diff --git a/dataset2rdf/utils.py b/dataset2rdf/utils.py
index 9646f7257f3236e6f86a17198da5f9374e77ec16..8be08f0f2f6480ce13156cab1e267882666c1ad2 100644
--- a/dataset2rdf/utils.py
+++ b/dataset2rdf/utils.py
@@ -795,38 +795,40 @@ def parse_active_composed_ofs(
)
elif 'restricted to:' in valueset:
#valueset = valueset.replace(",", ";")
- path_str, elements_str = valueset.split("restricted to:")
- property_path = [iri_header + format_property_name(x) for x in path_str.strip().split("->")]
- elements = [x.strip() for x in elements_str.split(";")]
- parsed_elements = []
- for_standard = None
- scope = None
- for element in elements:
- if standard in {'UCUM'}:
- element = parse_element(element)
- if element.startswith("for "):
- for_standard = extract_code(element, REGEX_MAP["for_standard"])
- if "descendant of:" in element:
- scope = "descendant of: "
- elif "child of:" in element:
- scope = "child of: "
- if for_standard and for_standard not in element:
- element = f"for {for_standard}: {scope if scope and scope not in element else ''}{element}"
- parsed_elements.append(element)
- else:
- element = f"{scope if scope and scope not in element else ''}{element}"
- parsed_elements.append(element)
+ restricted_to_expressions = parse_restricted_to_expression(valueset)
+ for expression in restricted_to_expressions:
+ path_str, elements_str = expression.split("restricted to:")
+ property_path = [iri_header + format_property_name(x) for x in path_str.strip().split("->")]
+ elements = [x.strip() for x in elements_str.split(";")]
+ parsed_elements = []
+ for_standard = None
+ scope = None
+ for element in elements:
+ if standard in {'UCUM'}:
+ element = parse_element(element)
+ if element.startswith("for "):
+ for_standard = extract_code(element, REGEX_MAP["for_standard"])
+ if "descendant of:" in element:
+ scope = "descendant of: "
+ elif "child of:" in element:
+ scope = "child of: "
+ if for_standard and for_standard not in element:
+ element = f"for {for_standard}: {scope if scope and scope not in element else ''}{element}"
+ parsed_elements.append(element)
+ else:
+ element = f"{scope if scope and scope not in element else ''}{element}"
+ parsed_elements.append(element)
- parse_standard_as_restriction(
- concept=concept,
- prop=prop,
- standard=standard,
- valueset=";".join(parsed_elements),
- property_path=property_path,
- prefix=prefix.lower(),
- add_info=add_info,
- config=config
- )
+ parse_standard_as_restriction(
+ concept=concept,
+ prop=prop,
+ standard=standard,
+ valueset=";".join(parsed_elements),
+ property_path=property_path,
+ prefix=prefix.lower(),
+ add_info=add_info,
+ config=config
+ )
elif valueset.lower().startswith("unit:"):
# UCUM code restriction on prop -> hasUnit -> hasCode
@@ -1901,6 +1903,8 @@ def add_code_as_restriction(
"""
logger_utils.debug("adding code as restriction: " + str(codes) +" for proppath: " + str(prop_path) + " and prop " + str(prop))
r_key = f"{concept.identifier}-{prop.identifier}"
+ if prop_path:
+ r_key = f"{r_key}-{'-'.join(prop_path)}"
if r_key in concept.restrictions:
restriction = concept.restrictions[r_key]
else:
@@ -2235,3 +2239,31 @@ def compare_composed_of_attributes(dataset: pd.DataFrame, upstream_record: Dict,
e = f"Type '{composed_of_type}' for composedOf '{name}' is not the same as the parent composedOf '{upstream_record[COLUMN_MAP['name']]}' with type '{parent_composed_of_type}'"
errors.append(e)
return errors
+
+
+def parse_restricted_to_expression(valueset: str) -> List:
+ """
+ Parse a given valueset string and check if there are 'restricted to' expressions.
+ If so, then split the string at the right delimiter and return a list where each
+ element is a 'restricted to' expression.
+
+ Args:
+ valueset: The valueset string
+
+ Return:
+ A list of 'restricted to' expressions
+
+ """
+ keywords = {'descendant of', 'child of', 'for '}
+ prepared_valueset = []
+ prepared_value = None
+ for value in valueset.split(";"):
+ if 'restricted to' in value:
+ # First property path restriction
+ if prepared_value:
+ prepared_valueset.append(prepared_value)
+ prepared_value = value
+ elif any(x not in value for x in keywords):
+ prepared_value += f";{value}"
+ prepared_valueset.append(prepared_value)
+ return prepared_valueset
\ No newline at end of file
diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py
index d7a0acb652974da2dc606e53ade865644ed896cc..093fef959f4ece197b059af04a6570f90a84c901 100644
--- a/tests/unit/test_utils.py
+++ b/tests/unit/test_utils.py
@@ -710,7 +710,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP8",
"label": "has p8",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP8": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP8-https://biomedit.ch/rdf/sphn-ontology/sphn#hasUnit-https://biomedit.ch/rdf/sphn-ontology/sphn#hasCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP8",
"some_values_from": [],
@@ -746,7 +746,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP9",
"label": "has p9",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP9": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP9-https://biomedit.ch/rdf/sphn-ontology/sphn#hasUnit-https://biomedit.ch/rdf/sphn-ontology/sphn#hasCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP9",
"some_values_from": [],
@@ -1089,7 +1089,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasUnit-https://biomedit.ch/rdf/sphn-ontology/sphn#hasCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1133,7 +1133,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasUnit-https://biomedit.ch/rdf/sphn-ontology/sphn#hasCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1175,7 +1175,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1216,7 +1216,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1230,6 +1230,10 @@ def test_parse_active_concept(record, expected):
"https://biomedit.ch/rdf/sphn-resource/chop/43.3"
],
"scope_notes": {'sphn:hasP18 no subclasses allowed'},
+ },
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
+ "property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"notes": {'sphn:hasP18 allowed coding system: SNOMED CT, CHOP'}
}
}
@@ -1260,7 +1264,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1272,10 +1276,16 @@ def test_parse_active_concept(record, expected):
"http://snomed.info/id/45353",
"https://biomedit.ch/rdf/sphn-resource/chop/23.1",
"https://biomedit.ch/rdf/sphn-resource/chop/43.3",
+ ],
+ "scope_notes": {'sphn:hasP18 no subclasses allowed'},
+ },
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
+ "property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
+ "some_values_from": [
"https://biomedit.ch/rdf/sphn-ontology/sphn#Code",
"https://biomedit.ch/rdf/sphn-ontology/sphn#Terminology"
],
- "scope_notes": {'sphn:hasP18 no subclasses allowed'},
"notes": {'sphn:hasP18 allowed coding system: SNOMED CT or other'}
}
}
@@ -1306,7 +1316,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1347,7 +1357,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1389,7 +1399,7 @@ def test_parse_active_concept(record, expected):
"identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"label": "has p18",
"restrictions": {
- "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18": {
+ "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB-https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18-https://biomedit.ch/rdf/sphn-ontology/sphn#hasMedicalDevice-https://biomedit.ch/rdf/sphn-ontology/sphn#hasTypeCode": {
"class_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#ConceptB",
"property_identifier": "https://biomedit.ch/rdf/sphn-ontology/sphn#hasP18",
"property_path": [
@@ -1432,6 +1442,7 @@ def test_parse_active_composed_ofs(record, expected_properties, expected_individ
concept = prop.domain[0]
if expected_properties["restrictions"]:
assert concept.restrictions
+ print(f">>> CONCEPT RESTRICTIONS:\n{concept.restrictions}")
for k,v in expected_properties['restrictions'].items():
assert k in concept.restrictions