[InterMine Dev] failed load malaria kegg data

J. Clark-Casey jc955 at cam.ac.uk
Fri Jul 17 13:21:34 BST 2015


Hi Pengcheng,

I'm a new developer on InterMine so Julie can correct me if there are 
mistakes in the following!

However, if you've added the kegg-pathway entry in your project.xml

<source name="kegg-pathway" type="kegg-pathway">
   <property name="src.data.dir" 
location="<malaria-data-root>/malaria/kegg/"/>
   <property name="kegg.organisms" value="36329"/>
</source>

then my guess would be that you haven't yet rerun the "ant db-model" 
step in your malariamine/dbmodel directory.

The additions file containing the Pathway class is at 
bio/sources/kegg-pathways/kegg-pathway_additions.xml.

When the "ant db-model" step is run, all the <source>_additions.xml 
files referenced by malariamine/project.xml get merged into a single 
file at malariamine/dbmodel/build/model/genomic_model.xml where I 
believe is the one used to create the data model in the database.

I'm not sure if you can run the db-model step again on an existing 
model.  If you want to be safe you might want to reload the data from 
scratch again.

I see that the kegg data is not mentioned in the tutorial at [1] though 
it is in the zipped data.  I don't know if this is deliberate.  However, 
when I set it up I was able to run the kegg-pathway source without 
errors (I haven't done much checking of the data actually loaded).

[1] http://intermine.readthedocs.org/en/latest/get-started/tutorial/

Best Regards,Hi Pengcheng,

I'm a new developer on InterMine so Julie can correct me if there are 
mistakes in the following!

However, if you've added the kegg-pathway entry in your project.xml

<source name="kegg-pathway" type="kegg-pathway">
   <property name="src.data.dir" 
location="<malaria-data-root>/malaria/kegg/"/>
   <property name="kegg.organisms" value="36329"/>
</source>

then my guess would be that you haven't yet rerun the "ant db-model" 
step in your malariamine/dbmodel directory.

The additions file containing the Pathway class is at 
bio/sources/kegg-pathways/kegg-pathway_additions.xml.

When the "ant db-model" step is run, all the <source>_additions.xml 
files referenced by malariamine/project.xml get merged into a single 
file at malariamine/dbmodel/build/model/genomic_model.xml where I 
believe is the one used to create the data model in the database.

I'm not sure if you can run the db-model step again on an existing 
model.  If you want to be safe you might want to reload the data from 
scratch again.

I see that the kegg data is not mentioned in the tutorial at [1] though 
it is in the zipped data.  I don't know if this is deliberate.  However, 
when I set it up I was able to run the kegg-pathway source without 
errors (I haven't done much checking of the data actually loaded).

[1] http://intermine.readthedocs.org/en/latest/get-started/tutorial/

All the best,

-- Justin Clark-Casey

On 2015-07-17 01:46, Pengcheng Yang wrote:
> 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
> 
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

-- Justin Clark-Casey

On 2015-07-17 01:46, Pengcheng Yang wrote:
> 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
> 
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



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