From c78cd7f95d0c3fdac60ed8d15e3e17209e79d984 Mon Sep 17 00:00:00 2001
From: Andrew Wen <Andrew.Wen@uth.tmc.edu>
Date: Mon, 23 Sep 2024 11:19:22 -0500
Subject: [PATCH] Bugfix: MedTator Schema names must match/be customizable

---
 pom.xml                                                   | 2 +-
 .../ohnlp/medtagger/backbone/MedtatorOutputTransform.java | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index f65d41d..f70c783 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.77</version>
+    <version>1.0.78</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 
diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedtatorOutputTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedtatorOutputTransform.java
index 4fb0006..253ca49 100644
--- a/src/main/java/org/ohnlp/medtagger/backbone/MedtatorOutputTransform.java
+++ b/src/main/java/org/ohnlp/medtagger/backbone/MedtatorOutputTransform.java
@@ -45,6 +45,12 @@ public class MedtatorOutputTransform extends LoadFromMany {
     )
     private String workingDir;
 
+    @ConfigurationProperty(
+            path = "taskName",
+            desc = "Task Name (the Schema Definition Name for MedTator)"
+    )
+    private String taskName;
+
     @ConfigurationProperty(
             path = "note_id_raw_col",
             desc = "The input column to use containing the note identifier from the raw text collection"
@@ -159,7 +165,7 @@ public void process(@Element Row input, OutputReceiver<String> out) {
                         Iterable<Row> anns = input.getRow("lhs").getIterable("annotations");
                         String rawText = input.getRow("rhs").getString(note_text_raw_col.getSourceColumnName());
                         Document doc = db.newDocument();
-                        org.w3c.dom.Element rootElement = doc.createElement("MedTagger");
+                        org.w3c.dom.Element rootElement = doc.createElement(taskName);
                         doc.appendChild(rootElement);
                         Node cdata = doc.createCDATASection(rawText);
                         org.w3c.dom.Element textElement = doc.createElement("TEXT");