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[bioontology-support] parsing error

Erick Antezana erick.antezana at gmail.com
Fri Feb 1 02:59:55 PST 2013


Hi,

I got similar error messages:

   BioPortal returned an error: Error Parsing Ontologies: [(Id: 1004) -
Ontology version with the given id does not exist]

any suggestions where to check?  log files or so?

cheers,
erick

On 25 January 2013 22:29, Holt, Jonathan <jonathan.holt at vanderbilt.edu>wrote:

>  When I tried to upload the ontology manually, I got the error,
>
>
>   "we are sorry, but something has gone wrong. We have been notified of
> this error."
>
>
>
>
>
>  jonathan
>
>
>  .................................
>          Jonathan Holt, DO, MS
>
>             Assistant Professor of Biomedical Informatics and Medicine
>    Departments of Biomedical Informatics & Medicine, Division of Genetic
> Medicine
>  Vanderbilt University Medical Center
> 2209 Garland Ave
>        412 Eskind Biomedical Library
>  Nashville, TN  37232-8340
>  Phone:  615-322-8683
>  Fax: 615-875-1424
>
>  jonathan.holt at vanderbilt.edu
>  http://dbmi.mc.vanderbilt.edu/people/holt.html
>
>
>
>
>
>
>
>
>
>
>  On Jan 25, 2013, at 3:02 PM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>
>  wrote:
>
>   One you uploaded the files, you can run the parser through this page:
> http://rest.bioontology.org/bioportal_admin/parseontologies.jsf****
>
>   *From:* Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu]
> *Sent:* Friday, January 25, 2013 2:38 PM
> *To:* Lian, Zonghui
> *Cc:* Paul R Alexander (palexander at stanford.edu); support at bioontology.orgSupport
> *Subject:* Re: [bioontology-support] parsing error****
>   ** **
>  any update?****
>  ** **
>   Thanks,****
>   ** **
>   Jonathan****
>   ** **
>   ** **
>      .................................****
>   Jonathan Holt, DO, MS****
>
>   Assistant Professor of Biomedical Informatics and Medicine****
>  Departments of Biomedical Informatics & Medicine, Division of Genetic
> Medicine****
>  Vanderbilt University Medical Center****
>   2209 Garland Ave
>
> ****
>   412 Eskind Biomedical Library****
>   Nashville, TN  37232-8340****
>   Phone:  615-322-8683****
>   Fax: 615-875-1424****
>
>   jonathan.holt at vanderbilt.edu****
>   http://dbmi.mc.vanderbilt.edu/people/holt.html****
>
>
>
>
>
>
>
>
> ** **
>  ** **
>   On Jan 21, 2013, at 11:01 AM, "Jonathan Holt, DO, MS" <
> jonathan.holt at vanderbilt.edu> wrote:****
>
>
> ****
>  sure, ****
>  ** **
>   mine is in a slightly different place. ****
>   ** **
>   for ICD-9 is is located in: /srv/ncbo/bioportal_resources/uploads/1101/1
> ****
>   ** **
>   see below: ****
>   ** **
>   root at ncbo 1]# pwd****
>   /srv/ncbo/bioportal_resources/uploads/1101/1****
>   [root at ncbo 1]# ls -hal****
>   total 25M****
>   drwxr-xr-x 2 tomcat tomcat 4.0K Jan 18 13:30 .****
>   drwxr-xr-x 3 tomcat tomcat 4.0K Jan 18 13:30 ..****
>   -rw-r--r-- 1 tomcat tomcat  25M Jan 18 13:30 icd9cm.rrf****
>    ** **
>   ** **
>   ** **
>   <Screen Shot 2013-01-21 at 11.01.05 AM.png>****
>   ** **
>   ** **
>   ** **
>   Thanks,****
>   ** **
>   Jonathan ****
>   ** **
>   ** **
>      .................................****
>   Jonathan Holt, DO, MS****
>
>   Assistant Professor of Biomedical Informatics and Medicine****
>  Departments of Biomedical Informatics & Medicine, Division of Genetic
> Medicine****
>  Vanderbilt University Medical Center****
>   2209 Garland Ave
>
> ****
>   412 Eskind Biomedical Library****
>   Nashville, TN  37232-8340****
>   Phone:  615-322-8683****
>   Fax: 615-875-1424****
>
>   jonathan.holt at vanderbilt.edu****
>   http://dbmi.mc.vanderbilt.edu/people/holt.html****
>
>
>
>
>
>
>
>
> ** **
>  ** **
>   On Jan 21, 2013, at 10:35 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>***
> *
>    wrote:****
>
>
> ****
>   Dr Holt,****
>    ****
>   The error may be caused by the file uploader. Can you check if the file
> was uploaded correctly? For example, for the below ontology, its ontology
> id is (1290).****
>    ****
>   <image001.png>****
>    ****
>   In the linux box, you can find its uploaded files are under****
>   <image006.png>****
>    ****
>   Please use this method to check the file for your case. As what I know,
> the file uploader is not stable when the file size is big. Once you find
> this file you can manually replace them with the right one.  (For rrf
> format, you need to unzip the zipped file) .****
>    ****
>   Thanks,****
>   -Lian****
>    ****
>    ****
>    ****
>    ****
>   *From:* Holt, Jonathan [mailto:jonathan.holt at Vanderbilt.Edu<http://vanderbilt.edu/>
> ]
> *Sent:* Friday, January 18, 2013 4:09 PM
> *To:* Lian, Zonghui
> *Cc:* support at bioontology.org Support
> *Subject:* Re: [bioontology-support] parsing error****
>    ****
>   Lian,****
>    ****
>   After trying to up load the zipped file i get, ****
>    ****
>   "we are sorry, but something has gone wrong. We have been notified of
> this error."  (see below) ****
>    ****
>   <image003.jpg>****
>    ****
>    ****
>   if i try from the import_ontologies.rb script and point to Stanford's
> server with my apikey,  I get a parsing error as shown below. ****
>    ****
>    ****
>   <image005.jpg>****
>    ****
>    ****
>    ****
>   Of note, this does NOT happen when I import an ontology in a different
> format, such as OWL or OBO, as shown in my other ontologies that I have
> successfully imported using the script. ****
>    ****
>    ****
>   I've tried getting a new build using: ****
>    ****
>   bpdeploy deployui****
>    ****
>   but that does help things either. ****
>    ****
>    ****
>    ****
>   Thanks,****
>    ****
>   Jonathan ****
>    ****
>    ****
>      .................................****
>   Jonathan Holt, DO, MS****
>    ****
>   Assistant Professor of Biomedical Informatics and Medicine****
>   Departments of Biomedical Informatics & Medicine, Division of Genetic
> Medicine****
>   Vanderbilt University Medical Center****
>   2209 Garland Ave
>
>
> ****
>   412 Eskind Biomedical Library****
>   Nashville, TN  37232-8340****
>   Phone:  615-322-8683****
>   Fax: 615-875-1424****
>    ****
>   jonathan.holt at vanderbilt.edu****
>   http://dbmi.mc.vanderbilt.edu/people/holt.html****
>     ****
>    ****
>    ****
>    ****
>    ****
>    ****
>    ****
>
>  ****
>    ****
>   On Jan 18, 2013, at 10:26 AM, "Lian, Zonghui" <Lian.Zonghui at mayo.edu>***
> *
>    wrote:****
>
>
>
> ****
>   Hi Dr Holt,****
>    ****
>   It looks like the rrf files you used may be not correct(in the figure
> 2, the icd9cm.rrf was incorrect). Can you download the rrf zip from
> http://bioportal.bioontology.org/ontologies? After that, you can unzip
> them into the upload folder and overwrite the old one. Please let me know
> if it works. Thanks.****
>    ****
>   -Lian****
>    ****
>    ****
>    ****
>   *From:* Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Thursday, January 17, 2013 4:11 PM
> *To:* Lian, Zonghui
> *Subject:* Fwd: [bioontology-support] parsing error****
>    ****
>    ****
>    ****
>   Begin forwarded message:****
>
>
>
>
> ****
>   *From: *"Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu>****
>   *Subject: [bioontology-support] parsing error*****
>   *Date: *January 9, 2013 3:04:05 PM PST****
>   *To: *"support at bioontology.org" <support at bioontology.org>****
>    ****
>   I have recently tried to get my ncbo virtual appliance back up and
> running. ****
>    ****
>   So, I tried to import some ontologies from the bioportal to my own
> hosted vm, but got a parsing error. ****
>    ****
>   I also tried to manually and still got a java error. ****
>    ****
>    ****
>   see attached.****
>    ****
>    ****
>   Any thoughts?****
>    ****
>    ****
>   Jonathan****
>    ****
>    ****
>    ****
>   <image002.jpg>****
>    ****
>   <image003.png><image005.jpg>****
>    ****
>    ****
>    ****
>    ****
>    ****
>      .................................****
>   Jonathan Holt, DO, MS****
>    ****
>   Assistant Professor of Biomedical Informatics and Medicine****
>   Departments of Biomedical Informatics & Medicine, Division of Genetic
> Medicine****
>   Vanderbilt University Medical Center****
>   2209 Garland Ave
>
>
>
> ****
>   412 Eskind Biomedical Library****
>   Nashville, TN  37232-8340****
>   Phone:  615-322-8683****
>   Fax: 615-936-1427****
>    ****
>   jonathan.holt at vanderbilt.edu****
>   http://dbmi.mc.vanderbilt.edu/people/holt.html****
>     ****
>    ****
>    ****
>    ****
>    ****
>    ****
>
>  ****
>    ****
>   _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support****
>     ** **
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
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