[InterMine Dev] Failing to release webapp

Richard Smith richard at flymine.org
Mon Mar 28 12:07:59 BST 2011


Hi James,
This looks like a different issue?  The previous error was with creating
the objectstore summary.

This one looks like a custom source that isn't configured quite right.
It seems to be a custom source called uniprot-proteins that is set up to
load intermine items XML but it's pointing at the original UniProt XML
file rather than an items XML file.

Cheers,
Richard.



On 28/03/2011 11:17, James Blackshaw wrote:
> Hi Richard,
> That is under -v, I'm afraid. I've changed how I'm loading it now
> though, spitting up the uniprot XML using the built-in funtion rather
> than a custom one I was using first to generate smaller test datasets. I
> get the error outlined below if I try to load in data for a couple of
> the organisms now. I am trying it with just one organism right now and
> will forward you the intermine.log file.
>
> -James
>
> -set-xml-tgt-file-includes:
> Skipped because property 'src.data.dir.includes' set.
>
> -set-xml-tgt-file:
>
> -retrieve-tgt-from-xml-file:
> Property "ignore.duplicates" has not been set
> [integrate] Processing file
> /data/datasets/uniprot/release_2010_11/Full/uniprot_sprot.xml
> [null] Exiting
> /home/jab250/intermine_09_03_edit_compare/bio/sources/uniprot-proteins/build.xml.
>
>
> BUILD FAILED
> /home/jab250/intermine_09_03_edit_compare/imbuild/integrate.xml:54: The
> following error occurred while executing this line:
> /home/jab250/intermine_09_03_edit_compare/imbuild/source.xml:201:
> Exception while reading from:
> /data/datasets/uniprot/release_2010_11/Full/uniprot_sprot.xml
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>
> 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)
>
> ... 32 more
> Caused by: java.lang.RuntimeException: no name given for reference with
> value: null
> at org.intermine.xml.full.FullHandler.startElement(FullHandler.java:72)
> at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
> at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
> at org.intermine.util.SAXParser.parse(SAXParser.java:59)
> at org.intermine.util.SAXParser.parse(SAXParser.java:42)
> at org.intermine.xml.full.FullParser.parse(FullParser.java:59)
> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
> ... 34 more
>
> Total time: 125 minutes 46 seconds
>
>
>
>
>
> On 28/03/2011 10:13, Richard Smith wrote:
>> Hi James,
>> When the summarise objectstore step fails there should be an error in
>> the webapp/intermine.log file. Or you could run with ant -v to get a
>> better error report. If let us know what the error is we can take a
>> look.
>>
>> Richard.
>>
>>
>>
>> On 24/03/2011 14:29, James Blackshaw wrote:
>>> Hi,
>>> I can release the webapp when I only load one organism's data in from
>>> Uniprot, but if I load any more organisms in, the webapp release fails.
>>> The build and integration beforehand both work fine, and I can see the
>>> data in MySQL. I just can't get the webapp released.
>>>
>>> -James
>>>
>>>
>>> The error:
>>>
>>> -init-summarise-objectstore:
>>>
>>> retrieve-objectstore-summary:
>>> [echo] Retrieving object store summary from os.production...
>>> [summarise-objectstore] summarising objectstore...
>>>
>>> BUILD FAILED
>>> /home/jab250/intermine_09_03_edit/imbuild/application.xml:29: failed to
>>> get the object store summary
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>




More information about the dev mailing list