From 66cfd2b0bfbbe06994ba2cae463de0abd0a54cd8 Mon Sep 17 00:00:00 2001
From: Andrew Wen <Andrew.Wen@uth.tmc.edu>
Date: Tue, 3 Sep 2024 15:50:32 -0500
Subject: [PATCH] Dynamically resolve section

---
 pom.xml                                       |  2 +-
 .../java/org/ohnlp/medtagger/fit/Main.java    | 28 ++++++++++++++++++-
 .../MedTaggerIEAggregateTAE.xml               |  7 -----
 3 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/pom.xml b/pom.xml
index 59bb63b..34f1bb5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.73</version>
+    <version>1.0.74</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 
diff --git a/src/main/java/org/ohnlp/medtagger/fit/Main.java b/src/main/java/org/ohnlp/medtagger/fit/Main.java
index b6f446e..7ac456e 100644
--- a/src/main/java/org/ohnlp/medtagger/fit/Main.java
+++ b/src/main/java/org/ohnlp/medtagger/fit/Main.java
@@ -5,8 +5,11 @@
 import org.apache.uima.collection.CollectionReaderDescription;
 import org.apache.uima.fit.factory.AnalysisEngineFactory;
 import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.ExternalResourceFactory;
 import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.resource.impl.FileLanguageResource_impl;
 import org.apache.uima.resource.metadata.ConfigurationParameterSettings;
+import org.apache.uima.resource.metadata.ResourceManagerConfiguration;
 import org.ohnlp.medtagger.cr.FileSystemReader;
 import org.ohnlp.medtagger.ie.cc.MedTatorWriter;
 
@@ -22,6 +25,10 @@ public static void main(String[] args) throws Exception {
         Path inputDirPath = Paths.get(args[0]);
         Path outputDirPath = Paths.get(args[1]);
         Path ruleDirPath = Paths.get(args[2]);
+        Path sectionPath = null;
+        if (args.length > 3) {
+            sectionPath = Paths.get(args[4]);
+        }
 
         CollectionReaderDescription reader =
                 CollectionReaderFactory.createReaderDescription(
@@ -31,10 +38,29 @@ public static void main(String[] args) throws Exception {
         System.out.println("Input Dir:\t" + inputDirPath.toAbsolutePath().toString());
         System.out.println("Output Dir:\t" + outputDirPath.toAbsolutePath().toString());
         System.out.println("IE Rules:\t" + ruleDirPath.toAbsolutePath().toUri().toString());
+        if (sectionPath != null) {
+            System.out.println("Section Rules:\t" + sectionPath.toAbsolutePath().toUri().toString());
+        }
 
         AnalysisEngineDescription descMedTaggerTAE = createEngineDescription(
                 "desc.medtaggeriedesc.aggregate_analysis_engine.MedTaggerIEAggregateTAE");
-
+        if (sectionPath != null) {
+            ResourceManagerConfiguration rmConfig = descMedTaggerTAE.getResourceManagerConfiguration();
+            rmConfig.addExternalResource(
+                    ExternalResourceFactory.createExternalResourceDescription(
+                            "section_map",
+                            "file:" + sectionPath.toFile().getAbsolutePath()
+                    )
+            );
+        } else {
+            ResourceManagerConfiguration rmConfig = descMedTaggerTAE.getResourceManagerConfiguration();
+            rmConfig.addExternalResource(
+                    ExternalResourceFactory.createExternalResourceDescription(
+                            "section_map",
+                            "file:medtaggerieresources/pad/Radiology_Section"
+                    )
+            );
+        }
         AnalysisEngineMetaData metadata = descMedTaggerTAE.getAnalysisEngineMetaData();
 
         ConfigurationParameterSettings settings = metadata.getConfigurationParameterSettings();
diff --git a/src/main/resources/desc/medtaggeriedesc/aggregate_analysis_engine/MedTaggerIEAggregateTAE.xml b/src/main/resources/desc/medtaggeriedesc/aggregate_analysis_engine/MedTaggerIEAggregateTAE.xml
index c9c626e..6b0a281 100644
--- a/src/main/resources/desc/medtaggeriedesc/aggregate_analysis_engine/MedTaggerIEAggregateTAE.xml
+++ b/src/main/resources/desc/medtaggeriedesc/aggregate_analysis_engine/MedTaggerIEAggregateTAE.xml
@@ -140,13 +140,6 @@
                 </fileResourceSpecifier>
             </externalResource>
 
-            <externalResource>
-                <name>section_map</name>
-                <description/>
-                <fileResourceSpecifier>
-                    <fileUrl>file:medtaggerieresources/pad/Radiology_Section</fileUrl>
-                </fileResourceSpecifier>
-            </externalResource>
 
             <externalResource>
                 <name>openclass</name>