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PathwayCommons / pcviz

Pathway Commons Bio Network Visualizer
http://www.pathwaycommons.org/pcviz/
MIT License
8 stars 3 forks source link

uniprot_scraper.sh error: StackOverFlow (endless loop) #24

Closed IgorRodchenkov closed 8 years ago

IgorRodchenkov commented 8 years ago

When I run the script (using a fresh and latest pcviz at localhost:8080/, configured properly, connecting to the pre-release PC2 v8 service at pathwaycommons.baderlab.org/, etc.), the pcviz console output grows large, and I can see errors like:

Mar 02, 2016 7:33:23 PM org.apache.catalina.core.ApplicationDispatcher invoke
SEVERE: Servlet.service() for servlet pcviz threw exception
java.lang.StackOverflowError
        at java.net.SocketOutputStream.socketWrite0(Native Method)
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
        at org.apache.coyote.http11.InternalOutputBuffer.realWriteBytes(InternalOutputBuffer.java:215)
        at org.apache.tomcat.util.buf.ByteChunk.flushBuffer(ByteChunk.java:462)
        at org.apache.coyote.http11.InternalOutputBuffer.flush(InternalOutputBuffer.java:119)
        at org.apache.coyote.http11.AbstractHttp11Processor.action(AbstractHttp11Processor.java:790)
        at org.apache.coyote.Response.action(Response.java:173)
        at org.apache.catalina.connector.OutputBuffer.doFlush(OutputBuffer.java:341)
        at org.apache.catalina.connector.OutputBuffer.flush(OutputBuffer.java:306)
        at org.apache.catalina.connector.CoyoteOutputStream.flush(CoyoteOutputStream.java:101)
        at sun.nio.cs.StreamEncoder.implFlush(StreamEncoder.java:297)
        at sun.nio.cs.StreamEncoder.flush(StreamEncoder.java:141)
        at java.io.OutputStreamWriter.flush(OutputStreamWriter.java:229)
        at org.springframework.util.StreamUtils.copy(StreamUtils.java:109)
        at org.springframework.http.converter.StringHttpMessageConverter.writeInternal(StringHttpMessageConverter.java:109)
        at org.springframework.http.converter.StringHttpMessageConverter.writeInternal(StringHttpMessageConverter.java:40)
        at org.springframework.http.converter.AbstractHttpMessageConverter.write(AbstractHttpMessageConverter.java:195)
        at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:238)
        at org.springframework.web.servlet.mvc.method.annotation.HttpEntityMethodProcessor.handleReturnValue(HttpEntityMethodProcessor.java:183)
        at org.springframework.web.method.support.HandlerMethodReturnValueHandlerComposite.handleReturnValue(HandlerMethodReturnValueHandlerComposite.java:80)
        at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:126)
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:814)
        at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:737)
        at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959)
...

and then the following trace gets repeated multiple times until the next such error happens - 

       at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:860)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
        at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:845)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:749)
        at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:605)
        at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:544)
        at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:160)
        at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:303)
        at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1243)
        at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:1027)
        at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:971)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:969)

I haven't seen this problem on the other pcviz instance that is normally used from web browsers (not by this scraper script...)

IgorRodchenkov commented 8 years ago

I also found (after trying two times with "AKT2") that this StackOverflowError may or may not happend, kind of by chance, when using the same gene name...