value: 1420095600 } } }
}
feature_list {
key: "MedicationRequest.authoredOn"
value { feature { int64_list { value: 1420095600 } } }
}
feature_list {
key: "eventId"
value { feature { int64_list { value: 1420095600 } } }
}
feature_list {
key: "MedicationRequest.contained.medication.code"
value { feature { bytes_list { value: "ndc:123" } } }
}
feature_list {
key: "encounterId"
value { feature { int64_list { value: 1420095600 } } }
}
}
""", example_pb2.SequenceExample())
got_stats = self._runTest(
"Patient/14", bundle, event_trigger_labels_list,
(("Patient/14:0-1@1420102800", expected_seqex, 1),))
# We only spot check a few counters here. The main goal is to make sure
# we get the counters back from c++ land.
self.assertEqual(1, got_stats.get("num-examples"))
def testMultipleTriggersAndExamples(self):
event_trigger1 = text_format.Parse(
"""
event_time { value_us: 1417424400000000 }
source { encounter_id { value: "1" } }
""", google_extensions_pb2.EventTrigger())
event_trigger2 = text_format.Parse(
"""
event_time { value_us: 1420102800000000 }
source { encounter_id { value: "2" } }
""", google_extensions_pb2.EventTrigger())
event_trigger_labels1 = (
event_trigger1,
list(),
)
event_trigger_labels2 = (
event_trigger2,
list(),
)
event_trigger_labels_list = (
event_trigger_labels1,
event_trigger_labels2,
)
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
} } }
entry {
resource { encounter {
id { value: "1" }
subject { patient_id { value: "14" } }
class_value {
system { value: "http://hl7.org/fhir/v3/ActCode" }
code { value: "IMP" }
}
reason {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "V410.9" }
display { value: "Standard issue" }
}
}
period {
start {
value_us: 1417420800000000 # "2014-12-01T08:00:00+00:00"
}
end {
value_us: 1417424400000000 # "2014-12-01T09:00:00+00:00"
}
}
} }
}
entry {
resource { encounter {
id { value: "2" }
subject { patient_id { value: "14" } }
class_value {
system { value: "http://hl7.org/fhir/v3/ActCode" }
code { value: "IMP" }
}
reason {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "191.4" }
display { value: "Malignant neoplasm of occipital lobe" }
}
}
period {
start {
value_us: 1420099200000000 # "2015-01-01T08:00:00+00:00"
}
end {
value_us: 1420102800000000 # "2015-01-01T09:00:00+00:00"
}
}
} }
}
""", resources_pb2.Bundle())
# pylint: disable=line-too-long
expected_seqex1 = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1417420800 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 2 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1417424400 } } }
}
feature_lists: {
feature_list {
key: "Encounter.class"
value { feature { bytes_list { value: "actcode:IMP" } } feature { bytes_list { value: "actcode:IMP" } } }
}
feature_list {
key: "Encounter.meta.lastUpdated"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } }
}
feature_list {
key: "Encounter.period.start"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } }
}
feature_list {
key: "Encounter.period.end"
value { feature { int64_list { } } feature { int64_list { value: 1417424400 } } }
}
feature_list {
key: "Encounter.reason"
value { feature { bytes_list { } } feature { bytes_list { value: "icd9:V410.9" } } }
}
feature_list {
key: "Encounter.reason.icd9"
value { feature { bytes_list { } } feature { bytes_list { value: "V410.9" } } }
}
feature_list {
key: "Encounter.reason.icd9.display.tokenized"
value { feature { bytes_list { } } feature { bytes_list { value: "standard" value: "issue" } } }
}
feature_list {
key: "encounterId"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } }
}
feature_list {
key: "eventId"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } }
}
}
""", example_pb2.SequenceExample())
expected_seqex2 = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1420099200 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 4 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1420102800 } } }
}
feature_lists: {
feature_list {
key: "Encounter.class"
value {
feature { bytes_list { value: "actcode:IMP" } } feature { bytes_list { value: "actcode:IMP" } } feature { bytes_list { value: "actcode:IMP" } } feature { bytes_list { value: "actcode:IMP" } }
}
}
feature_list {
key: "Encounter.meta.lastUpdated"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420102800 } } }
}
feature_list {
key: "Encounter.period.start"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } }
}
}
feature_list {
key: "Encounter.period.end"
value {
feature { int64_list { } } feature { int64_list { value: 1417424400 } } feature { int64_list { } } feature { int64_list { value: 1420102800 } }
}
}
feature_list {
key: "Encounter.reason"
value {
feature { bytes_list { } } feature { bytes_list { value: "icd9:V410.9" } } feature { bytes_list { } } feature { bytes_list { value: "icd9:191.4" } }
}
}
feature_list {
key: "Encounter.reason.icd9"
value {
feature { bytes_list { } } feature { bytes_list { value: "V410.9" } } feature { bytes_list { } } feature { bytes_list { value: "191.4" } }
}
}
feature_list {
key: "Encounter.reason.icd9.display.tokenized"
value {
feature { bytes_list { } } feature { bytes_list { value: "standard" value: "issue" } } feature { bytes_list { } } feature { bytes_list { value: "malignant" value: "neoplasm" value: "of" value: "occipital" value: "lobe" } }
}
}
feature_list {
key: "encounterId"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } }
}
}
feature_list {
key: "eventId"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420102800 } }
}
}
}
""", example_pb2.SequenceExample())
# pylint: enable=line-too-long
_ = self._runTest("Patient/14", bundle, event_trigger_labels_list, (
("Patient/14:0-2@1417424400:Encounter/1", expected_seqex1, 2),
("Patient/14:0-4@1420102800:Encounter/2", expected_seqex2, 4),
))
def testSingleTriggerAndLabel(self):
event_trigger = text_format.Parse(
"""
event_time { value_us: 1420102800000000 }
source { encounter_id { value: "1" } }
""", google_extensions_pb2.EventTrigger())
event_label = text_format.Parse(
"""
patient { patient_id { value: "14" } }
type { code { value: "test1" }}
event_time { value_us: 1420102800000000 }
label {
class_name {
system { value: "urn:test:label"
}
code { value: "red" }
}
}
""", google_extensions_pb2.EventLabel())
event_trigger_labels = (
event_trigger,
(event_label,),
)
event_trigger_labels_list = (event_trigger_labels,)
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
} } }
entry { resource { condition {
id { value: "1" }
subject { patient_id { value: "14" } }
code { coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "bar" }
} }
asserted_date {
value_us: 1417392000000000 # "2014-12-01T00:00:00+00:00"
}
} } }
entry { resource { condition {
id { value: "2" }
subject { patient_id { value: "14" } }
code { coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "baz" }
} }
asserted_date {
value_us: 1420099200000000 # "2015-01-01T08:00:00+00:00"
}
} } }
entry { resource { composition {
id { value: "1" }
subject { patient_id { value: "14" } }
encounter { encounter_id { value: "1" } }
section { text { div { value: "test text" } } }
date {
value_us: 1420102800000000
timezone: "UTC"
precision: SECOND
}
} } }
entry { resource { encounter {
id { value: "1" }
subject { patient_id { value: "14" } }
class_value {
system { value: "http://hl7.org/fhir/v3/ActCode" }
code { value: "IMP" }
}
reason {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "191.4" }
display { value: "Malignant neoplasm of occipital lobe" }
}
}
period {
start {
value_us: 1420099200000000 # "2015-01-01T08:00:00+00:00"
}
end {
value_us: 1420102800000000 # "2015-01-01T09:00:00+00:00"
}
}
} } }
""", resources_pb2.Bundle())
# pylint: disable=line-too-long
expected_seqex = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1420099200 } }
}
feature {
key: "label.test1.class"
value { bytes_list { value: "red" } }
}
feature {
key: "label.test1.timestamp_secs"
value { int64_list { value: 1420102800 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 5 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1420102800 } }
}
}
feature_lists: {
feature_list {
key: "Composition.meta.lastUpdated"
value { feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { value: 1420102800 } } feature { int64_list { } } }
}
feature_list {
key: "Composition.date"
value { feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { value: 1420102800 } } feature { int64_list { } } }
}
feature_list {
key: "Composition.section.text.div.tokenized"
value { feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { value: "test" value: "text" } } feature { bytes_list { } } }
}
feature_list {
key: "Condition.meta.lastUpdated"
value { feature { int64_list { value: 1417392000 } } feature { int64_list { value: 1420099200 } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } }
}
feature_list {
key: "Condition.code"
value { feature { bytes_list { value: "icd9:bar" } } feature { bytes_list { value: "icd9:baz" } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } }
}
feature_list {
key: "Condition.code.icd9"
value { feature { bytes_list { value: "bar" } } feature { bytes_list { value: "baz" } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } }
}
feature_list {
key: "Condition.assertedDate"
value { feature { int64_list { value: 1417392000 } } feature { int64_list { value: 1420099200 } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } }
}
feature_list {
key: "Encounter.class"
value { feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { value: "actcode:IMP" } } feature { bytes_list { } } feature { bytes_list { value: "actcode:IMP" } } }
}
feature_list {
key: "Encounter.meta.lastUpdated"
value { feature { int64_list { } } feature { int64_list { } } feature { int64_list { value: 1420099200 } } feature { int64_list { } } feature { int64_list { value: 1420102800 } } }
}
feature_list {
key: "Encounter.period.start"
value { feature { int64_list { } } feature { int64_list { } } feature { int64_list { value: 1420099200 } } feature { int64_list { } } feature { int64_list { value: 1420099200 } } }
}
feature_list {
key: "Encounter.period.end"
value { feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { } } feature { int64_list { value: 1420102800 } } }
}
feature_list {
key: "Encounter.reason"
value { feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { value: "icd9:191.4" } } }
}
feature_list {
key: "Encounter.reason.icd9"
value { feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { value: "191.4" } } }
}
feature_list {
key: "Encounter.reason.icd9.display.tokenized"
value { feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { } } feature { bytes_list { value: "malignant" value: "neoplasm" value: "of" value: "occipital" value: "lobe" } } }
}
feature_list {
key: "encounterId"
value { feature { int64_list { value: 1417392000 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } } }
}
feature_list {
key: "eventId"
value { feature { int64_list { value: 1417392000 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420102800 } } feature { int64_list { value: 1420102800 } } }
}
}
""", example_pb2.SequenceExample())
# pylint: enable=line-too-long
_ = self._runTest(
"Patient/14", bundle, event_trigger_labels_list,
(("Patient/14:0-5@1420102800:Encounter/1", expected_seqex, 5),))
def testBundleAndLabelsToSeqexDoFn(self):
event_trigger1 = text_format.Parse(
"""
event_time { value_us: 1417424400000000 }
source { encounter_id { value: "1" } }
""", google_extensions_pb2.EventTrigger())
event_trigger2 = text_format.Parse(
"""
event_time { value_us: 1420102800000000 }
source { encounter_id { value: "2" } }
""", google_extensions_pb2.EventTrigger())
event_trigger_labels1 = (
event_trigger1,
list(),
)
event_trigger_labels2 = (
event_trigger2,
list(),
)
event_trigger_labels_list = [
event_trigger_labels1,
event_trigger_labels2,
]
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
} } }
entry {
resource { encounter {
id { value: "1" }
subject { patient_id { value: "14" } }
class_value {
system { value: "http://hl7.org/fhir/v3/ActCode" }
code { value: "IMP" }
}
reason {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "V410.9" }
display { value: "Standard issue" }
}
}
period {
start {
value_us: 1417420800000000 # "2014-12-01T08:00:00+00:00"
}
end {
value_us: 1417424400000000 # "2014-12-01T09:00:00+00:00"
}
}
} }
}
entry {
resource { encounter {
id { value: "2" }
subject { patient_id { value: "14" } }
class_value {
system { value: "http://hl7.org/fhir/v3/ActCode" }
code { value: "IMP" }
}
reason {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "191.4" }
display { value: "Malignant neoplasm of occipital lobe" }
}
}
period {
start {
value_us: 1420099200000000 # "2015-01-01T08:00:00+00:00"
}
end {
value_us: 1420102800000000 # "2015-01-01T09:00:00+00:00"
}
}
} }
}
""", resources_pb2.Bundle())
# pylint: disable=line-too-long
expected_seqex1 = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1417420800 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 2 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1417424400 } } }
}
feature_lists: {
feature_list {
key: "Encounter.class"
value { feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } } feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } } }
}
feature_list {
key: "Encounter.meta.lastUpdated"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } }
}
feature_list {
key: "Encounter.period.start"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } }
}
feature_list {
key: "Encounter.period.end"
value { feature { int64_list { } } feature { int64_list { value: 1417424400 } } }
}
feature_list {
key: "Encounter.reason.http-hl7-org-fhir-sid-icd-9-cm-diagnosis"
value { feature { bytes_list { } } feature { bytes_list { value: "V410.9" } } }
}
feature_list {
key: "Encounter.reason.http-hl7-org-fhir-sid-icd-9-cm-diagnosis.display.tokenized"
value { feature { bytes_list { } } feature { bytes_list { value: "standard" value: "issue" } } }
}
feature_list {
key: "encounterId"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } }
}
feature_list {
key: "eventId"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } }
}
}
""", example_pb2.SequenceExample())
expected_seqex2 = text_format.Parse(
"""
context: {
feature {
key: "currentEncounterId"
value { int64_list { value: 1420099200 } }
}
feature {
key: "patientId"
value { bytes_list { value: "14" } }
}
feature {
key: "sequenceLength"
value { int64_list { value: 4 } }
}
feature {
key: "timestamp"
value { int64_list { value: 1420102800 } } }
}
feature_lists: {
feature_list {
key: "Encounter.class"
value {
feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } } feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } } feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } } feature { bytes_list { value: "http-hl7-org-fhir-v3-ActCode:IMP" } }
}
}
feature_list {
key: "Encounter.meta.lastUpdated"
value { feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420102800 } } }
}
feature_list {
key: "Encounter.period.start"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } }
}
}
feature_list {
key: "Encounter.period.end"
value {
feature { int64_list { } } feature { int64_list { value: 1417424400 } } feature { int64_list { } } feature { int64_list { value: 1420102800 } }
}
}
feature_list {
key: "Encounter.reason.http-hl7-org-fhir-sid-icd-9-cm-diagnosis"
value {
feature { bytes_list { } } feature { bytes_list { value: "V410.9" } } feature { bytes_list { } } feature { bytes_list { value: "191.4" } }
}
}
feature_list {
key: "Encounter.reason.http-hl7-org-fhir-sid-icd-9-cm-diagnosis.display.tokenized"
value {
feature { bytes_list { } } feature { bytes_list { value: "standard" value: "issue" } } feature { bytes_list { } } feature { bytes_list { value: "malignant" value: "neoplasm" value: "of" value: "occipital" value: "lobe" } }
}
}
feature_list {
key: "encounterId"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420099200 } }
}
}
feature_list {
key: "eventId"
value {
feature { int64_list { value: 1417420800 } } feature { int64_list { value: 1417424400 } } feature { int64_list { value: 1420099200 } } feature { int64_list { value: 1420102800 } }
}
}
}
""", example_pb2.SequenceExample())
with test_pipeline.TestPipeline() as p:
result = (
p
| beam.Create([(b"Patient/14", (bundle, event_trigger_labels_list))])
| "BundleAndLabelsToSeqex" >> beam.ParDo(
bundle_to_seqex.BundleAndLabelsToSeqexDoFn(
version_config=self._version_config,
enable_attribution=False,
generate_sequence_label=False)))
def check_result(got):
try:
self.assertLen(got, 2, "got: %s" % got)
got_seqex1 = got[0]
got_seqex2 = got[1]
self.assertProtoEqual(expected_seqex1, got_seqex1)
self.assertProtoEqual(expected_seqex2, got_seqex2)
except AssertionError as err:
raise util.BeamAssertException(err)
util.assert_that(result, check_result)
def testCreateBundleAndLabels(self):
bundle1 = text_format.Parse(
"""
entry { resource { patient {
id { value: "14" }
} } }
entry { resource { condition {
id { value: "1" }
subject { patient_id { value: "14" } }
code {
coding {
system { value: "http://hl7.org/fhir/sid/icd-9-cm/diagnosis" }
code { value: "bar" }
}
}
asserted_date {
value_us: 1417392000000000 # "2014-12-01T00:00:00+00:00"
}
} } }""", resources_pb2.Bundle())
bundle1_event_trigger = text_format.Parse(
"""
event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00"
""", google_extensions_pb2.EventTrigger())
# For the purpose of testing, bundle2 does not exist.
bundle2_event_trigger = text_format.Parse(
"""
event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00"
""", google_extensions_pb2.EventTrigger())
bundle3 = text_format.Parse(
"""
entry { resource { patient {
id { value: "30" }
} } }""", resources_pb2.Bundle())
bundle1_event_trigger_labels_list = [
(
bundle1_event_trigger,
list(),
),
]
bundle2_event_trigger_labels_list = [
(
bundle2_event_trigger,
list(),
),
]
with test_pipeline.TestPipeline() as p:
bundle_pcoll = p | "CreateBundles" >> beam.Create([
(b"Patient/14", bundle1),
(b"Patient/30", bundle3),
])
trigger_list_pcoll = p | "CreateTriggerLists" >> beam.Create([
(b"Patient/14", bundle1_event_trigger_labels_list),
(b"Patient/20", bundle2_event_trigger_labels_list),
])
result = bundle_to_seqex.CreateBundleAndLabels(bundle_pcoll,
trigger_list_pcoll)
def check_result(got):
try:
self.assertLen(got, 1)
(got_key, got_bundle_and_labels) = got[0]
self.assertEqual(b"Patient/14", got_key)
(got_bundle, got_trigger_labels_list) = got_bundle_and_labels
self.assertProtoEqual(got_bundle, bundle1)
self.assertLen(got_trigger_labels_list, 1)
self.assertProtoEqual(got_trigger_labels_list[0][0],
bundle1_event_trigger)
self.assertFalse(len(got_trigger_labels_list[0][1]))
except AssertionError as err:
raise util.BeamAssertException(err)
util.assert_that(result, check_result)
def test_get_trigger_labels_pair(self):
# pylint: disable=line-too-long
bundle = text_format.Parse(
"""
entry { resource { patient {
id { value: "20" }
} } }
entry { resource { encounter {
id { value: "1" }
extension {
url { value: "https://g.co/fhir/StructureDefinition/eventTrigger" }
extension {
url { value: "type" }
value { coding {
system { value: "urn:test:trigger"}
code { value: "at_discharge" }
} }
}
extension {
url { value: "eventTime" }
value { date_time {
value_us: 1388566800000000 # "2014-01-01T09:00:00+00:00"
} }
}
}
extension {
url { value: "https://g.co/fhir/StructureDefinition/eventLabel" }
extension {
url { value: "type" }
value { coding {
system { value: "urn:test:label" }
code { value: "test1" }
} }
}
extension {
url { value: "eventTime" }
value { date_time { value_us: 1388566800000000 } }
}
extension {
url { value: "source" }
value { reference { encounter_id { value: "1" } } }
}
}
} } }
entry { resource { encounter {
id { value: "2" }
extension {
url { value: "https://g.co/fhir/StructureDefinition/eventTrigger" }
extension {
url { value: "type" }
value { coding {
system { value: "urn:test:trigger"}
code { value: "at_discharge" }
} }
}
extension {
url { value: "eventTime" }
value { date_time {
value_us: 1420102800000000 # "2015-01-01T09:00:00+00:00"
} }
}
}
extension {
url { value: "https://g.co/fhir/StructureDefinition/eventLabel" }
extension {
url { value: "type" }
value { coding {
system { value: "urn:test:label" }
code { value: "test1" }
} }
}
extension {
url { value: "source" }
value { reference { encounter_id { value: "2" } } }
}
extension {
url { value: "label" }
extension {
url { value: "className" }
value { coding {
system { value: "urn:test:label:test1" }
code { value: "red" }
} }
}
}
}
} } }
""", resources_pb2.Bundle())
trigger1 = text_format.Parse(
"""
type {
system { value: "urn:test:trigger" }
code { value: "at_discharge" }
}
event_time { value_us: 1388566800000000 } # "2014-01-01T09:00:00+00:00"
""", google_extensions_pb2.EventTrigger())
trigger2 = text_format.Parse(
"""
type {
system { value: "urn:test:trigger" }
code { value: "at_discharge" }
}
event_time { value_us: 1420102800000000 } # "2015-01-01T09:00:00+00:00"
""", google_extensions_pb2.EventTrigger())
label1 = text_format.Parse(
"""
type {
system { value: "urn:test:label" }
code { value: "test1" }
}
event_time { value_us: 1388566800000000 }
source { encounter_id { value: "1" } }
""", google_extensions_pb2.EventLabel())
label2 = text_format.Parse(
"""
type {
system { value: "urn:test:label" }
code { value: "test1" }
}
source { encounter_id { value: "2" } }
label {
class_name {
system { value: "urn:test:label:test1" }
code { value: "red" }
}
}
""", google_extensions_pb2.EventLabel())
# pylint: enable=line-too-long
(filtered_count, got_list) = bundle_to_seqex_util.get_trigger_labels_pair(
bundle, [b"test1"], b"at_discharge")
self.assertEqual(0, filtered_count)
self.assertLen(got_list, 2)
(got_trigger_1, got_label_list1) = got_list[0]
(got_trigger_2, got_label_list2) = got_list[1]
self.assertProtoEqual(got_trigger_1, trigger1)
self.assertLen(got_label_list1, 1)
self.assertProtoEqual(got_label_list1[0], label1)
self.assertProtoEqual(got_trigger_2, trigger2)
self.assertLen(got_label_list2, 1)
self.assertProtoEqual(got_label_list2[0], label2)
