Added back -Dpaxtools.CollectionProvider etc.

PathwayCommons · Apr 29, 2024 · e0fdcec · e0fdcec
1 parent 869f37d
commit e0fdcec
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -28,7 +28,7 @@
     <validator.version>6.0.0-SNAPSHOT</validator.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <lucene.version>9.10.0</lucene.version>
-    <jvm.options>-Xmx3g -Dfile.encoding=UTF-8 -ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED</jvm.options>
+    <jvm.options>-Xmx3g -Dfile.encoding=UTF-8 -ea -Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED</jvm.options>
     <agent>${settings.localRepository}/org/springframework/spring-instrument/${spring-framework.version}/spring-instrument-${spring-framework.version}.jar</agent>
     <!-- this copy is created by maven-dependency-plugin -->
 <!--    <agent>target/spring-instrument.jar</agent>-->

diff --git a/src/main/java/cpath/service/ConsoleApplication.java b/src/main/java/cpath/service/ConsoleApplication.java
@@ -45,7 +45,9 @@
 public class ConsoleApplication implements CommandLineRunner {
   private static final Logger LOG = LoggerFactory.getLogger(ConsoleApplication.class);
   private static final String JAVA_PAXTOOLS = "$JAVA_HOME/bin/java -Xmx64g " +
-      "-Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true -jar paxtools.jar";
+      "-Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider " +
+      "-Dpaxtools.normalizer.use-latest-registry=true " +
+      "-Dpaxtools.core.use-latest-genenames=true -jar paxtools.jar";
 
   @Autowired
   private Service service;

diff --git a/work/cpath2.sh b/work/cpath2.sh
@@ -5,7 +5,7 @@ export CPATH2_HOME="."
 JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED"
 DEBUG_OPTS=""
 #DEBUG_OPTS="-Dlogback.configurationFile=logback.xml -Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=12345"
-BASE_OPTS="-Dlogback.configurationFile=logback.xml -Dfile.encoding=UTF-8 -Xss32m -Xmx60g -Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true"
+BASE_OPTS="-Dlogback.configurationFile=logback.xml -Dfile.encoding=UTF-8 -Xss32m -Xmx60g -Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProvider -Dpaxtools.normalizer.use-latest-registry=true -Dpaxtools.core.use-latest-genenames=true"
 #use List instead Map collections for read-only BioPAX model if we start the Web app but not if building the instance/data
 EXTRA_OPTS="$BASE_OPTS -server"