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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****
> ** **
>
>
>
> _______________________________________________
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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