fmax is not a number error

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fmax is not a number error

Chris Childers
Hi all,

Has anyone else seen this error? It seems like we get it with some regularity (at least a few times a week), but I'm not sure what is causing it.  I was wondering if this might be one of the causes of our instability.  I haven't seen any mention in it in github issues section, or in the apollo listserv.  It is even harder to track the issue down since I'm not sure which instance this was in.

Thanks,
Chris



Feb 08, 2016 10:03:54 AM org.apache.coyote.http11.AbstractHttp11Processor process
INFO: Error parsing HTTP request header
 Note: further occurrences of HTTP header parsing errors will be logged at DEBUG level.
10:49:10.708 [http-bio-8080-exec-7] ERROR  - Problem parsing offset string: Scaffold2796
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: fmax is not a number error

Colin
Hi Chris,

It looks like maybe there are two separate errors near each other in the log file, one is in the selectTracks page, and another is during addTranscript. That is pretty weird but here's what it looks like to me

error 1.
10:49:10.708 [http-bio-8080-exec-7] ERROR  - Problem parsing offset string: Scaffold2796

error 2.
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)


Error 1 is part of the selectTracks page and says that the "offset" for the pages that it is processing was something unexpected (weird..)

Error 2 seems like maybe data that was loaded into apollo doesn't conform to expectations (maybe data loading issue)

As far as being able to tell which error comes from which instance, I would maybe look into using the configurable log4j logging paths. There are some details about configuring that for WA1 here http://webapollo.readthedocs.org/en/1.0.4/Configure/

Let me know if any of that helps!

-Colin

On Tue, Feb 9, 2016 at 2:37 PM, Chris Childers <[hidden email]> wrote:
Hi all,

Has anyone else seen this error? It seems like we get it with some regularity (at least a few times a week), but I'm not sure what is causing it.  I was wondering if this might be one of the causes of our instability.  I haven't seen any mention in it in github issues section, or in the apollo listserv.  It is even harder to track the issue down since I'm not sure which instance this was in.

Thanks,
Chris



Feb 08, 2016 10:03:54 AM org.apache.coyote.http11.AbstractHttp11Processor process
INFO: Error parsing HTTP request header
 Note: further occurrences of HTTP header parsing errors will be logged at DEBUG level.
10:49:10.708 [http-bio-8080-exec-7] ERROR  - Problem parsing offset string: Scaffold2796
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)
org.json.JSONException: JSONObject["fmax"] is not a number.
        at org.json.JSONObject.getDouble(JSONObject.java:543)
        at org.json.JSONObject.getInt(JSONObject.java:560)
        at org.bbop.apollo.web.util.JSONUtil.convertJSONToFeatureLocation(JSONUtil.java:226)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:4167)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1259)
        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1243)
        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:369)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
        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.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.