Hi,
Ive been loading in data to Mitominer, and most of the old files are failing to integrate, giving the same exception, but no line number of where the error occurred in the file. It's clearly something in the xml, but I can't see what. Could you offer any ideas on where to look for the problem? Regards, James BUILD FAILED /home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following error occurred while executing this line: /home/jab250/intermine_rebuild/imbuild/source.xml:201: Exception while reading from: /data/datasets/mitominer/gfp_xml/gfp.xml at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:390) at org.apache.tools.ant.Target.performTasks(Target.java:411) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38) at org.apache.tools.ant.Project.executeTargets(Project.java:1212) at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441) at org.intermine.task.Integrate.performAction(Integrate.java:223) at org.intermine.task.Integrate.performAction(Integrate.java:135) at org.intermine.task.Integrate.execute(Integrate.java:127) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:390) at org.apache.tools.ant.Target.performTasks(Target.java:411) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) at org.apache.tools.ant.Project.executeTarget(Project.java:1329) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1212) at org.apache.tools.ant.Main.runBuild(Main.java:801) at org.apache.tools.ant.Main.startAnt(Main.java:218) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) Caused by: org.intermine.InterMineException: Error during unmarshalling at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64) at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68) at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160) ... 31 more Caused by: java.lang.NullPointerException at java.lang.Class.isAssignableFrom(Native Method) at org.intermine.xml.full.FullParser.populateObject(FullParser.java:205) at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:134) at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77) at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62) ... 33 more Total time: 47 seconds _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
Hello,
Tracked this down to the fact that my *_keys.properties files were uing the old formatting of [item]=[key], not [item].[key]=[field with the key in it]. It's sorted now. -James On 26/11/2010 16:36, James Blackshaw wrote: > Hi, > Ive been loading in data to Mitominer, and most of the old files are > failing to integrate, giving the same exception, but no line number of > where the error occurred in the file. It's clearly something in the > xml, but I can't see what. Could you offer any ideas on where to look > for the problem? > Regards, > James > > BUILD FAILED > /home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following > error occurred while executing this line: > /home/jab250/intermine_rebuild/imbuild/source.xml:201: Exception while > reading from: /data/datasets/mitominer/gfp_xml/gfp.xml > at > org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170) > at > org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:616) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) > at org.apache.tools.ant.Target.execute(Target.java:390) > at org.apache.tools.ant.Target.performTasks(Target.java:411) > at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) > at > org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38) > at org.apache.tools.ant.Project.executeTargets(Project.java:1212) > at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441) > at org.intermine.task.Integrate.performAction(Integrate.java:223) > at org.intermine.task.Integrate.performAction(Integrate.java:135) > at org.intermine.task.Integrate.execute(Integrate.java:127) > at > org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:616) > at > org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) > at org.apache.tools.ant.Target.execute(Target.java:390) > at org.apache.tools.ant.Target.performTasks(Target.java:411) > at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) > at org.apache.tools.ant.Project.executeTarget(Project.java:1329) > at > org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) > at org.apache.tools.ant.Project.executeTargets(Project.java:1212) > at org.apache.tools.ant.Main.runBuild(Main.java:801) > at org.apache.tools.ant.Main.startAnt(Main.java:218) > at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) > at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) > Caused by: org.intermine.InterMineException: Error during unmarshalling > at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64) > at > org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68) > at > org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160) > ... 31 more > Caused by: java.lang.NullPointerException > at java.lang.Class.isAssignableFrom(Native Method) > at > org.intermine.xml.full.FullParser.populateObject(FullParser.java:205) > at > org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:134) > at > org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77) > at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62) > ... 33 more > > Total time: 47 seconds > _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
Hi James,
Good to hear you got this working. I don't think the keys would have been the problem - they shouldn't be read until after the XML has successfully been parsed. So maybe something else you did fixed it. The original error looks like there was an Item in the XML without a classname (or implementations) field set. Let us know if the problem comes back. Cheers, Richard. On 29/11/2010 17:11, James Blackshaw wrote: > Hello, > Tracked this down to the fact that my *_keys.properties files were uing > the old formatting of [item]=[key], not [item].[key]=[field with the key > in it]. It's sorted now. > -James > > On 26/11/2010 16:36, James Blackshaw wrote: >> Hi, >> Ive been loading in data to Mitominer, and most of the old files are >> failing to integrate, giving the same exception, but no line number of >> where the error occurred in the file. It's clearly something in the >> xml, but I can't see what. Could you offer any ideas on where to look >> for the problem? >> Regards, >> James >> >> BUILD FAILED >> /home/jab250/intermine_rebuild/imbuild/integrate.xml:54: The following >> error occurred while executing this line: >> /home/jab250/intermine_rebuild/imbuild/source.xml:201: Exception while >> reading from: /data/datasets/mitominer/gfp_xml/gfp.xml >> at >> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170) >> >> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) >> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> >> at java.lang.reflect.Method.invoke(Method.java:616) >> at >> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) >> >> at org.apache.tools.ant.Task.perform(Task.java:348) >> at org.apache.tools.ant.Target.execute(Target.java:390) >> at org.apache.tools.ant.Target.performTasks(Target.java:411) >> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) >> at >> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38) >> >> at org.apache.tools.ant.Project.executeTargets(Project.java:1212) >> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441) >> at org.intermine.task.Integrate.performAction(Integrate.java:223) >> at org.intermine.task.Integrate.performAction(Integrate.java:135) >> at org.intermine.task.Integrate.execute(Integrate.java:127) >> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) >> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> >> at java.lang.reflect.Method.invoke(Method.java:616) >> at >> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) >> >> at org.apache.tools.ant.Task.perform(Task.java:348) >> at org.apache.tools.ant.Target.execute(Target.java:390) >> at org.apache.tools.ant.Target.performTasks(Target.java:411) >> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360) >> at org.apache.tools.ant.Project.executeTarget(Project.java:1329) >> at >> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) >> >> at org.apache.tools.ant.Project.executeTargets(Project.java:1212) >> at org.apache.tools.ant.Main.runBuild(Main.java:801) >> at org.apache.tools.ant.Main.startAnt(Main.java:218) >> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) >> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109) >> Caused by: org.intermine.InterMineException: Error during unmarshalling >> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64) >> at >> org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68) >> at >> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160) >> >> ... 31 more >> Caused by: java.lang.NullPointerException >> at java.lang.Class.isAssignableFrom(Native Method) >> at org.intermine.xml.full.FullParser.populateObject(FullParser.java:205) >> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:134) >> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:77) >> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62) >> ... 33 more >> >> Total time: 47 seconds >> > > > _______________________________________________ > dev mailing list > [hidden email] > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev > _______________________________________________ dev mailing list [hidden email] http://mail.intermine.org/cgi-bin/mailman/listinfo/dev |
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