<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi everyone,<div><br></div><div>I just upgraded our install of the API from version 59 to 60 and all of my code stopped working.</div><div>I tracked down the problem to the registry not being able to connect to the database... I guess?... Or at least I get zero results back when I try to query the database.</div><div>This simple piece of test code works perfectly on my v59 install but stops working when I try and use the freshly installed v60:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><span style="color: #c900f9">require </span>Bio::EnsEMBL::Registry<span style="color: #d71200">;</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><span style="color: #c900f9">my </span><span style="color: #000000">$</span><span style="color: #ca00f9">registry</span><span style="color: #000000"> </span><span style="color: #d71200">= </span>'Bio::EnsEMBL::Registry'<span style="color: #d71200">; </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><font class="Apple-style-span" color="#D90023"><font class="Apple-style-span" color="#000000"><br></font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; ">$<span style="color: #ca00f9">registry</span><span style="color: #d71200">-></span>load_registry_from_db<span style="color: #d71200">(</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><span style="color: #d71200"> -</span><span style="color: #000000">host </span><span style="color: #d71200">=> </span>'ensembldb.ensembl.org'<span style="color: #d71200">,</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><span style="color: #d71200"> -</span><span style="color: #000000">user </span><span style="color: #d71200">=> </span>'anonymous'<span style="color: #d71200">,</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(215, 18, 0); "><span class="Apple-tab-span" style="white-space:pre"> </span>-<span style="color: #000000">port </span>=> <span style="color: #c61400">5306</span>,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(215, 18, 0); ">);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #c900f9">my </span><span style="color: #000000">@</span>db_adaptors<span style="color: #000000"> </span><span style="color: #d71200">= </span><span style="color: #000000">@</span>{ $registry->get_all_DBAdaptors() }<span style="color: #d71200">;</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #c900f9">foreach my </span><span style="color: #000000">$</span>db_adaptor<span style="color: #000000"> </span><span style="color: #d71200">(</span><span style="color: #000000">@</span>db_adaptors<span style="color: #d71200">) {</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #d71200"> </span><span style="color: #c900f9">my </span><span style="color: #000000">$</span>db_connection<span style="color: #000000"> </span><span style="color: #d71200">= </span><span style="color: #000000">$</span>db_adaptor<span style="color: #d71200">-></span><span style="color: #000000">dbc</span><span style="color: #d71200">();</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #d71200"> </span>printf<span style="color: #d71200">(</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><span style="color: #d71200"> </span>"species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n"<span style="color: #d71200">,</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(215, 18, 0); "> <span style="color: #000000">$</span><span style="color: #ca00f9">db_adaptor</span>-><span style="color: #000000">species</span>(), <span style="color: #000000">$</span><span style="color: #ca00f9">db_adaptor</span>-><span style="color: #000000">group</span>(),</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #d71200"> </span><span style="color: #000000">$</span>db_connection<span style="color: #d71200">-></span><span style="color: #000000">dbname</span><span style="color: #d71200">(), </span><span style="color: #000000">$</span>db_connection<span style="color: #d71200">-></span><span style="color: #000000">host</span><span style="color: #d71200">(),</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(202, 0, 249); "><span style="color: #d71200"> </span><span style="color: #000000">$</span>db_connection<span style="color: #d71200">-></span><span style="color: #000000">port</span><span style="color: #d71200">()</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(215, 18, 0); "> );</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(215, 18, 0); ">}</div></div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><font class="Apple-style-span" color="#C900F9"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; color: rgb(43, 0, 255); "><font class="Apple-style-span" color="#D71200"><font class="Apple-style-span" color="#C900F9"><br></font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"></font><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; ">I receive no errors when I execute the code making this a hard problem to debug. Any kind of slice I try to get from any adaptor on my registry will return undefined . When I use the mysql client on my server:</span><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; "> mysql -u anonymous -h <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> -P 5306, and perfrom a show databases I get to see the database just fine: "</span><span class="Apple-style-span" style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; ">homo_sapiens_core_60_37e" is in the list so the mysql connection does not seem to be the cause of all this.</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="background-color: transparent; font-size: 12px;">Installation was done exactly as described in the online tutorial (the files from my v 59 and v60 install look exactly the same on my machine, with the correct permissions set...)</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="background-color: transparent; font-size: 12px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="background-color: transparent; font-size: 12px;">The perldoc for the Bio/EnsEMBL/Registry.pm does not mention any changes in the way we are supposed to connect to the database, nor does the online manual.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="background-color: transparent; font-size: 12px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="background-color: transparent; font-size: 12px;">Anyone has any pointers as to what i am doing wrong?</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">Kind regards,</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><font class="Apple-style-span" color="#000000" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><br></span></font></div></font></div></div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; font-size: 13px; white-space: pre-wrap; ">Bram De Wilde, MD
Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.050
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 332 4812 (phone) | +32 9 332 6549 (fax)
<a href="http://medgen.ugent.be/">http://medgen.ugent.be/</a>
<a href="mailto:Bram.DeWilde@UGent.be">Bram.DeWilde@UGent.be</a> </span></div><div><br></div></span><br class="Apple-interchange-newline">
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