[ensembl-dev] a caching question?

Tue May 1 16:37:14 BST 2012

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/

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