this looks like the stack trace from the earlier error. the latest error
you mentioned was related to the table method, not search.
error: Error during compilation of /usr/local/www/meest/html/index.html:
>> Can't locate object method "table" via package "ESTdb::Organism" at
>> /usr/lib/perl5/site_perl/5.8.0/ESTdb/Organism.pm line 3
>>
>>
i would clear out the obj files, which will be a different locations
depending on your setup. try locate mason_data to see where they might
be. i would also restart the web server to make sure you aren't dealing
with page caching issues. if that doesn't work, then you should expand
your script to include all of the method that you are calling in the
mason page, using the exact same syntax. you basically take the code in
your mason page and strip out the apache- and mason-specific bits. if
that doesn't work, then i'm at a loss.
Rojas, Fernando (CIAT) wrote:
> This is the stack-trace:
>
> Trace begun at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Exceptions.pm line
> 131
> HTML::Mason::Exceptions::rethrow_exception('Can\'t locate object method
> "search" via package "ESTdb::Organism" at
> /usr/local/www/meest/html/index.html line 41.^J') called at
> /usr/local/www/meest/html/index.html line 41
> HTML::Mason::Commands::__ANON__ at
> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Component.pm line 136
> HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH(0x924c900)')
> called at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1074
> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1068
> HTML::Mason::Request::comp(undef, undef) called at
> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 760
> HTML::Mason::Request::call_next('HTML::Mason::Request::ApacheHandler=HASH(0x926642c)')
> called at /usr/local/www/meest/html/autohandler line 3
> HTML::Mason::Commands::__ANON__ at
> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Component.pm line 136
> HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH(0x8b3a9d0)')
> called at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1069
> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1068
> HTML::Mason::Request::comp(undef, undef, undef) called at
> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 338
> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 338
> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 297
> HTML::Mason::Request::exec('HTML::Mason::Request::ApacheHandler=HASH(0x926642c)')
> called at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line 128
> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line
> 128
> HTML::Mason::Request::ApacheHandler::exec('HTML::Mason::Request::ApacheHandler=HASH(0x926642c)')
> called at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line 825
> HTML::Mason::ApacheHandler::handle_request('HTML::Mason::ApacheHandler=HASH(0x82ad010)',
> 'Apache=SCALAR(0x9219438)') called at /usr/local/apache/conf/handler.pl line
> 32
> MyMason::MyApp::handler('Apache=SCALAR(0x9219438)') called at /dev/null line 0
> eval {...} at /dev/null line 0
>
> Thanks
>
> -----Original Message-----
> From: Sherrard Burton [mailto:[EMAIL PROTECTED]
> Sent: Monday, August 06, 2007 9:41 AM
> To: Rojas, Fernando (CIAT)
> Cc: Mason-Users
> Subject: Re: [Mason] Can't locate object method "search" via package
>
> but you don't seem to be calling all of the same methods from the script that
> you are trying to use from the web interface.
>
> from the stack trace you should be able to see which line in your mason
> component called the method that eventually led to this error.
>
> ps--you should use reply-all so that these discussions stay on-list where
> everybody can benefit.
>
> Rojas, Fernando (CIAT) wrote:
>> TY for your help; I have this script that was attached to the end of my
>> e-mail and it runs ok:
>>
>> #!/usr/bin/perl
>>>> use strict;
>>>> use ESTdb::Organism;
>>>> use ESTdb::Library;
>>>> my $species = 'Manihot esculenta';
>>>> my $orgn = 99;
>>>> print "$orgn >>>\n";
>>>> print "$species :";
>>>> my $orgn = (ESTdb::Organism->search(name => $species))[0]; print
>>>> "$orgn :\n"; my $library = 0; my $name = 'aflp'; print "$name "; my
>>>> $library = (ESTdb::Library->search(name => $name))[0]; print
>>>> "$library \n";
>> In this case im querying 2 tables of database organism and library and runs
>> ok:
>>
>> Ty for your help again.
>>
>> -----Original Message-----
>> From: Sherrard Burton [mailto:[EMAIL PROTECTED]
>> Sent: Monday, August 06, 2007 9:32 AM
>> To: Rojas, Fernando (CIAT)
>> Subject: Re: [Mason] Can't locate object method "search" via package
>>
>> it sounds like you are having perl problems. are you sure the same code
>> works from a command-line script?
>>
>> that message usually means that you haven't "use"ed the package that exports
>> that method, or that that method doesn't exist in the package.
>>
>> maybe you should prototype the code in a perl script or module called from
>> the command line first so that you can distinguish the simple perl errors
>> from any that are mason-specific.
>>
>> good luck
>>
>>
>> Rojas, Fernando (CIAT) wrote:
>>> TY for your answer; I tried it; now im getting:
>>>
>>> error: Error during compilation of /usr/local/www/meest/html/index.html:
>>> Can't locate object method "table" via package "ESTdb::Organism" at
>>> /usr/lib/perl5/site_perl/5.8.0/ESTdb/Organism.pm line 3
>>>
>>> TY.
>>>
>>> -----Original Message-----
>>> From: Sherrard Burton [mailto:[EMAIL PROTECTED]
>>> Sent: Monday, August 06, 2007 7:23 AM
>>> To: Rojas, Fernando (CIAT)
>>> Cc: mason-users@lists.sourceforge.net
>>> Subject: Re: [Mason] Can't locate object method "search" via package
>>>
>>> i'm not sure, but i'm guessing you should be using
>>>
>>> use ESTdb::Organism;
>>> use ESTdb::Library;
>>>
>>> in your mason code instead of
>>>
>>> use base 'ESTdb::Organism';
>>> use base 'ESTdb::Library';
>>>
>>>
>>>
>>> Rojas, Fernando (CIAT) wrote:
>>>> ______________________________________________
>>>> *From: * Rojas, Fernando (CIAT)
>>>> *Sent: * Friday, August 03, 2007 5:47 PM
>>>> *To: * 'mason-users@lists.sourceforge.net'
>>>> *Subject: *
>>>>
>>>> HI: I have a web-site running in this environment:
>>>>
>>>> Linux (Red Hat 8.0 3-2-7); Apache 1.3.24 Mod-Perl 1.29 Perl 5.8.5;
>>>> Html-Mason-1.27; MySql 4.1.20; Al CPAN Modules installed
>>>>
>>>> Im getting this error running my web aplication:
>>>>
>>>> *error:* Can't locate object method "search" via package
>>>> "ESTdb::Organism" at /usr/local/www/meest/html/index.html line 41.
>>>> *context:*
>>>> *...*
>>>> *37:* use base 'ESTdb::Library';
>>>> *38:* my $root = $m->comp('/root');
>>>> *39:* my $species = $m->comp('/species');
>>>> *40:* print "$species \n";
>>>> *41:* my $orgn = (ESTdb::Organism->search(name => $species))[0];
>>>> *42:* </%init>
>>>> *43:*
>>>> *code stack:* /usr/local/www/meest/html/index.html:41
>>>> /usr/local/www/meest/html/autohandler:3
>>>>
>>>> *The index.html is:*
>>>> <h1><% $orgn->name() %> ESTs</h1>
>>>> <p/>
>>>> <table>
>>>> <tbody>
>>>> <tr> <th>ESTs </th>
>>>> <td> <%
>>>> ESTdb::Library->sql_nests_by_species($orgn)->select_val
>>>> %> <% 1 ? '' : ESTdb::Est->rel_count({clone => {library =>
>>>> {organism => {organism=> $orgn}}}})%> </td></tr>
>>>> <tr> <th>non redondant contigs </th>
>>>> <td> <% ESTdb::Library->sql_ncontig_by_species(1, 999999,
>>>> $orgn)->select_val %> <td></tr>
>>>> <tr> <th>Contigs : </th>
>>>> <td><% ESTdb::Library->sql_ncontig_by_species(2, 99999,
>>>> $orgn)->select_val%></td></tr>
>>>> <tr> <th>Singletons : </th>
>>>> <td><% ESTdb::Library->sql_ncontig_by_species(1, 1,
>>>> $orgn)->select_val%></td></tr> </tbody> </table> <hr/>
>>>> <h2>Search</h2> <ul> <li>search <a
>>>> href="<%$root%>/byfactor/factor.html">by
>>>> factor</a></li> <li>search <a href="<%$root%>/bylib/library.html">by
>>>> lib</a></li> <li>search <a href="<%$root%>/byest/est.html">by
>>>> est</a></li> <li>search <a href="<%$root%>/bycn/cn.html">by
>>>> contig</a></li> </ul> <hr/> <h2>Blast</h2> <a
>>>> href="<%$root%>/blast/blast">blast</a>
>>>> <!--
>>>> <ul>
>>>> <li>blast on <a href="blast/ests/">ESTs</a></li> <li>blast on <a
>>>> href="blast/contigs/">Contigs</li>
>>>> </ul>
>>>> -->
>>>> <%init>
>>>> use strict;
>>>> use base 'ESTdb::Organism';
>>>> use base 'ESTdb::Library';
>>>> my $root = $m->comp('/root');
>>>> my $species = $m->comp('/species');
>>>> print "$species \n";
>>>> my $orgn = (ESTdb::Organism->search(name => $species))[0]; </%init>
>>>>
>>>> *Organism.pm code is:*
>>>> package ESTdb::Organism;
>>>> use base 'ESTdb::DBI';
>>>> __PACKAGE__->table('organism');
>>>> __PACKAGE__->columns(All => qw/ organism name/);
>>>> __PACKAGE__->has_many(libs => 'ESTdb::Library');
>>>>
>>>> *DBI.pm is:*
>>>> package ESTdb::DBI;
>>>> use strict;
>>>> use base 'Class::DBI';
>>>> use Data::Dumper;
>>>> my $dsn = 'DBI:mysql:dbname=est;host=localhost;port=3306';
>>>> my $user = 'root';
>>>> my $password = 'ciatroot';
>>>> __PACKAGE__->connection($dsn, $user, $password);
>>>> #Class::DBI->connection($dsn, $user, $password);
>>>> #__PACKAGE__->set_db('Main', $dsn, $user, $password); ..
>>>>
>>>> *Someone could give me some ideas. What's happening.??* *I have
>>>> this Perl Script and when I run as root or as another user it runs
>>>> ok connecting to the database and retrieving information.*
>>>>
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use ESTdb::Organism;
>>>> use ESTdb::Library;
>>>> my $species = 'Manihot esculenta';
>>>> my $orgn = 99;
>>>> print "$orgn >>>\n";
>>>> print "$species :";
>>>> my $orgn = (ESTdb::Organism->search(name => $species))[0]; print
>>>> "$orgn :\n"; my $library = 0; my $name = 'aflp'; print "$name "; my
>>>> $library = (ESTdb::Library->search(name => $name))[0]; print
>>>> "$library \n";
>>>>
>>>>
>>>> Sorry for the long mail;; I hope some help THANKS.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> FERNANDO ROJAS
>>>> Ingeniero de Sistemas y Computación
>>>> Unidad de Sistemas de Información
>>>> Centro Internacional de Agricultura Tropical (CIAT)
>>>> E-mail: [EMAIL PROTECTED]
>>>> Phone:(57-2)445-01-00 Ext 3647
>>>>
>>>>
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>>>>
>>>> _______________________________________________
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>>>> Mason-users@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/mason-users
>
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