[InterMine Dev] Error retrieving organisms

Paulo Nuin paulo.nuin at gmail.com
Tue Nov 22 19:29:57 GMT 2016


Hi Joel

Thanks a lot, we are on 1.6.6. I will checkout a newer version and try.

Cheers
Paulo


> On Nov 22, 2016, at 12:19 PM, Joel Richardson <Joel.Richardson at jax.org> wrote:
> 
> 
> Hi Paolo,
> 
> Looks like this might be related to NCBI¹s switch from http to https.
> What version of InterMine are you using? I think you need 1.6.7 or later.
> 
> Joel
> 
> -- 
> Joel E. Richardson, Ph.D.
> Sr. Research Scientist
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, Maine 04609
> 207-288-6435
> joel.richardson at jax.org
> 
> 
> 
> 
> 
> On 11/22/16, 1:49 PM, "dev on behalf of Paulo Nuin"
> <dev-bounces at lists.intermine.org on behalf of paulo.nuin at gmail.com> wrote:
> 
>> Hi everyone
>> 
>> I am getting a strange error on retrieving organisms from Entrez, and I
>> never saw something like this
>> 
>> /Users/nuin/intermine/imbuild/integrate.xml:54: The following error
>> occurred while executing this line:
>> /Users/nuin/intermine/bio/sources/entrez-organism/build.xml:18: exception
>> while retrieving organisms
>> 	at 
>> org.intermine.bio.dataconversion.EntrezOrganismRetriever.execute(EntrezOrg
>> anismRetriever.java:127)
>> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>> 	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> 	at 
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorIm
>> pl.java:43)
>> 	at java.lang.reflect.Method.invoke(Method.java:498)
>> 	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(SingleCheck
>> Executor.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:219)
>> 	at org.intermine.task.Integrate.performAction(Integrate.java:131)
>> 	at org.intermine.task.Integrate.execute(Integrate.java:123)
>> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>> 	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>> 	at 
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorIm
>> pl.java:43)
>> 	at java.lang.reflect.Method.invoke(Method.java:498)
>> 	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:854)
>> 	at org.apache.tools.ant.Main.startAnt(Main.java:236)
>> 	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:285)
>> 	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
>> Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber:
>> 50; White spaces are required between publicId and systemId.
>> 
>> I am using this Java version
>> 
>> java version "1.8.0_74"
>> Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
>> Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)
>> 
>> Any help appreciated
>> 
>> Paulo
>> _______________________________________________
>> dev mailing list
>> dev at lists.intermine.org
>> https://lists.intermine.org/mailman/listinfo/dev
> 
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