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NcML aggregation works in ToolsUI, fails in THREDDS #245

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dopplershift opened this issue Oct 20, 2015 · 1 comment
Open

NcML aggregation works in ToolsUI, fails in THREDDS #245

dopplershift opened this issue Oct 20, 2015 · 1 comment
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Area: NcML Area: TDS

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@dopplershift
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dopplershift commented Oct 20, 2015 •
edited by lesserwhirls

From e-support BZZ-321180:

"
Package Version: 4.6.2
Operating System: Windows Server 2012 R2
Hardware:
Description of problem: Hi,
I've created a catalog with an aggregation using NcML, this is the catalog definition I've used:
"

<catalog xmlns="https://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0" xmlns:xlink="https://www.w3.org/1999/xlink" name="Unidata THREDDS Data Server" version="1.0.3">
        <service name="all" base="" serviceType="compound">
                <service name="odap" serviceType="OpenDAP" base="/thredds/dodsC/" />
        </service>
        <dataset name="11903" ID="11903" urlPath="11903/11903.nc">
                <serviceName>all</serviceName>
                <netcdf xmlns="https://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
                        <aggregation dimName="TIME" type="joinExisting">
                                <scan location="E:/Thredds/ROOS/11903/" suffix= ".nc" subdirs="false"/>
                        </aggregation>
                </netcdf>
        </dataset>
</catalog>

"
when I try to read data (ASCII or BINARY) via "OPeNDAP Dataset Access Form" the browser return
an HTTP 500 error and the error; in the threddsServlet.log is:
"

*************************************************************
2015-10-16T15:46:14.715 +0200 [ 281328308][ 12] INFO - threddsServlet - Remote host: 0:0:0:0:0:0:0:1 - Request: "GET /thredds/dodsC/11903/11903.nc.ascii?TEMP[0:1:1][0:1:0] HTTP/1.1"
2015-10-16T15:46:14.731 +0200 [ 281328324][ 12] ERROR - thredds.server.opendap.NcSDArray - NcSDArray read TEMP TIME(0,1,1) DEPTH(0,1,0)
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method) ~[?:1.8.0_51]
at ucar.ma2.Array.arraycopy(Array.java:300) ~[cdm-4.6.2.jar:4.6.2]
at ucar.nc2.ncml.AggregationOuterDimension.reallyRead(AggregationOuterDimension.java:382) ~[cdm-4.6.2.jar:4.6.2]
at ucar.nc2.dataset.VariableDS._read(VariableDS.java:507) ~[cdm-4.6.2.jar:?]
at ucar.nc2.dataset.VariableDS._read(VariableDS.java:531) ~[cdm-4.6.2.jar:?]
at ucar.nc2.Variable.read(Variable.java:703) ~[cdm-4.6.2.jar:?]
at ucar.nc2.Variable.read(Variable.java:677) ~[cdm-4.6.2.jar:?]
at thredds.server.opendap.NcSDArray.read(NcSDArray.java:115) [NcSDArray.class:?]
at opendap.servlet.AsciiWriter.writeAsc(AsciiWriter.java:107) [opendap-4.6.2.jar:?]
at opendap.servlet.AsciiWriter.toASCII(AsciiWriter.java:68) [opendap-4.6.2.jar:?]
at thredds.server.opendap.OpendapServlet.doGetASC(OpendapServlet.java:315) [OpendapServlet.class:?]
at thredds.server.opendap.OpendapServlet.doGet(OpendapServlet.java:220) [OpendapServlet.class:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622) [servlet-api.jar:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) [servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.CookieFilter.doFilter(CookieFilter.java:55) [CookieFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestQueryFilter.doFilter(RequestQueryFilter.java:118) [RequestQueryFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat-websocket.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestCORSFilter.doFilterInternal(RequestCORSFilter.java:49) [RequestCORSFilter.class:?]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestPathFilter.doFilter(RequestPathFilter.java:94) [RequestPathFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.server.RequestBracketingLogMessageFilter.doFilter(RequestBracketingLogMessageFilter.java:81) [RequestBracketingLogMessageFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.logging.log4j.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:71) [log4j-web-2.2.jar:2.2]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [catalina.jar:8.0.24]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) [catalina.jar:8.0.24]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [catalina.jar:8.0.24]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:617) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [catalina.jar:8.0.24]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:518) [catalina.jar:8.0.24]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091) [tomcat-coyote.jar:8.0.24]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668) [tomcat-coyote.jar:8.0.24]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1527) [tomcat-coyote.jar:8.0.24]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1484) [tomcat-coyote.jar:8.0.24]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:1.8.0_51]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:1.8.0_51]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.0.24]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_51]
2015-10-16T15:46:14.731 +0200 [ 281328324][ 12] ERROR - thredds.server.opendap.OpendapServlet - path2= /11903/11903.nc.ascii
java.lang.RuntimeException: NcSDArray java.lang.ArrayIndexOutOfBoundsException=null for request= NcSDArray read TEMP TIME(0,1,1) DEPTH(0,1,0) dataset= 11903/11903.nc
at thredds.server.opendap.NcSDArray.read(NcSDArray.java:120) ~[NcSDArray.class:?]
at opendap.servlet.AsciiWriter.writeAsc(AsciiWriter.java:107) ~[opendap-4.6.2.jar:?]
at opendap.servlet.AsciiWriter.toASCII(AsciiWriter.java:68) ~[opendap-4.6.2.jar:?]
at thredds.server.opendap.OpendapServlet.doGetASC(OpendapServlet.java:315) ~[OpendapServlet.class:?]
at thredds.server.opendap.OpendapServlet.doGet(OpendapServlet.java:220) [OpendapServlet.class:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622) [servlet-api.jar:?]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) [servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.CookieFilter.doFilter(CookieFilter.java:55) [CookieFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestQueryFilter.doFilter(RequestQueryFilter.java:118) [RequestQueryFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat-websocket.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestCORSFilter.doFilterInternal(RequestCORSFilter.java:49) [RequestCORSFilter.class:?]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.servlet.filter.RequestPathFilter.doFilter(RequestPathFilter.java:94) [RequestPathFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at thredds.server.RequestBracketingLogMessageFilter.doFilter(RequestBracketingLogMessageFilter.java:81) [RequestBracketingLogMessageFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.logging.log4j.web.Log4jServletFilter.doFilter(Log4jServletFilter.java:71) [log4j-web-2.2.jar:2.2]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) [catalina.jar:8.0.24]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [catalina.jar:8.0.24]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) [catalina.jar:8.0.24]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [catalina.jar:8.0.24]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:617) [catalina.jar:8.0.24]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [catalina.jar:8.0.24]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:518) [catalina.jar:8.0.24]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091) [tomcat-coyote.jar:8.0.24]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668) [tomcat-coyote.jar:8.0.24]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1527) [tomcat-coyote.jar:8.0.24]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1484) [tomcat-coyote.jar:8.0.24]
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:1.8.0_51]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:1.8.0_51]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.0.24]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_51]
2015-10-16T15:46:14.731 +0200 [ 281328324][ 12] INFO - threddsServlet - Request Completed - 500 - -1 - 16
*************************************************************

Using the same NcMLin toolsUI-4.6 I can read data without problem.

Attached the two file in the "E:/Thredds/ROOS/11903/" directory

I don't known if the problem are the file or the aggregation used.

Thanks
@dopplershift
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Here are the files mentioned:
GL_LATEST_TS_DB_11903_20151001.nc | uploaded via ZenHub

GL_LATEST_TS_DB_11903_20150930.nc | uploaded via ZenHub

@dopplershift dopplershift self-assigned this Oct 20, 2015
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