Merge pull request #34 from ccb-hms/development

Fix Cache Ontology Set Bug
ccb-hms · May 10, 2023 · fa91e27 · fa91e27
2 parents 3e1816b + 70d95c2
commit fa91e27
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/test/simple-test.py b/test/simple-test.py
@@ -10,8 +10,9 @@ def main():
 	# 	cached_onto = text2term.cache_ontology("EFO")
 	# 	# df = cached_onto.map_terms(["asthma", "disease location", "obsolete food allergy"], excl_deprecated=True, term_type="classes")
 	# 	print("Cache exists:", cached_onto.cache_exists())
-	# df = text2term.map_terms(["asthma", "disease location", "obsolete food allergy"], "EFO", excl_deprecated=True, use_cache=True, term_type="classes")
-	df = text2term.map_terms(["contains", "asthma"], "EFO", term_type="classes")
+	caches = text2term.cache_ontology_set("text2term/resources/ontologies.csv")
+	df = text2term.map_terms(["asthma", "disease location", "obsolete food allergy"], "EFO", excl_deprecated=True, use_cache=True, term_type="classes")
+	# df = text2term.map_terms(["contains", "asthma"], "EFO", term_type="classes")
 	print(df.to_string())
 
 if __name__ == '__main__':

diff --git a/text2term/config.py b/text2term/config.py
@@ -1 +1 @@
-VERSION = "2.3.0"
+VERSION = "2.3.1"
diff --git a/text2term/onto_cache.py b/text2term/onto_cache.py
@@ -3,6 +3,8 @@
 import os
 from shutil import rmtree
 import sys
+import pandas as pd
+import owlready2
 
 """
 CACHING FUNCTIONS -- Public
@@ -16,7 +18,8 @@ def cache_ontology_set(ontology_registry_path):
             cache = text2term.cache_ontology(row.url, row.acronym)
             cache_set.update({row.acronym : cache})
         except Exception as err:
-            sys.stderr.write("Could not cache ontology", row.acronym, "due to error:", err)
+            err_message = "Could not cache ontology " + row.acronym + " due to error: " + str(err)
+            sys.stderr.write(err_message)
         owlready2.default_world.ontologies.clear()
     return cache_set