Fix default resource loading from jarfile

OHNLP · Feb 2, 2022 · 16a2744 · 16a2744
1 parent eb0d8f1
commit 16a2744
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Showing 3 changed files with 26 additions and 24 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.ohnlp.medtagger</groupId>
     <artifactId>medtagger</artifactId>
-    <version>1.0.21</version>
+    <version>1.0.22</version>
     <description>The MedTagger biomedical information extraction pipeline</description>
 
 

diff --git a/src/main/java/org/ohnlp/medtagger/ae/AhoCorasickLookupAnnotator.java b/src/main/java/org/ohnlp/medtagger/ae/AhoCorasickLookupAnnotator.java
@@ -80,21 +80,22 @@ public void initialize(UimaContext aContext)
             lvg = new LvgLookup(aContext);
             String dictfile = (String) aContext
                     .getConfigParameterValue("dict_file");
+            InputStream is;
             if (dictfile == null) {
-                dictfile = AhoCorasickLookupAnnotator.class.getResource("/medtaggerresources/lookup/PASC.lookup.dict")
-						.toURI().toString();
+                is = AhoCorasickLookupAnnotator.class.getResourceAsStream("/medtaggerresources/lookup/PASC.lookup.dict");
+            } else {
+                is = Files.newInputStream(Paths.get(URI.create(dictfile)));
             }
-            btac = new AhoCorasickDict(Files.newInputStream(Paths.get(URI.create(dictfile))));
+            btac = new AhoCorasickDict(is);
 			String stpfile = (String) aContext
 					.getConfigParameterValue("stop_file");
 			if (stpfile == null) {
-				stpfile = AhoCorasickLookupAnnotator.class.getResource("/medtaggerresources/lookup/stop.615")
-						.toURI().toString();
-			}
+				is = AhoCorasickLookupAnnotator.class.getResourceAsStream("/medtaggerresources/lookup/stop.615");
+			} else {
+                is = Files.newInputStream(Paths.get(URI.create(stpfile)));
+            }
             stop = new HashSet<String>();
-            BufferedReader br = new BufferedReader(new InputStreamReader(
-                    Files.newInputStream(Paths.get(URI.create(stpfile)))
-            ));
+            BufferedReader br = new BufferedReader(new InputStreamReader(is));
             while (br.ready()) {
                 String line = br.readLine();
                 if (line.startsWith("#")) continue;
@@ -107,12 +108,11 @@ public void initialize(UimaContext aContext)
             String abrfile = (String) aContext
                     .getConfigParameterValue("abbr_file");
 			if (abrfile == null) {
-				abrfile = AhoCorasickLookupAnnotator.class.getResource("/medtaggerresources/lookup/OHNLP_ohdsi.abbr")
-						.toURI().toString();
-			}
-            br = new BufferedReader(new InputStreamReader(
-                    Files.newInputStream(Paths.get(URI.create(abrfile)))
-            ));
+				is = AhoCorasickLookupAnnotator.class.getResourceAsStream("/medtaggerresources/lookup/OHNLP_ohdsi.abbr");
+			} else {
+                is =  Files.newInputStream(Paths.get(URI.create(abrfile)));
+            }
+            br = new BufferedReader(new InputStreamReader(is));
             while (br.ready()) {
                 String line = br.readLine();
                 if (line.startsWith("#")) continue;
@@ -123,7 +123,7 @@ public void initialize(UimaContext aContext)
             }
             br.close();
 
-        } catch (ResourceAccessException | IOException | URISyntaxException e) {
+        } catch (ResourceAccessException | IOException e) {
             throw new ResourceInitializationException(e);
         }
 

diff --git a/src/main/java/org/ohnlp/medtagger/context/RuleContextAnnotator.java b/src/main/java/org/ohnlp/medtagger/context/RuleContextAnnotator.java
@@ -41,10 +41,14 @@
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystemNotFoundException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.nio.file.spi.FileSystemProvider;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.regex.MatchResult;
@@ -68,21 +72,19 @@ public class RuleContextAnnotator extends JCasAnnotator_ImplBase {
     public void initialize(UimaContext ctxt) throws ResourceInitializationException {
         super.initialize(ctxt);
         String ruleset = (String) ctxt.getConfigParameterValue("context_ruleset");
-
+        InputStream is  = null;
         try {
             if (ruleset == null) {
-                ruleset = ConTexTSettings.class.getResource("/medtaggerresources/context/contextRule.txt").toURI().toString();
+                is = ConTexTSettings.class.getResourceAsStream("/medtaggerresources/context/contextRule.txt");
             } else {
-                ruleset = Paths.get(URI.create(ruleset)).resolve("context").resolve("contextRule.txt").toUri().toString();
+                is = Files.newInputStream(Paths.get(URI.create(ruleset)).resolve("context").resolve("contextRule.txt"));
             }
             contextSettings = new LinkedList<>();
             for (int priority : RULE_PRIORITIES) {
-                contextSettings.add(new ConTexTSettings(Files.newInputStream(Paths.get(URI.create(ruleset))), priority));
+                contextSettings.add(new ConTexTSettings(is, priority));
             }
-        } catch (FileNotFoundException | URISyntaxException e) {
-            throw new ResourceInitializationException(e);
         } catch (IOException e) {
-            e.printStackTrace();
+            throw new ResourceInitializationException(e);
         }
     }