ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

Standardizer InvocationTargetException (5.11.3 & 5.11.4)

User 4b347806a7

21-11-2012 14:50:12

Hello,


We just upgraded to 5.11.3 (& just now 5.11.4) and now get this error when recalculating molecule tables with jcman.  The tables seem to be recalculate.  Just this error appears at the outset.  We also see this error when doing substructure searching within our web application.  Does anyone know what this might be?  Thank you!


 



java.lang.reflect.InvocationTargetException


        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


 


        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)


 


        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou


rce)


        at java.lang.reflect.Constructor.newInstance(Unknown Source)


        at chemaxon.standardizer.StandardizerActionFactory.getStandardizerAction


(StandardizerActionFactory.java:260)


        at chemaxon.standardizer.StandardizerActionFactory.getAvailableStandardi


zerActions(StandardizerActionFactory.java:182)


        at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.ini


tializeMap(StandardizerSAXHandler.java:91)


        at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<in


it>(StandardizerSAXHandler.java:80)


        at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<in


it>(StandardizerSAXHandler.java:57)


        at chemaxon.standardizer.configuration.reader.StandardizerXMLReader.<ini


t>(StandardizerXMLReader.java:56)


        at chemaxon.standardizer.StandardizerUtil.initializeReader(StandardizerU


til.java:148)


        at chemaxon.standardizer.Standardizer.<init>(Standardizer.java:162)


        at chemaxon.reaction.Standardizer.<init>(Standardizer.java:297)


        at chemaxon.descriptors.MDParameters.createStandardizer(MDParameters.jav


a:1005)


        at chemaxon.descriptors.MDParameters.processDocument(MDParameters.java:9


65)


        at chemaxon.descriptors.MarkushDescriptorParameters.processDocument(Mark


ushDescriptorParameters.java:199)


        at chemaxon.descriptors.MDParameters.initParameters(MDParameters.java:20


6)


        at chemaxon.descriptors.MarkushDescriptorParameters.<init>(MarkushDescri


ptorParameters.java:71)


        at chemaxon.jchem.db.MarkushTableInfo$DefaultConfigSingleTable.getMDTabl


eInfoArray(MarkushTableInfo.java:283)


        at chemaxon.jchem.db.MarkushTableInfo.<clinit>(MarkushTableInfo.java:124


)


        at chemaxon.jchem.db.Updater.getMarkushTablesToUpgrade(Updater.java:1216


)


        at chemaxon.jchem.db.Updater.getUpdateInfoForUpgradingMarkushDescriptorT


ables(Updater.java:597)


        at chemaxon.jchem.db.Updater.getNextUpdateInfo(Updater.java:203)


        at chemaxon.jchem.connection.UpdateInfoProvider.doInBackground(UpdateInf


oProvider.java:32)


        at chemaxon.jchem.connection.UpdateInfoProvider.doInBackground(UpdateInf


oProvider.java:18)


        at javax.swing.SwingWorker$1.call(Unknown Source)


        at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)


        at java.util.concurrent.FutureTask.run(Unknown Source)


        at javax.swing.SwingWorker.run(Unknown Source)


        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)


        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)


        at java.lang.Thread.run(Unknown Source)


Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 1


4


        at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)


        at chemaxon.marvin.io.formats.peptide.AminoAcidSource.getExportMols(Amin


oAcidSource.java:340)


        at chemaxon.standardizer.advancedactions.GroupList.getDefaultAminoAcids(


GroupList.java:166)


        at chemaxon.standardizer.advancedactions.GroupList.setAll(GroupList.java


:269)


        at chemaxon.standardizer.advancedactions.CreateGroupAction.createGroupLi


st(CreateGroupAction.java:94)


        at chemaxon.standardizer.advancedactions.CreateGroupAction.<init>(Create


GroupAction.java:47)


        ... 32 more



ChemAxon d9cc14700b

21-11-2012 16:03:09

Dear Customer,


As far as I can see, this stack trace relates to the error occued when you tried to regenerate the database. Could you please send a stack trace of the other case, when you run a search fro your web application?


Thanks and Regards,
Gabor 

User 4b347806a7

21-11-2012 22:27:51

Hi Gabor,


Thanks for your help.  This is the stacktrace when doing structure search in our app:



About to check registration integrity for SMALL MOLECULE


java.lang.reflect.InvocationTargetException


at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)


at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)


at java.lang.reflect.Constructor.newInstance(Constructor.java:513)


at chemaxon.standardizer.StandardizerActionFactory.getStandardizerAction(StandardizerActionFactory.java:260)


at chemaxon.standardizer.StandardizerActionFactory.getAvailableStandardizerActions(StandardizerActionFactory.java:182)


at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.initializeMap(StandardizerSAXHandler.java:91)


at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<init>(StandardizerSAXHandler.java:80)


at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<init>(StandardizerSAXHandler.java:57)


at chemaxon.standardizer.configuration.reader.StandardizerXMLReader.<init>(StandardizerXMLReader.java:56)


at chemaxon.standardizer.StandardizerUtil.initializeReader(StandardizerUtil.java:148)


at chemaxon.standardizer.Standardizer.<init>(Standardizer.java:162)


at com.coreinformatics.chemistry.util.SmallMoleculeRegistrationIntegrity.checkIntegrity(SmallMoleculeRegistrationIntegrity.java:128)


at com.coreinformatics.core.dao.EntityDAO.checkIntegrity(EntityDAO.java:9335)


at com.coreinformatics.core.dao.EntityDAO.instantiateEntity(EntityDAO.java:2370)


at com.coreinformatics.core.dao.SampleDAO.instantiate(SampleDAO.java:379)


at com.coreinformatics.core.dao.SampleDAO.instantiate(SampleDAO.java:384)


at com.coreinformatics.core.command.SampleCreateCommand.performTask(SampleCreateCommand.java:111)


at com.coreinformatics.core.command.LIMSCommand.execute(LIMSCommand.java:176)


at com.coreinformatics.core.servlet.CoreServlet.service(CoreServlet.java:714)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)


at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)


at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)


at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)


at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)


at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)


at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)


at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)


at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)


at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)


at java.lang.Thread.run(Thread.java:662)


Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 14


at chemaxon.struc.MoleculeGraph.getAtom(Unknown Source)


at chemaxon.marvin.io.formats.peptide.AminoAcidSource.getExportMols(AminoAcidSource.java:340)


at chemaxon.standardizer.advancedactions.GroupList.getDefaultAminoAcids(GroupList.java:166)


at chemaxon.standardizer.advancedactions.GroupList.setAll(GroupList.java:269)


at chemaxon.standardizer.advancedactions.CreateGroupAction.createGroupList(CreateGroupAction.java:94)


at chemaxon.standardizer.advancedactions.CreateGroupAction.<init>(CreateGroupAction.java:47)


... 33 more


Found 0 matching structures.


ChemAxon d9cc14700b

22-11-2012 11:06:24

Hi,


Thanks for the info. Based on the stack traces I suspect that the dictionary of amino acids is corrupt. Do you have custom amino acids by any chance?


Thanks and Regards,
Gabor

User 4b347806a7

22-11-2012 13:24:42

That was it!  An old custom amino file that wasn't formatted correctly.  Thank you!!