[ensembl-dev] a caching question?
Jay Humphrey
jhumphre at ebi.ac.uk
Tue May 1 16:41:38 BST 2012
It was "External database type" until recently
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-webcode/modules/EnsEMBL/Web/Component.pm?root=ensembl&r1=1.228&r2=1.229
I'm also positive that is the right place to change to column header.
Maybe you have an outdated instance running? Kill all your apache/httpd
processes and double-check the server config (such as port number).
On 01/05/2012 16:37, Simon Brent wrote:
> You are looking in the right place, in theory.
>
> However, the Ensembl code has the header of this column as "External
> database", not "External database type", which to me says you have a
> plugin somewhere with the _matches function overwritten.
>
> Simon
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
> Of Thomason, James
> Sent: 01 May 2012 15:35
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] a caching question?
>
> I still haven't gotten it going. Again, on my example page:
>
> http://dev.gramene.org/Arabidopsis_thaliana/Transcript/Similarity?db=cor
> e;g=AT3G52430;oid=1;r=3:19431371-19434403;t=AT3G52430.1
>
> Alternatively, you can hit the table directly at:
>
> http://dev.gramene.org/Arabidopsis_thaliana/Component/Transcript/Web/Sim
> ilarityMatches?db=core;g=AT3G52430;oid=1;r=3:19431371-19434403;t=AT3G524
> 30.1;time=1335882643495.495
>
> Incidentally, for those with issues loading the page, firefox seems to
> complain the first time you go to it, but after reloading it never
> complains again. That is very bizarre and I'd love to know what's going
> on there as well, but it's a side issue. Chrome and Safari have had no
> issues for me, fwiw.
>
> All I'm trying to do now is change the value of the header on the page
> from "External database type" to....anything else. It looks like this
> table is generated through EnsEMBL::Web::Component's _matches method,
> due to the fact that it's one of the very very few modules that actually
> contains the text "External database type". But changing it does me no
> good.
>
> I dove through our entire ensembl install looking for that string and
> changed all of 'em, but the blasted page still refuses to budge. That
> string is altered everywhere in the codebase that I can discern. AFAIK,
> I've checked and re-checked all the plugin directories and everything's
> altered. The server's been restarted multiple times.
>
> I've either missed a plugin somewhere, something's cached to disk that
> refuses to let go, or I'm looking at the wrong code entirely and the
> table's actually generated elsewhere.
>
> This change is, of course, trivial, but I'm just trying to implement it
> to confirm that I'm looking at the right bit of code so I can walk
> through it and figure out how to pull out the actual data I need.
>
> Can someone familiar with the internals confirm that I'm looking in the
> right spot? What else could I be missing here? I'm utterly stumped.
>
> Many thanks, as always.
>
> -Jim...
>
> On Apr 27, 2012, at 9:18 AM, Jay Humphrey wrote:
>
>> You are running Ensembl with the 'plants' plugin. The priority of the
> plugins is set in conf/Plugins.pm. That file should show a list of
> plugin directories, and eg-plugins/plants preceeds eg-plugins/common,
> and both have priority over the default Ensembl webcode.
>> Plugins work by overriding functions, or adding new modules or
> functions. For example, if
> eg-plugins/plants/modules/Ensembl/Object/Gene.pm exists, the functions
> in it will be executed. And code under eg-plugins/plants will override
> anything under eg-plugins/common.
>> If you're using Apache::Reload, make sure the plugin directories are
> in the path.
>> On 27/04/2012 15:00, Thomason, James wrote:
>>> I've gotta have something else going on then, I've been restarting
> the web server between all of my edits and still can't get them to show
> up. I was hoping I was running into an issue where the page was being
> cached on disk and that was something I could clear out.
>>> Here's what I'm doing -
>>>
>>> Hitting this page:
>>>
> http://dev.gramene.org/Arabidopsis_thaliana/Transcript/Ontology/Table?db
> =core;g=AT3G52430;oid=1;r=3:19431371-19434403;t=AT3G52430.1
>>> And clicking on the "General Identifiers" link on the left under
> External References. It looks like the result is rendered out of code in
> Ensembl::Web::Component, specifically in the _matches method. But no
> matter how much I mess with it, I can't change the output on the page.
>>> If it's not a caching issue, then I have to just be looking in the
> wrong spot. Could someone point me in the right direction?
>>> On Apr 26, 2012, at 3:18 AM, Jay Humphrey wrote:
>>>
>>> Yes, there is caching of the source code. You woul have to restart
> the server every time you make a change, or add Apache2::Reload to the
> apache/mod_perl configuration.
>>> In conf/httpd.conf, just before the<Perl> section, add:...
>>>
>>> On 26/04/2012 00:01, Thomason, James wrote:
>>> Gang,
>>>
>>> I'm working on another exporting gimmick and am having trouble. I've
> mostly tracked it down, but am trying to isolate what looks like a bug
> to me. My issue is that no matter where I seem to add in debugging code
> to ensembl to trace it back, it's never getting executed. I'm trying to
> add some debugging lines to EnsEMBL::Web::Component, but nothing's
> showing up.
>>> So my questions -
>>> 1) Is there some cache that's butting in here? And, can I clear it
> out easily enough?
>>> or
>>> 2) Is there some other file I should be editing instead? A plugin or
> something?
>>> Many thanks, as always.
>>>
>>> --
>>> -Jim Thomason...
>>>
>>> Scientific Informatics Developer @ The Ware Lab,
>>> a USDA-ARS Laboratory at Cold Spring Harbor Laboratory
>>> http://www.warelab.org/
>>> http://www.cshl.edu/
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org<mailto:Dev at ensembl.org>
>>> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>> --
>>> Jay Humphrey Ensembl Genomes Web Developer
>>> EMBL-EBI Tel: +44-(0)1223-492682
>>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org<mailto:Dev at ensembl.org>
>>> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>> --
>>> -Jim Thomason...
>>>
>>> Scientific Informatics Developer @ The Ware Lab,
>>> a USDA-ARS Laboratory at Cold Spring Harbor Laboratory
>>> http://www.warelab.org/
>>> http://www.cshl.edu/
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>> --
>> Jay Humphrey Ensembl Genomes Web Developer
>> EMBL-EBI Tel: +44-(0)1223-492682
>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
--
Jay Humphrey Ensembl Genomes Web Developer
EMBL-EBI Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
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