/Library/Java/JavaVirtualMachines/jdk1.8.0_291.jdk/Contents/Home/lib

ant-javafx.jar	ct.sym		dt.jar		ir.idl		javafx-mx.jar	jconsole.jar	orb.idl		packager.jar	sa-jdi.jar	tools.jar	visualvm

/Library/Java/JavaVirtualMachines/zulu8.62.0.19-ca-fx-jdk8.0.332-macosx_x64/zulu-8.jdk/Contents/Home/lib

ant-javafx.jar	ct.sym		dt.jar		ir.idl		javafx-mx.jar	jconsole.jar	orb.idl		packager.jar	sa-jdi.jar	tools.jar

/Library/Java/JavaVirtualMachines/zulu11.60.19-ca-fx-jdk11.0.17-macosx_x64/zulu-11.jdk/Contents/Home/lib

classlist			libdecora_sse.dylib		libjava.dylib			libmanagement_agent.dylib	librmi.dylib
ct.sym				libdt_socket.dylib		libjavafx_font.dylib		libmanagement_ext.dylib		libsaproc.dylib
fontconfig.bfc			libextnet.dylib			libjavafx_iio.dylib		libmlib_image.dylib		libsplashscreen.dylib
fontconfig.properties.src	libfontmanager.dylib		libjavajpeg.dylib		libnet.dylib			libsunec.dylib
javafx-swt.jar			libfreetype.dylib		libjawt.dylib			libnio.dylib			libunpack.dylib
javafx.properties		libfxplugins.dylib		libjdwp.dylib			libosx.dylib			libverify.dylib
jfr				libglass.dylib			libjfxmedia.dylib		libosxapp.dylib			libzip.dylib
jli				libglib-lite.dylib		libjfxmedia_avf.dylib		libosxkrb5.dylib		modules
jrt-fs.jar			libgstreamer-lite.dylib		libjfxwebkit.dylib		libosxsecurity.dylib		psfont.properties.ja
jspawnhelper			libinstrument.dylib		libjimage.dylib			libosxui.dylib			psfontj2d.properties
jvm.cfg				libj2gss.dylib			libjsig.dylib			libprefs.dylib			security
libattach.dylib			libj2pcsc.dylib			libjsound.dylib			libprism_common.dylib		server
libawt.dylib			libj2pkcs11.dylib		liblcms.dylib			libprism_es2.dylib		src.zip
libawt_lwawt.dylib		libjaas.dylib			libmanagement.dylib		libprism_sw.dylib		tzdb.dat

Blog on fixing sun.* imports: https://winterbe.com/posts/2018/08/29/migrate-maven-projects-to-java-11-jigsaw/

Removal of javadoc doclet API: https://bugs.openjdk.org/browse/JDK-8215587

This is where the IGB code came from in Cytoscape: https://www.javatips.net/api/cytoscape-api-master/taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java

This is the newer refactored code from cytoscape: https://github.com/cytoscape/cytoscape-api/blob/d2446a8e5ef6991ed38f7c0699c41b29b5505b48/taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java

Cytoscape refactoring taglets commit: https://github.com/cytoscape/cytoscape-api/commit/d2446a8e5ef6991ed38f7c0699c41b29b5505b48

Documentation on jkd.javadoc.doclet: https://docs.oracle.com/en/java/javase/11/docs/api/jdk.javadoc/jdk/javadoc/doclet/package-summary.html

Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/0da7d0a013c3f821ded6da40a3a05c83e672182b

I used the refactored Cytoscape code base to update ModuleInfoTaglet.java. I'm not entirely sure what this class is needed for, as it is only used in the parent pom.xml, but I think it has to do with IGB apps. The original code for ModuleInfoTaglet.java appears to come straight from cytoscape, so I used their refactored code. I have pushed the changes to the IGBF-3275 branch.

The Netbeans IDE is no longer complaining about the taglets package, however, I am unclear how to test my changes as IGB is not yet running with JDK 11.

To test:
Pull the latest changes to the IGBF-3275 branch.
Clean and build IGB (mvn clean install).
IGB should build successfully, but the jar will not run.

Discussion during scrum:

Try:

• Migrate new cytoscape code over to the master branch.
• Attempt to build and run the code.
• If it works, rebase the JDK 11 branch on master.

Code has been migrated to master branch.
IGB builds and runs, however, I am unsure of what the taglets are doing, so I am not sure if the new changes are working correctly. The taglets are included in the parent pom as part of the maven-javadoc-plugin. The code for ModuleInfoTaglet.java was added in this commit with the comment "added javadoc for context-menu-api".

I think the code was included as part of a tutorial(?) for the context menu api: https://wiki.bioviz.org/confluence/display/igbdevelopers/Context+Menu+API+QuickStart

There is a Jira ticket (https://jira.bioviz.org/browse/IGBF-1089) that mentions the context menu api and is dated around the same time that David made the above commit.

Suggestion: Search Jira for "javadoc" and see what comes up.

This commit may be relevant, but there is no information in the commit other than a link to the IGB developer's guide. Searching the developer's guide for javadoc returns no results.

I am able to install apps via the IGB App Store as well as the IGB App Manager (tested ProtAnnot and Super Simple IGB App). I think that the context-menu-api quickstart app may demonstrate/use the taglets based on David's commit, but I cannot get it to run as there are a number of errors.

My commit to my Java 8 branch: https://bitbucket.org/nfreese/nowlanfork-igb/commits/14582a8a688838129e42c5131b62b2674b1f9869

Since the changes do not appear to break IGB (on Java 8) but we are unclear of what the changes are doing, I have pushed the changes to the IGBF-3275 branch (Java 11) but we will not push them to master.

Closing ticket.