Bugfix: define inputcolumn source tag metadata

OHNLP · Nov 18, 2024 · 25c54eb · 25c54eb
1 parent be085ec
commit 25c54eb
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Showing 2 changed files with 20 additions and 1 deletion.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.81</version>
+    <version>1.0.82</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
@@ -14,6 +14,7 @@
 import org.checkerframework.checker.nullness.qual.UnknownKeyFor;
 import org.ohnlp.backbone.api.annotations.ComponentDescription;
 import org.ohnlp.backbone.api.annotations.ConfigurationProperty;
+import org.ohnlp.backbone.api.annotations.InputColumnProperty;
 import org.ohnlp.backbone.api.components.LoadFromMany;
 import org.ohnlp.backbone.api.config.InputColumn;
 import org.ohnlp.backbone.api.exceptions.ComponentInitializationException;
@@ -55,30 +56,45 @@ public class MedtatorOutputTransform extends LoadFromMany {
             path = "note_id_raw_col",
             desc = "The input column to use containing the note identifier from the raw text collection"
     )
+    @InputColumnProperty(
+            sourceTags = {"Raw Text"}
+    )
     private InputColumn note_identifer_raw_col;
 
     @ConfigurationProperty(
             path = "note_text_raw_col",
             desc = "The input column to use containing the note text from the annotated entities"
     )
+    @InputColumnProperty(
+            sourceTags = {"Entity Annotations"}
+    )
     private InputColumn note_text_raw_col;
 
     @ConfigurationProperty(
             path = "note_id_ann_col",
             desc = "The input column to use containing the note identifier from the annotated entities"
     )
+    @InputColumnProperty(
+            sourceTags = {"Entity Annotations"}
+    )
     private InputColumn note_identifer_ann_col;
 
     @ConfigurationProperty(
             path = "note_ann_start_col",
             desc = "The input column to use containing the annotation start index from the annotated entities"
     )
+    @InputColumnProperty(
+            sourceTags = {"Entity Annotations"}
+    )
     private InputColumn ann_start_ann_col;
 
     @ConfigurationProperty(
             path = "note_ann_end_col",
             desc = "The input column to use containing the annotation end index from the annotated entities"
     )
+    @InputColumnProperty(
+            sourceTags = {"Entity Annotations"}
+    )
     private InputColumn ann_end_ann_col;
 
     @ConfigurationProperty(
@@ -87,6 +103,9 @@ public class MedtatorOutputTransform extends LoadFromMany {
                     "Defaults to \"ConceptMention\" if left blank",
             required = false
     )
+    @InputColumnProperty(
+            sourceTags = {"Entity Annotations"}
+    )
     private InputColumn ann_type_col;
 
     @Override