<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Sydney,
<div class=""><br class="">
</div>
<div class="">I’m glad it’s working for you now.</div>
<div class=""><br class="">
</div>
<div class="">If you run into anything similar in the future, another issue could be a corrupt entry in the cache. You can clear the application caches via the “Admin" page in the user interface:</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes" id="C182DEF5-D217-454F-AC95-C3CB13D36D34" src="cid:2F751492-B7CE-49BF-AACB-C1008A4CFCB7@stanford.edu" class=""></div>
<div class="">For Goo::Base::AttributeNotLoaded errors, you’d want to try flushing the Goo cache.</div>
<div class=""><br class="">
</div>
<div class="">Another item of potential interest is turning on more extensive logging in order to debug issues like the one you saw. You would need to uncomment a couple of lines in your unicorn.rb file, i.e.:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://github.com/ncbo/virtual_appliance/blob/master/appliance_config/ontologies_api/config/unicorn.rb#L11" class="">https://github.com/ncbo/virtual_appliance/blob/master/appliance_config/ontologies_api/config/unicorn.rb#L11</a></div>
<div class=""><br class="">
</div>
<div class="">… and restart your system.</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class="">Jennifer</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 5, 2018, at 1:48 PM, Sydney Hoppe <<a href="mailto:hoppesyd@umich.edu" class="">hoppesyd@umich.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello!
<div class=""><br class="">
</div>
<div class="">I just wanted to send an update with a very simple fix. (So simple that it just went right over my head). Because my local instance did not recognize that Ontology XYZ existed, it did not object to me submitting a 'new' ontology with the same
 name and data. This solved the issue!</div>
<div class=""><br class="">
</div>
<div class="">Thanks for taking the time to help me out.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Sydney</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Thu, Jul 5, 2018 at 2:15 PM, Sydney Hoppe <span dir="ltr" class="">
<<a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">unfortunately that returns 'nil'</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Thu, Jul 5, 2018 at 2:08 PM, Jennifer Leigh Vendetti <span dir="ltr" class="">
<<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space" class="">Are you able to access the ontology object from a console session using the following syntax:
<div class=""><br class="">
</div>
<div class="">ont = LinkedData::Models::Ontology.f<wbr class="">ind(RDF::URI.new("<a href="http://data.bioontology.org/ontologies/IEV" target="_blank" class="">http://data.<wbr class="">bioontology.org/ontologies/IEV</a><wbr class="">")).first</div>
<div class=""><br class="">
</div>
<div class="">You would need to replace the URL passed to the new() method with your domain name and your problematic ontology acronym. If you get an object back, you should then be able to call delete on it.</div>
<span class="m_-1541430849830455117HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Jennifer</div>
</font></span>
<div class="">
<div class="m_-1541430849830455117h5">
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 5, 2018, at 11:59 AM, Sydney Hoppe <<a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a>> wrote:</div>
<br class="m_-1541430849830455117m_3418506120203847031Apple-interchange-newline">
<div class="">
<div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
Originally I was issuing a REST API call in order to delete the ontology. When that failed I have since tried both methods</div>
<div class="gmail_extra" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br class="">
<div class="gmail_quote">On Thu, Jul 5, 2018 at 1:57 PM, Jennifer Leigh Vendetti<span class="m_-1541430849830455117m_3418506120203847031Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.ed<wbr class="">u</a>></span><span class="m_-1541430849830455117m_3418506120203847031Apple-converted-space"> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space" class="">Apologies - you already included that information and I missed it upon first reading.
<div class=""><br class="">
</div>
<div class="">Are you issuing a REST API call to delete the ontology? Or, are you doing it via a console session, as described here:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_delete_an_ontology.3F" target="_blank" class="">https://www.bioontology.org/wi<wbr class="">ki/Virtual_Appliance_FAQ#How_d<wbr class="">o_I_delete_an_ontology.3F</a></div>
<span class="m_-1541430849830455117m_3418506120203847031HOEnZb"><font color="#888888" class="">
<div class=""><br class="">
</div>
<div class="">Jennifer</div>
</font></span>
<div class="">
<div class="m_-1541430849830455117m_3418506120203847031h5">
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 5, 2018, at 11:52 AM, Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" target="_blank" class="">vendetti@stanford.edu</a>> wrote:</div>
<br class="m_-1541430849830455117m_3418506120203847031m_-866572977335314297Apple-interchange-newline">
<div class="">
<div style="word-wrap:break-word;line-break:after-white-space" class="">Hello Sydney,
<div class=""><br class="">
</div>
<div class="">Could you please clarify for us if you’re working on the main BioPortal, or a virtual appliance instance?</div>
<div class=""><br class="">
</div>
<div class="">Jennifer</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <<a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a>> wrote:</div>
<br class="m_-1541430849830455117m_3418506120203847031m_-866572977335314297Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello,
<div class=""><br class="">
</div>
<div class="">I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background. </div>
<div class=""><br class="">
</div>
<div class="">Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/curre<wbr class="">nt/helpers/application_helper.<wbr class="">rb
 file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :</div>
<div class=""><br class="">
</div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class="">
<div class="">class: Goo::Base::AttributeNotLoaded</div>
</div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px" class="">
<div class="">
<div class="">message: Persistent object with `acronym` not loaded</div>
</div>
<div class=""><br class="">
</div>
</blockquote>
</blockquote>
For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined
 which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology
 XYZ but, an ontology with that acronym can not be found.
<div class=""><br class="">
</div>
<div class="">To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it. </div>
<div class=""><br class="">
</div>
<div class="">Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your help!<br class="">
<div class="">--<span class="m_-1541430849830455117m_3418506120203847031Apple-converted-space"> </span><br class="">
<div class="m_-1541430849830455117m_3418506120203847031m_-866572977335314297gmail_signature">
<div dir="ltr" class=""><font face="times new roman, serif" class=""><span style="font-size:12px" class=""><b class="">Sydney Hoppe</b></span></font><br class="">
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class=""><font face="times new roman, serif" class="">University of Michigan, Ann Arbor</font></div>
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class=""><font face="times new roman, serif" class="">B.S.E. in Engineering, 2019</font></div>
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class="">
<div style="line-height:normal" class=""><font face="times new roman, serif" class=""><a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a> </font><span style="font-family:"times new roman",serif" class="">| 614.282.1314</span></div>
</div>
</div>
</div>
</div>
</div>
</div>
______________________________<wbr class="">_________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" target="_blank" class="">bioontology-support@lists.stan<wbr class="">ford.edu</a><br class="">
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" target="_blank" class="">https://mailman.stanford.edu/m<wbr class="">ailman/listinfo/bioontology-su<wbr class="">pport</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
______________________________<wbr class="">_________________<br class="">
bioontology-support mailing list<br class="">
<a href="mailto:bioontology-support@lists.stanford.edu" target="_blank" class="">bioontology-support@lists.stan<wbr class="">ford.edu</a><br class="">
<a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" target="_blank" class="">https://mailman.stanford.edu/m<wbr class="">ailman/listinfo/bioontology-su<wbr class="">pport</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
<br clear="all" class="">
<div class=""><br class="">
</div>
--<span class="m_-1541430849830455117m_3418506120203847031Apple-converted-space"> </span><br class="">
<div class="m_-1541430849830455117m_3418506120203847031gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class=""><font face="times new roman, serif" class=""><span style="font-size:12px" class=""><b class="">Sydney Hoppe</b></span></font><br class="">
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class=""><font face="times new roman, serif" class="">University of Michigan, Ann Arbor</font></div>
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class=""><font face="times new roman, serif" class="">B.S.E. in Engineering, 2019</font></div>
<div style="font-family:Helvetica;font-size:12px;line-height:normal" class="">
<div style="line-height:normal" class=""><font face="times new roman, serif" class=""><a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a> </font><span style="font-family:"times new roman",serif" class="">| 614.282.1314</span></div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
<br clear="all" class="">
<div class=""><br class="">
</div>
-- <br class="">
<div class="m_-1541430849830455117gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class=""><font face="times new roman, serif" class=""><span style="font-size:12px" class=""><b class="">Sydney Hoppe</b></span></font><br class="">
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<font face="times new roman, serif" class="">University of Michigan, Ann Arbor</font></div>
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<font face="times new roman, serif" class="">B.S.E. in Engineering, 2019</font></div>
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<div style="line-height:normal" class=""><font face="times new roman, serif" class=""><a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a> </font><span style="font-family:'times new roman',serif" class="">| 614.282.1314</span></div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
<br clear="all" class="">
<div class=""><br class="">
</div>
-- <br class="">
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class=""><font face="times new roman, serif" class=""><span style="font-size:12px" class=""><b class="">Sydney Hoppe</b></span></font><br class="">
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<font face="times new roman, serif" class="">University of Michigan, Ann Arbor</font></div>
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<font face="times new roman, serif" class="">B.S.E. in Engineering, 2019</font></div>
<div style="font-family: Helvetica; font-size: 12px; line-height: normal;" class="">
<div style="line-height:normal" class=""><font face="times new roman, serif" class=""><a href="mailto:hoppesyd@umich.edu" target="_blank" class="">hoppesyd@umich.edu</a> </font><span style="font-family:'times new roman',serif" class="">| 614.282.1314</span></div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>