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[bioontology-support] [BioPortal] Feedback from rakesh

Rakesh Nagarajan rakesh at pieriandx.com
Wed Aug 12 19:05:52 PDT 2020


Jennifer,
     We'd love to upgrade to v3.0 of the appliance as soon as our DevOps
has the bandwidth to do so. Thanks for checking on this and I am glad my
issue is at least reproducible. I'll await further feedback from you after
you've had a chance to connect with your colleagues tomorrow.

Thanks a ton,
Rakesh

On Wed, Aug 12, 2020 at 7:49 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Rakesh,
>
> OK - I’m sorry to say that I don’t have a satisfactory answer for you at
> the moment. I installed a virtual appliance instance in my local
> development environment and attempted to upload the SNOMED CT TTL file. I
> reproduced the 500 error that you reported. Unfortunately, the log files
> where I would usually look for errors don’t contain anything enlightening
> (appliance.log, unicorn.stderr.log, unicorn.stdout.log). I’ve pinged our IT
> person in charge of packaging the appliance to see what other log files
> might contain error output, and will get back to you with what I find out.
>
> A few things to note:
>
> 1). There's a new version of the appliance out (3.0.2). Not sure if this
> is of interest to you in terms of possibly upgrading. I was testing with
> 3.0.2, so it won’t help with your immediate issue.
>
> 2). The REST API logging is turned off by default in version 2.5 of the
> appliance. If you want to turn it on in order to examine log output, you’ll
> need to uncomment stderr_path and stdout_path in
> /srv/ncbo/ontologies_api/current/config/unicorn.rb. Again, this may not
> help with your immediate issue since I have REST API logging turned on in
> my local instance and the log files didn’t reveal anything obvious. If you
> turn on logging, the files should be located in
> /srv/ncbo/ontologies_api/current/log.
>
> I should be able to speak with a couple of colleagues tomorrow and hope to
> have other tips for you.
>
> Kind regards,
> Jennifer
>
>
> On Aug 12, 2020, at 2:32 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
> wrote:
>
> Jennifer,
>      No worries at all. I did track this down last night and tried to use
> the API and 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 Wed, Aug 12, 2020 at 2:48 PM Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Sorry about that Rakesh - I meant to send a link to this script in our
>> sample code repository:
>>
>>
>> https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb
>>
>>
>>
>> On Aug 11, 2020, at 6:31 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
>>> <http://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
>> contents and notify the sender of the error by reply email.
>>
>>
>>
>>
>>
>
> --
>
> *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.
>
>
>
>
>

-- 

*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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