When using the OMEZarrReader Build from #82 on the microervices dependencies I got an error (at the end of this issue) from the microservices. The error message does not have a lot of information.
I think one of the possible changes which may cause the error is the using awssdk dependency (2.17.100):
I have tried to upgrade the aws-java-sdk on the microservice dependencies to use the same version in the OMEZarrReader (2.17.100) but got the same error,
I have checked the other microservice dependencies, and found out that s3fs using version 2.2.3, one of the dependencies of this package is:
aws-java-sdk-s3 version 1.11.232
The latest version of this package (2.2.3, 2018) is the one which microservices is using
java.lang.NullPointerException: cause
at io.netty.util.internal.ObjectUtil.checkNotNull(ObjectUtil.java:39)
at io.netty.channel.AbstractChannelHandlerContext.invokeExceptionCaught(AbstractChannelHandlerContext.java:278)
at io.netty.channel.DefaultChannelPipeline.fireExceptionCaught(DefaultChannelPipeline.java:907)
at io.vertx.core.net.impl.VertxHandler.fail(VertxHandler.java:97)
at io.vertx.core.net.impl.ConnectionBase.fail(ConnectionBase.java:86)
at io.vertx.core.http.impl.Http1xServerConnection.handleError(Http1xServerConnection.java:480)
at io.vertx.core.http.impl.Http1xServerConnection.handleMessage(Http1xServerConnection.java:121)
at io.vertx.core.impl.ContextImpl.executeTask(ContextImpl.java:369)
at io.vertx.core.impl.EventLoopContext.execute(EventLoopContext.java:43)
at io.vertx.core.impl.ContextImpl.executeFromIO(ContextImpl.java:232)
at io.vertx.core.net.impl.VertxHandler.channelRead(VertxHandler.java:173)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.ChannelInboundHandlerAdapter.channelRead(ChannelInboundHandlerAdapter.java:93)
at io.netty.handler.codec.http.websocketx.extensions.WebSocketServerExtensionHandler.channelRead(WebSocketServerExtensionHandler.java:99)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at io.vertx.core.http.impl.Http1xUpgradeToH2CHandler.channelRead(Http1xUpgradeToH2CHandler.java:109)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:324)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:296)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at io.vertx.core.http.impl.Http1xOrH2CHandler.end(Http1xOrH2CHandler.java:61)
at io.vertx.core.http.impl.Http1xOrH2CHandler.channelRead(Http1xOrH2CHandler.java:38)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1410)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:919)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:166)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:719)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:655)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:581)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:493)
at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:986)
at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
at java.lang.Thread.run(Thread.java:750)
When using the OMEZarrReader Build from #82 on the microervices dependencies I got an error (at the end of this issue) from the microservices. The error message does not have a lot of information.
I think one of the possible changes which may cause the error is the using
awssdkdependency (2.17.100):I have tried to upgrade the aws-java-sdk on the microservice dependencies to use the same version in the OMEZarrReader (2.17.100) but got the same error,
I have checked the other microservice dependencies, and found out that s3fs using version 2.2.3, one of the dependencies of this package is: aws-java-sdk-s3 version 1.11.232
The latest version of this package (2.2.3, 2018) is the one which microservices is using
2024-03-26 01:41:48,854 [vert.x-eventloop-thread-0] ERROR io.vertx.core.impl.ContextImpl - Unhandled exception
java.lang.NullPointerException: cause at io.netty.util.internal.ObjectUtil.checkNotNull(ObjectUtil.java:39) at io.netty.channel.AbstractChannelHandlerContext.invokeExceptionCaught(AbstractChannelHandlerContext.java:278) at io.netty.channel.DefaultChannelPipeline.fireExceptionCaught(DefaultChannelPipeline.java:907) at io.vertx.core.net.impl.VertxHandler.fail(VertxHandler.java:97) at io.vertx.core.net.impl.ConnectionBase.fail(ConnectionBase.java:86) at io.vertx.core.http.impl.Http1xServerConnection.handleError(Http1xServerConnection.java:480) at io.vertx.core.http.impl.Http1xServerConnection.handleMessage(Http1xServerConnection.java:121) at io.vertx.core.impl.ContextImpl.executeTask(ContextImpl.java:369) at io.vertx.core.impl.EventLoopContext.execute(EventLoopContext.java:43) at io.vertx.core.impl.ContextImpl.executeFromIO(ContextImpl.java:232) at io.vertx.core.net.impl.VertxHandler.channelRead(VertxHandler.java:173) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.ChannelInboundHandlerAdapter.channelRead(ChannelInboundHandlerAdapter.java:93) at io.netty.handler.codec.http.websocketx.extensions.WebSocketServerExtensionHandler.channelRead(WebSocketServerExtensionHandler.java:99) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357) at io.vertx.core.http.impl.Http1xUpgradeToH2CHandler.channelRead(Http1xUpgradeToH2CHandler.java:109) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:324) at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:296) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357) at io.vertx.core.http.impl.Http1xOrH2CHandler.end(Http1xOrH2CHandler.java:61) at io.vertx.core.http.impl.Http1xOrH2CHandler.channelRead(Http1xOrH2CHandler.java:38) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357) at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1410) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379) at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365) at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:919) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:166) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:719) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:655) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:581) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:493) at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:986) at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) at java.lang.Thread.run(Thread.java:750)