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Developing PlugIns with MacOSX running Catalina

I've followed the instructions for upgrading to Geneious Prime and am running 2020.0.4 on a Mac with OS version Catalina (v 10.15.1). I've also downloaded the latest plugin kit (geneious-2020.0.4-devkit). I'm trying to run a plugin that ran previously on a Mac running Mojave and Geneious Primer 2019.2.1 with the associated plugin kit (2019.2.1). When I try to run the plugin under my current setting with Catalina and the 2020.0.4 client and devkit using open JDK 11.0.5, I get these errors:

/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home/bin/java -XX:+UseCompressedOops -XX:+UseConcMarkSweepGC -ea -Xss512K -Xms256M -Xmx768M -XX:MaxPermSize=256M -Djava.util.logging.config.file=no_logging.properties --add-opens=java.base/jdk.internal.reflect=ALL-UNNAMED -Djava.library.path=/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles "-javaagent:/Applications/IntelliJ IDEA.app/Contents/lib/idea_rt.jar=64668:/Applications/IntelliJ IDEA.app/Contents/bin" -Dfile.encoding=UTF-8 -classpath /Users/speters/Projects/ProteinTargetDbExportPlugin/production/ProteinTargetDbExportPlugin:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/converter-gson-2.5.0.jar:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/gson-2.8.2.jar:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/logging-interceptor-3.14.1.jar:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/okhttp-3.14.1.jar:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/okio-1.17.2.jar:/Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/lib/retrofit-2.5.0.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/gag.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jdom.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jebl.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/mail.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/common.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/crypto.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/flexlm.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/fop-2.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/bytecode.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/dynclass.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jna-4.5.1.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/oro-2.0.8.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/activation.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/i4jruntime.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jcommander.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/ObjCBridge.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/PrivateAPI.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/biojava-1.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-cli.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/epsgraphics.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/piccolo_xml.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/EccpressoAll.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jdom-contrib.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jsr305-1.3.9.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/log4j-1.2.17.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/truezip-6.8.3.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/batik-all-1.10.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-io-2.6.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/guava-25.0-jre.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/talkbackShared.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/webservices-rt.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/CryptoUtilities.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/oshi-core-3.5.0.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/webservices-api.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-dbcp-1.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-io-2.2.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/MacOsIntegration.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/slf4j-api-1.7.25.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/threetenbp-1.3.6.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/bcpg-jdk15on-1.47.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-math3-3.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-net-1.4.1.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/flexnetActivation.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/GeneiousPublicAPI.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/interpolatd-1.0.0.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/lucene-core-2.9.3.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-pool-1.5.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-util-2.1.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jackson-core-2.7.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jakarta-regexp-1.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jna-platform-4.5.1.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/piccolo2d-core-1.3.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/VersionTestLibrary.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/WindowsIntegration.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/bcprov-jdk15on-1.47.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-lang3-3.3.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-logging-1.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/javassist-3.18.2-GA.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/UsageTrackingShared.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/xml-apis-ext-1.3.04.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/geneiouscliapi-11.0.3.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/avalon-framework-4.1.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-compress-1.4.1.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/flexnetInstallerHelper.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphics2d-2.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphicsio-2.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jackson-databind-2.7.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/juniversalchardet-1.0.3.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/xmlgraphics-commons-2.2.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/commons-collections4-4.1.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphicsbase-2.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/glazedlists-1.6.0_java15.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/MaskedShellFolderManager.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/jackson-annotations-2.7.5.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphicsio-emf-2.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphicsio-swf-2.4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/org-netbeans-swing-outline.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/freehep-graphicsio-java-2.4.jar:/Users/speters/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.0.0-M4/junit-jupiter-api-5.0.0-M4.jar:/Users/speters/.m2/repository/org/opentest4j/opentest4j/1.0.0-M2/opentest4j-1.0.0-M2.jar:/Users/speters/.m2/repository/org/junit/platform/junit-platform-commons/1.0.0-M4/junit-platform-commons-1.0.0-M4.jar:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/iSeek.jar com.biomatters.iseek.application.ISeekMain extraPlugins=com.absci.geneious.proteindbexport.ProteinTargetDbExportPlugin
OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.biomatters.utilities.FilePreferencesFactory (file:/Users/speters/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib/common.jar) to constructor java.util.prefs.MacOSXPreferencesFactory()
WARNING: Please consider reporting this to the maintainers of com.biomatters.utilities.FilePreferencesFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
16:11:27.708 WARNING: Exception: java.lang.RuntimeException: java.lang.IllegalStateException: Should not fail to list contents of application folder: /Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/resources/images
at com.biomatters.utilities.Utils.c(Utils.java:860)
at com.biomatters.iseek.application.ISeekMain.j(ISeekMain.java:146)
at com.biomatters.iseek.application.ISeekMain.a(ISeekMain.java:764)
at com.biomatters.iseek.application.ISeekMain.main(ISeekMain.java:685)
Caused by: java.lang.IllegalStateException: Should not fail to list contents of application folder: /Users/speters/Projects/geneious/geneious/ProteinTargetDbExportPlugin/resources/images
at com.biomatters.security.gui.SplashWindow.getSplashBackgroundImage(SplashWindow.java:475)
at com.biomatters.security.gui.SplashWindow.<init>(SplashWindow.java:77)
at com.biomatters.iseek.application.ISeekMain.lambda$showSplashScreen$0(ISeekMain.java:147)
at com.biomatters.geneious.publicapi.utilities.ThreadUtilities.lambda$invokeAndWait$0(ThreadUtilities.java:107)
at org.virion.jam.util.Utils$1.run(Utils.java:130)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:303)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Process finished with exit code 1

Are these error due to the MacOS or an incorrect project setting in IntelliJ? Please see the project .iml file below:

?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager">
<output url="file://$MODULE_DIR$/../../../ProteinTargetDbExportPlugin/production/ProteinTargetDbExportPlugin" />
<output-test url="file://$MODULE_DIR$/../../../ProteinTargetDbExportPlugin/test/ProteinTargetDbExportPlugin" />
<exclude-output />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/test" isTestSource="true" />
</content>
<orderEntry type="jdk" jdkName="11 (2)" jdkType="JavaSDK" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/converter-gson-2.5.0.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/gson-2.8.2.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/logging-interceptor-3.14.1.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/okhttp-3.14.1.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/okio-1.17.2.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="jar://$MODULE_DIR$/lib/retrofit-2.5.0.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
</orderEntry>
<orderEntry type="module-library" exported="">
<library>
<CLASSES>
<root url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib" />
</CLASSES>
<JAVADOC />
<SOURCES>
<root url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib" />
</SOURCES>
<jarDirectory url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib" recursive="false" />
<jarDirectory url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles/lib" recursive="false" type="SOURCES" />
</library>
</orderEntry>
<orderEntry type="library" name="org.junit.jupiter:junit-jupiter-api:5.0.0-M4" level="project" />
<orderEntry type="library" scope="TEST" name="junit:junit:4.13-rc-2" level="project" />
<orderEntry type="module-library">
<library>
<CLASSES>
<root url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles" />
</CLASSES>
<JAVADOC />
<NATIVE>
<root url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles" />
</NATIVE>
<SOURCES />
<jarDirectory url="file://$USER_HOME$/Downloads/geneious-2020.0.4-devkit/examples/GeneiousFiles" recursive="false" />
</library>
</orderEntry>
</component>
</module>

 

Sandra Peters

Official comment

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Hi,

Looks like this issue is caused by your runtime configuration, not by the .iml file: 

The WORKING_DIRECTORY in your runtime configuration has to be set to 'GeneiousFiles', e.g.:

<option name="WORKING_DIRECTORY" value="file://$MODULE_DIR$/../GeneiousFiles" />

In addition to that, in your iml file you should replace all the <orderEntry> sections that refer in different variations to GeneiousFiles with this one reference:

<orderEntry type="module" module-name="GeneiousFiles" />
Jonas Kuhn
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