[netcdf-java] no IOException for shortened file

• To: Java NetCDF <netcdf-java@xxxxxxxxxxxxxxxx>
• Subject: [netcdf-java] no IOException for shortened file
• From: Bob Simons - NOAA Federal <bob.simons@xxxxxxxx>
• Date: Tue, 18 Oct 2016 10:56:32 -0700

In our system, and I suspect elsewhere, sometimes .nc files don't get
completely copied from one place to another. Normally, this is caught and
dealt with (e.g., by the script doing the copying), but sometimes it isn't
(e.g., a computer is restarted while a script is running), leaving a
shortened file in place.

I wanted to understand how netcdf-java (v4.6.6) reacted to these shorted
files. So I made the attached file by copying only the first 1/6th of a
valid file. Then I tried to read it with this code

            NetcdfFile ncFile =
NetcdfFile.open("/git/erddapTest/nc/invalidShortened.nc");
            try {
                Variable var = ncFile.findVariable("MWcdom");
 //size=[1,1,2321,4001]
                Array array = var.read();
                System.out.println("shape=" +
Arrays.toString(array.getShape()));

                array = var.read("0,0,0:2000:1000,0:4000:1000");
                System.out.println("shape=" +
Arrays.toString(array.getShape()));

                //System.out.println(array.toString());
                System.out.println("Shouldn't get here!");
                ncFile.close();
            } catch (Throwable t) {
                try {
                    ncFile.close();
                } catch (Throwable t2) {
                }
                System.out.println("caught: " + t.toString());
            }

Note that Variable.read() documentation says that the method throws an
IOException.

To my surprise, the above code doesn't throw any exception.
netcdf-java says it can read the entire var and read the specified section
(which gets values from throughout the variable).

Is that what you expected?
Am I doing something wrong in my test?
Doesn't netcdf-java check the validity of the file?
Why don't the read()s cause an IOException?

Thank you for looking into this.

-- 
Sincerely,

Bob Simons
IT Specialist
Environmental Research Division
NOAA Southwest Fisheries Science Center
99 Pacific St., Suite 255A      (New!)
Monterey, CA 93940               (New!)
Phone: (831)333-9878            (New!)
Fax:   (831)648-8440
Email: bob.simons@xxxxxxxx

The contents of this message are mine personally and
do not necessarily reflect any position of the
Government or the National Oceanic and Atmospheric Administration.
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Attachment: invalidShortened.nc
Description: Cdf file

• Follow-Ups:
  • Re: [netcdf-java] no IOException for shortened file
    • From: Christian Ward-Garrison