Print-wiki-tables

The process described on this page is obsolete. The process described on Chado Schema Documentation HOWTO is the the current one. This page should be deleted once the new process has been fully adopted.

<perl>

1. !/usr/bin/perl -w

=head1 NAME

print-wiki-tables.pl

=head1 SYNOPSIS

Examples:

 >print-wiki-tables.pl -m cv > cv.wiki

or

 >print-wiki-tables.pl -all > allmodules.wiki

=head1 DESCRIPTION

The postgresql_autodoc script will create an HTML schema diagram. For example:

>postgresql_autodoc -f chado -u user -d chado --password=passwd -l .

This creates a "chado.html" file when the argument to "-f" is set to "chado" as in the example above. The HTML can be customized by modifying the html.tmpl file from the postgresql_autodoc package. Use the "-l" argument if you need to tell postgresql_autodoc where your custom html.tmpl file is.

The script prints out Wiki text for the tables in these modules, taken from chado.html. Run this script in the same directory as "chado.html" and pass the script the name of one or more Chado modules.

=cut

my $tables = { companalysis => [qw( analysis analysisfeature analysisprop)], contact => [qw( contact contact_relationship)], cv => [qw( cv cvprop cvterm cvterm_dbxref cvterm_relationship cvtermpath cvtermprop cvtermsynonym dbxrefprop)], expression => [qw( eimage expression expression_cvterm expression_image expression_pub feature_expression)], general => [qw( db dbxref project tableinfo)], genetic => [qw( environment environment_cvterm feature_genotype genotype phendesc phenotype_comparison phenstatement)], library => [qw( library library_cvterm library_feature library_pub library_synonym libraryprop)], map => [qw( featuremap featuremap_pub featurepos featurerange)], organism => [qw( organism organism_dbxref organismprop)], phenotype => [qw( feature_phenotype phenotype phenotypeprop phenotype_cvterm)], phylogeny => [qw( phylonode phylonode_dbxref phylonode_organism phylonode_pub phylonode_relationship phylonodeprop phylotree phylotree_pub)],

</pub => [qw( pub pub_dbxref pub_relationship pubauthor pubprop)], mage => [qw( acquisition acquisition_relationship acquisitionprop arraydesign arraydesignprop assay assay_biomaterial assay_project assayprop biomaterial biomaterial_dbxref biomaterial_relationship biomaterial_treatment biomaterialprop channel control element element_relationship elementresult elementresult_relationship magedocumentation mageml protocol protocolparam quantification quantification_relationship quantificationprop study study_assay studydesign studydesignprop studyfactor studyfactorvalue treatment)], sequence => [qw( feature feature_cvterm feature_cvterm_dbxref feature_cvterm_pub feature_cvtermprop feature_dbxref feature_pub feature_pubprop feature_relationship feature_relationship_pub feature_relationshipprop feature_relationshipprop_pub feature_synonym featureloc featureloc_pub featureprop featureprop_pub synonym)], stock => [qw( stock stock_cvterm stock_dbxref stock_genotype stock_pub stock_relationship stock_relationship_pub stockcollection stockcollection_stock stockcollectionprop stockprop stockprop_pub)], www => [qw( wwwuser wwwuser_author wwwuser_cvterm wwwuser_expression wwwuser_feature wwwuser_genotype wwwuser_interaction wwwuser_organism wwwuser_phenotype wwwuser_project wwwuser_pub wwwuserrelationship)], natural_diversity => [qw( nd_geolocation nd_experiment nd_experiment_project nd_experimentprop nd_experiment_pub nd_geolocationprop nd_protocol nd_reagent nd_protocol_reagent nd_protocolprop nd_experiment_stock nd_experiment_protocol nd_experiment_phenotype nd_experiment_genotype nd_reagent_relationship nd_reagentprop nd_experiment_stockprop nd_experiment_stock_dbxref nd_experiment_dbxref nd_experiment_contact )], };

my ($help,@modules,$all);

GetOptions( "m=s" => \@modules,

           "h"   => \$help,
                          "all" => \$all );

@modules = split(/,/,join(',',@modules)); @modules = keys %$tables if ($all);

usage() if ($help || !@modules);

my $file = "chado.html";

my $wc = HTML::WikiConverter->new(dialect => 'MediaWiki');

my $html = extract($file);

my $wikitext = $wc->html2wiki($html);

my @tables = split /^(?===\s*Table:.+)/m, $wikitext;

for my $module (@modules) {

       print "No such module: $module\n" if (!exists $tables->{$module});
       for my $table (@tables) {
               for my $tablename ( @{$tables->{$module}} ) {
                       print "$table\n\n" if ($table =~ /\+\s+public.$tablename\s+Structure/);
               }
       }

}

sub extract {

       my $file = shift;
       local $/ = undef;
       open MYIN, $file;
       my $str = <MYIN>;
       $str;

}

sub usage {

       exec('perldoc',$0);
       exit(0);

}

__END__

</perl>