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Revision 1.7 - (download) (annotate)
Tue Apr 29 08:18:58 2008 UTC (11 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.6: +1 -1 lines
Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.

#!/usr/bin/perl -w
#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
#
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#


BEGIN {
    # Print the HTML header.
    print "CONTENT-TYPE: text/html\n\n";
}

=head1 Similarity Block Form Generator

This script generates the form used to request similarity comparisons
between genome sets. The form allows the user to select which of the
available genomes should be put in each set. When the form is
submitted, the processing script will invoke the B<Compare> method
of the B<SimBlocks> object to generate a comparison summary.

For debugging purposes, you can specify the B<Trace> parameter to
set the tracing level. So, for example,

    http://myseedurl/CGI/SimBlockForm.cgi?Trace=3

runs the standard processing script at a trace level of 3. Normally, only the
script itself and B<Tracer> tracing is active; however, you can activate other tracing modules
by appending them to the trace level. Thus,

    http://myseedurl/CGI/SimBlockForm.cgi?Trace=3%20SimBlocks%20ERDBObject

activates tracing for the similarity block module (C<SimBlocks.pm>) and the data
base object (C<ERDBObject.pm>).

=cut

use strict;
use CGI;
use Tracer;
use PageBuilder;
use SimBlocks;

my ($query, $varHash) = Tracer::ScriptSetup();
eval {
    # Create the similarity block object.
    my $simBlocks = SimBlocks->new();
    # Begin building the main part of the output page.
    my $webData = "";
    # We intend to loop through the genomes, generating a table row for each.
    # The table row is built from a template string in the
    # SimBlockGenomeFragment.html file.
    my $rowTemplate = Tracer::GetFile("Html/SimBlockGenomeFragment.html");
    # Create a hash to use for the template variables in the genome row.
    my %varHash = ( GenomeID => "error", GenomeDescription => "error");
    # Now we get the genome list from the database.
    my @genomes = $simBlocks->GetList(['Genome'], "ORDER BY Genome(group-name), Genome(id)");
    # Loop through the genomes, generating table rows.
    for my $genome (@genomes) {
        # Copy the genome fields into the variable hash.
        ($varHash{GenomeID}, $varHash{GenomeDescription}) =
            $genome->Values(['Genome(id)', 'Genome(description)']);
        # Substitute the variables and write them out.
        my $row = PageBuilder::Build($rowTemplate, \%varHash);
        $webData .= $row;
    }
    # Store the page data.
    $varHash->{Data} = $webData;
};
# Trace any error that occurred.
if ($@) {
    Trace($@) if T(0);
}
# Write out the web page.
Tracer::ScriptFinish("Html/SimBlockForm.html", $varHash);

1;

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