Data resource publishing problems. (Oracle database)
Hello there,
I'm trying to install the IPT RC3 acording to the instruction on the web page of the project and everything goes well until I try to publish the resource.
It return the next error: (see attachment screenshot.1.png) ------------------------------------------------------------------------------------------------------------------- Feb 1, 2011 8:55:38 AM
Failed. Fatal error!
Continue to resource overview.
Log Messages Archive generation started for resource cr-inbio 8:55:38 AM Start writing data file for Darwin Core Occurrence 8:55:38 AM
Exception org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:423) org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) java.util.concurrent.FutureTask.run(FutureTask.java:138) java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) java.lang.Thread.run(Thread.java:619) -------------------------------------------------------------------------------------------------------------------
If I check the errors it shows this:
------------------------------------------------------------------------------------------------------------------- ERROR 01-Feb-2011 08:51:46 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:51:46 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:51:46 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException ERROR 01-Feb-2011 08:55:38 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:55:38 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:55:38 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException -------------------------------------------------------------------------------------------------------------------
I have been searching if its a problem in my database (by the way its an oracle 9i) and found this[0]
The question is, is there a way to bypass this problem?
should I add this as a bug? in the project site?
[0] http://opensource.atlassian.com/projects/hibernate/browse/HHH-682
-- Saludos, Aurelio Sanabria http://informatics.inbio.ac.cr/
Hi Aurelio, there is indeed a simple bug in the IPT RC3 that prevents the use of oracle data sources. We have fixed this in the trunk, but if you could try yourself if the following simple change will do the trick we'd be glad to know:
Stop tomcat and open the following file in your expanded tomcat webapp: IPT/WEB-INF/classes/jdbc.properties
change the line for the oracle driver to this one: oracle.driver=oracle.jdbc.driver.OracleDriver
Restart tomcat and try again to see if its working.
Many thanks for discovering this bug, we currently dont have access to an oracle test database, so its great to have someone reporting this!
Markus
On Feb 1, 2011, at 16:20, Aurelio Sanabria wrote:
Hello there,
I'm trying to install the IPT RC3 acording to the instruction on the web page of the project and everything goes well until I try to publish the resource.
It return the next error: (see attachment screenshot.1.png)
Feb 1, 2011 8:55:38 AM
Failed. Fatal error!
Continue to resource overview.
Log Messages Archive generation started for resource cr-inbio 8:55:38 AM Start writing data file for Darwin Core Occurrence 8:55:38 AM
Exception org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:423) org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) java.util.concurrent.FutureTask.run(FutureTask.java:138) java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) java.lang.Thread.run(Thread.java:619)
If I check the errors it shows this:
ERROR 01-Feb-2011 08:51:46 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:51:46 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:51:46 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException ERROR 01-Feb-2011 08:55:38 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:55:38 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:55:38 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException
I have been searching if its a problem in my database (by the way its an oracle 9i) and found this[0]
The question is, is there a way to bypass this problem?
should I add this as a bug? in the project site?
[0] http://opensource.atlassian.com/projects/hibernate/browse/HHH-682
-- Saludos, Aurelio Sanabria http://informatics.inbio.ac.cr/ _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
nice, its working now.
2011/2/2 "Markus Döring (GBIF)" mdoering@gbif.org:
Hi Aurelio, there is indeed a simple bug in the IPT RC3 that prevents the use of oracle data sources. We have fixed this in the trunk, but if you could try yourself if the following simple change will do the trick we'd be glad to know:
Stop tomcat and open the following file in your expanded tomcat webapp: IPT/WEB-INF/classes/jdbc.properties
change the line for the oracle driver to this one: oracle.driver=oracle.jdbc.driver.OracleDriver
Restart tomcat and try again to see if its working.
Many thanks for discovering this bug, we currently dont have access to an oracle test database, so its great to have someone reporting this!
Markus
On Feb 1, 2011, at 16:20, Aurelio Sanabria wrote:
Hello there,
I'm trying to install the IPT RC3 acording to the instruction on the web page of the project and everything goes well until I try to publish the resource.
It return the next error: (see attachment screenshot.1.png)
Feb 1, 2011 8:55:38 AM
Failed. Fatal error!
Continue to resource overview.
Log Messages Archive generation started for resource cr-inbio 8:55:38 AM Start writing data file for Darwin Core Occurrence 8:55:38 AM
Exception org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:423) org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) java.util.concurrent.FutureTask.run(FutureTask.java:138) java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) java.lang.Thread.run(Thread.java:619)
If I check the errors it shows this:
ERROR 01-Feb-2011 08:51:46 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:51:46 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:51:46 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException ERROR 01-Feb-2011 08:55:38 java.sql.SQLException: Invalid argument(s) in call: setFetchSize ERROR 01-Feb-2011 08:55:38 Fatal DwC-A Generator Error org.gbif.ipt.service.SourceException: Cant build iterator for source biodiversidaddecostarica :Invalid argument(s) in call: setFetchSize at org.gbif.ipt.service.manage.impl.SourceManagerImpl.rowIterator(SourceManagerImpl.java:572) at org.gbif.ipt.task.GenerateDwca.dumpData(GenerateDwca.java:346) at org.gbif.ipt.task.GenerateDwca.addDataFile(GenerateDwca.java:140) at org.gbif.ipt.task.GenerateDwca.createDataFiles(GenerateDwca.java:260) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:205) at org.gbif.ipt.task.GenerateDwca.call(GenerateDwca.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) ERROR 01-Feb-2011 08:55:38 Process for resource cr-inbio aborted due to error: org.gbif.ipt.task.GeneratorException: java.lang.NullPointerException
I have been searching if its a problem in my database (by the way its an oracle 9i) and found this[0]
The question is, is there a way to bypass this problem?
should I add this as a bug? in the project site?
[0] http://opensource.atlassian.com/projects/hibernate/browse/HHH-682
-- Saludos, Aurelio Sanabria http://informatics.inbio.ac.cr/ _______________________________________________ IPT mailing list IPT@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ipt
participants (2)
-
"Markus Döring (GBIF)" -
Aurelio Sanabria