dont add medtagger prefix as it messes with legacy configs

OHNLP · Feb 15, 2023 · d1815f9 · d1815f9
1 parent d399138
commit d1815f9
Show file tree

Hide file tree

Showing 3 changed files with 23 additions and 23 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.51</version>
+    <version>1.0.52</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
@@ -72,16 +72,16 @@ public void initFromConfig(JsonNode config) throws ComponentInitializationExcept
     @Override
     public Schema calculateOutputSchema(Schema schema) {
         List<Schema.Field> fields = new ArrayList<>(schema.getFields());
-        fields.add(Schema.Field.of("medtagger_matched_text", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_concept_code", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_matched_sentence", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_section_id", Schema.FieldType.INT32));
-        fields.add(Schema.Field.of("medtagger_nlp_run_dtm", Schema.FieldType.DATETIME));
-        fields.add(Schema.Field.of("medtagger_certainty", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_experiencer", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_status", Schema.FieldType.STRING));
-        fields.add(Schema.Field.of("medtagger_offset", Schema.FieldType.INT32));
-        fields.add(Schema.Field.of("medtagger_semgroups", Schema.FieldType.STRING).withNullable(true));
+        fields.add(Schema.Field.of("matched_text", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("concept_code", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("matched_sentence", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("section_id", Schema.FieldType.INT32));
+        fields.add(Schema.Field.of("nlp_run_dtm", Schema.FieldType.DATETIME));
+        fields.add(Schema.Field.of("certainty", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("experiencer", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("status", Schema.FieldType.STRING));
+        fields.add(Schema.Field.of("offset", Schema.FieldType.INT32));
+        fields.add(Schema.Field.of("semgroups", Schema.FieldType.STRING).withNullable(true));
         this.outputSchema = Schema.of(fields.toArray(new Schema.Field[0]));
         return this.outputSchema;
     }

diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerOutputToOHDSIFormatTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerOutputToOHDSIFormatTransform.java
@@ -99,42 +99,42 @@ public void processElement(@Element Row input, OutputReceiver<Row> output) throw
                 // Generate an output row
                 Row.Builder rowBuild = Row.withSchema(schema)
                         .addValues(input.getValues())
-                        .addValue(input.getInt32("medtagger_section_id"))
-                        .addValue(input.getString("medtagger_matched_text"))
-                        .addValue(input.getString("medtagger_matched_sentence"));
+                        .addValue(input.getInt32("section_id"))
+                        .addValue(input.getString("matched_text"))
+                        .addValue(input.getString("matched_sentence"));
                 switch (resources.toUpperCase(Locale.ROOT)) {
                     case "NONE": {
                         try {
-                            rowBuild = rowBuild.addValue(Integer.valueOf(Optional.ofNullable(input.getString("medtagger_concept_code")).orElse("0")));
+                            rowBuild = rowBuild.addValue(Integer.valueOf(Optional.ofNullable(input.getString("concept_code")).orElse("0")));
                         } catch (NumberFormatException e) {
                             throw new IllegalArgumentException("OHDSI requires integer concept codes, value "
-                                    + input.getString("medtagger_concept_code") + " was instead provided with mapping ruleset 'NONE'");
+                                    + input.getString("concept_code") + " was instead provided with mapping ruleset 'NONE'");
                         }
                         break;
                     }
                     case "UMLS": {
-                        String conceptCode = input.getString("medtagger_concept_code");
+                        String conceptCode = input.getString("concept_code");
                         // Only take first portion as CUI, remainder is top freq lexeme in current dict format.
                         String cui = conceptCode.contains(":") ? conceptCode.split(":")[0].toUpperCase(Locale.ROOT)
                                 : conceptCode.toUpperCase(Locale.ROOT);
                         int ohdsicid = ohdsiConceptMap.getOrDefault(cui, -99999);
                         rowBuild = rowBuild.addValue(ohdsicid);
                     }
                     default: {
-                        rowBuild = rowBuild.addValue(ohdsiConceptMap.getOrDefault(input.getString("medtagger_concept_code"), 0));
+                        rowBuild = rowBuild.addValue(ohdsiConceptMap.getOrDefault(input.getString("concept_code"), 0));
                     }
                 }
                 Row out = rowBuild
                         .addValue(0)
-                        .addValue(input.getDateTime("medtagger_nlp_run_dtm"))
+                        .addValue(input.getDateTime("nlp_run_dtm"))
                         .addValue(
                                 String.format("certainty=%1$s,experiencer=%2$s,status=%3$s",
-                                        input.getString("medtagger_certainty"),
-                                        input.getString("medtagger_experiencer"),
-                                        input.getString("medtagger_status")
+                                        input.getString("certainty"),
+                                        input.getString("experiencer"),
+                                        input.getString("status")
                                 )
                         )
-                        .addValue(input.getInt32("medtagger_offset"))
+                        .addValue(input.getInt32("offset"))
                         .addValue(version.trim())
                         .build();
                 output.output(out);