From 2922957611a4d3de8a0bf36ef918c1520208600b Mon Sep 17 00:00:00 2001
From: Andrew Wen <Andrew.Wen@uth.tmc.edu>
Date: Sat, 9 Sep 2023 17:25:55 -0500
Subject: [PATCH] Don't attempt splits for zero-length lines

---
 pom.xml                                                        | 2 +-
 .../ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java   | 2 +-
 .../ohnlp/medtagger/backbone/SectionResolutionTransform.java   | 3 +++
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index d852e7c..7a0c45e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.69</version>
+    <version>1.0.70</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 
diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java
index a143582..1c145d1 100644
--- a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java
+++ b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java
@@ -264,7 +264,7 @@ public void init() throws IOException, InvalidXMLException, URISyntaxException,
                         ae.add(AnalysisEngineFactory.createEngineDescription(RuleContextAnnotator.class, "context_ruleset", contextURI.toString()));
                     }
                 } else {
-                    if (mode.equals(RunMode.STANDALONE_DICT_ONLY) || mode.equals(RunMode.STANDALONE_DICT_ONLY)) {
+                    if (mode.equals(RunMode.STANDALONE_DICT_ONLY) || mode.equals(RunMode.GENERAL_CLINICAL)) {
                         if (this.context.equalsIgnoreCase("DEFAULT")) {
                             ae.add(AnalysisEngineFactory.createEngineDescription(RuleContextAnnotator.class));
                         } else {
diff --git a/src/main/java/org/ohnlp/medtagger/backbone/SectionResolutionTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/SectionResolutionTransform.java
index b0f64da..539f03d 100644
--- a/src/main/java/org/ohnlp/medtagger/backbone/SectionResolutionTransform.java
+++ b/src/main/java/org/ohnlp/medtagger/backbone/SectionResolutionTransform.java
@@ -62,6 +62,9 @@ public void process(ProcessContext pc) {
                 // First, split by newlines
                 Arrays.stream(raw.split("\\r?\\n")).forEach(s -> {
                     // Now split by colon and add first part to candidates
+                    if (s.trim().length() == 0) {
+                        return;
+                    }
                     String cand = s.split(":")[0].trim();
                     if (cand.length() > 0) {
                         // And output