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Hi Rakesh,
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<div class="">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.</div>
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<div class="">A few things to note:</div>
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<div class="">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.</div>
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<div class="">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.</div>
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<div class="">I should be able to speak with a couple of colleagues tomorrow and hope to have other tips for you.</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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<div class="">On Aug 12, 2020, at 2:32 PM, Rakesh Nagarajan <<a href="mailto:rakesh@pieriandx.com" class="">rakesh@pieriandx.com</a>> wrote:</div>
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<div dir="ltr" class="">Jennifer,<input name="virtru-metadata" type="hidden" value="{"email-policy":{"state":"closed","expirationUnit":"days","disableCopyPaste":false,"disablePrint":false,"disableForwarding":false,"enableNoauth":false,"persistentProtection":false,"expandedWatermarking":false,"expires":false,"isManaged":false},"attachments":{},"compose-id":"19","compose-window":{"secure":false}}" class="">
<div class="">     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?</div>
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<div class="">Thanks so much for your help,</div>
<div class="">Rakesh</div>
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<div dir="ltr" class="gmail_attr">On Wed, Aug 12, 2020 at 2:48 PM Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" class="">vendetti@stanford.edu</a>> wrote:<br class="">
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<div style="overflow-wrap: break-word;" class="">Sorry about that Rakesh - I meant to send a link to this script in our sample code repository:
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<div class=""><a href="https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb" target="_blank" class="">https://github.com/ncbo/ncbo_rest_sample_code/blob/master/ruby/bioportal_ontologies_import.rb</a></div>
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<div class="">On Aug 11, 2020, at 6:31 PM, Rakesh Nagarajan <<a href="mailto:rakesh@pieriandx.com" target="_blank" class="">rakesh@pieriandx.com</a>> wrote:</div>
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<div dir="ltr" class="">Jennifer,
<div class="">     Thanks! Can you confirm the last link where you refer to a script but that link is the same as the previous link?</div>
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<div class="">Thanks,</div>
<div class="">Rakesh</div>
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<div dir="ltr" class="gmail_attr">On Tue, Aug 11, 2020 at 6:18 PM Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>> wrote:<br class="">
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<div class="">Hi Rakesh,
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<div class="">On Aug 10, 2020, at 5:18 PM, <a href="mailto:support@bioontology.org" target="_blank" class="">
support@bioontology.org</a> wrote:</div>
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<p class="">Name: rakesh </p>
<p class=""><a href="mailto:rakesh@pieriandx.com" target="_blank" class="">Email: rakesh@pieriandx.com</a>
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<p class="">Location: https%3A%2F%<a href="http://2fbioportal.bioontology.org/" target="_blank" class="">2Fbioportal.bioontology.org</a>%2F
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<strong class="">Feedback:</strong> </p>
<p class="">Hello, <br class="">
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?
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<div class="">There are some instructions for locating log files here:</div>
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<div class=""><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing" target="_blank" class="">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing</a></div>
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<p class="">Any other ideas to help troubleshoot? Finally are there commands to load directly on the server I may use?</p>
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<div class="">I’m not certain this is what you’re asking for, but you can manually re-parse an ontology submission using this methodology:</div>
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<div class=""><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console" target="_blank" class="">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console</a></div>
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<div class="">It’s also possible to upload ontologies programmatically. An appliance user submitted the following script to our code sample repository:</div>
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<div class=""><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console" target="_blank" class="">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console</a></div>
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<div class="">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.</div>
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<div class="">Kind regards,</div>
<div class="">Jennifer</div>
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