null org.oostethys.model.impl.ObservationNetcdf.processVarConfig(Unknown Source)

[GoogleCodeExporter]

check.jsp failed with the error shown below.

The steps to get to this error were:

1. Dowloaded and deployed
http://oostethys.googlecode.com/files/oostethys.war (http://mmisw.org/oost/)

2. Edited oostethys.xml (as indicated in
http://mmisw.org/oost/instructions.html). The updated file is attached, but
here is the relevant part:

  <oostethys-netcdf
  xmlns="http://www.oostethys.org/schemas/0.1.0/oostethys-netcdf">

  <!--   URL of the NETCDF file or OPENDAP link. It could also be a
relative path to
  the WEB_INF/classes folder in the web application -->

<fileURL>http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m0/20060
7/hourlyM0_20060731.nc</fileURL>

      <!--   ShortName of each variable. At least
             lat, lon and time coordinates should be given 
            -->

  <variables>
      <variable shortName="LONGITUDE"/>
      <variable shortName="LATITUDE"/>
      <variable shortName="HR_TIME_ADCP"/>
      <variable shortName="HR_DEPTH_ADCP"/>
  </variables>
  </oostethys-netcdf>

I picked the shortNames by looking at
http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m0/200607/hourlyM
0_20060731.nc.html.
In particular, I chose HR_TIME_ADCP for the required time coordinate
(perhaps this was not an appropriate selection?).

3. Ran the check:  http://mmisw.org/oost/check.jsp
which returned:
----
Results of your OOSTethys configuration

The following problem was detected:

null
org.oostethys.model.impl.ObservationNetcdf.processVarConfig(Unknown Source)
org.oostethys.model.impl.ObservationNetcdf.process(Unknown Source)
org.oostethys.sos.Netcdf2sos100.processSystem(Unknown Source)
org.oostethys.sos.Netcdf2sos100.doComponents(Unknown Source)
org.oostethys.sos.Netcdf2sos100.doComponents(Unknown Source)
org.oostethys.sos.Netcdf2sos100.doComponents(Unknown Source)
org.oostethys.sos.Netcdf2sos100.process(Unknown Source)
org.oostethys.sos.Netcdf2sos100.processForTest(Unknown Source)
org.apache.jsp.check_jsp._jspService(check_jsp.java:84)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:337)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilt
erChain.java:290)
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.
java:206)
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:2
33)
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:1
75)
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109
)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)
org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697)
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889
)
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:69
0)
java.lang.Thread.run(Thread.java:613)

To send this error to OOSTethys click here. 
----

I'm also attaching oost.error.log with output generated (in catalina.out)
during the check operation.

Original issue reported on code.google.com by caru...@gmail.com on 9 Apr 2009 at 7:25

Attachments:

• oostethys.xml
• oost.error.log

[GoogleCodeExporter]

An update.

I was able to create the release from sources (thanks Rick!), and reproduce the
stack-trace with line numbers so it's easier to examine the problem (I 
previously
updated check.jsp to show the name of the exception class--this is checked in):

----
The following problem was detected:

java.lang.NullPointerException: null
org.oostethys.model.impl.ObservationNetcdf.processVarConfig(ObservationNetcdf.ja
va:630)
org.oostethys.model.impl.ObservationNetcdf.process(ObservationNetcdf.java:326)
org.oostethys.sos.Netcdf2sos100.processSystem(Netcdf2sos100.java:435)
org.oostethys.sos.Netcdf2sos100.doComponents(Netcdf2sos100.java:159)
org.oostethys.sos.Netcdf2sos100.doComponents(Netcdf2sos100.java:160)
org.oostethys.sos.Netcdf2sos100.doComponents(Netcdf2sos100.java:160)
org.oostethys.sos.Netcdf2sos100.process(Netcdf2sos100.java:330)
org.oostethys.sos.Netcdf2sos100.processForTest(Netcdf2sos100.java:292)
org.apache.jsp.check_jsp._jspService(check_jsp.java:84)
...
----

Original comment by caru...@gmail.com on 9 Apr 2009 at 9:11

[GoogleCodeExporter]

Looks like a problem in the config.  It cannot map the short name HR_DEPTH_ADCP 
to a urn.  This causes an 
error in the nc variable mapping.  Does the HR_DEPTH_ADCP occur in the nc file?

Rick

Original comment by blairsrh...@gmail.com on 17 Apr 2009 at 8:07

[GoogleCodeExporter]

Hi Rick, did you created a test file ? 
I created a new test org.oostethys.test.TestIssue18.java
and added to src/test  oostethys-18.xml

Original comment by ber...@gmail.com on 18 Apr 2009 at 12:36

[GoogleCodeExporter]

I think the file is not netcdf compliant. There is missing a standard name 
attribute
 double HR_DEPTH_ADCP(HR_DEPTH_ADCP=11);
     :units = "METERS";
     :positive = "down";
     :point_spacing = "even";
     :axis = "Z";
     :_CoordinateAxisType = "Height";
     :_CoordinateZisPositive = "down";

The method that needs to be checked is:
 public void assignURItoVarConfig(VariableQuantity variableQuantity)
ObservationNetcdf.java

Original comment by ber...@gmail.com on 18 Apr 2009 at 12:58

[GoogleCodeExporter]

Couldn't go ahead and retry with the latest codes updates as of today because 
the
dataset that I originally used is not available at the moment:

http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m0/200607/hourlyM
0_20060731.nc.html
(returns an empty page).

However, I tried with a different dataset; please see issue #19

Original comment by caru...@gmail.com on 29 Apr 2009 at 7:08

[GoogleCodeExporter]

Original comment by ber...@gmail.com on 27 May 2009 at 5:35

• Changed state: Fixed

[GoogleCodeExporter]

I verified this a while ago.

Original comment by caru...@gmail.com on 27 May 2009 at 5:37

• Changed state: Verified