def test_get_field_mappings(self):
expected = {
self.procedure_concept_id: self.condition_concept_id,
self.procedure_type_concept_id: self.condition_type_concept_id,
self.procedure_source_concept_id: self.condition_source_concept_id
}
self.assertDictEqual(
domain_mapping.get_field_mappings(self.condition_table,
self.procedure_table), expected)
self.assertDictEqual(
domain_mapping.get_field_mappings(self.procedure_table,
self.condition_table), {})
def resolve_specific_field_mappings(_src_table, _dest_table,
_dest_specific_fields):
"""
This function generates a list of field mappings between _src_table and _dest_table for the domain specific fields.
E.g. The fields value_as_number and value_as_concept_id can be mapped between observation and measurement.
:param _src_table: the source CDM table
:param _dest_table: the destination CDM table
:param _dest_specific_fields: an array that contains the specific destination fields
:return:
"""
specific_field_mappings = OrderedDict()
# If the src_table and dest_table are the same, map all the fields onto themselves.
if _src_table == _dest_table:
for dest_specific_field in _dest_specific_fields:
specific_field_mappings[dest_specific_field] = dest_specific_field
else:
# Retrieve the field mappings and put them into the dict
specific_field_mappings.update(
get_field_mappings(_src_table, _dest_table))
# For dest_specific_field that is not defined, map it to NULL
for dest_specific_field in _dest_specific_fields:
if dest_specific_field not in specific_field_mappings:
specific_field_mappings[dest_specific_field] = NULL_VALUE
return specific_field_mappings
def resolve_field_mappings(src_table, dest_table):
"""
This function generates the content of SQL select statement for the given src_table and dest_table.
:param src_table: the source CDM table for rerouting
:param dest_table: the destination CDM table for rerouting
:return: the content of the SQL select statements
"""
select_statements = []
field_mappings = domain_mapping.get_field_mappings(src_table, dest_table)
for dest_field, src_field in field_mappings.items():
if domain_mapping.value_requires_translation(src_table, dest_table,
src_field, dest_field):
value_mappings = domain_mapping.get_value_mappings(
src_table, dest_table, src_field, dest_field)
if len(value_mappings) == 0:
if field_mapping.is_field_required(dest_table, dest_field):
case_statements = ZERO_AS_DEST_FIELD.format(
dest_field=dest_field)
else:
case_statements = NULL_AS_DEST_FIELD.format(
dest_field=dest_field)
else:
case_statements = '\n\t\t'.join([
WHEN_STATEMENT.format(src_value=s, dest_value=d)
for d, s in value_mappings.items()
])
dummy_value = fetch_dummy_value(
dest_table, dest_field) if field_mapping.is_field_required(
dest_table, dest_field) else NULL_VALUE
case_statements = CASE_STATEMENT.format(
src_field=src_field,
dest_field=dest_field,
dummy_value=dummy_value,
statements=case_statements)
select_statements.append(case_statements)
else:
select_statements.append(
SRC_FIELD_AS_DEST_FIELD.format(src_field=src_field,
dest_field=dest_field))
return ',\n\t'.join(select_statements)