Added units

Author: ddooley

script/oca_to_linkml.py

@@ -10,7 +10,7 @@
 # typically, in some DH web/templates/[schema folder]/, which reads by default
 # a file called oca_bundle.json
 #
-# > python3 ../../../script/oca_to_linkml.py [-i oca_bundle_file_name]
+# > python3 ../../../script/oca_to_linkml.py [-i [oca_bundle_file_name.json]]
 #
 # Output: 
 #
@@ -254,6 +254,7 @@
 	"title",
 	"range",
 	"range_2",
+	"unit",
 	"identifier",
 	"multivalued",
 	"minimum_cardinality",
@@ -397,6 +398,8 @@ def writeSchemaCore():
 
 	return SCHEMA;
 
+
+################################ SLOT OUTPUT ################################
 def writeSlots():
 	# Ensure SCHEMA_SLOTS has language variation
 	addLocaleHeaders(SCHEMA_SLOTS, ["slot_group","title","description","comments","examples"]);
@@ -410,9 +413,11 @@ def writeSlots():
 		slot['class_name'] = SCHEMA["name"];
 		slot['name'] = slot_name;
 		slot['title'] = oca_labels[slot_name];
-		slot['range'] = oca_attributes[slot_name]; # Yeilds Type
-		slot['pattern'] = oca_formats[slot_name];
-		slot['description'] = oca_informations[slot_name];
+		slot['range'] = oca_attributes[slot_name]; # Type is a required field?
+		if slot_name in oca_formats:
+			slot['pattern'] = oca_formats[slot_name];
+		if slot_name in oca_informations:
+			slot['description'] = oca_informations[slot_name]; 
 
 		# Minnum and maximum number of values in array of a multivalued field.
 		# See https://oca.colossi.network/specification/#cardinality-overlay
@@ -490,6 +495,16 @@ def writeSlots():
 			case "Boolean":
 				pass
 
+		# OCA mentions a oca_overlays["unit"]["metric_system"] (usually = "SI"),
+		# So here is a place to do unit conversion to UCUM if possible.
+		# https://ucum.nlm.nih.gov/ucum-lhc/demo.html
+		if slot_name in oca_units:
+			# slot unit: / ucum_code: cm
+			if "metric_system" in oca_overlays["unit"]:
+				slot['unit'] = oca_overlays["unit"]["metric_system"] + ":" + oca_units[slot_name];
+			else:
+				slot['unit'] = oca_units[slot_name];
+
     # Now convert any slot datatypes where pattern matches OCA-specific data type
 		for type_name in SCHEMA["types"]:
 			if "pattern" in SCHEMA["types"][type_name]:
@@ -509,11 +524,10 @@ def writeSlots():
 				#slot['comments_'+locale] # No OCA equivalent
 				#slot['examples_'+locale] # No OCA equivalent
 
-
-
 	save_tsv("schema_slots.tsv", SCHEMA_SLOTS, slots);
 
 
+################################ ENUM OUTPUT ################################
 def writeEnums():
 	addLocaleHeaders(SCHEMA_ENUMS, ["title", "menu_1"]);
 	enums = [];
@@ -545,8 +559,8 @@ def writeEnums():
 
 # Load OCA schema bundle specification
 if options.input_oca_file and os.path.isfile(options.input_oca_file):
-    with open(options.input_oca_file, "r") as f:
-        oca_obj = json.load(f);
+    with open(options.input_oca_file, "r") as file_handle:
+        oca_obj = json.load(file_handle);
 else:
 	os.exit("- [Input OCA bundle file is required]")
 
@@ -599,6 +613,12 @@ def writeEnums():
 # attribute_entries is dictionary of [enumeration name]: {code, label}
 oca_entry_labels = oca_overlays["entry"][0]["attribute_entries"];
 
+# Also has   "metric_system": "SI",
+if "unit" in oca_overlays:
+	oca_units = oca_overlays["unit"]["attribute_units"];
+else:
+	oca_units = {}
+
 SCHEMA = writeSchemaCore();
 writeSlots();
 writeEnums();

script/tabular_to_schema.py

@@ -114,18 +114,27 @@ def set_examples (slot, example_string):
 		slot['examples'] = examples;
 
 # Parse annotation_string into slot.examples. Works for multilingual slot locale
-def set_annotations (slot, annotation_string):
-				
-	if annotation_string > '':
+def set_attribute (slot, attribute, content):
+	print (content)	
+	if content > '':
 		annotations = {};
-		for v in annotation_string.split(';'):
-			(key, value) = v.split(':');
-			value = value.strip();
-			if value.lower() == 'true':
-				value = bool(value);
-			annotations[key.strip()] = value;
-
-		slot['annotations'] = annotations;
+		for v in content.split(';'):
+			if ':' in v:
+				(key, value) = v.split(':');
+				key = key.strip();
+				value = value.strip();
+				if value.lower() == 'true':
+					value = bool(value);
+				
+				if attribute == 'unit' and key != 'ucum_code':
+					# FUTURE: do unit conversion here
+					annotations['ucum_code'] = value;
+				else:
+					annotations[key] = value;
+			else:
+				if attribute == 'unit':
+					annotations['ucum_code'] = value;
+		slot[attribute] = annotations;
 
 
 # A slot's or enum's exact_mappings array gets populated with all the 
@@ -273,6 +282,7 @@ def set_classes(schema_slot_path, schema, locale_schemas, export_format, warning
 
 					slot_range =							row.get('range','');
 					slot_range_2 =						row.get('range_2','');
+					slot_unit =						row.get('unit','');
 					slot_pattern = 						row.get('pattern','');
 					slot_structured_pattern = row.get('structured_pattern','');
 					slot_minimum_value =			row.get('minimum_value','');
@@ -296,8 +306,10 @@ def set_classes(schema_slot_path, schema, locale_schemas, export_format, warning
 
 					if slot_minimum_cardinality > '':	slot['minimum_cardinality'] = int(slot_minimum_cardinality);
 					if slot_maximum_cardinality > '':	slot['maximum_cardinality'] = int(slot_maximum_cardinality);
-					
+
 					set_range(slot, slot_range, slot_range_2);
+					if slot_unit > '':							slot['unit'] = slot_unit;
+
 					set_min_max(slot, slot_minimum_value, slot_maximum_value);
 					if slot_pattern > '':						slot['pattern'] = slot_pattern;		
 					if slot_structured_pattern > '':
@@ -307,8 +319,9 @@ def set_classes(schema_slot_path, schema, locale_schemas, export_format, warning
 																						'interpolated': True
 																					}
 
+					set_attribute(slot, "unit", slot_unit);
 					set_examples(slot, slot_examples);
-					set_annotations(slot, slot_annotations);
+					set_attribute(slot, "annotations", slot_annotations);
 					set_mappings(slot, row, export_format);
 
 					# If slot has already been set up in schema['slots'] then compare