Dynamic context loading for backbone

OHNLP · Jan 26, 2022 · d21f0dc · d21f0dc
1 parent 2d4da10
commit d21f0dc
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Showing 2 changed files with 23 additions and 4 deletions.
diff --git a/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java b/src/main/java/org/ohnlp/medtagger/backbone/MedTaggerBackboneTransform.java
@@ -91,11 +91,12 @@ public void init() throws IOException, InvalidXMLException, URISyntaxException,
             // Tokenization, Sentence Splitting, Section Detection, etc.
             ae.add(createEngineDescription("desc.backbone.aes.PreConceptExtractionAE"));
             // Add the appropriate NER/normalization component depending on run mode
+            URI uri = null;
             switch (mode) {
                 case OHNLPTK_DEFINED: // Ruleset from a web service
                     throw new UnsupportedOperationException("Remote Served IE Rulesets not yet implemented");
                 case STANDALONE:
-                    final URI uri = MedTaggerPipelineFunction.class.getResource("/resources/" + this.resourceFolder).toURI();
+                    uri = MedTaggerPipelineFunction.class.getResource("/resources/" + this.resourceFolder).toURI();
                     Map<String, String> env = new HashMap<>();
                     env.put("create", "true");
                     try {
@@ -111,7 +112,11 @@ public void init() throws IOException, InvalidXMLException, URISyntaxException,
             }
 
             // Add Context handling
-            ae.add(AnalysisEngineFactory.createEngineDescription(RuleContextAnnotator.class));
+            if (uri != null) {
+                ae.add(AnalysisEngineFactory.createEngineDescription(RuleContextAnnotator.class, "context_ruleset", uri.toString()));
+            } else {
+                ae.add(AnalysisEngineFactory.createEngineDescription(RuleContextAnnotator.class));
+            }
 
             this.resMgr = ResourceManagerFactory.newResourceManager();
             this.aae = UIMAFramework.produceAnalysisEngine(ae.createAggregateDescription(), resMgr, null);

diff --git a/src/main/java/org/ohnlp/medtagger/context/RuleContextAnnotator.java b/src/main/java/org/ohnlp/medtagger/context/RuleContextAnnotator.java
@@ -40,6 +40,11 @@
 import org.ohnlp.typesystem.type.textspan.Sentence;
 
 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.regex.MatchResult;
@@ -62,12 +67,21 @@ public class RuleContextAnnotator extends JCasAnnotator_ImplBase {
     @Override
     public void initialize(UimaContext ctxt) throws ResourceInitializationException {
         super.initialize(ctxt);
+        String ruleset = (String) ctxt.getConfigParameterValue("context_ruleset");
+
         try {
+            if (ruleset == null) {
+                ruleset = ConTexTSettings.class.getResource("/medtaggerresources/context/contextRule.txt").toURI().toString();
+            } else {
+                ruleset = Paths.get(URI.create(ruleset)).resolve("context").resolve("contextRule.txt").toUri().toString();
+            }
             contextSettings = new LinkedList<>();
             for (int priority : RULE_PRIORITIES) {
-                contextSettings.add(new ConTexTSettings(ConTexTSettings.class.getResourceAsStream("/medtaggerresources/context/contextRule.txt"), priority));
+                contextSettings.add(new ConTexTSettings(Files.newInputStream(Paths.get(URI.create(ruleset))), priority));
             }
-        } catch (FileNotFoundException e) {
+        } catch (FileNotFoundException | URISyntaxException e) {
+            throw new ResourceInitializationException(e);
+        } catch (IOException e) {
             e.printStackTrace();
         }
     }