Update abstract parsing regex

calvinlu3 · Jun 14, 2024 · 4d573cd · 4d573cd
1 parent 7d926ad
commit 4d573cd
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/web/src/main/java/org/mskcc/cbio/oncokb/controller/DriveAnnotationParser.java b/web/src/main/java/org/mskcc/cbio/oncokb/controller/DriveAnnotationParser.java
@@ -10,8 +10,6 @@
 import org.json.JSONObject;
 import org.mskcc.cbio.oncokb.bo.*;
 import org.mskcc.cbio.oncokb.model.*;
-import org.mskcc.cbio.oncokb.model.TumorType;
-import org.mskcc.cbio.oncokb.bo.OncokbTranscriptService;
 import org.mskcc.cbio.oncokb.model.clinicalTrialsMathcing.Tumor;
 import org.mskcc.cbio.oncokb.util.*;
 import org.springframework.stereotype.Controller;
@@ -962,7 +960,7 @@ private void setDocuments(String str, Evidence evidence) {
         Set<Article> docs = new HashSet<>();
         ArticleBo articleBo = ApplicationContextSingleton.getArticleBo();
         Pattern pmidPattern = Pattern.compile("PMIDs?:?\\s*([\\d,\\s*]+)", Pattern.CASE_INSENSITIVE);
-        Pattern abstractPattern = Pattern.compile("\\(?\\s*Abstract\\s*:([^\\)]*);?\\s*\\)?", Pattern.CASE_INSENSITIVE);
+        Pattern abstractPattern = Pattern.compile("\\(?\\s*Abstract\\s*:(.*(?:\\([^()]*\\).*?)*);?\\s*\\)", Pattern.CASE_INSENSITIVE);
         Pattern abItemPattern = Pattern.compile("(.*?)\\.\\s*(http.*)", Pattern.CASE_INSENSITIVE);
         Matcher m = pmidPattern.matcher(str);
         int start = 0;