#387 drastic changes: REMOVAL OF ONTOBIO from kg2_util and validation

validate/run-validation-tests.sh

@@ -58,8 +58,8 @@ ${curl_get} ${infores_catalog_yaml_url} -o ${infores_catalog_yaml}
 ${python_command} -u ${VALIDATE_CODE_DIR}/validate_curies_to_categories_yaml.py \
            ${curies_to_categories_file} \
            ${curies_to_urls_file} \
-           ${biolink_model_owl_url} \
-           ${biolink_model_owl_local_file}
+           ${biolink_model_yaml_url} \
+           ${biolink_model_yaml_local_file}
 
 ${python_command} -u ${VALIDATE_CODE_DIR}/validate_curies_to_urls_map_yaml.py \
            ${curies_to_urls_file} \

validate/validate_curies_to_categories_yaml.py

@@ -7,7 +7,7 @@
 
 __author__ = 'Stephen Ramsey'
 __copyright__ = 'Oregon State University'
-__credits__ = ['Stephen Ramsey']
+__credits__ = ['Stephen Ramsey', 'Erica Wood']
 __license__ = 'MIT'
 __version__ = '0.1.0'
 __maintainer__ = ''
@@ -22,8 +22,8 @@ def make_arg_parser():
     arg_parser = argparse.ArgumentParser(description='validate_curies_to_categories.py: checks the file `curies-to-categories.yaml` for correctness.')
     arg_parser.add_argument('curiesToCategoriesFile', type=str)
     arg_parser.add_argument('curiesToURLsMapFile', type=str)
-    arg_parser.add_argument('biolinkModelOWLURL', type=str)
-    arg_parser.add_argument('biolinkModelOWLLocalFile', type=str)
+    arg_parser.add_argument('biolinkModelYAMLURL', type=str)
+    arg_parser.add_argument('biolinkModelYAMLLocalFile', type=str)
     return arg_parser
 
 
@@ -37,8 +37,8 @@ def make_arg_parser():
 curies_to_url_map_data_bidir = {next(iter(listitem.keys())) for listitem in curies_to_url_map_data['use_for_bidirectional_mapping']}
 
 kg2_util.download_file_if_not_exist_locally(biolink_model_url, biolink_model_file_name)
-biolink_ont = kg2_util.make_ontology_from_local_file(biolink_model_file_name)
-biolink_categories_ontology_depths = kg2_util.get_biolink_categories_ontology_depths(biolink_ont)
+biolink_model = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(biolink_model_file_name))
+_, biolink_categories = kg2_util.identify_biolink_terms(biolink_model)
 
 for prefix in curies_to_categories_data['prefix-mappings'].keys():
     assert prefix in curies_to_url_map_data_bidir, prefix
@@ -53,4 +53,4 @@ def make_arg_parser():
 for category in categories_to_check:
     category_camelcase = kg2_util.convert_space_case_to_camel_case(category)
     category_curie = kg2_util.CURIE_PREFIX_BIOLINK + ':' + category_camelcase
-    assert category_curie in biolink_categories_ontology_depths, category_curie
+    assert category_curie in biolink_categories, category_curie

validate/validate_kg2_util_curies_urls_categories.py

@@ -17,10 +17,6 @@
 import kg2_util
 import json
 
-DESCENDANT_KEY = "is_a"
-BASE_PREDICATE = "related to"
-BASE_CATEGORY = "named thing"
-
 def make_arg_parser():
     arg_parser = argparse.ArgumentParser(description='validate_kg2_util_curies_urls_categories.py: ' +
                                          'checks the file `kg2_util.py` for correctness for its CURIE IDs, Base URLs, and biolink categories.')
@@ -29,34 +25,6 @@ def make_arg_parser():
     arg_parser.add_argument('biolinkModelLocalFile', type=str)
     return arg_parser
 
-def construct_biolink_term_set(is_a_base, biolink_terms):
-    output_set = set()
-    for key in biolink_terms:
-        key_is_a = biolink_terms[key]
-        if key_is_a == is_a_base:
-            for item in construct_biolink_term_set(key, biolink_terms):
-                output_set.add(item)
-    output_set.add(is_a_base)
-    return output_set
-
-def identify_biolink_terms(biolink_model):
-    biolink_predicate_terms = dict()
-    biolink_category_terms = dict()
-    for predicate in biolink_model["slots"]:
-        if DESCENDANT_KEY in biolink_model["slots"][predicate]:
-            biolink_predicate_terms[predicate] = biolink_model["slots"][predicate][DESCENDANT_KEY]
-
-    for category in biolink_model["classes"]:
-        if DESCENDANT_KEY in biolink_model["classes"][category]:
-            biolink_category_terms[category] = biolink_model["classes"][category][DESCENDANT_KEY]
-
-    biolink_predicates = construct_biolink_term_set("related to", biolink_predicate_terms)
-    biolink_categories = construct_biolink_term_set("named thing", biolink_category_terms)
-
-    return list(biolink_predicates), list(biolink_categories)
-
-
-
 args = make_arg_parser().parse_args()
 biolink_model_url = args.biolinkModelURL
 biolink_model_file_name = args.biolinkModelLocalFile
@@ -73,7 +41,7 @@ def identify_biolink_terms(biolink_model):
 
 kg2_util.download_file_if_not_exist_locally(biolink_model_url, biolink_model_file_name)
 biolink_model = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(biolink_model_file_name))
-biolink_edge_labels, biolink_categories = identify_biolink_terms(biolink_model)
+biolink_edge_labels, biolink_categories = kg2_util.identify_biolink_terms(biolink_model)
 
 for variable_name in dir(kg2_util):
     variable_value = getattr(kg2_util, variable_name)
@@ -84,14 +52,12 @@ def identify_biolink_terms(biolink_model):
         assert url_str in valid_base_urls, url_str
     elif variable_name.startswith('BIOLINK_CATEGORY_'):
         category_label = variable_value
-        category_camelcase = kg2_util.convert_space_case_to_camel_case(category_label)
-        category_curie = kg2_util.CURIE_PREFIX_BIOLINK + ':' + category_camelcase
-        assert category_curie in biolink_categories, category_curie
+        assert category_label in biolink_categories, category_curie
         #  assert category_label in categories_to_check, category_label
     elif variable_name.startswith('CURIE_ID_'):
         curie_id = variable_value
         assert ':' in curie_id, variable_name
         assert curie_id.split(':')[0] in curies_to_url_map_data_bidir, variable_name
     elif variable_name.startswith('EDGE_LABEL_BIOLINK_'):
-        relation_label = variable_value
-        assert kg2_util.CURIE_PREFIX_BIOLINK + ':' + relation_label in biolink_edge_labels, relation_label
+        relation_label = variable_value.replace('_', ' ')
+        assert relation_label in biolink_edge_labels, relation_label