[InterMine Dev] Error retrieving organisms

Joel Richardson Joel.Richardson at jax.org
Tue Nov 22 19:19:37 GMT 2016


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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