Dynamically resolve section

OHNLP · Sep 3, 2024 · 66cfd2b · 66cfd2b
1 parent abe2c0a
commit 66cfd2b
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Showing 3 changed files with 28 additions and 9 deletions.
diff --git 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
@@ -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/...main/resources/desc/medtaggeriedesc/aggregate_analysis_engine/MedTaggerIEAggregateTAE.xml b/...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>