lib/CXGN/Cview/MapFactory/ChlamyBase.pm

   1
   2 use strict;
   3
   4 package CXGN::Cview::MapFactory::ChlamyBase;
   5
   6 use base qw | CXGN::DB::Object | ;
   7
   8 use CXGN::Cview::Map::SGN::Genetic;
   9
  10 sub new {
  11     my $class = shift;
  12     my $dbh = shift;
  13     my $self = $class->SUPER::new($dbh);
  14
  15     return $self;
  16 }
  17
  18
  19 sub create {
  20     my $self = shift;
  21     my $hashref = shift;
  22
  23     #print STDERR "Hashref = map_id => $hashref->{map_id}, map_version_id => $hashref->{map_version_id}\n";
  24
  25     if (!exists($hashref->{map_id}) && !exists($hashref->{map_version_id})) {
  26         die "[CXGN::Cview::MapFactory] Need either a map_id or map_version_id.\n";
  27     }
  28     if ($hashref->{map_id} && $hashref->{map_version_id}) {
  29         die "[CXGN::Cview::MapFactory] Need either a map_id or map_version_id - not both.\n";
  30     }
  31     if ($hashref->{map_id}) {
  32         $hashref->{map_version_id}=CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), $hashref->{map_id});
  33     }
  34
  35     # now, we only deal with map_versions...
  36     #
  37     my $id = $hashref->{map_version_id};
  38
  39     #print STDERR "MapFactory: dealing with id = $id\n";
  40
  41     # if the map_version_id is purely numeric,
  42     # check if the map is in the maps table and generate the
  43     # appropriate map
  44
  45     if ($id=~/^\d+$/) {
  46         my $query = "SELECT map_version_id, map_type, map_id, short_name FROM sgn.map join sgn.map_version using(map_id) WHERE map_version_id=?";
  47         my $sth = $self->get_dbh()->prepare($query);
  48         $sth->execute($id);
  49         my ($id, $map_type) = $sth->fetchrow_array();
  50         if ($map_type =~ /genetic/i) {
  51             return CXGN::Cview::Map::SGN::Genetic->new($self->get_dbh(), $id);
  52         }
  53     }
  54     print STDERR "Map NOT FOUND!!!!!!!!!!!!!!!!!!\n\n";
  55     return undef;
  56
  57 }
  58
  59 =head2 function get_all_maps()
  60
  61   Synopsis:
  62   Arguments:    none
  63   Returns:      a list of all maps currently defined, as
  64                 CXGN::Cview::Map objects (and subclasses)
  65   Side effects: Queries the database for certain maps
  66   Description:
  67
  68 =cut
  69
  70 sub get_all_maps {
  71     my $self = shift;
  72
  73     my @system_maps = $self->get_system_maps();
  74     my @user_maps = $self->get_user_maps();
  75     my @maps = (@system_maps, @user_maps);
  76     return @maps;
  77
  78 }
  79
  80
  81 =head2 get_system_maps
  82
  83   Usage:        my @system_maps = $map_factory->get_system_maps();
  84   Desc:         retrieves a list of system maps (from the sgn
  85                 database) as a list of CXGN::Cview::Map objects
  86   Ret:
  87   Args:
  88   Side Effects:
  89   Example:
  90
  91 =cut
  92
  93 sub get_system_maps {
  94     my $self = shift;
  95
  96     my @maps = ();
  97
  98     my $query = "SELECT map.map_id FROM sgn.map LEFT JOIN sgn.map_version USING(map_id) LEFT JOIN sgn.accession on(parent_1=accession.accession_id) LEFT JOIN sgn.organism USING(organism_id) LEFT JOIN common_name USING(common_name_id) WHERE current_version='t' ORDER by common_name.common_name";
  99     my $sth = $self->get_dbh()->prepare($query);
 100     $sth->execute();
 101
 102     while (my ($map_id) = $sth->fetchrow_array()) {
 103         my $map = $self->create({ map_id => $map_id });
 104         if ($map) { push @maps, $map; }
 105     }
 106
 107     # push il, physical, contig, and agp map
 108     #
 109     foreach my $id ("il6.5", "il6.9", "p9", "c9", "agp") {
 110         my $map = $self->create( {map_id=>$id} );
 111         if ($map) { push @maps, $map; }
 112     }
 113
 114     return @maps;
 115 }
 116
 117
 118
 119 =head2 get_user_maps
 120
 121  Usage:
 122  Desc:         retrieves the current user maps of the logged in user.
 123  Ret:          a list of CXGN::Cview::Map objects
 124  Args:         none
 125  Side Effects: none
 126  Example:
 127
 128 =cut
 129
 130 sub get_user_maps {
 131     my $self = shift;
 132     # push the maps that are specific to that user and not public, if somebody is logged in...
 133     #
 134     my @maps = ();
 135     my $login = CXGN::Login->new($self->get_dbh());
 136     my $user_id = $login->has_session();
 137     if ($user_id) {
 138         my $q3 = "SELECT user_map_id FROM sgn_people.user_map WHERE obsolete='f' AND sp_person_id=?";
 139         my $h3 = $self->get_dbh()->prepare($q3);
 140         $h3->execute($user_id);
 141         while (my ($user_map_id) = $h3->fetchrow_array()) {
 142             my $map = $self->create( {map_id=>"u".$user_map_id} );
 143
 144             if ($map) { push @maps, $map; }
 145         }
 146     }
 147     return @maps;
 148 }
 149
 150
 151
 152 return 1;
 153