Add required column schema

OHNLP · Mar 9, 2023 · eb3ff76 · eb3ff76
1 parent 093efe1
commit eb3ff76
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java
@@ -85,12 +85,7 @@ public void init() throws ComponentInitializationException {
     }
 
     @Override
-    public boolean hasRequiredColumns() {
-        return true;
-    }
-
-    @Override
-    public Schema getRequiredColumns() {
+    public Schema getRequiredColumns(String inputTag) {
         return Schema.of(
                 Schema.Field.of(this.noteIdField, Schema.FieldType.STRING),
                 Schema.Field.of(this.inputField, Schema.FieldType.STRING)

diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerOutputToOHDSIFormatTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerOutputToOHDSIFormatTransform.java
@@ -61,6 +61,21 @@ public Schema calculateOutputSchema(Schema schema) {
         return this.schema;
     }
 
+    @Override
+    public Schema getRequiredColumns(String inputTag) {
+        return Schema.of(
+                Schema.Field.of("nlp_run_dtm", Schema.FieldType.DATETIME),
+                Schema.Field.of("certainty", Schema.FieldType.STRING),
+                Schema.Field.of("experiencer", Schema.FieldType.STRING),
+                Schema.Field.of("status", Schema.FieldType.STRING),
+                Schema.Field.of("offset", Schema.FieldType.INT32),
+                Schema.Field.of("concept_code", Schema.FieldType.STRING),
+                Schema.Field.of("section_id", Schema.FieldType.INT32),
+                Schema.Field.of("matched_text", Schema.FieldType.STRING),
+                Schema.Field.of("matched_sentence", Schema.FieldType.STRING)
+        );
+    }
+
     @Override
     public PCollection<Row> expand(PCollection<Row> input) {
         return input.apply(ParDo.of(new DoFn<Row, Row>() {