Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

CeSymm broken on many java versions #104

Closed
sbliven opened this issue Nov 10, 2021 · 4 comments
Closed

CeSymm broken on many java versions #104

sbliven opened this issue Nov 10, 2021 · 4 comments

Comments

@sbliven
Copy link
Collaborator

sbliven commented Nov 10, 2021

Biojava and cesymm officially support Java 1.8+. However the CeSymm jar file includes many dependencies which break this compatiblity.

Java 8

❌ Broken due to jgrapht

java -jar 'symmetry-tools/target/CeSymm-2.2.0-SNAPSHOT.jar' 1tim.A
Structure       NumRepeats      SymmGroup       Reason
Exception in thread "pool-2-thread-1" java.lang.UnsupportedClassVersionError: org/jgrapht/Graph has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
        at workers.CeSymmWorker.run(CeSymmWorker.java:65)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

Jgrapht dropped java 8 support after 1.3.0, so BioJava needs to pin that version upstream.

Java 11

⚠️ Works, but warnings:

java -jar 'symmetry-tools/target/CeSymm-2.2.0-SNAPSHOT.jar' 1tim.A
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Structure       NumRepeats      SymmGroup       Reason
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/Users/bliven_s/git/biojava_ws/symmetry/symmetry-tools/target/CeSymm-2.2.0-SNAPSHOT.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int)
WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector
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
1tim.A  2       C2      Significant (TM=0,56)

com.sun.xml was removed in Java 11. BioJava gets around this by bundling it as a dependency, but the warnings indicate the bundled JAXB version is not fully compatible.

Java 15 and 17

❌ Broken

java -jar 'symmetry-tools/target/CeSymm-2.2.0-SNAPSHOT.jar' 1tim.A
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Structure       NumRepeats      SymmGroup       Reason
Nov 10, 2021 9:43:22 PM com.sun.xml.bind.v2.runtime.reflect.opt.Injector <clinit>
SEVERE: null
java.security.PrivilegedActionException: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass(java.lang.String,[B,int,int,java.lang.ClassLoader,java.security.ProtectionDomain)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:573)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.java:166)
        at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:51)
        at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:157)
        at com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:255)
        at com.sun.xml.bind.v2.runtime.property.SingleElementLeafProperty.<init>(SingleElementLeafProperty.java:62)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
        at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:99)
        at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:150)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:493)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:512)
        at com.sun.xml.bind.v2.runtime.ArrayBeanInfoImpl.<init>(ArrayBeanInfoImpl.java:48)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:502)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:304)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:109)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1142)
        at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:141)
        at com.sun.xml.bind.v2.JAXBContextFactory.createContext(JAXBContextFactory.java:35)
        at javax.xml.bind.ContextFinder.find(ContextFinder.java:404)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:721)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:662)
        at org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot.fromXML(SpaceGroupMapRoot.java:77)
        at org.biojava.nbio.structure.xtal.SymoplibParser.parseSpaceGroupsXML(SymoplibParser.java:140)
        at org.biojava.nbio.structure.xtal.SymoplibParser.parseSpaceGroupsXML(SymoplibParser.java:104)
        at org.biojava.nbio.structure.xtal.SymoplibParser.<clinit>(SymoplibParser.java:58)
        at org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl.consumeSymmetry(CifStructureConsumerImpl.java:1099)
        at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromCifFile(CifStructureConverter.java:156)
        at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromInputStream(CifStructureConverter.java:83)
        at org.biojava.nbio.structure.io.BcifFileReader.getStructure(BcifFileReader.java:41)
        at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructureById(LocalPDBDirectory.java:349)
        at org.biojava.nbio.structure.align.util.AtomCache.loadStructureFromBcifByPdbId(AtomCache.java:893)
        at org.biojava.nbio.structure.align.util.AtomCache.getStructureForPdbId(AtomCache.java:831)
        at org.biojava.nbio.structure.SubstructureIdentifier.loadStructure(SubstructureIdentifier.java:324)
        at org.biojava.nbio.structure.align.client.StructureName.loadStructure(StructureName.java:517)
        at org.biojava.nbio.structure.align.util.AtomCache.getStructure(AtomCache.java:503)
        at workers.CeSymmWorker.run(CeSymmWorker.java:58)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass(java.lang.String,[B,int,int,java.lang.ClassLoader,java.security.ProtectionDomain)
        at java.base/java.lang.Class.getMethod(Class.java:2227)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$3.run(Injector.java:170)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector$3.run(Injector.java:166)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
        ... 42 more

Exception in thread "pool-2-thread-1" java.lang.ExceptionInInitializerError
        at org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl.consumeSymmetry(CifStructureConsumerImpl.java:1099)
        at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromCifFile(CifStructureConverter.java:156)
        at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromInputStream(CifStructureConverter.java:83)
        at org.biojava.nbio.structure.io.BcifFileReader.getStructure(BcifFileReader.java:41)
        at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructureById(LocalPDBDirectory.java:349)
        at org.biojava.nbio.structure.align.util.AtomCache.loadStructureFromBcifByPdbId(AtomCache.java:893)
        at org.biojava.nbio.structure.align.util.AtomCache.getStructureForPdbId(AtomCache.java:831)
        at org.biojava.nbio.structure.SubstructureIdentifier.loadStructure(SubstructureIdentifier.java:324)
        at org.biojava.nbio.structure.align.client.StructureName.loadStructure(StructureName.java:517)
        at org.biojava.nbio.structure.align.util.AtomCache.getStructure(AtomCache.java:503)
        at workers.CeSymmWorker.run(CeSymmWorker.java:58)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NullPointerException: Cannot invoke "java.lang.reflect.Method.invoke(Object, Object[])" because "com.sun.xml.bind.v2.runtime.reflect.opt.Injector.defineClass" is null
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.inject(Injector.java:294)
        at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.inject(Injector.java:66)
        at com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:57)
        at com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:157)
        at com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:255)
        at com.sun.xml.bind.v2.runtime.property.SingleElementLeafProperty.<init>(SingleElementLeafProperty.java:62)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
        at com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:99)
        at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:150)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:493)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:512)
        at com.sun.xml.bind.v2.runtime.ArrayBeanInfoImpl.<init>(ArrayBeanInfoImpl.java:48)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:502)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:304)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:109)
        at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1142)
        at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:141)
        at com.sun.xml.bind.v2.JAXBContextFactory.createContext(JAXBContextFactory.java:35)
        at javax.xml.bind.ContextFinder.find(ContextFinder.java:404)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:721)
        at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:662)
        at org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot.fromXML(SpaceGroupMapRoot.java:77)
        at org.biojava.nbio.structure.xtal.SymoplibParser.parseSpaceGroupsXML(SymoplibParser.java:140)
        at org.biojava.nbio.structure.xtal.SymoplibParser.parseSpaceGroupsXML(SymoplibParser.java:104)
        at org.biojava.nbio.structure.xtal.SymoplibParser.<clinit>(SymoplibParser.java:58)
        ... 14 more

XML parsing seems completely broken with the bundled JAXB. The code runs fine for me in VSCode, so I believe the problem is introduced in the shade step, which includes dependencies without stringent compatibility checks.
@josemduarte
Copy link
Member

I suppose you are using the latest biojava release (6.0.0)?

Also another comment, have you tried the explicit dependencies solution for this project? I.e. what this PR did for biojava: https://github.com/biojava/biojava/pull/805/files

@sbliven
Copy link
Collaborator Author

sbliven commented Nov 10, 2021

@josemduarte I need to look into it more, but I think that PR probably broke it for Java 15. CeSymm uses mvn shade, so all of biojava's dependencies get pulled recursively including the JAXB implementation.

The protein-comparison-tool also uses shade and is also broken on java 15, although it gives a different exception.

I think the solution to this is probably to switch biojava to use a different XML implementation.

@sbliven sbliven mentioned this issue Nov 11, 2021
Merged
@sbliven
Copy link
Collaborator Author

sbliven commented Nov 11, 2021

The glassfish implementation fixed the problem. Should be fixed after merging biojava/biojava#996 upstream

@sbliven
Copy link
Collaborator Author

sbliven commented Jan 4, 2022

Fixed in #112 with biojava 6.0.3

@sbliven sbliven closed this as completed Jan 4, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@sbliven @josemduarte