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[bioontology-support] [BioPortal] Feedback from rakesh

Rakesh Nagarajan rakesh at pieriandx.com
Tue Aug 11 20:52:40 PDT 2020


Jennifer,
     I was able to track the code down on your code repository and tried to
use the API but again got an Internal Server Error. The submission itself
isn't succeeding so there is no submission ID created on the server and so
I can't check logs there. Is there a way to check any other internal
application server (nginx, tomcat?) logs to see why the submission is
failing? I have tried to restart the VM and flushed the goo cache per the
instructions as well. I also validated the TTL file in Protege which was
able to successfully load the complete SNOMEDCT file without errors. Any
other ideas?

Thanks so much for your help,
Rakesh

On Tue, Aug 11, 2020 at 8:31 PM Rakesh Nagarajan <rakesh at pieriandx.com>
wrote:

> Jennifer,
>      Thanks! Can you confirm the last link where you refer to a script but
> that link is the same as the previous link?
>
> Thanks,
> Rakesh
>
> On Tue, Aug 11, 2020 at 6:18 PM Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hi Rakesh,
>>
>>
>> On Aug 10, 2020, at 5:18 PM, support at bioontology.org wrote:
>>
>> Name: rakesh
>>
>> Email: rakesh at pieriandx.com <rakesh at pieriandx.com>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org%2F
>>
>>
>> *Feedback:*
>>
>> Hello,
>> I am using v2.5 of the Ontoportal appliance and have successfully loaded
>> NCIT a few times now. I am now attempting to load SNOMED-CT after
>> conversion from the UMLS using umls2rdf as a .ttl file. I have selected
>> UMLS as the format but I have now tried twice to upload via UI and the
>> server threw an error saying 'something went wrong and administrators have
>> been notified. However I dont know what happened. Are there logs on the
>> server to check?
>>
>>
>> There are some instructions for locating log files here:
>>
>>
>> https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing
>>
>> Any other ideas to help troubleshoot? Finally are there commands to load
>> directly on the server I may use?
>>
>>
>>
>> I’m not certain this is what you’re asking for, but you can manually
>> re-parse an ontology submission using this methodology:
>>
>>
>> https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console
>>
>> It’s also possible to upload ontologies programmatically. An appliance
>> user submitted the following script to our code sample repository:
>>
>>
>> https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console
>>
>> It’s a script that imports ontologies from on appliance instance to
>> another, which is not what you’re doing. However, I thought that some
>> portions of the code might be of interest to you.
>>
>> Kind regards,
>> Jennifer
>>
>>
>
> --
>
> *Rakesh Nagarajan*
>
> Founder, President, and Chief Technology & Visionary Officer
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> Wisdom in Every Report™
>
> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
> the use of the intended recipient and may contain privileged, confidential
> or other legally protected information. If you are not the intended
> recipient, please destroy all copies without reading or disclosing their
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>
>
>
>

-- 

*Rakesh Nagarajan*

Founder, President, and Chief Technology & Visionary Officer

m: 314-504-5620
e: rakesh at pieriandx.com

[image: pierian-logo-trans-light-background]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report™

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
use of the intended recipient and may contain privileged, confidential or
other legally protected information. If you are not the intended recipient,
please destroy all copies without reading or disclosing their contents and
notify the sender of the error by reply email.
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