[InterMine Dev] failed load malaria kegg data

Pengcheng Yang pengchy at gmail.com
Fri Jul 17 01:46:42 BST 2015


Hi,

Errors were encountered when I load the example kegg data 
(map_title.tab  and pfa_gene_map.tab data given by malariamine data) [1].

I have searched the intermine email list archive and have tried the 
method suggested at 
http://gmod.827538.n3.nabble.com/errors-when-loading-kegg-pathway-data-td3508893.html#a3509095 
. but the errors still the same as below. What is the model 
"org.intermine.model.bio.Pathway"? Where to find it?

Any suggestions are welcome and be appreciated.

Thank you in advance.

Best,
Pengcheng Yang



[1] error messages for w/without pfa_gene_map.tab file.

BUILD FAILED
/home/pengchy/Soft/05.SystemBiology/intermine/imbuild/integrate.xml:54: 
The following error occurred while executing this line:
/home/pengchy/Soft/05.SystemBiology/intermine/imbuild/source.xml:145: 
java.lang.IllegalArgumentException: class 
"org.intermine.model.bio.Pathway" is not in the Model
         at 
org.intermine.xml.full.Item.getClassDescriptorByName(Item.java:546)
         at org.intermine.xml.full.Item.setClassName(Item.java:128)
         at 
org.intermine.xml.full.ItemFactory.makeItem(ItemFactory.java:115)
         at 
org.intermine.dataconversion.DataConverter.createItem(DataConverter.java:104)
         at 
org.intermine.bio.dataconversion.KeggPathwayConverter.getPathway(KeggPathwayConverter.java:251)
         at 
org.intermine.bio.dataconversion.KeggPathwayConverter.processPathway(KeggPathwayConverter.java:241)
         at 
org.intermine.bio.dataconversion.KeggPathwayConverter.process(KeggPathwayConverter.java:135)
         at 
org.intermine.task.FileConverterTask.execute(FileConverterTask.java:116)
         at 
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:497)
         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:435)
         at org.apache.tools.ant.Target.performTasks(Target.java:456)
         at 
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
         at 
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
         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:293)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:497)
         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:435)
         at org.apache.tools.ant.Target.performTasks(Target.java:456)
         at 
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
         at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
         at 
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
         at org.apache.tools.ant.Main.runBuild(Main.java:853)
         at org.apache.tools.ant.Main.startAnt(Main.java:235)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:285)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)

Total time: 22 seconds



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