Documentation + bug fix

script/dh-validate.py

@@ -419,16 +419,35 @@ def getLinkMLTransform(SCHEMA, template, row_data):
  if slot['multivalued'] == True:
  output_val = [x.strip() for x in re.split(DELIMITERS, output_val)];
 
- # If key isn't in snake_case, then convert it to that, since 
- # linkml-validate insists on that:
+
  # ISSUE: () preserved rather than eliminated
  # ISSUE: diagnostic pcr Ct value 1 not transformed to diagnostic_pcr_ct_value_1
- # ISSUE: geo_loc_name_(state_province_territory) not transformed to geo_loc_name_(state_province_territory)
- # ISSUE: NML submitted specimen type not transformed to nml_submitted_specimen_type
- # ISSUE: specimen collector sample ID not transformed to specimen_collector_sample_id 
-
- # This relabling of key helps
- key = re.sub("[-]","",re.sub("[ /]","_", key)); #LinkML doesn't convert to lowercase
+ # ISSUE: 
+
+
+ # For validation, LinkML will transform both schema and slot labels into
+ # what it considers are standardized names, so we have to anticipate what
+ # new slot label will be via search and replace. Convert keys to 
+ # **snake_case** since linkml-validate insists on that. However: 
+ # - Forward slashes and parentheses are preserved though this is 
+ # nonstandard, so:
+ # "geo_loc name (state/province/territory)"
+ # is changed to
+ # "geo_loc_name_(state/province/territory)"
+ # - Case is preserved though that is non-standard. So 
+ # "specimen collector sample ID" 
+ # is changed to 
+ # "specimen_collector_sample_ID"
+ #
+ # - Validating caps CamelCase Enums is hard, e.g. if an Enum is named 
+ # "geo_loc_name (state/province/territory) menu"
+ # LinkML will automatically rename this to 
+ # "GeoLocName(state/province/territory)Menu"
+ # However, it doesn't update the name in slot range expressions!
+ # Hence these must be renamed in source schema.
+
+ The GeoLocName(state/province/territory)Menu
+ key = re.sub("[-]","",re.sub("[ ]","_", key)); # Accepts ()/ in field name.
  data[key] = output_val;
 
  return data;

script/tabular_to_schema.py

@@ -149,19 +149,37 @@ def set_range(slot, slot_range, slot_range_2):
 def set_min_max(slot, slot_minimum_value, slot_maximum_value):
 
  if slot_minimum_value > '':
- if slot_minimum_value.isnumeric():
+ if isInteger(slot_minimum_value):
  slot['minimum_value'] = int(slot_minimum_value);
+ elif isDecimal(slot_minimum_value):
+ slot['minimum_value'] = float(slot_minimum_value);
  else:
  slot['todos'] = ['>=' + slot_minimum_value];
  if slot_maximum_value > '':
- if slot_maximum_value.isnumeric():
+ if isInteger(slot_maximum_value):
  slot['maximum_value'] = int(slot_maximum_value);
+ elif isDecimal(slot_maximum_value):
+ slot['maximum_value'] = float(slot_maximum_value);
  else:
  if slot['todos']:
  slot['todos'].append('<=' + slot_maximum_value);
  else:
  slot['todos'] = ['<=' + slot_maximum_value];
 
+def isDecimal(x):
+ try:
+ float(x);
+ return True
+ except ValueError:
+ return False
+
+def isInteger(x):
+ try: 
+ int(x)
+ except ValueError:
+ return False
+ else:
+ return True
 
 def set_classes(schema_slot_path, schema, locale_schemas, export_format, warnings):
 
@@ -356,9 +374,8 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings):
  reader = csv.DictReader(tsvfile, dialect='excel-tab');
 
  enumerations = schema['enums'];
-
- name = ''; # running title for chunks of enumeration rows
- menu_path = [];
+ name = ''; # running name for chunks of enumeration rows
+ choice_path = [];
  enum = {};
 
  for row in reader:
@@ -368,21 +385,18 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings):
  row[field] = row[field].strip();
 
  # Each enumeration begins with a row that provides the name of the enum.
- if row.get('title','') > '':
+ # subsequent rows may not have a name.
+ if row.get('name','') > '' or row.get('title','') > '':
 
  # Process default language title
-
+ name = row.get('name');
  title = row.get('title');
- name = row.get('name','');
- if name == '': name = title;
- print ("name:", name)
-
- description = row.get('description','');
+ if not name: # For enumerations that don't have separate name field
+ name = title;
  if not (name in enumerations):
  enum = {
  'name': name,
  'title': title,
- 'description': description,
  'permissible_values': {}
  };
  enumerations[name] = enum;
@@ -393,58 +407,52 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings):
  for lcode in locale_schemas.keys():
  locale_schema = locale_schemas[lcode];
  locale_schema['enums'][name] = {
- 'name': name, # default (usu. english) name acts as key 
+ 'name': name, # Acts as key 
  'permissible_values': {}
  };
 
  # Provide translation title if available for this menu.
  locale_title = row.get('title_' + lcode, '');
  if locale_title > '':
- locale_schema['enums'][name]['title'] = row.get('title_' + lcode, title);
-
- # Provide translation description if available for this menu.
- locale_description = row.get('description_' + lcode, '');
- if locale_description > '':
- locale_schema['enums'][name]['description'] = locale_description;
-
+ locale_schema['enums'][name]['title'] = locale_title;
 
- # If there is a title (or name) of an emum at play
- if name and name > '':
+ if name > '':
  # Text is label of a particular menu choice
  # Loop scans through columns until it gets a value
  for depth in range(1,6):
  menu_x = 'menu_' + str(depth);
- choice_value = row.get(menu_x);
+ choice_text = row.get(menu_x);
  # Here there is a menu item to process
- if choice_value > '':
- del menu_path[depth-1:] # Menu path always points to parent
+ if choice_text > '':
+ del choice_path[depth-1:] # Menu path always points to parent
 
  description = row.get('description','');
  meaning = row.get('meaning','');
 
- choice = {'text' : choice_value}
+ choice = {'text' : choice_text}
  if description > '': choice['description'] = description;
  if meaning > '': choice['meaning'] = meaning;
 
  # Export mappings can be established for any enumeration items too.
  set_mappings(choice, row, export_format);
 
  # IMPLEMENTS FLAT LIST WITH IS_A HIERARCHY
- if len(menu_path) > 0:
- choice['is_a'] = menu_path[-1]; # Last item in path
+ if len(choice_path) > 0:
+ choice['is_a'] = choice_path[-1]; # Last item in path
 
- enum['permissible_values'][choice_value] = choice
- menu_path.append(choice_value)
+ enum['permissible_values'][choice_text] = choice;
+ choice_path.append(choice_text);
 
  for lcode in locale_schemas.keys():
  translation = row.get(menu_x + '_' + lcode, '');
- if translation > '':
+ if translation > '' and translation != choice['text']:
 
- local_choice = copy.deepcopy(choice);
- del local_choice['text']; # in language variant files this isn't needed.
- local_choice['title'] = translation;
+ local_choice = {'title': translation}
+ description = row.get(description + '_' + lcode, '');
+ if description:
+ local_choice['description': description];
 
- locale_schemas[lcode]['enums'][name]['permissible_values'][choice_value] = local_choice;
+ locale_schemas[lcode]['enums'][name]['permissible_values'][choice_text] = local_choice;
 
  break;