Removed old wikipathways cleaner; added new paxtools jvm opt;

PathwayCommons · Feb 21, 2024 · 5f5185a · 5f5185a
1 parent b320921
commit 5f5185a
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Showing 3 changed files with 3 additions and 92 deletions.
diff --git a/src/main/java/cpath/cleaner/WikipathwaysCleaner.java b/src/main/java/cpath/cleaner/WikipathwaysCleaner.java
diff --git a/src/main/java/cpath/service/ConsoleApplication.java b/src/main/java/cpath/service/ConsoleApplication.java
@@ -44,7 +44,8 @@
 @Profile({"admin"})
 public class ConsoleApplication implements CommandLineRunner {
   private static final Logger LOG = LoggerFactory.getLogger(ConsoleApplication.class);
-  private static final String javaRunPaxtools = "nohup $JAVA_HOME/bin/java -Xmx60g -jar paxtools.jar";
+  private static final String javaRunPaxtools = "nohup $JAVA_HOME/bin/java -Xmx64g " +
+      "-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="-Dfile.encoding=UTF-8 -Xss32m -Xmx60g -Dpaxtools.normalizer.use-latest-registry=true"
+BASE_OPTS="-Dfile.encoding=UTF-8 -Xss32m -Xmx60g -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 -Dpaxtools.model.safeset=list -server"