sorry, the versioning is rather baroque. the bug is fixed in version >=
2.2.22.14
theres a readme file inside each jar that has this number in it, in case
theres any doubt
Nick Bower wrote:
> Ok. Could you clarify the version number? I'm on 2.2.22 now - you mentioned
> 2.22.14 just now. Is there that much difference between the two?
>
>
> John Caron wrote:
>> release 2.22.14 should fix this problem. be sure to call flush() after
>> writing and before reading
>>
>> Nick Bower wrote:
>>> Adding an ncFile.flush() to the submitted test case as suggested does
>>> not resolve the problem. I think it needs to be marked as a bug
>>> until a documented way around it surfaces.
>>>
>>>
>>> Ethan Davis wrote:
>>>
>>>> Hi Nick,
>>>>
>>>> I'm not sure if this is a recommended way but you might try to
>>>> flush() the NetcdfFileWriteable before reading.
>>>>
>>>> John might have another answer. He is out of the office this week so
>>>> his email may be spotty.
>>>>
>>>> Hope that helps,
>>>>
>>>> Ethan
>>>>
>>>> Nick Bower wrote:
>>>>
>>>>> Hello. Is the lack of response here because this is not considered
>>>>> a bug? Is there a another recommended way perhaps to safely
>>>>> increase a dimension and invalidate the memory cache in the process?
>>>>>
>>>>> Nick
>>>>>
>>>>>
>>>>> Nick Bower wrote:
>>>>>
>>>>>
>>>>>> I've found a problem in which cache/memory and disk shape
>>>>>> information about variables will disagree with v2.2.22 of Java
>>>>>> Netcdf library.
>>>>>>
>>>>>> When you add a new value to a variable, automatically increasing
>>>>>> the length of a dimension, subsequent reads can throw EOFException
>>>>>> because RandomAccessFile is instructed to read more values than
>>>>>> the file contains - the cached and actual shapes disagree.
>>>>>>
>>>>>> I've created a runnable test case below to explain and demonstrate
>>>>>> success and failure conditions.
>>>>>>
>>>>>> I am getting around this now by not interleaving read/write
>>>>>> operations on variables, but instead reading all variables' data
>>>>>> to memory, then performing any writes I need to after.
>>>>>>
>>>>>> TestInsertRecord.java:
>>>>>>
>>>>>>
>>>>>> package com.metoceanengineers.datafeeds.netcdf.test;
>>>>>>
>>>>>> import java.io.File;
>>>>>> import java.io.IOException;
>>>>>> import java.text.DateFormat;
>>>>>> import java.text.SimpleDateFormat;
>>>>>>
>>>>>> import junit.framework.TestCase;
>>>>>> import ucar.ma2.Array;
>>>>>> import ucar.ma2.ArrayInt;
>>>>>> import ucar.ma2.DataType;
>>>>>> import ucar.nc2.Dimension;
>>>>>> import ucar.nc2.NetcdfFileWriteable;
>>>>>>
>>>>>> public class TestInsertRecord extends TestCase {
>>>>>> DateFormat dateFormat = new SimpleDateFormat("yyyyMMdd HHMM");
>>>>>> protected NetcdfFileWriteable createNc(String prefix) throws
>>>>>> IOException {
>>>>>> File mainline = File.createTempFile(prefix+"-", ".nc");
>>>>>> NetcdfFileWriteable mainlineNc =
>>>>>> NetcdfFileWriteable.createNew(mainline.getAbsolutePath(), false);
>>>>>>
>>>>>> Dimension recordsDim =
>>>>>> mainlineNc.addUnlimitedDimension("records");
>>>>>> Dimension timeDims[] = {recordsDim};
>>>>>> Dimension var1Dims[] = {recordsDim}; // 1D
>>>>>> mainlineNc.addVariable("time", DataType.INT, timeDims);
>>>>>> mainlineNc.addVariable("var1", DataType.INT, var1Dims);
>>>>>>
>>>>>> mainlineNc.create();
>>>>>> return mainlineNc;
>>>>>> }
>>>>>>
>>>>>>
>>>>>> protected String getNcInstance() throws Exception {
>>>>>>
>>>>>> NetcdfFileWriteable mainlineNc = createNc("testfile");
>>>>>> int[] origin = {0};
>>>>>> ArrayInt.D1 timeArr = new ArrayInt.D1(2);
>>>>>> timeArr.set(0, (int)dateFormat.parse("20071130
>>>>>> 0924").getTime());
>>>>>> timeArr.set(1, (int)dateFormat.parse("20071130
>>>>>> 0926").getTime());
>>>>>> mainlineNc.write("time", origin, timeArr);
>>>>>> ArrayInt.D1 var1Arr = new ArrayInt.D1(2);
>>>>>> var1Arr.set(0, 10);
>>>>>> var1Arr.set(1, 12);
>>>>>> mainlineNc.write("var1", origin, var1Arr);
>>>>>>
>>>>>> mainlineNc.close();
>>>>>>
>>>>>> return mainlineNc.getLocation();
>>>>>> }
>>>>>> /**
>>>>>> * Append new data to end of existing variables.
>>>>>> *
>>>>>> * @throws Exception
>>>>>> */
>>>>>> public void testAppendWorksOk() throws Exception {
>>>>>> String ncFilename = getNcInstance();
>>>>>> NetcdfFileWriteable ncFile =
>>>>>> NetcdfFileWriteable.openExisting(ncFilename, false);
>>>>>>
>>>>>> /*
>>>>>> * Append value (20071130 0924, 11) into (time, var1)
>>>>>> */
>>>>>> ArrayInt.D1 newTimeValue = new ArrayInt.D1(1);
>>>>>> newTimeValue.set(0, (int)dateFormat.parse("20071130
>>>>>> 0925").getTime());
>>>>>>
>>>>>> ArrayInt.D1 newVarValue = new ArrayInt.D1(1);
>>>>>> newVarValue.set(0, 11);
>>>>>> int[] origin = {2};
>>>>>>
>>>>>> /* The first write will expand the variables,
>>>>>> * but second write ok as we're just writing
>>>>>> * and not reading */
>>>>>> ncFile.write("time", origin, newTimeValue);
>>>>>> ncFile.write("var1", origin, newVarValue);
>>>>>> assertEquals(3,
>>>>>> ncFile.findDimension("records").getLength());
>>>>>> }
>>>>>>
>>>>>> /**
>>>>>> * Test insertion of a record in between the 2 existing
>>>>>> * records by reading the existing tail, inserting new data
>>>>>> * and re-appending.
>>>>>> *
>>>>>> * Triggers EOFException through interleaved read/writes
>>>>>> *
>>>>>> * @throws Exception
>>>>>> */
>>>>>> public void testInsertFails() throws Exception {
>>>>>> String ncFilename = getNcInstance();
>>>>>> NetcdfFileWriteable ncFile =
>>>>>> NetcdfFileWriteable.openExisting(ncFilename, false);
>>>>>>
>>>>>> ArrayInt.D1 newTimeValue = new ArrayInt.D1(1);
>>>>>> newTimeValue.set(0, (int)dateFormat.parse("20071130
>>>>>> 0925").getTime());
>>>>>>
>>>>>> ArrayInt.D1 newVarValue = new ArrayInt.D1(1);
>>>>>> newVarValue.set(0, 11);
>>>>>> /* Going to insert at 1, so read existing value,
>>>>>> * write down new one, and re-append old tail.
>>>>>> */
>>>>>> int[] insertPointOrigin = {1};
>>>>>> int[] appendOrigin = {2};
>>>>>> int[] shape = {1};
>>>>>> Array tailTime =
>>>>>> ncFile.findVariable("time").read(insertPointOrigin, shape);
>>>>>> ncFile.write("time", insertPointOrigin, newTimeValue);
>>>>>> ncFile.write("time", appendOrigin, tailTime);
>>>>>> /* Next line excepts - why? Because the last write
>>>>>> above at
>>>>>> * records index 2 triggers an increase in the CACHED/MEMORY
>>>>>> * length of all variables to 3, but on disk it's still the
>>>>>> * original length 2.
>>>>>> *
>>>>>> * Therefore we get EOFException.
>>>>>> */
>>>>>> Array tailVar1 =
>>>>>> ncFile.findVariable("var1").read(insertPointOrigin, shape);
>>>>>> ncFile.write("var1", insertPointOrigin, newVarValue);
>>>>>> ncFile.write("var1", appendOrigin, tailVar1);
>>>>>> assertEquals(3,
>>>>>> ncFile.findDimension("records").getLength());
>>>>>> }
>>>>>>
>>>>>> }
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
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