def _get_start_stop_datetime(self, form_config):
"""
Returns a start datetime for the Visit and the Encounter, and a
stop_datetime for the Visit
"""
if form_config.openmrs_start_datetime:
cc_start_datetime_str = form_config.openmrs_start_datetime._get_commcare_value(self.info)
if cc_start_datetime_str is None:
raise ConfigurationError(
'A form config for form XMLNS "{}" uses "openmrs_start_datetime" to get the start of '
'the visit but no value was found in the form.'.format(form_config.xmlns)
)
try:
cc_start_datetime = string_to_utc_datetime(cc_start_datetime_str)
except ValueError:
raise ConfigurationError(
'A form config for form XMLNS "{}" uses "openmrs_start_datetime" to get the start of '
'the visit but an invalid value was found in the form.'.format(form_config.xmlns)
)
cc_stop_datetime = cc_start_datetime + timedelta(days=1) - timedelta(seconds=1)
# We need to use openmrs_start_datetime.serialize()
# for both values because they could be either
# OpenMRS datetimes or OpenMRS dates, and their data
# types must match.
start_datetime = form_config.openmrs_start_datetime.serialize(cc_start_datetime)
stop_datetime = form_config.openmrs_start_datetime.serialize(cc_stop_datetime)
else:
cc_start_datetime = string_to_utc_datetime(self.form_json['form']['meta']['timeEnd'])
cc_stop_datetime = cc_start_datetime + timedelta(days=1) - timedelta(seconds=1)
start_datetime = to_omrs_datetime(cc_start_datetime)
stop_datetime = to_omrs_datetime(cc_stop_datetime)
return start_datetime, stop_datetime
def validate_parent_ref(parent_ref, parent_resource_type):
"""
Validates that ``parent_ref`` is a relative reference with an
expected resource type. e.g. "Patient/12345"
"""
try:
resource_type_name, resource_id = parent_ref.split('/')
except (AttributeError, ValueError):
raise ConfigurationError(f'Unexpected reference format {parent_ref!r}')
if resource_type_name != parent_resource_type.name:
raise ConfigurationError(
'Resource type does not match expected parent resource type')
def save(self, *args, **kwargs):
if (self.case_property and
self.case_property.case_type != self.resource_type.case_type):
raise ConfigurationError(
"Invalid FHIRResourceProperty: case_property case type "
f"'{self.case_property.case_type}' does not match "
f"resource_type case type '{self.resource_type.case_type}'.")
if ((self.case_property or self.jsonpath or self.value_map)
and self.value_source_config):
raise ConfigurationError(
"Invalid FHIRResourceProperty: Unable to set "
"'value_source_config' when 'case_property', 'jsonpath' or "
"'value_map' are set.")
super().save(*args, **kwargs)
def get_case_properties(patient, importer):
"""
Returns case name and dictionary of case properties to update
Raises ConfigurationError if a value cannot be deserialized using
the data types given in a column mapping.
"""
name_columns = importer.name_columns.split(' ')
case_name = ' '.join([patient[column] for column in name_columns])
errors = []
fields_to_update = {}
tz = importer.get_timezone()
for mapping in importer.column_map:
value = patient[mapping.column]
try:
fields_to_update[mapping.property] = deserialize(
mapping, value, tz)
except (TypeError, ValueError) as err:
errors.append(
f'Unable to deserialize value {repr(value)} '
f'in column "{mapping.column}" for case property '
f'"{mapping.property}". OpenMRS data type is given as '
f'"{mapping.data_type}". CommCare data type is given as '
f'"{mapping.commcare_data_type}": {err}')
if errors:
raise ConfigurationError(f'Errors importing from {importer}:\n' +
'\n'.join(errors))
return case_name, fields_to_update
def get_case_block_for_indexed_case(mapping, external_data, parent_case_id,
parent_case_type, default_owner_id):
relationship = mapping.indexed_case_mapping.relationship
case_block_kwargs = {
"index": {
mapping.indexed_case_mapping.identifier:
IndexAttrs(
parent_case_type,
parent_case_id,
relationship,
)
},
"update": {}
}
for value_source in mapping.indexed_case_mapping.case_properties:
value = value_source.get_import_value(external_data)
if value_source.case_property in CASE_BLOCK_ARGS:
case_block_kwargs[value_source.case_property] = value
else:
case_block_kwargs["update"][value_source.case_property] = value
case_id = uuid.uuid4().hex
case_type = mapping.indexed_case_mapping.case_type
case_block_kwargs.setdefault("owner_id", default_owner_id)
if not case_block_kwargs["owner_id"]:
raise ConfigurationError(
_(f'Unable to determine mobile worker to own new "{case_type}" '
f'{relationship} case or parent case "{parent_case_id}"'))
case_block = CaseBlock(create=True,
case_id=case_id,
case_type=case_type,
**case_block_kwargs)
return case_block
def import_patients_of_owner(requests,
importer,
domain_name,
owner_id,
location=None):
try:
openmrs_patients = get_openmrs_patients(requests, importer, location)
except RequestException as err:
requests.notify_exception(
f'Unable to import patients for project space "{domain_name}" '
f'using {importer}: Error calling API: {err}')
return
except (KeyError, IndexError, TypeError, ValueError) as err:
requests.notify_exception(
f'Unable to import patients for project space "{domain_name}" '
f'using {importer}: Unexpected response format: {err}')
return
case_blocks = []
for i, patient in enumerate(openmrs_patients):
try:
patient_id = str(patient[importer.external_id_column])
except KeyError:
raise ConfigurationError(
f'Error importing patients for project space "{importer.domain}" '
f'from OpenMRS Importer "{importer}": External ID column '
f'"{importer.external_id_column}" not found in patient data.')
case, error = importer_util.lookup_case(EXTERNAL_ID, patient_id,
domain_name,
importer.case_type)
if error is None:
case_block = get_updatepatient_caseblock(case, patient, importer)
case_blocks.append(RowAndCase(i, case_block))
elif error == LookupErrors.NotFound:
case_block = get_addpatient_caseblock(patient, importer, owner_id)
case_blocks.append(RowAndCase(i, case_block))
elif error == LookupErrors.MultipleResults:
raise ConfigurationError(
f'Error importing patients for project space "{importer.domain}" '
f'from OpenMRS Importer "{importer}": {importer.case_type}'
f'.{EXTERNAL_ID} "{patient_id}" is not unique.')
submit_case_blocks(
[cb.case.as_text() for cb in case_blocks],
domain_name,
device_id=f'{OPENMRS_IMPORTER_DEVICE_ID_PREFIX}{importer.get_id}',
xmlns=XMLNS_OPENMRS,
)
def update_patient(repeater, patient_uuid):
"""
Fetch patient from OpenMRS, submit case update for all mapped case
properties.
.. NOTE:: OpenMRS UUID must be saved to "external_id" case property
"""
if len(repeater.white_listed_case_types) != 1:
raise ConfigurationError(
_(f'{repeater.domain}: {repeater}: Error in settings: Unable to update '
f'patients from OpenMRS unless only one case type is specified.')
)
case_type = repeater.white_listed_case_types[0]
try:
patient = get_patient_by_uuid(repeater.requests, patient_uuid)
except (RequestException, ValueError) as err:
raise OpenmrsException(
_(f'{repeater.domain}: {repeater}: Error fetching Patient '
f'{patient_uuid!r}: {err}')) from err
case, error = importer_util.lookup_case(
EXTERNAL_ID,
patient_uuid,
repeater.domain,
case_type=case_type,
)
if error == LookupErrors.NotFound:
if not repeater.openmrs_config.case_config.import_creates_cases:
# We can't create cases via the Atom feed, just update them.
# Nothing to do here.
return
default_owner: Optional[CommCareUser] = repeater.first_user
case_block = get_addpatient_caseblock(case_type, default_owner,
patient, repeater)
elif error == LookupErrors.MultipleResults:
# Multiple cases have been matched to the same patient.
# Could be caused by:
# * The cases were given the same identifier value. It could
# be user error, or case config assumed identifier was
# unique but it wasn't.
# * PatientFinder matched badly.
# * Race condition where a patient was previously added to
# both CommCare and OpenMRS.
raise DuplicateCaseMatch(
_(f'{repeater.domain}: {repeater}: More than one case found '
f'matching unique OpenMRS UUID. case external_id: "{patient_uuid}"'
))
else:
case_block = get_updatepatient_caseblock(case, patient, repeater)
if case_block:
submit_case_blocks(
[case_block.as_text()],
repeater.domain,
xmlns=XMLNS_OPENMRS,
device_id=OPENMRS_ATOM_FEED_DEVICE_ID + repeater.get_id,
)
def get_owner(self):
if not self.owner_id:
raise ConfigurationError('Owner ID missing')
try:
if self.owner_type == OWNER_TYPE_GROUP:
return Group.get(self.owner_id)
elif self.owner_type == OWNER_TYPE_LOCATION:
return SQLLocation.objects.get(location_id=self.owner_id)
elif self.owner_type == OWNER_TYPE_USER:
user = CouchUser.get_by_user_id(self.owner_id)
if user:
return user
else:
raise ResourceNotFound()
else:
raise ConfigurationError(f'Unknown owner type {self.owner_type!r}')
except (ResourceNotFound, SQLLocation.DoesNotExist):
raise ConfigurationError(f'{self.owner_type.capitalize()} '
f'{self.owner_id!r} does not exist')
def validate_resource(self, fhir_resource):
schema = self.get_json_schema()
resolver = RefResolver(base_uri=f'file://{self._schema_file}',
referrer=schema)
try:
validate(fhir_resource, schema, resolver=resolver)
except JSONValidationError as err:
raise ConfigurationError(
f'Validation failed for resource {fhir_resource!r}: {err}'
) from err
def get_auth(self):
if not self.last_token:
raise ConfigurationError(
_('OAuth1 authentication workflow has not been followed for '
f'Connection "{self.connection_settings}"'))
resource_owner_key = self.last_token['oauth_token']
resource_owner_secret = self.last_token['oauth_token_secret']
return OAuth1(self.client_id,
client_secret=self.client_secret,
resource_owner_key=resource_owner_key,
resource_owner_secret=resource_owner_secret)
def get_external_value(self, external_data):
if self.jsonpath is not None:
try:
jsonpath = parse_jsonpath(self.jsonpath)
except Exception as err:
raise JsonpathError from err
matches = jsonpath.find(external_data)
values = [m.value for m in matches]
if not values:
return None
elif len(values) == 1:
return values[0]
else:
return values
raise ConfigurationError(f"{self} is not configured to parse external data")
def get_value_source(self) -> ValueSource:
"""
Returns a ValueSource for building FHIR resources.
"""
if self.value_source_config:
return as_value_source(self.value_source_config)
if not (self.case_property and self.jsonpath):
raise ConfigurationError(
'Unable to set FHIR resource property value without case '
'property and JSONPath.')
value_source_config = {
'case_property': self.case_property.name,
'jsonpath': self.jsonpath,
}
if self.value_map:
value_source_config['value_map'] = self.value_map
return as_value_source(value_source_config)
def set_external_value(self, external_data: dict, info: CaseTriggerInfo):
"""
Builds ``external_data`` by reference.
Currently implemented for dicts using JSONPath but could be
implemented for other types as long as they are mutable.
"""
if self.jsonpath is None:
raise ConfigurationError(f"{self} is not configured to navigate "
"external data")
value = self.get_value(info)
if value is None:
# Don't set external value if CommCare has no value
return
try:
jsonpath = parse_jsonpath(self.jsonpath)
except Exception as err:
raise JsonpathError from err
jsonpath.update_or_create(external_data, value)
def get_addpatient_caseblock(
case_type: str,
default_owner: Optional[CommCareUser],
patient: dict,
repeater: OpenmrsRepeater,
) -> CaseBlock:
case_block_kwargs = get_case_block_kwargs_from_patient(patient, repeater)
if default_owner:
case_block_kwargs.setdefault("owner_id", default_owner.user_id)
if not case_block_kwargs.get("owner_id"):
raise ConfigurationError(
_(f'No users found at location "{repeater.location_id}" to own '
'patients added from OpenMRS Atom feed.'))
case_id = uuid.uuid4().hex
return CaseBlock.deprecated_init(create=True,
case_id=case_id,
case_type=case_type,
external_id=patient['uuid'],
**case_block_kwargs)
def get_json_schema(self) -> dict:
"""
Returns the JSON schema of this resource type.
>>> resource_type = FHIRResourceType(
... case_type=CaseType(name='mother'),
... name='Patient',
... )
>>> schema = resource_type.get_json_schema()
>>> schema['$ref']
'#/definitions/Patient'
"""
try:
with open(self._schema_file, 'r') as file:
return json.load(file)
except FileNotFoundError:
raise ConfigurationError(
f'Unknown resource type {self.name!r} for FHIR version '
f'{self.fhir_version}')
def create_parent_indices(
importer: FHIRImportConfig,
child_cases: List[ParentInfo],
):
"""
Creates parent-child relationships on imported cases.
If ``ResourceTypeRelationship.related_resource_is_parent`` is
``True`` then this function will add an ``index`` on the child case
to its parent case.
"""
if not child_cases:
return
case_blocks = []
for child_case_id, parent_ref, parent_resource_type in child_cases:
resource_type_name, external_id = parent_ref.split('/')
parent_case = get_case_by_external_id(
parent_resource_type.domain,
external_id,
parent_resource_type.case_type.name,
)
if not parent_case:
raise ConfigurationError(
f'Case not found with external_id {external_id!r}')
case_blocks.append(
CaseBlock(
child_case_id,
index={'parent': (parent_case.type, parent_case.case_id)},
))
submit_case_blocks(
[cb.as_text() for cb in case_blocks],
importer.domain,
xmlns=XMLNS_FHIR,
device_id=f'FHIRImportConfig-{importer.pk}',
)