<div dir="ltr"><div dir="ltr">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":"3","compose-window":{"secure":false}}"><div>     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?</div><div><br></div><div>Thanks so much for your help,</div><div>Rakesh</div></div><br><div class="gmail_quote" style=""><div dir="ltr" class="gmail_attr">On Tue, Aug 11, 2020 at 8:31 PM Rakesh Nagarajan <<a href="mailto:rakesh@pieriandx.com">rakesh@pieriandx.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">Jennifer,<div>     Thanks! Can you confirm the last link where you refer to a script but that link is the same as the previous link?</div><div><br></div><div>Thanks,</div><div>Rakesh</div></div><br><div class="gmail_quote"><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">vendetti@stanford.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">



<div>
Hi Rakesh,
<div><br>
<div><br>
<blockquote type="cite">
<div>On Aug 10, 2020, at 5:18 PM, <a href="mailto:support@bioontology.org" target="_blank">
support@bioontology.org</a> wrote:</div>
<br>
<div>
<div>
<p>Name: rakesh </p>
<p><a href="mailto:rakesh@pieriandx.com" target="_blank">Email: rakesh@pieriandx.com</a>
</p>
<p>Location: https%3A%2F%<a href="http://2Fbioportal.bioontology.org" target="_blank">2Fbioportal.bioontology.org</a>%2F
</p>
<p><br>
<strong>Feedback:</strong> </p>
<p>Hello, <br>
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?
</p>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>There are some instructions for locating log files here:</div>
<div><br>
</div>
<div><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing" target="_blank">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing</a></div>
<br>
<blockquote type="cite">
<div>
<div>
<p>Any other ideas to help troubleshoot? Finally are there commands to load directly on the server I may use?</p>
<div><br>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div><br>
</div>
<div>I’m not certain this is what you’re asking for, but you can manually re-parse an ontology submission using this methodology:</div>
<div><br>
</div>
<div><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console" target="_blank">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console</a></div>
<div><br>
</div>
<div>It’s also possible to upload ontologies programmatically. An appliance user submitted the following script to our code sample repository:</div>
<div><br>
</div>
<div><a href="https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console" target="_blank">https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-using-the-ruby-console</a></div>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>Kind regards,</div>
<div>Jennifer</div>
<div><br>
</div>
</div>
</div>
</div>

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