Fix nbactions namespace, remove System.exit from ChemicalFormatParser

asad · asad · commit 20e7dc8e0917 · 2026-03-23T21:40:36.000Z
- Fix 4 nbactions XML files: uk.ac.ebi → com.bioinceptionlabs
- ChemicalFormatParser: replace exit(1) with FileNotFoundException
  (CML) and continue (RXN loop) — library should not kill the JVM
- Remove unused System.exit import

All 135 tests pass.

Author: Syed Asad Rahman &lt;asad.rahman@bioinceptionlabs.com&gt;
diff --git a/nbactions-local.xml b/nbactions-local.xml
@@ -10,7 +10,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
@@ -24,7 +24,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <jpda.listen>true</jpda.listen>
         </properties>
@@ -39,7 +39,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
diff --git a/nbactions-ossrh.xml b/nbactions-ossrh.xml
@@ -10,7 +10,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
@@ -24,7 +24,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <jpda.listen>true</jpda.listen>
         </properties>
@@ -39,7 +39,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
diff --git a/nbactions-release-profile.xml b/nbactions-release-profile.xml
@@ -10,7 +10,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
@@ -24,7 +24,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <jpda.listen>true</jpda.listen>
         </properties>
@@ -39,7 +39,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.5.0:exec</goal>
         </goals>
         <properties>
-            <exec.args>-classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
         </properties>
     </action>
diff --git a/nbactions.xml b/nbactions.xml
@@ -10,7 +10,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
         </goals>
         <properties>
-            <exec.args>-Xms4G -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-Xms4G -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <exec.workingdir>/Users/asad/github/ReactionDecoder</exec.workingdir>
         </properties>
@@ -25,7 +25,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
         </goals>
         <properties>
-            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -Xms4G -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address} -Xms4G -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <jpda.listen>true</jpda.listen>
             <exec.workingdir>/Users/asad/github/ReactionDecoder</exec.workingdir>
@@ -41,7 +41,7 @@
             <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
         </goals>
         <properties>
-            <exec.args>-Xms4G -classpath %classpath uk.ac.ebi.aamtool.ReactionDecoder</exec.args>
+            <exec.args>-Xms4G -classpath %classpath com.bioinceptionlabs.aamtool.ReactionDecoder</exec.args>
             <exec.executable>java</exec.executable>
             <exec.workingdir>/Users/asad/github/ReactionDecoder</exec.workingdir>
         </properties>
diff --git a/src/main/java/com/bioinceptionlabs/aamtool/ChemicalFormatParser.java b/src/main/java/com/bioinceptionlabs/aamtool/ChemicalFormatParser.java
@@ -24,7 +24,6 @@
 import java.io.FileReader;
 import java.io.IOException;
 import static java.lang.String.format;
-import static java.lang.System.exit;
 import static java.lang.System.getProperty;
 import java.util.ArrayList;
 import java.util.List;
@@ -60,8 +59,7 @@ class ChemicalFormatParser {
     protected static IReaction parseCML(String input) throws FileNotFoundException, CDKException {
         File f = new File(input);
         if (!f.isFile()) {
-            LOGGER.warn(WARNING, format("CML file not found! " + f.getName()));
-            exit(1);
+            throw new FileNotFoundException("CML file not found: " + f.getName());
         }
         String[] split = f.getName().split("\\.cml");
         try (FileInputStream fis = new FileInputStream(input);
@@ -92,7 +90,7 @@ protected static List<IReaction> parseRXN(String fileNames) {
             File filepath = new File(fileName);
             if (!filepath.isFile()) {
                 LOGGER.error(WARNING, format("RXN file not found! %s", filepath.getName()));
-                exit(1);
+                continue;
             }
             LOGGER.info(INFO, "Annotating Reaction {0}", filepath.getName());
             IReaction rxnReactions;
