lib/CXGN/Chado/Db.pm

   1 =head1 NAME
   2
   3 CXGN::Chado::Db - a class to handle Db terms.
   4
   5 implements an object for the Chado 'db' database table:
   6
   7   Column    |          Type          |                       Modifiers
   8   db_id       | integer                | not null default nextval('public.db_db_id_seq'::text)
   9   name        | character varying(255) | not null
  10   description | character varying(255) |
  11   urlprefix   | character varying(255) |
  12   url         | character varying(255) |
  13
  14
  15 =head1 SYNOPSIS
  16
  17 my $db=CXGN::Chado::Db->new($dbh, $db_id);
  18 my $db_name= $db->get_db_name();
  19
  20 #do an update:
  21 $db->set_description("new description for SGN db");
  22 $db->store();
  23
  24
  25 #OR store a new db :
  26 my $db=CXGN::Chado::Db->new($dbh);
  27 $db->set_db_name($db_name);
  28 $db->set_urlprefix($prefix);
  29 $db->set_url($url);
  30 my $db_id=$db->store();
  31
  32
  33 =head1 AUTHOR
  34
  35  Naama Menda <nm249@cornell.edu>
  36  Lukas Mueller <lam87@cornell.edu> (added implementation of Bio::Ontology::TermI)
  37
  38 =cut
  39 use strict;
  40
  41 package CXGN::Chado::Db;
  42
  43 use base qw / CXGN::DB::Object /;
  44
  45
  46 =head2 new
  47
  48  Usage: CXGN::Chado::Db->new($dbh, $id)
  49  Desc:  a new Db object
  50  Ret:   Db object
  51  Args:  a database handle, a database db_id (optional)
  52  Side Effects: none
  53  Example:
  54
  55 =cut
  56
  57 sub new {
  58     my $class = shift;
  59     my $dbh = shift;
  60     my $id = shift;
  61     my $self= $class->SUPER::new($dbh);
  62
  63     if ($id) {
  64         $self->set_db_id($id);
  65         $self->fetch();
  66     }
  67     return $self;
  68 }
  69
  70 =head2 new_with_name
  71
  72  Usage:        my $db = CXGN::Chado::Db->new_with_name($dbh, "GO");
  73  Desc:         an alternate constructor that takes a db name as parameter
  74                db name is case insensitive, but if more than one is found
  75                only one db_id is returned + a warning.
  76  Side Effects: accesses the database.
  77  Example:
  78
  79 =cut
  80
  81 sub new_with_name {
  82     my $class = shift;
  83     my $dbh = shift;
  84     my $name = shift;
  85
  86     my $query = "SELECT db_id FROM db WHERE name ilike ?";
  87     my $sth = $dbh->prepare($query);
  88     $sth->execute($name);
  89     my @ids=();
  90     while (my ($id) = $sth->fetchrow_array()) {
  91         push @ids, $id;
  92     }
  93     if (scalar(@ids) > 1 ) { warn "Db.pm: new with name found more than one db with iname $name! Please check your databse."; }
  94     my $db_id= $ids[0] || undef; #return only the 1st id
  95     my $self = CXGN::Chado::Db->new($dbh, $db_id);
  96     return $self;
  97 }
  98
  99
 100
 101
 102 sub fetch {
 103     my $self = shift;
 104     my $query = "SELECT name, description, urlprefix, url
 105                    FROM db
 106                   WHERE db_id=?";
 107     my $sth = $self->get_dbh()->prepare($query);
 108     $sth->execute($self->get_db_id());
 109     my ($name, $description, $urlprefix, $url) =
 110         $sth->fetchrow_array();
 111
 112     $self->set_db_name($name);
 113     $self->set_description($description);
 114     $self->set_urlprefix($urlprefix);
 115     $self->set_url($url);
 116 }
 117
 118 =head2 store
 119
 120  Usage: $db->store()
 121  Desc:   store a new db in the database (update if db_id exists)
 122  Ret:   a database id (db_id)
 123  Args:  none
 124  Side Effects: accesses the database
 125  Example:
 126
 127 =cut
 128
 129
 130 sub store {
 131     my $self= shift;
 132     my $db_id= $self->get_db_id();
 133     if (!$db_id) {
 134
 135         my $query = "INSERT INTO public.db (name, description, urlprefix,url) VALUES(?,?,?,?)";
 136         my $sth= $self->get_dbh()->prepare($query);
 137         $self->d( "Db.pm: storing * " . $self->get_db_name() . "\n\n");
 138         $sth->execute($self->get_db_name, $self->get_description, $self->get_urlprefix, $self->get_url());
 139         $db_id=  $self->get_dbh()->last_insert_id("db", "public");
 140         $self->set_db_id($db_id);
 141     }else {
 142         my $query = "UPDATE public.db SET description=?, urlprefix=? , url=? WHERE db_id=?";
 143         my $sth= $self->get_dbh()->prepare($query);
 144         $sth->execute($self->get_description(), $self->get_urlprefix(),$self->get_url(), $db_id);
 145     }
 146     return $db_id;
 147 }
 148
 149 =head2 Class properties
 150
 151 The following class properties have accessors (get_db_id, set_db_id...):
 152
 153     db_id
 154     db_name
 155     description
 156     urlprefix
 157     url
 158
 159 =cut
 160
 161
 162 sub get_db_id {
 163   my $self=shift;
 164   return $self->{db_id};
 165 }
 166
 167 sub set_db_id {
 168   my $self=shift;
 169   $self->{db_id}=shift;
 170 }
 171
 172
 173 sub get_db_name {
 174   my $self=shift;
 175   return $self->{db_name};
 176 }
 177
 178
 179 sub set_db_name {
 180   my $self=shift;
 181   $self->{db_name}=shift;
 182 }
 183
 184
 185 sub get_description {
 186   my $self=shift;
 187   return $self->{description};
 188 }
 189
 190 sub set_description {
 191   my $self=shift;
 192   $self->{description}=shift;
 193 }
 194
 195
 196 sub get_urlprefix {
 197   my $self=shift;
 198   return $self->{urlprefix};
 199 }
 200
 201 sub set_urlprefix {
 202   my $self=shift;
 203   $self->{urlprefix}=shift;
 204 }
 205
 206 sub get_url {
 207   my $self=shift;
 208   return $self->{url};
 209 }
 210
 211 sub set_url {
 212   my $self=shift;
 213   $self->{url}=shift;
 214 }
 215
 216
 217
 218 return 1;