[InterMine Dev] Error retrieving organisms

Paulo Nuin paulo.nuin at gmail.com
Tue Nov 22 18:49:14 GMT 2016


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(EntrezOrganismRetriever.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: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(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: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(DelegatingMethodAccessorImpl.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


More information about the dev mailing list