chado-utils 1.31-3 / usr / share / gmod / chado / bin / dbi.tt2

[% MACRO printPackage(node) BLOCK %]
########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 %]