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</o:shapelayout></xml><![endif]--></head><body lang=EN-NZ link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hi,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have just upgraded the my local Ensembl instance to the latest (from version 69 to version 74), and I have a question regarding how to handle species with no DAS url.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>In version 69 having no DAS registry URL specified was no problem, but with version 74 this causes Ensembl to break, as explained below.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Why it breaks:<o:p></o:p></p><p class=MsoNormal>At SpeciesDefs.pm line 533:<o:p></o:p></p><p class=MsoNormal><a href="https://github.com/Ensembl/ensembl-webcode/blob/release/74/modules/EnsEMBL/Web/SpeciesDefs.pm#L533">https://github.com/Ensembl/ensembl-webcode/blob/release/74/modules/EnsEMBL/Web/SpeciesDefs.pm#L533</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>sub _merge_db_tree {<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> my ($self, $tree, $db_tree, $key) = @_;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> Hash::Merge::set_behavior('RIGHT_PRECEDENT');<o:p></o:p></span></p><p class=MsoNormal style='background:#FFFFCC'><span style='font-size:10.0pt;font-family:"Courier New"'> my $t = merge($tree->{$key}, $db_tree->{$key});<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> $tree->{$key} = $t;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>}<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal>When no DAS is available <span style='font-size:10.0pt;font-family:"Courier New"'>$db_tree->{$key} </span>returns ‘undef’ when $dbtree is a das_tree object, which overwrites (due to RIGHT PRECEDENT merge behaviour) the original $tree, thus returning an empty tree which is later stored. This results in the main config file config.packed having missing hash values which should have been loaded from the species.ini/DEAFULTS.ini config files.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have found 2 solutions(outlined at the end of this email) however both solutions involve altering the Ensembl code in SpecesDefs.pm, which I would rather not do. So is there some other way to disable the DAS so this doesn’t happen, perhaps in the species.ini/DEAFULTS.ini or SiteDefs.pm?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have tried un-setting the 'DAS_REGISTRY_URL' in DEFAULTS.ini, which does stop Ensembl trying to connect to the default DAS registry, but does not prevent the afore-mentioned behaviour.<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>(Hacky) solutions I have found:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>1. Change merge precedence at SpeciesDefs.pm line 532:<o:p></o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> Hash::Merge::set_behavior('RIGHT_PRECEDENT');<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> To<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> Hash::Merge::set_behavior(LEFT_PRECEDENT');<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'> * This means the original config tree has priority over any DAS config<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>2. Only try to process DAS if a DAS_REGISTRY_URL is available<o:p></o:p></p><p class=MsoNormal> * best way to do this seems to be to test for the URL at SpeciesDefs.pm line 630:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-family:"Courier New"'> if ($species ne 'MULTI') {<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-family:"Courier New"'> $self->process_ini_files($species, 'das', $config_packer, $defaults);<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-family:"Courier New"'> $self->_merge_db_tree($tree, $das_tree, $species);<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-family:"Courier New"'> }<o:p></o:p></span></p><p class=MsoNormal style='margin-left:36.0pt'><span style='font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal> * Change <o:p></o:p></p><p class=MsoNormal> <span style='font-family:"Courier New"'>if ($species ne 'MULTI')<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Courier New"'> </span>to<o:p></o:p></p><p class=MsoNormal><span style='font-family:"Courier New"'> if ($tree->{$species}{'DAS_REGISTRY_URL'} && $species ne 'MULTI')</span><span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal>N.B. These snippets of SpeciesDefs.pm code do not seem to have changed since version 69, so something else must have changed to cause this issue, though I cannot find what that change is... Also this issue exists in version 73 as well (I tried that for comparison).<span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal>Kind Regards<span style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Ben Warren</span></b><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Research Technologist<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><div><p class=MsoNormal><a href="http://www.plantandfood.co.nz/"><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:blue;text-decoration:none'><img border=0 width=210 height=70 id="_x0000_i1025" src="cid:image001.gif@01CF113E.2BEC6170" alt="Plant & Food Research"></span></a><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Arial","sans-serif"'>T: +64 9 925 8615<br>F: +64 9 925 7001<br>E: ben.warren@plantandfood.co.nz<br>www.plantandfood.co.nz<br>The New Zealand Institute for Plant & Food Research Limited<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><div><p class=MsoNormal><b><span style='font-size:8.5pt;font-family:"Arial","sans-serif"'>Postal Address:</span></b><span style='font-size:8.5pt;font-family:"Arial","sans-serif"'> Plant & Food Research<br>Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand<br></span><b><span style='font-size:8.5pt;font-family:"Arial","sans-serif"'>Physical Address:</span></b><span style='font-size:8.5pt;font-family:"Arial","sans-serif"'> Plant & Food Research<br>120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p></div></body></html>
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