/usr/share/gmod/chado/bin/dbi.tt2 is in chado-utils 1.31-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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########Bio::Chado::CDBI::[% format_node(node.name) %]########
package Bio::Chado::CDBI::[% format_node(node.name) %];
use base '[% baseclass %]';
use Class::DBI::Pager;
no warnings qw(redefine);
Bio::Chado::CDBI::[% format_node(node.name) %]->set_up_table('[% node.table.name %]');
[% printPKAccessors(node.primary_key, node.table.name) %]
[% printHasA(node.edges, node) %]
[% printHasMany(node.edges, node) %]
[% printHasCompound(node.compoundedges, node.hyperedges, node.name) %]
1;
[% END %]
[% MACRO printPKAccessors(array, name) BLOCK %]
#
# Primary key accessors
#
[% FOREACH item = array %]
[% IF item != "id" %]sub id { shift->[% item %] }[% END %]
[% IF item != name %]sub [% name %] { shift->[% item %] }[% END %]
[% END %] [% END %] [% MACRO printHasA(edges, name) BLOCK %]
[% FOREACH edge = edges %]
[% IF loop.first() %]
#
# Has A
#
[% END %] [% IF edge.type == 'import' %]
Bio::Chado::CDBI::[% format_node(node.name) %]->has_a([% edge.thisfield.name %] => 'Bio::Chado::CDBI::[% format_node(edge.thatnode.name) %]');
[% IF node.has(edge.thatnode.name) < 2 %]
sub Bio::Chado::CDBI::[% format_node(node.name) %]::[% edge.thatnode.table.name %] { return shift->[% edge.thisfield.name %] }
[% ELSE %]
sub [% format_fk(edge.thisnode.table.name,edge.thisfield.name) %] { return shift->[% edge.thisfield.name %] }
[% END %] [% END %] [% END %] [% END %]
[%- MACRO printHasMany(edges, node) BLOCK -%]
[%- FOREACH edge = edges -%]
[% IF loop.first() %]
#
# Has Many
#
[% END %] [% IF edge.type == 'export' %]
Bio::Chado::CDBI::[% format_node(node.name) %]->has_many('[% edge.thatnode.table.name %]_[% edge.thatfield.name %]', 'Bio::Chado::CDBI::[% format_node(edge.thatnode.name) %]' => '[% edge.thatfield.name %]');
[% IF node.via(edge.thatnode.name) >= 1 %]
sub [% edge.thatnode.table.name %]_[% format_fk(edge.thatnode.table.name,edge.thatfield.name) %]s { return shift->[% edge.thatnode.table.name %]_[% edge.thatfield.name %] }
#sub [% format_refers(edge.thatnode.table.name,edge.thatfield.name) %] {}
[% ELSIF edge.thatnode.table.is_data %]
[% IF node.edgecount(edge.thatnode.name) > 1 %]
sub [% edge.thatnode.table.name %]_[% format_fk(edge.thatnode.name,edge.thatfield.name) %]_ids { my $self = shift; return $self->[% edge.thatnode.table.name %]_[% edge.thatfield.name %](@_) }
[% ELSE %]
sub [% edge.thatnode.table.name %]s { return shift->[% edge.thatnode.table.name %]_[% edge.thatfield.name %] }
[% END %] [% END %] [%- END -%] [%- END -%] [%- END -%]
[% MACRO printHasCompound(cedges,hedges,name) BLOCK %]
[% FOREACH cedge = cedges %]
[% IF loop.first() %]
#
# Has Compound Many (many to many relationships in all their flavors)
#
[% END %] [% FOREACH edge = cedge.edges %]
[% NEXT IF edge.thisnode.name != name %]
sub [% cedge.via.table.name %]_[% format_fk(edge.thatnode.table.name,edge.thatfield.name) %]s { return shift->[% cedge.via.table.name %]_[% edge.thatfield.name %] }
[% END %] [% END %]
# one to many to one
[% seen = 0 %] [% FOREACH h = hedges %]
[% NEXT UNLESS h.type == 'one2one' %]
[% IF seen == 0 ; seen = 1 %]# one2one #[% END %]
sub [% h.thatnode.table.name %]s { my $self = shift; return map $_->[% h.thatviafield.name %], $self->[% h.vianode.table.name %]_[% h.thisviafield.name %] }
[% END %]
# one to many to many
[% seen = 0 %] [% FOREACH h = hedges %]
[% NEXT UNLESS h.type == 'one2many' %]
[% IF seen == 0 ; seen = 1 %]# one2many #[% END %]
[% thisnode = h.thisnode_index(0) %]
[% i = 0 %]
[% FOREACH thatnode = h.thatnode %]
[% NEXT UNLESS h.thisviafield_index(i).name %]
sub [% h.vianode.table.name %]_[% format_fk(h.vianode,h.thatviafield_index(0).name) %]s { my $self = shift; return map $_->[% h.thatviafield_index(0).name %], $self->[% h.vianode.table.name %]_[% h.thisviafield_index(i).name %] }
[% i = i + 1 %]
[% END %] [% END %]
#many to many to one
[% seen = 0 %] [% FOREACH h = hedges %]
[% NEXT UNLESS h.type == 'many2one' %]
[% IF seen == 0 ; seen = 1 %]# many2one #[% END %]
[% i = 0 %]
[% FOREACH thisnode = h.thisnode %]
sub [% h.vianode.table.name %]_[% format_fk(h.vianode,h.thisviafield_index(i).name) %]_[% format_fk(h.vianode,h.thatviafield_index(0).name) %]s { my $self = shift; return map $_->[% h.thatviafield_index(0).name %], $self->[% h.vianode.table.name %]_[% h.thisviafield_index(i).name %] }
[% i = i + 1 %]
[% END %] [% END %]
#many to many to many
[% seen = 0 %]
[% FOREACH h = hedges %]
[% NEXT UNLESS h.type == 'many2many' %]
[% IF seen == 0 ; seen = 1 %]# many2many #[% END %]
[% i = 0 %]
[% FOREACH thisnode = h.thisnode %]
[% j = 0 %]
[% FOREACH thatnode = h.thatnode %]
sub [% h.vianode.table.name %]_[% format_fk(h.vianode,h.thisviafield_index(i).name) %]_[% format_fk(h.vianode,h.thatviafield_index(j).name) %]s { my $self = shift; return map $_->[% h.vianode.table.name %]_[% format_fk(h.vianode,h.thatviafield_index(j).name) %]s, $self->[% h.vianode.table.name %]_[% format_fk(h.vianode,h.thisviafield_index(i).name) %]s }
[% j = j + 1 %]
[% END %]
[% i = i + 1 %]
[% END %] [% END %] [% END %]
########DBI########
package [% baseclass %];
# Created by SQL::Translator::Producer::TTSchema
# Template used: dbi.tt2
use strict;
use Data::Dumper;
use Bio::GMOD::Config;
use Bio::GMOD::DB::Config;
no warnings 'redefine';
use base qw(Class::DBI::Pg);
# This is how you normally connect with Class DBI's connection pooling but
# its very fragile for me on FC2. I'm replacing it with the db_Main method below
#[% baseclass %]->set_db('Main', '[% db_dsn %]', '[% db_user %]', '[% db_pass %]');
my $db_options = { __PACKAGE__->_default_attributes };
__PACKAGE__->_remember_handle('Main'); # so dbi_commit works
$db_options->{AutoCommit} = 0;
sub db_Main {
my $DBPROFILE ||= 'default'; #might want to allow passing this in somehow
my $gmod_conf = Bio::GMOD::Config->new();
my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE );
my $dbname = $db_conf->name;
my $dbhost = $db_conf->host;
my $dbport = $db_conf->port;
my $dbuser = $db_conf->user;
my $dbpass = $db_conf->password;
my $dbh;
$dbh = DBI->connect_cached(
"dbi:Pg:dbname=$dbname;host=$dbhost;port=$dbport",
$dbuser,
$dbpass,
$db_options );
# clear the connection cache if can't ping
if ($dbh->ping() < 1) {
my $CachedKids_hashref = $dbh->{Driver}->{CachedKids};
%$CachedKids_hashref = () if $CachedKids_hashref;
$dbh = DBI->connect_cached(
"dbi:Pg:dbname=$dbname;host=$dbhost;port=$dbport",
$dbuser,
$dbpass,
$db_options );
warn("Database handle reset!: ".$dbh." ping: ".$dbh->ping());
}
return($dbh);
}
sub search_ilike { shift->_do_search(ILIKE => [% "\@\_" %] ) }
sub search_lower {
my $c = shift;
my %q = @_;
my %t;
foreach my $k (keys %q){
$t{"lower($k)"} = lc($q{$k});
}
$c->_do_search(LIKE => %t);
}
# debug method
sub dump {
my $self = shift;
my %arg = %{shift @_};
$arg{'indent'} ||= 1;
$arg{'depth'} ||= 3;
$Data::Dumper::Maxdepth = $arg{'depth'} if defined $arg{'depth'};
$Data::Dumper::Indent = $arg{'indent'} if defined $arg{'indent'};
return(Dumper($arg{'object'}));
}
#
#
# NOT PART OF THE API, but useful function which returns a single row
# and throws an error if more than one is returned
#
# Added as a utility function for modware
#
sub get_single_row {
my ($proto, @args) = @_;
my $class = ref $proto || $proto;
my @rows = $class->search( @args );
my $count = @rows;
die "only one row expected, @rows returned" if @rows > 1;
return $rows[0];
}
1;
[% graph = schema.as_graph %]
[% FOREACH n = graph.node %][% NEXT UNLESS n.isa('UNIVERSAL') %][% printPackage(n) %][% END %]
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