Error retrieving organisms

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Error retrieving organisms

Paulo Nuin
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
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Re: Error retrieving organisms

Joel Richardson-2

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
[hidden email]





On 11/22/16, 1:49 PM, "dev on behalf of Paulo Nuin"
<[hidden email] on behalf of [hidden email]> 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
>[hidden email]
>https://lists.intermine.org/mailman/listinfo/dev

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Re: Error retrieving organisms

Paulo Nuin
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 <[hidden email]> 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
> [hidden email]
>
>
>
>
>
> On 11/22/16, 1:49 PM, "dev on behalf of Paulo Nuin"
> <[hidden email] on behalf of [hidden email]> 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
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> ---
>
> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
>

_______________________________________________
dev mailing list
[hidden email]
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