Another stab at fixing integer typecasting on retrieval

Author: qqndrew

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.84</version>
+    <version>1.0.85</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 

src/main/java/org/ohnlp/medtagger/backbone/MedtatorOutputTransform.java

@@ -193,8 +193,18 @@ public void process(@Element Row input, OutputReceiver<String> out) {
                         org.w3c.dom.Element tagsElement = doc.createElement("TAGS");
                         int tagId = 0;
                         for (Row ann : anns) {
-                            int start = Integer.valueOf(ann.getValue(ann_start_ann_col.getSourceColumnName()));
-                            int end = Integer.valueOf(ann.getValue(ann_end_ann_col.getSourceColumnName()));
+                            Integer start = null;
+                            Integer end = null;
+                            if (ann.getSchema().getField(ann_start_ann_col.getSourceColumnName()).getType().typesEqual(Schema.FieldType.STRING)) {
+                                start = Integer.valueOf(ann.getString(ann_start_ann_col.getSourceColumnName()));
+                            } else {
+                                start = ann.getInt32(ann_start_ann_col.getSourceColumnName());
+                            }
+                            if (ann.getSchema().getField(ann_end_ann_col.getSourceColumnName()).getType().typesEqual(Schema.FieldType.STRING)) {
+                                end = Integer.valueOf(ann.getString(ann_end_ann_col.getSourceColumnName()));
+                            } else {
+                                end = ann.getInt32(ann_end_ann_col.getSourceColumnName());
+                            }
                             String type = "CM";
                             if (ann_type_col != null) {
                                 type = ann.getString(ann_type_col.getSourceColumnName());