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<p class="MsoNormal"><span style="color:#1F497D">Sorry, I forgot that “load_registry()” was a subroutine in my own code. The full code is:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal">my $version = software_version();<o:p></o:p></p>
<p class="MsoNormal">my $registry = load_registry();<o:p></o:p></p>
<p class="MsoNormal">my $GO_adapter = $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );<o:p></o:p></p>
<p class="MsoNormal">die "Couldn't get GO adaptor from $version" unless ($GO_adapter);<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">sub load_registry {<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> my $registry = 'Bio::EnsEMBL::Registry';<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> $registry->load_registry_from_db(<o:p></o:p></p>
<p class="MsoNormal"> -host => 'ensembldb.ensembl.org',<o:p></o:p></p>
<p class="MsoNormal"> -user => 'anonymous'<o:p></o:p></p>
<p class="MsoNormal"> );<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> return $registry;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">}<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">I had a similar problem with ensemblgenomes before (should be in the list archives) and was given a work round by directly connecting to a different database to get the GO DBA, but hopefully this can be fixed
in the main registry.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Simon. </span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-GB"> Simon Andrews
<br>
<b>Sent:</b> 27 September 2018 09:07<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> Can't get GO adapter from latest registry<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve just updated our code to the latest API release and one of our processing scripts is now failing.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">You can reproduce this with:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">my $version = software_version();<o:p></o:p></p>
<p class="MsoNormal">my $registry = load_registry();<o:p></o:p></p>
<p class="MsoNormal">my $GO_adapter = $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );<o:p></o:p></p>
<p class="MsoNormal">die "Couldn't get GO adaptor from $version" unless ($GO_adapter);<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">..where I get:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Couldn't get GO adaptor from 93<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can this be fixed at the Ensembl end, or is there a more immediate work round I can apply locally?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Simon.<o:p></o:p></p>
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