Merge branch 'develop' of https://github.com/ClarityNLP/ClarityNLP in…

…to develop
ClarityNLP · Aug 26, 2019 · 0558fe1 · 0558fe1
2 parents 3bfa930 + add2928
commit 0558fe1
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diff --git a/nlp/nlpql/nlpql.py b/nlp/nlpql/nlpql.py
@@ -601,7 +601,7 @@ def run_nlpql_parser(nlpql_txt: str):
 
 
 if __name__ == '__main__':
-    with open('samples/simple.nlpql') as f:
+    with open('samples/sample2.nlpql') as f:
         nlpql_txt = f.read()
         results = run_nlpql_parser(nlpql_txt)
         if results['has_errors'] or results['has_warnings']:

diff --git a/nlp/nlpql/nlpql_parser.g4 b/nlp/nlpql/nlpql_parser.g4
@@ -153,7 +153,8 @@ unaryOperator:
 
 logicalOperator:
     AND |
-    OR
+    OR |
+    NOT
     ;
 
 comparisonOperator:

diff --git a/nlp/nlpql/nlpql_parser.interp b/nlp/nlpql/nlpql_parser.interp
diff --git a/nlp/nlpql/nlpql_parserParser.py b/nlp/nlpql/nlpql_parserParser.py
@@ -44,7 +44,7 @@ def serializedATN():
         buf.write("\n,\3-\3-\3-\3-\3-\3-\3-\3-\3-\3-\3-\3-\5-\u0187\n-\3")
         buf.write("-\2\4\60\66.\2\4\6\b\n\f\16\20\22\24\26\30\32\34\36 \"")
         buf.write("$&(*,.\60\62\64\668:<>@BDFHJLNPRTVX\2\n\4\2\"\"PP\4\2")
-        buf.write("#$PP\3\2&\'\4\2++\65\65\3\2)*\3\2\4\5\4\2\"\"UU\6\2\t")
+        buf.write("#$PP\3\2&\'\4\2++\65\65\3\2)+\3\2\4\5\4\2\"\"UU\6\2\t")
         buf.write("\t\f\30\33\35\37!\2\u019f\2]\3\2\2\2\4p\3\2\2\2\6t\3\2")
         buf.write("\2\2\bv\3\2\2\2\ny\3\2\2\2\f|\3\2\2\2\16~\3\2\2\2\20\u0083")
         buf.write("\3\2\2\2\22\u0086\3\2\2\2\24\u008b\3\2\2\2\26\u0093\3")
@@ -2033,6 +2033,9 @@ def AND(self):
         def OR(self):
             return self.getToken(nlpql_parserParser.OR, 0)
 
+        def NOT(self):
+            return self.getToken(nlpql_parserParser.NOT, 0)
+
         def getRuleIndex(self):
             return nlpql_parserParser.RULE_logicalOperator
 
@@ -2048,7 +2051,7 @@ def logicalOperator(self):
             self.enterOuterAlt(localctx, 1)
             self.state = 283
             _la = self._input.LA(1)
-            if not(_la==nlpql_parserParser.AND or _la==nlpql_parserParser.OR):
+            if not((((_la) & ~0x3f) == 0 and ((1 << _la) & ((1 << nlpql_parserParser.AND) | (1 << nlpql_parserParser.OR) | (1 << nlpql_parserParser.NOT))) != 0)):
                 self._errHandler.recoverInline(self)
             else:
                 self._errHandler.reportMatch(self)

diff --git a/nlp/nlpql/samples/simple.nlpql → nlp/nlpql/samples/sample1.nlpql b/nlp/nlpql/samples/simple.nlpql → nlp/nlpql/samples/sample1.nlpql
diff --git a/nlp/nlpql/samples/sample2.nlpql b/nlp/nlpql/samples/sample2.nlpql
@@ -0,0 +1,76 @@
+limit 100;
+phenotype "Test Setdiff" version "1";
+include ClarityCore version "1.0" called Clarity;
+///////////////////////////////////////////////////////////////////////////////
+//
+//                          Documents
+//
+///////////////////////////////////////////////////////////////////////////////
+// documentset Docs:
+//     Clarity.createDocumentSet({
+//         "report_types":[
+//             "Physician",
+//             "Nurse",
+//             "Note",
+//             "Discharge Summary"
+//         ],
+//         "source":"MIMIC"
+//     });
+///////////////////////////////////////////////////////////////////////////////
+//
+//                          Termsets
+//
+///////////////////////////////////////////////////////////////////////////////
+termset RigorsTerms: [
+    "Rigors",
+    "Rigoring",
+    "Shivers",
+    "Shivering"
+];
+termset DyspneaTerms: [
+    "Labored respiration",
+    "Shortness of breath",
+    "Short of breath",
+    "SOB",
+    "Respiration labored",
+    "Labored breathing",
+    "Dyspnea",
+    "Difficulty breathing"
+];
+///////////////////////////////////////////////////////////////////////////////
+//
+//                          Provider Assertions
+//
+///////////////////////////////////////////////////////////////////////////////
+define hasRigors:
+    Clarity.ProviderAssertion({
+        termset: [RigorsTerms]
+    });
+define hasDyspnea:
+    Clarity.ProviderAssertion({
+        termset: [DyspneaTerms]
+    });
+
+///////////////////////////////////////////////////////////////////////////////
+//
+//                         Context
+//
+///////////////////////////////////////////////////////////////////////////////
+context Patient;
+///////////////////////////////////////////////////////////////////////////////
+//
+//                         Expressions
+//
+///////////////////////////////////////////////////////////////////////////////
+define RigorsOrDyspnea:
+    where hasRigors OR hasDyspnea;
+define RigorsAndDyspnea:
+    where hasRigors AND hasDyspnea;
+define hasRigorsOrDyspneaButNotBoth:
+    where (hasRigors OR hasDyspnea) NOT (hasRigors AND hasDyspnea);
+define complexNotLogic:
+    where (hasTachycardia OR hasShock OR hasRigors) NOT ( (hasTachycardia AND hasShock) OR (hasTachycardia AND hasRigors) OR (hasShock AND hasRigors) );
+define LogicAndMath1:
+    where (hasRigors OR hasDyspnea OR hasTachycardia) NOT ( (Temperature.value >= 100.4) AND (Temperature.value <= 102) );
+define LogicAndMath2:
+    where (Lesion.dimension_X > 10 AND Lesion.dimension_X < 30) NOT (hasRigors OR hasTachycardia OR hasDyspnea);
diff --git a/nlp/tasks/TermFinderTask.py b/nlp/tasks/TermFinderTask.py
@@ -123,8 +123,8 @@ def run_term_finder(name, filters, pipeline_config, temp_file, mongo_client, doc
 
     for doc in docs:
         objs = get_cached_terms(name, doc[util.solr_report_id_field], pipeline_config.terms, pipeline_config.
-                                synonyms, pipeline_config
-                                .descendants, pipeline_config.ancestors, pipeline_config
+                                include_synonyms, pipeline_config
+                                .include_descendants, pipeline_config.include_ancestors, pipeline_config
                                 .vocabulary, filters, has_special_filters)
         if objs and len(objs) > 0:
             for obj in objs: