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imagej / imagej-server

A RESTful web server for ImageJ [EXPERIMENTAL]
Apache License 2.0
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error launching imagej-server on linux64 #22

Closed kephale closed 6 years ago

kephale commented 6 years ago

fresh Fiji on a Dell Ubuntu, installed imagej-server update site.

Fiji.app$ ./ImageJ-linux64 --server
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalStateException: Unable to acquire the logger context
    at io.dropwizard.logging.LoggingUtil.getLoggerContext(LoggingUtil.java:46)
    at io.dropwizard.logging.BootstrapLogging.bootstrap(BootstrapLogging.java:45)
    at io.dropwizard.Application.bootstrapLogging(Application.java:38)
    at io.dropwizard.Application.<init>(Application.java:26)
    at net.imagej.server.ImageJServer.<init>(ImageJServer.java:64)
    at net.imagej.server.DefaultImageJServerService$1.<init>(DefaultImageJServerService.java:66)
    at net.imagej.server.DefaultImageJServerService.start(DefaultImageJServerService.java:66)
    at net.imagej.server.console.ServerArgument.handle(ServerArgument.java:76)
    at org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:102)
    at net.imagej.legacy.LegacyConsoleService.processArgs(LegacyConsoleService.java:81)
    at org.scijava.AbstractGateway.launch(AbstractGateway.java:97)
    at net.imagej.Main.main(Main.java:55)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
ctrueden commented 6 years ago

@kephale Was there also an SLF4J binding error beforehand? Or nothing else? See e.g. this SO post, which might be related.

kephale commented 6 years ago

Yes, that seems to be true. It looks like there are 2 Loggers on the classpath:

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/kharrington/Fiji.app/jars/slf4j-simple-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/kharrington/Fiji.app/jars/logback-classic-1.2.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalStateException: Unable to acquire the logger context
    at io.dropwizard.logging.LoggingUtil.getLoggerContext(LoggingUtil.java:46)
    at io.dropwizard.logging.BootstrapLogging.bootstrap(BootstrapLogging.java:45)
    at io.dropwizard.Application.bootstrapLogging(Application.java:38)
    at io.dropwizard.Application.<init>(Application.java:26)
    at net.imagej.server.ImageJServer.<init>(ImageJServer.java:64)
    at net.imagej.server.DefaultImageJServerService$1.<init>(DefaultImageJServerService.java:66)
    at net.imagej.server.DefaultImageJServerService.start(DefaultImageJServerService.java:66)
    at net.imagej.server.console.ServerArgument.handle(ServerArgument.java:76)
    at org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:102)
    at net.imagej.legacy.LegacyConsoleService.processArgs(LegacyConsoleService.java:81)
    at org.scijava.AbstractGateway.launch(AbstractGateway.java:97)
    at net.imagej.Main.main(Main.java:55)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
kephale commented 6 years ago

I tracked this down to a slf4j dependency coming in through SciView. If I uninstall it, then imagej-server works just fine.

Should I add slf4j exclusions into SciView (like the ones in the imagej-server pom.xml)?

ctrueden commented 6 years ago

I believe the issue is not a Maven-related problem with SciView, since SciView marks the slf4j-simple dependency as runtime+optional, so it won't affect downstream projects depending on it.

The problem is one of deployment: unfortunately, Dropwizard has a hard assumption about its SLF4J logging implementaiton, which is evil, but not easy to work around. So for now (as long as imagej-server is built on dropwizard), the easiest way to avoid this issue is to ensure that only one SLF4J binding is on the classpath: Dropwizard's assumed binding. That means slf4j-simple has to go. The slf4j-simple JAR was uploaded to the SciView update site, but should not be necessary—I have now marked it obsolete, which hopefully avoids the exception above.

See also this Gitter discussion.