<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Bummer,<div><br></div><div>Apparently I had the version 61 of the code as was show by enabling the verbosity option, Thanx!!!</div><div><br></div><div>Strange enough though, because I had downloaded the code from the ensembl website ( <a href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a> ) where the hyperlink clearly suggests that I was downloading version 60... <a href="<a href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-60&view=tar">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-60&view=tar</a>">ensembl</a> possibly other people will get confused?...</div><div><br></div><div>Oh well, now I got a taste of the CVS way of installing I'm never going back, so thanx again. I got it all working now.</div><div><br></div><div>Kind regards,</div><div><br></div><div>Bram</div><div><br></div><div><br><div><div>On 26-dec-2010, at 20:23, Ian wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div bgcolor="#FFFFFF"><div>This only happens when the API and the database selected are not the same version.</div><div>Use -verbose => 1 in load_registry_from_db to see what version it is trying to load.</div><div><br></div><div>It is usually best to delete the version of the API and install the new one as cvs can sometimes get confused when over writing. </div><div><br>So if you get a new checkout and make sure this is in a new directory you should be okay.</div><div>But add the verbose option to see what the registry is trying to do.</div><div><br></div><div>If the problem continues please let us know what the verbose option gives you.</div><div><br></div><div>Ian longden</div><div>Ensembl developer.</div><div><br>On Dec 26, 2010, at 5:28 PM, Bram De Wilde <<a href="mailto:gbramdewilde@gmail.com">gbramdewilde@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>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">$</span><span style="color: #ca00f9">registry</span><span style="color: #000000"> </span><span style="color: #d71200">= </span>'Bio::EnsEMBL::Registry'<span style="color: #d71200">; </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; min-height: 15px; "><font class="Apple-style-span" color="#D90023"><font class="Apple-style-span"><br></font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; ">$<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" face="Helvetica" size="3"></font><span class="Apple-style-span" style="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="font-family: Helvetica; font-size: 12px; "> mysql -u anonymous -h <a href="http://ensembldb.ensembl.org/"></a><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="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" 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" 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" 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" 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" 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" 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" 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" 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" 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" 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; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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/"></a><a href="http://medgen.ugent.be/">http://medgen.ugent.be/</a>
<a href="mailto:Bram.DeWilde@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">
</div>
<br></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>Dev mailing list</span><br><span><a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a></span><br><span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a></span><br></div></blockquote></div></blockquote></div><br></div></body></html>