Merge pull request #43 from callahantiff/development

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callahantiff · Oct 5, 2020 · 599086d · 599086d
2 parents 7f13f83 + 47ddc2e
commit 599086d
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Showing 2 changed files with 13 additions and 19 deletions.
diff --git a/omop2obo/string_similarity.py b/omop2obo/string_similarity.py
@@ -22,6 +22,8 @@
 
 from omop2obo.utils import column_splitter, data_frame_subsetter, merge_dictionaries
 
+# TODO: Update script so all ontologies in the ont list (i.e. ontology_dictionary keys) are processed in parallel.
+
 # load stopwords into environment -- horrible workaround until Travis is fixed
 # nltk.download('wordnet')
 stopwords = ['i', 'me', 'my', 'myself', 'we', 'our', 'ours', 'ourselves', 'you', "you're", "you've", "you'll", "you'd",

diff --git a/omop2obo/utils/data_utils.py b/omop2obo/utils/data_utils.py
@@ -518,29 +518,21 @@ def assigns_mapping_category(mapping_result: List, map_evidence: str) -> str:
          mapping_category: A string containing the mapping category.
     """
 
-    if len(mapping_result[0]) == 1:
-        if 'CONCEPT_SIMILARITY:' in map_evidence:
-            if len(map_evidence.split(' | ')) == 1:
-                mapping_category = 'Manual Exact - Concept Similarity'
-            else:
-                mapping_category = 'Automatic Exact - Concept'
+    if 'CONCEPT_SIMILARITY:' in map_evidence:
+        if len(map_evidence.split(' | ')) > 1:
+            mapping_category = 'Automatic Constructor - Concept'
         else:
-            mapping_category = 'Automatic Exact - '
-    elif len(mapping_result[0]) > 1:
-        if 'CONCEPT_SIMILARITY:' in map_evidence:
+            mapping_category = 'Manual Exact - Concept Similarity'
+    elif any(x for x in ['ANCESTOR_CODE', 'ANCESTOR_SYNONYM', 'ANCESTOR_LABEL'] if x not in map_evidence):
+        if len(mapping_result[0]) > 1:
             mapping_category = 'Automatic Constructor - Concept'
         else:
-            mapping_category = 'Automatic Constructor - '
+            mapping_category = 'Automatic Exact - Concept'
     else:
-        mapping_category = ''
-
-    # determine mapping level (i.e. concept or ancestor)
-    if any(x for x in ['CONCEPT_CODE', 'CONCEPT_SYNONYM', 'CONCEPT_LABEL'] if x in map_evidence):
-        mapping_category = mapping_category + 'Concept'
-    elif any(x for x in ['ANCESTOR_CODE', 'ANCESTOR_SYNONYM', 'ANCESTOR_LABEL'] if x in map_evidence):
-        mapping_category = mapping_category + 'Ancestor'
-    else:
-        mapping_category = mapping_category + ''
+        if len(mapping_result[0]) > 1:
+            mapping_category = 'Automatic Constructor - Ancestor'
+        else:
+            mapping_category = 'Automatic Exact - Ancestor'
 
     return mapping_category