Updates

[egonw]

• CDK 2.7.1 with JNA InChI (replacing the JNI library)
• Newer Bnd tool
• Cytoscape 3.9.0

I only tested the SMILES depiction. Please let me know what things I should check.

[egonw]

Okay, I found one problem:

Native library (linux-x86-64/libjnainchi.so) not found in resource path (/opt/Cytoscape_v3.9.1/framework/lib/boot/branding-3.9.1.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/karaf-launcher-3.9.1.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/opendmk_jmxremote_optional_jar-1.0-b01-ea.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/org.apache.karaf.diagnostic.boot-4.2.8.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/org.apache.karaf.jaas.boot-4.2.8.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/org.apache.karaf.main-4.2.8.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/org.apache.karaf.specs.activator-4.2.8.jar:/opt/Cytoscape_v3.9.1/framework/lib/boot/osgi.core-6.0.0.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/istack-commons-runtime-3.0.10.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/jakarta.xml.bind-api-2.3.2.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/javax.activation-1.2.0.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/javax.annotation-api-1.3.1.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/jaxb-runtime-2.3.2.jar:/opt/Cytoscape_v3.9.1/framework/lib/jdk9plus/txw2-2.3.2.jar)
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:301) ~[!/:?]
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:461) ~[!/:?]
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:403) ~[!/:?]
        at io.github.dan2097.jnainchi.inchi.InchiLibrary.<clinit>(InchiLibrary.java:33) ~[!/:?]
        at io.github.dan2097.jnainchi.JnaInchi.<clinit>(JnaInchi.java:61) ~[!/:?]
        ... 13 more
        Suppressed: java.lang.UnsatisfiedLinkError: libjnainchi.so: cannot open shared object file: No such file or directory
                at com.sun.jna.Native.open(Native Method) ~[!/:?]
                at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:191) ~[!/:?]
                at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:461) ~[!/:?]
                at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:403) ~[!/:?]
                at io.github.dan2097.jnainchi.inchi.InchiLibrary.<clinit>(InchiLibrary.java:33) ~[!/:?]
                at io.github.dan2097.jnainchi.JnaInchi.<clinit>(JnaInchi.java:61) ~[!/:?]
                at org.openscience.cdk.inchi.InChIToStructure.<init>(InChIToStructure.java:116) ~[!/:?]
                at org.openscience.cdk.inchi.InChIToStructure.<init>(InChIToStructure.java:127) ~[!/:?]
                at org.openscience.cdk.inchi.InChIGeneratorFactory.getInChIToStructure(InChIGeneratorFactory.java:211) ~[!/:?]
                at edu.ucsf.rbvi.chemViz2.internal.model.Compound.convertInchiToSmiles(Compound.java:394) [!/:?]

[egonw]

Does either of you have a lead I can follow up on, @johnmay and @dan2097?

[johnmay]

Like the SO is getting stripped out?

[egonw]

Like the SO is getting stripped out?

my current thought is that they are still there, but in inside the jna-inchi jars which are in the chemViz2-1.2.0.jar plugins jar, and that this double archiving makes them unfindable?

$ jar tvf chemViz2-1.2.0.jar  | grep jna
1756400 Mon Jan 10 15:18:46 CET 2022 jna-5.10.0.jar
 76056 Thu Mar 24 12:09:58 CET 2022 jna-inchi-api-1.1.jar
  1688 Thu Mar 24 12:09:58 CET 2022 jna-inchi-core-1.1.jar
659168 Thu Mar 24 12:09:58 CET 2022 jna-inchi-darwin-aarch64-1.1.jar
700925 Thu Mar 24 12:09:58 CET 2022 jna-inchi-darwin-x86-64-1.1.jar
612015 Thu Mar 24 12:09:58 CET 2022 jna-inchi-linux-arm-1.1.jar
639995 Thu Mar 24 12:10:00 CET 2022 jna-inchi-linux-x86-1.1.jar
674110 Thu Mar 24 12:10:00 CET 2022 jna-inchi-linux-x86-64-1.1.jar
567074 Thu Mar 24 12:10:00 CET 2022 jna-inchi-win32-x86-1.1.jar
682583 Thu Mar 24 12:10:00 CET 2022 jna-inchi-win32-x86-64-1.1.jar
 13656 Fri Dec 31 09:46:18 CET 2021 jnati-core-0.4.jar
 32831 Fri Dec 31 09:46:18 CET 2021 jnati-deploy-0.4.jar

[dan2097]

I think the double archiving may be intentional to work with OSGI. Is there an easy way to reproduce the error you mentioned? I can produce the packaged jar on Java 11.
If I were to take a guess I wonder whether it's an issue with the maven-bundle-plugin configuration, as as far as I'm aware JNA supports OSGI... but I'm not personally at all familiar with OSGI!

Unrelatedly, the build fails on Java 8 with the following error:

[ERROR] /C:/My Documents/workspace/chemViz2/src/main/java/edu/ucsf/rbvi/chemViz2/internal/tasks/ChemInfoSettingsTask.java:[6,26] cannot access org.cytoscape.work.AbstractTask
  bad class file: C:\Users\Daniel\.m2\repository\org\cytoscape\work-api\3.9.0\work-api-3.9.0.jar(org/cytoscape/work/AbstractTask.class)
    class file has wrong version 55.0, should be 52.0
    Please remove or make sure it appears in the correct subdirectory of the classpath.

[egonw]

@dan2097, @johnmay, okay, this was silliest mistake in 2022. It's working fine now.

@scootermorris, this PR is ready to get merged in.

[dan2097]

@egonw I'm still a bit confused as to why this would fix the issue, while jna-inchi-all does include the native binaries, jna-inchi-core also does! [jna-inchi-all also pulls in code for reading SMILES]

[egonw]

@egonw I'm still a bit confused as to why this would fix the issue, while jna-inchi-all does include the native binaries, jna-inchi-core also does! [jna-inchi-all also pulls in code for reading SMILES]

Mmm... not sure. It just made it work for me.