def test_unique_list(input_value, output):
assert unique_list(input_value) == output
assert unique_list(unique_list(input_value)) == unique_list(input_value)
def merge_fhir_json(filepath: str, new_cs: CodeSystem):
existing_cs = CodeSystem.parse_file(filepath)
click.echo(f"there is an existing file at {filepath}, merging...")
validation_errors = validate_attributes_match(existing_cs, new_cs)
if len(validation_errors) > 0:
click.echo("there were validation messages when merging:\n " +
',\n '.join(validation_errors),
err=True,
color=True)
return None
new_codes = list(c.code for c in new_cs.concept)
concept_missing_in_existing = [
concept for concept in existing_cs.concept
if concept.code not in new_codes
]
if len(concept_missing_in_existing) > 0:
click.echo("codes missing in the existing CodeSystem: " +
", ".join(f"'{c.code}'='{c.display}'"
for c in concept_missing_in_existing))
click.echo("")
existing_codes = list(c.code for c in existing_cs.concept)
concept_missing_in_new = [
concept for concept in new_cs.concept
if concept.code not in existing_codes
]
if len(concept_missing_in_new) > 0:
click.echo("codes missing in the new CodeSystem: " +
", ".join(f"'{c.code}'='{c.display}'"
for c in concept_missing_in_new))
click.echo("")
all_codes = unique_list(new_codes + existing_codes)
common_codes = list(c for c in all_codes
if c in existing_codes and c in new_codes)
concepts_in_both_old = {
c.code: c
for c in existing_cs.concept if c in common_codes
}
concepts_in_both_new = {
c.code: c
for c in new_cs.concept if c in common_codes
}
merge_errors = []
for code in concepts_in_both_old.keys():
assert (code in concepts_in_both_new.keys())
old_concept: CodeSystemConcept = concepts_in_both_old[code]
new_concept: CodeSystemConcept = concepts_in_both_new[code]
if old_concept.display != new_concept.display:
merge_errors.append(
f"code '{code}' has different display, old '{old_concept.display}' vs new '{new_concept.display}'"
)
old_parent = None
new_parent = None
if "property" in old_concept.json():
old_parent = [
p for p in old_concept.property if p.code == "parent"
]
if "property" in new_concept.json():
new_parent = [
p for p in new_concept.property if p.code == "parent"
]
if old_parent != None and new_parent == None or old_parent == None and new_parent != None:
merge_errors.append(
f"unhandled parent for code '{code}' in only one code system, please handle."
)
elif old_parent != None and new_parent != None and len(
old_parent) > 0 and len(new_parent) > 0:
if old_parent[0].valueCode != new_parent[0].valueCode:
merge_errors.append(
f"code '{code}' has different parent value, old '{old_parent.valueCode}' vs new '{new_parent.valueCode}'"
)
if len(merge_errors) > 0:
click.echo("there were differences detected in the concepts: \n " +
"\n ".join(merge_errors),
err=True,
color=True)
return None
existing_cs.concept.extend(concept_missing_in_existing)
return existing_cs
