Bugfix: MedTator Schema names must match/be customizable

OHNLP · Sep 23, 2024 · c78cd7f · c78cd7f
1 parent 03cf299
commit c78cd7f
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git 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
@@ -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");