def get_medications(self):
medications = []
entries = self._tree.get_entries_by_template(Root.MEDICATION)
for entry in entries:
medication = messages.Medication()
medication.product = messages.Product()
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
medication.date_range = messages.DateRange(**date_range)
product_node = entry.getElementsByTagName('manufacturedProduct')[0]
product_code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(product_code_node)
medication.product.code = messages.Code(**product_code)
quantity_nodes = entry.getElementsByTagName('doseQuantity')
if quantity_nodes:
node = quantity_nodes[0]
medication.dose_quantity = CcdaTree.get_quantity_message_from_node(
node)
rate_nodes = entry.getElementsByTagName('rateQuantity')
if rate_nodes:
node = rate_nodes[0]
medication.rate_quantity = CcdaTree.get_quantity_message_from_node(
node)
# TODO: precondition, reason, route, vehicle, administration, prescriber.
medications.append(medication)
return medications
def get_vitals(self):
vitals = []
entries = self._tree.get_entries_by_template(Root.VITAL)
for entry in entries:
vital = messages.Vital()
vital.date = CcdaTree.get_date_from_effective_time(entry)
vital.results = []
result_entries = entry.getElementsByTagName('component')
for result_entry in result_entries:
vital_result = messages.VitalResult()
code_node = result_entry.getElementsByTagName('code')[0]
value_node = result_entry.getElementsByTagName('value')[0]
vital_result_code = CcdaTree.get_code_from_node(code_node)
vital_result.code = messages.Code(**vital_result_code)
vital_result.value = int(
float(value_node.getAttribute('value')))
vital_result.unit = value_node.getAttribute('unit')
vital.results.append(vital_result)
vitals.append(vital)
return vitals
def get_procedures(self):
procedures = []
procedure_parent = self._tree.get_entries_by_template(
Root.PROCEDURE)[0]
entries = procedure_parent.getElementsByTagName('entry')
for entry in entries:
procedure = messages.Procedure()
code_node = entry.getElementsByTagName('code')[0]
# print(entry.getchildren())
# print(messages.Code(**CcdaTree.get_code_from_node(code_node)))
procedure_code = CcdaTree.get_code_from_node(code_node)
procedure.code = messages.Code(**procedure_code)
procedure.date = CcdaTree.get_date_from_effective_time(entry)
# TODO: Implement specimen, performer, device.
procedures.append(procedure)
# x = dom.createElement("foo")
# txt = dom.createTextNode("hello, world!") # creates "hello, world!"
# x.appendChild(txt) # results in <foo>hello, world!</foo>
return procedures
def to_message(self):
"""Converts the CCDA document to a ProtoRPC message."""
# TODO: Remove duplicate code.
doc = messages.CcdaDocument()
# Demographics.
doc.demographics = messages.Demographic()
doc.demographics.dob = self._tree.get_dob()
doc.demographics.gender = messages.Code(**self._tree.get_gender())
doc.demographics.marital_status = messages.Code(
**self._tree.get_marital_status())
doc.demographics.language = self._tree.get_language()
doc.demographics.race = messages.Code(**self._tree.get_race())
doc.demographics.ethnicity = messages.Code(
**self._tree.get_ethnicity())
doc.demographics.religion = messages.Code(**self._tree.get_religion())
doc.demographics.birthplace = messages.Address(
**self._tree.get_birthplace())
# Allergies.
# TODO: Implement allergies.
doc.allergies = []
entries = self._tree.get_entries_by_template(Root.ALLERGY)
for entry in entries:
allergy = messages.Allergy()
participantVal = entry.getElementsByTagName('participant')
if participantVal:
participantRoleVal = participantVal[0].getElementsByTagName(
'participantRole')
if participantRoleVal:
playingEntityVal = participantRoleVal[
0].getElementsByTagName('playingEntity')
if playingEntityVal:
codeVals = playingEntityVal[0].getElementsByTagName(
'code')
if codeVals:
codeVal = codeVals[0]
allergy.code = messages.Code()
allergy.code.code = codeVal.getAttribute('code')
allergy.code.name = codeVal.getAttribute(
'displayName')
allergy.code.code_system = codeVal.getAttribute(
'codeSystem')
allergy.code.code_system_name = codeVal.getAttribute(
'codeSystemName')
allergyReactionNode = self._tree.get_entries_by_template(
Root.ALLERGY_REACTION, entry)
if allergyReactionNode:
allergyReactionObservationNode = allergyReactionNode[0]
if allergyReactionObservationNode:
valueVals = allergyReactionObservationNode.getElementsByTagName(
'value')
if valueVals:
valueval = valueVals[0]
allergy.reaction = messages.Code()
allergy.reaction.code = valueval.getAttribute('code')
allergy.reaction.name = valueval.getAttribute(
'displayName')
allergy.reaction.code_system = valueval.getAttribute(
'codeSystem')
allergy.reaction.code_system_name = valueval.getAttribute(
'codeSystemName')
allergySeverityNode = self._tree.get_entries_by_template(
Root.ALLERGY_SEVERITY, entry)
if allergySeverityNode:
allergySeverityObservationNode = allergySeverityNode[0]
if allergySeverityObservationNode:
valueVals = allergySeverityObservationNode.getElementsByTagName(
'value')
if valueVals:
valueval = valueVals[0]
allergy.severity = messages.Code()
allergy.severity.code = valueval.getAttribute('code')
allergy.severity.name = valueval.getAttribute(
'displayName')
allergy.severity.code_system = valueval.getAttribute(
'codeSystem')
allergy.severity.code_system_name = valueval.getAttribute(
'codeSystemName')
doc.allergies.append(allergy)
# Immunizations.
doc.immunizations = []
entries = self._tree.get_entries_by_template(Root.IMMUNIZATION)
for entry in entries:
product_nodes = self._tree.get_entries_by_template(
Root.IMMUNIZATION_PRODUCT, parent=entry)
if product_nodes:
product_node = product_nodes[0]
immunization = messages.Immunization()
immunization.date = CcdaTree.get_date_from_effective_time(
entry)
immunization.product = messages.Product()
code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(code_node)
immunization.product.code = messages.Code(**product_code)
doc.immunizations.append(immunization)
# Labs.
doc.labs = []
lab_parent = self._tree.get_entries_by_template(Root.LAB)
if lab_parent:
entries = lab_parent[0].getElementsByTagName('entry')
for entry in entries:
lab = messages.Lab()
code_node = entry.getElementsByTagName('code')[0]
lab_code = CcdaTree.get_code_from_node(code_node)
lab.code = messages.Code(**lab_code)
lab.results = []
component_nodes = entry.getElementsByTagName('component')
for component_node in component_nodes:
result_code_nodes = component_node.getElementsByTagName(
'code')
lab_result = messages.LabResult()
if result_code_nodes:
result_code_node = result_code_nodes[0]
result_code = CcdaTree.get_code_from_node(
result_code_node)
lab_result.code = messages.Code(**result_code)
valueVals = component_node.getElementsByTagName('value')
if valueVals:
lab_result.value = valueVals[0].getAttribute('value')
if lab_result.value:
lab_result.unit = valueVals[0].getAttribute('unit')
else:
if valueVals[0].firstChild:
lab_result.value = valueVals[
0].firstChild.nodeValue
lab_result.date = CcdaTree.get_date_from_effective_time(
component_node)
lab.results.append(lab_result)
doc.labs.append(lab)
# Medications.
doc.medications = []
entries = self._tree.get_entries_by_template(Root.MEDICATION)
for entry in entries:
medication = messages.Medication()
medication.product = messages.Product()
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
medication.date_range = messages.DateRange(**date_range)
product_node = entry.getElementsByTagName('manufacturedProduct')[0]
product_code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(product_code_node)
medication.product.code = messages.Code(**product_code)
quantity_nodes = entry.getElementsByTagName('doseQuantity')
if quantity_nodes:
node = quantity_nodes[0]
medication.dose_quantity = CcdaTree.get_quantity_message_from_node(
node)
rate_nodes = entry.getElementsByTagName('rateQuantity')
if rate_nodes:
node = rate_nodes[0]
medication.rate_quantity = CcdaTree.get_quantity_message_from_node(
node)
# TODO: precondition, reason, route, vehicle, administration, prescriber.
doc.medications.append(medication)
# Problems.
doc.problems = []
entries = self._tree.get_entries_by_template(Root.PROBLEM)
for entry in entries:
problem = messages.Problem()
code_node = entry.getElementsByTagName('value')
# problem_code = CcdaTree.get_code_from_node(code_node)
# problem.code = messages.Code(**problem_code)
if code_node:
valueval = code_node[0]
problem.code = messages.Code()
problem.code.code = valueval.getAttribute('code')
problem.code.name = valueval.getAttribute('displayName')
problem.code.code_system = valueval.getAttribute('codeSystem')
problem.code.code_system_name = valueval.getAttribute(
'codeSystemName')
date_nodes = entry.getElementsByTagName('effectiveTime')
for date_node in date_nodes:
date_range = CcdaTree.get_date_range_from_node(date_node)
problem.date_range = messages.DateRange(**date_range)
status_nodes = self._tree.get_entries_by_template(
Root.PROBLEM_STATUS, parent=entry)
if status_nodes:
status_node = status_nodes[0]
entry_node = status_node.getElementsByTagName('value')[0]
problem.status = entry_node.getAttribute('displayName')
# TODO: Implement problem.age.
doc.problems.append(problem)
# Procedures.
doc.procedures = []
procedure_parent = self._tree.get_entries_by_template(Root.PROCEDURE)
if procedure_parent:
entries = procedure_parent[0].getElementsByTagName('entry')
for entry in entries:
procedure = messages.Procedure()
code_node = entry.getElementsByTagName('code')[0]
procedure_code = CcdaTree.get_code_from_node(code_node)
procedure.code = messages.Code(**procedure_code)
procedure.date = CcdaTree.get_date_from_effective_time(entry)
# TODO: Implement specimen, performer, device.
doc.procedures.append(procedure)
# Vitals.
doc.vitals = []
vitals_parent = self._tree.get_entries_by_template(Root.VITAL)
if vitals_parent:
entries = vitals_parent[0].getElementsByTagName('entry')
for entry in entries:
vital = messages.Vital()
vital.date = CcdaTree.get_date_from_effective_time(entry)
vital.results = []
result_entries = entry.getElementsByTagName('component')
for result_entry in result_entries:
vital_result = messages.VitalResult()
code_node = result_entry.getElementsByTagName('code')[0]
value_node = result_entry.getElementsByTagName('value')[0]
vital_result_code = CcdaTree.get_code_from_node(code_node)
vital_result.code = messages.Code(**vital_result_code)
value_attribute = value_node.getAttribute('value')
if value_attribute:
#if not value_attribute.isalnum():
try:
vital_result.value = long(float(value_attribute))
except ValueError:
vital_result.value = None
else:
vital_result.value = None
vital_result.unit = value_node.getAttribute('unit')
vital.results.append(vital_result)
doc.vitals.append(vital)
return doc
def to_message(self):
"""Converts the CCDA document to a ProtoRPC message."""
# TODO: Remove duplicate code.
doc = messages.CcdaDocument()
# Allergies.
# TODO: Implement allergies.
doc.allergies = [messages.Allergy()]
# Demographics.
doc.demographics = messages.Demographic()
doc.demographics.dob = self._tree.get_dob()
doc.demographics.gender = messages.Code(**self._tree.get_gender())
doc.demographics.marital_status = messages.Code(
**self._tree.get_marital_status())
doc.demographics.language = self._tree.get_language()
doc.demographics.race = messages.Code(**self._tree.get_race())
doc.demographics.ethnicity = messages.Code(
**self._tree.get_ethnicity())
doc.demographics.religion = messages.Code(**self._tree.get_religion())
doc.demographics.birthplace = messages.Address(
**self._tree.get_birthplace())
# Immunizations.
doc.immunizations = []
entries = self._tree.get_entries_by_template(Root.IMMUNIZATION)
for entry in entries:
product_node = self._tree.get_entries_by_template(
Root.IMMUNIZATION_PRODUCT, parent=entry)[0]
immunization = messages.Immunization()
immunization.date = CcdaTree.get_date_from_effective_time(entry)
immunization.product = messages.Product()
code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(code_node)
immunization.product.code = messages.Code(**product_code)
# Labs.
doc.labs = []
lab_parent = self._tree.get_entries_by_template(Root.LAB)[0]
entries = lab_parent.getElementsByTagName('entry')
for entry in entries:
lab = messages.Lab()
code_node = entry.getElementsByTagName('code')[0]
lab_code = CcdaTree.get_code_from_node(code_node)
lab.code = messages.Code(**lab_code)
lab.result = messages.LabResult()
component_node = entry.getElementsByTagName('component')[0]
result_code_node = component_node.getElementsByTagName('code')[0]
result_code = CcdaTree.get_code_from_node(result_code_node)
lab.result.code = messages.Code(**result_code)
doc.labs.append(lab)
# Medications.
doc.medications = []
entries = self._tree.get_entries_by_template(Root.MEDICATION)
for entry in entries:
medication = messages.Medication()
medication.product = messages.Product()
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
medication.date_range = messages.DateRange(**date_range)
product_node = entry.getElementsByTagName('manufacturedProduct')[0]
product_code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(product_code_node)
medication.product.code = messages.Code(**product_code)
quantity_nodes = entry.getElementsByTagName('doseQuantity')
if quantity_nodes:
node = quantity_nodes[0]
medication.dose_quantity = CcdaTree.get_quantity_message_from_node(
node)
rate_nodes = entry.getElementsByTagName('rateQuantity')
if rate_nodes:
node = rate_nodes[0]
medication.rate_quantity = CcdaTree.get_quantity_message_from_node(
node)
# TODO: precondition, reason, route, vehicle, administration, prescriber.
doc.medications.append(medication)
# Problems.
doc.problems = []
entries = self._tree.get_entries_by_template(Root.PROBLEM)
for entry in entries:
problem = messages.Problem()
code_node = entry.getElementsByTagName('code')[0]
problem_code = CcdaTree.get_code_from_node(code_node)
problem.code = messages.Code(**problem_code)
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
problem.date_range = messages.DateRange(**date_range)
status_nodes = self._tree.get_entries_by_template(
Root.PROBLEM_STATUS, parent=entry)
if status_nodes:
status_node = status_nodes[0]
entry_node = status_node.getElementsByTagName('value')[0]
problem.status = entry_node.getAttribute('displayName')
# TODO: Implement problem.age.
doc.problems.append(problem)
# Procedures.
doc.procedures = []
procedure_parent = self._tree.get_entries_by_template(
Root.PROCEDURE)[0]
entries = procedure_parent.getElementsByTagName('entry')
for entry in entries:
procedure = messages.Procedure()
code_node = entry.getElementsByTagName('code')[0]
procedure_code = CcdaTree.get_code_from_node(code_node)
procedure.code = messages.Code(**procedure_code)
procedure.date = CcdaTree.get_date_from_effective_time(entry)
# TODO: Implement specimen, performer, device.
doc.procedures.append(procedure)
# Vitals.
doc.vitals = []
entries = self._tree.get_entries_by_template(Root.VITAL)
for entry in entries:
vital = messages.Vital()
vital.date = CcdaTree.get_date_from_effective_time(entry)
vital.results = []
result_entries = entry.getElementsByTagName('component')
for result_entry in result_entries:
vital_result = messages.VitalResult()
code_node = result_entry.getElementsByTagName('code')[0]
value_node = result_entry.getElementsByTagName('value')[0]
vital_result_code = CcdaTree.get_code_from_node(code_node)
vital_result.code = messages.Code(**vital_result_code)
vital_result.value = int(
float(value_node.getAttribute('value')))
vital_result.unit = value_node.getAttribute('unit')
vital.results.append(vital_result)
doc.vitals.append(vital)
return doc
def to_message(self):
"""Converts the CCDA document to a ProtoRPC message."""
# TODO: Remove duplicate code.
doc = messages.CcdaDocument()
''' Not of interest
# Demographics.
doc.demographics = messages.Demographic()
doc.demographics.dob = self._tree.get_dob()
doc.demographics.gender = messages.Code(**self._tree.get_gender())
doc.demographics.marital_status = messages.Code(
**self._tree.get_marital_status())
doc.demographics.language = self._tree.get_language()
doc.demographics.race = messages.Code(
**self._tree.get_race())
doc.demographics.ethnicity = messages.Code(
**self._tree.get_ethnicity())
doc.demographics.religion = messages.Code(
**self._tree.get_religion())
doc.demographics.birthplace = messages.Address(
**self._tree.get_birthplace())
'''
# Labs.
doc.labs = []
lab_parent = self._tree.get_entries_by_template(Root.LAB)[0]
entries = lab_parent.getElementsByTagName('entry')
for entry in entries:
#prettyentry_string = entry.toprettyxml()
lab = messages.Lab()
observationEntries = entry.getElementsByTagName('observation')
for observationEntry in observationEntries:
observation = messages.Observation()
ValueNode = observationEntry.getElementsByTagName('value')
DateNode = observationEntry.getElementsByTagName(
'effectiveTime')
try:
observation.name = ''
observation.value = ValueNode[0].attributes.getNamedItem(
'value').value
observation.unit = ValueNode[0].attributes.getNamedItem(
'unit').value
observation.date = datetime.datetime.strptime(
DateNode[0].attributes.getNamedItem('value').value,
'%Y%m%d%H%M%S-%f')
lab.observations.append(observation)
except:
observation.name = ''
observation.value = "error"
observation.unit = "error"
observation.date = datetime.datetime.strptime(
'29000101', '%Y%m%d')
doc.labs.append(lab)
# Medications.
doc.medications = []
entries = self._tree.get_entries_by_template(Root.MEDICATION)
for entry in entries:
prettyentry_string = entry.toprettyxml()
medication = messages.Medication()
medication.product = messages.Product()
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
medication.date_range = messages.DateRange(**date_range)
product_node = entry.getElementsByTagName('manufacturedProduct')[0]
product_code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(product_code_node)
medication.product.code = messages.Code(**product_code)
quantity_nodes = entry.getElementsByTagName('doseQuantity')
if quantity_nodes:
node = quantity_nodes[0]
medication.dose_quantity = CcdaTree.get_quantity_message_from_node(
node)
rate_nodes = entry.getElementsByTagName('rateQuantity')
if rate_nodes:
node = rate_nodes[0]
medication.rate_quantity = CcdaTree.get_quantity_message_from_node(
node)
# TODO: precondition, reason, route, vehicle, administration, prescriber.
doc.medications.append(medication)
# Problems.
doc.problems = []
entries = self._tree.get_entries_by_template(Root.PROBLEM)
for entry in entries:
problem = messages.Problem()
code_node = entry.getElementsByTagName('code')[0]
problem_code = CcdaTree.get_code_from_node(code_node)
problem.code = messages.Code(**problem_code)
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
problem.date_range = messages.DateRange(**date_range)
status_nodes = self._tree.get_entries_by_template(
Root.PROBLEM_STATUS, parent=entry)
if status_nodes:
status_node = status_nodes[0]
entry_node = status_node.getElementsByTagName('value')[0]
problem.status = entry_node.getAttribute('displayName')
# TODO: Implement problem.age.
doc.problems.append(problem)
# Procedures.
doc.procedures = []
procedure_parent = self._tree.get_entries_by_template(
Root.PROCEDURE)[0]
entries = procedure_parent.getElementsByTagName('entry')
for entry in entries:
procedure = messages.Procedure()
code_node = entry.getElementsByTagName('code')[0]
procedure_code = CcdaTree.get_code_from_node(code_node)
procedure.code = messages.Code(**procedure_code)
procedure.date = CcdaTree.get_date_from_effective_time(entry)
# TODO: Implement specimen, performer, device.
doc.procedures.append(procedure)
# Vitals.
doc.vitals = []
entries = self._tree.get_entries_by_template(Root.VITAL)
for entry in entries:
vital = messages.Vital()
vital.date = CcdaTree.get_date_from_effective_time(entry)
vital.results = []
result_entries = entry.getElementsByTagName('component')
for result_entry in result_entries:
vital_result = messages.VitalResult()
code_node = result_entry.getElementsByTagName('code')[0]
value_node = result_entry.getElementsByTagName('value')[0]
vital_result_code = CcdaTree.get_code_from_node(code_node)
vital_result.code = messages.Code(**vital_result_code)
vital_result.value = long(
float(value_node.getAttribute('value')))
vital_result.unit = value_node.getAttribute('unit')
vital.results.append(vital_result)
doc.vitals.append(vital)
return doc
def to_message(self):
"""Converts the CCDA document to a ProtoRPC message."""
# TODO: Remove duplicate code.
doc = messages.CcdaDocument()
# Allergies.
''' My modification starts here ..'''
doc.allergies = [
] # Create a list to store details of allergies from given C-CDA Xml file.
entries = self._tree.get_entries_by_template(Root.ALLERGY)
''' entries is a list. It holds DOMs (Document Object Model) for templates with attribute (root) value is
Root.ALLERGY from a given C-CDA Xml. Regarding each DOM, we need to access tags and their attributes by using
entry. '''
for entry in entries:
allergy = messages.Allergy(
) # For each DOM, use messages.py to create an object of class Allergy to store
# information about an allergy.
''' Enter allergy observation details '''
date_node = entry.getElementsByTagName('effectiveTime')[
0] # date_node is first DOM for tag <effectiveTime>.
date_range = CcdaTree.get_date_range_from_node(date_node)
allergy.date_range = messages.DateRange(**date_range)
participant = entry.getElementsByTagName('participant')[0]
''' # [0] for first participant object from a list of objects for <participant> under entry '''
if participant:
participantRole = participant.getElementsByTagName(
'participantRole')[0]
''' # [0] for first participantRole object from a list of objects for <participantRole> under <participant> '''
if participantRole:
playingEntity = participantRole.getElementsByTagName(
'playingEntity')[0]
''' # [0] for first playingEntity object from a list of objects for <playingEntity> under <participantRole> '''
code_node = playingEntity.getElementsByTagName('code')[0]
''' # [0] for first code object from a list of objects for <code> under <playingEntity> '''
allergy_code = CcdaTree.get_code_from_node(code_node)
''' get_code_from_node(code_node) assigns and returns values for attributes (code, codeSystem.. e.t.c) for <code>
as code = '7982', displayName = 'Penicillin G benezathine, .... etc'''
allergy.code = messages.Code(**allergy_code)
''' **kwargs is used to specify any number of arguments for a function and then it makes a dictionary from those arguments '''
''' Enter allergy status details '''
allergy_status = self._tree.get_entries_by_template(
Root.ALLERGY_STATUS, parent=entry)[0]
allergy_status_value_node = allergy_status.getElementsByTagName(
'value')[0]
allergy_status_value = CcdaTree.get_code_from_node(
allergy_status_value_node)
allergy.allergen = messages.Code(**allergy_status_value)
''' Enter allergy reaction details '''
allergy_reaction = self._tree.get_entries_by_template(
Root.ALLERGY_RECATION, parent=entry)[0]
allergy_reaction_value_node = allergy_reaction.getElementsByTagName(
'value')[0]
allergy_reaction_value = CcdaTree.get_code_from_node(
allergy_reaction_value_node)
allergy.reaction = messages.Code(**allergy_reaction_value)
''' Enter allergy severity details '''
allergy_severity = self._tree.get_entries_by_template(
Root.ALLERGY_SEVERITY, parent=entry)[0]
allergy_severity_value_node = allergy_severity.getElementsByTagName(
'value')[0]
allergy.severity = allergy_severity_value_node.getAttribute(
'displayName')
doc.allergies.append(allergy)
''' For each entry, adds allergy object to prepare ProtoRPC message for allergies '''
''' My modification ends here ....'''
# Demographics.
doc.demographics = messages.Demographic()
doc.demographics.dob = self._tree.get_dob()
doc.demographics.gender = messages.Code(**self._tree.get_gender())
doc.demographics.marital_status = messages.Code(
**self._tree.get_marital_status())
doc.demographics.language = self._tree.get_language()
doc.demographics.race = messages.Code(**self._tree.get_race())
doc.demographics.ethnicity = messages.Code(
**self._tree.get_ethnicity())
doc.demographics.religion = messages.Code(**self._tree.get_religion())
doc.demographics.birthplace = messages.Address(
**self._tree.get_birthplace())
# Immunizations.
doc.immunizations = []
entries = self._tree.get_entries_by_template(Root.IMMUNIZATION)
for entry in entries:
product_node = self._tree.get_entries_by_template(
Root.IMMUNIZATION_PRODUCT, parent=entry)[0]
immunization = messages.Immunization()
immunization.date = CcdaTree.get_date_from_effective_time(entry)
immunization.product = messages.Product()
code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(code_node)
immunization.product.code = messages.Code(**product_code)
doc.immunizations.append(immunization)
# Labs.
doc.labs = []
lab_parent = self._tree.get_entries_by_template(Root.LAB)[0]
entries = lab_parent.getElementsByTagName('entry')
for entry in entries:
lab = messages.Lab()
code_node = entry.getElementsByTagName('code')[0]
lab_code = CcdaTree.get_code_from_node(code_node)
lab.code = messages.Code(**lab_code)
lab.result = messages.LabResult()
component_node = entry.getElementsByTagName('component')[0]
result_code_node = component_node.getElementsByTagName('code')[0]
result_code = CcdaTree.get_code_from_node(result_code_node)
lab.result.code = messages.Code(**result_code)
doc.labs.append(lab)
# Medications.
doc.medications = []
entries = self._tree.get_entries_by_template(Root.MEDICATION)
for entry in entries:
medication = messages.Medication()
medication.product = messages.Product()
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
medication.date_range = messages.DateRange(**date_range)
product_node = entry.getElementsByTagName('manufacturedProduct')[0]
product_code_node = product_node.getElementsByTagName('code')[0]
product_code = CcdaTree.get_code_from_node(product_code_node)
medication.product.code = messages.Code(**product_code)
quantity_nodes = entry.getElementsByTagName('doseQuantity')
if quantity_nodes:
node = quantity_nodes[0]
medication.dose_quantity = CcdaTree.get_quantity_message_from_node(
node)
rate_nodes = entry.getElementsByTagName('rateQuantity')
if rate_nodes:
node = rate_nodes[0]
medication.rate_quantity = CcdaTree.get_quantity_message_from_node(
node)
# TODO: precondition, reason, route, vehicle, administration, prescriber.
doc.medications.append(medication)
# Problems.
doc.problems = []
entries = self._tree.get_entries_by_template(Root.PROBLEM)
for entry in entries:
problem = messages.Problem()
code_node = entry.getElementsByTagName('code')[0]
problem_code = CcdaTree.get_code_from_node(code_node)
problem.code = messages.Code(**problem_code)
date_node = entry.getElementsByTagName('effectiveTime')[0]
date_range = CcdaTree.get_date_range_from_node(date_node)
problem.date_range = messages.DateRange(**date_range)
status_nodes = self._tree.get_entries_by_template(
Root.PROBLEM_STATUS, parent=entry)
if status_nodes:
status_node = status_nodes[0]
entry_node = status_node.getElementsByTagName('value')[0]
problem.status = entry_node.getAttribute('displayName')
# TODO: Implement problem.age.
doc.problems.append(problem)
# Procedures.
doc.procedures = []
procedure_parent = self._tree.get_entries_by_template(
Root.PROCEDURE)[0]
entries = procedure_parent.getElementsByTagName('entry')
for entry in entries:
procedure = messages.Procedure()
code_node = entry.getElementsByTagName('code')[0]
procedure_code = CcdaTree.get_code_from_node(code_node)
procedure.code = messages.Code(**procedure_code)
procedure.date = CcdaTree.get_date_from_effective_time(entry)
# TODO: Implement specimen, performer, device.
doc.procedures.append(procedure)
# Vitals.
doc.vitals = []
entries = self._tree.get_entries_by_template(Root.VITAL)
for entry in entries:
vital = messages.Vital()
vital.date = CcdaTree.get_date_from_effective_time(entry)
vital.results = []
result_entries = entry.getElementsByTagName('component')
for result_entry in result_entries:
vital_result = messages.VitalResult()
code_node = result_entry.getElementsByTagName('code')[0]
value_node = result_entry.getElementsByTagName('value')[0]
vital_result_code = CcdaTree.get_code_from_node(code_node)
vital_result.code = messages.Code(**vital_result_code)
vital_result.value = long(
float(value_node.getAttribute('value')))
vital_result.unit = value_node.getAttribute('unit')
vital.results.append(vital_result)
doc.vitals.append(vital)
return doc