EdgeExpressDB

 view release on metacpan or  search on metacpan

lib/EEDB/Chrom.pm  view on Meta::CPAN

=head2 update

  Description  : updates the data of this instance. require the Chrom to have been
                 fetched from database. It must have database() and primary_id()
  Returntype   : $self
  Exceptions   : none

=cut

sub update {
  my $self = shift;
  
  return undef unless($self->database and $self->id);
  
  my $dbh = $self->database->get_connection;  
  my $sql = "UPDATE chrom set chrom_length=?, description=?, chrom_type=? where chrom_id=?";
  my $sth = $dbh->prepare($sql);
  $sth->execute($self->chrom_length, 
                $self->description,
                $self->chrom_type,

lib/EEDB/Experiment.pm  view on Meta::CPAN

  my $mdata_list = $self->metadataset->metadata_list;
  foreach my $mdata (@$mdata_list) {
    if(!defined($mdata->primary_id)) { 
      $mdata->store($self->database);
      $mdata->store_link_to_experiment($self);
    }
  }
}

sub update {
  my $self = shift;

  die("error no database set\n") unless($self->database);
  dies("Experiment with undef id") unless(defined($self->primary_id));
  
  my $dbc = $self->database->get_connection;  
  my $sql = "UPDATE experiment SET display_name=? WHERE experiment_id=?";
  my $sth = $dbc->prepare($sql);
  $sth->execute($self->display_name,
                $self->id);

lib/EEDB/Feature.pm  view on Meta::CPAN

  #first do insert ignore to make sure symbol is in the database
  my $dbc = $self->database->get_connection;  
  my $sql = "INSERT ignore INTO edge ".
            "(feature1_id, feature2_id, direction, sub_type, weight, edge_source_id) VALUES(?,?,?,?,?,0)";
  my $sth = $dbc->prepare($sql);
  $sth->execute($self->id, $feature->id, $dir, $link_type, $weight);
  $sth->finish;
}

sub update_location {
  my $self = shift;

  die("error no database set\n") unless($self->database);
  dies("Feature with undef id") unless(defined($self->primary_id));
  
  my $chrom_id = undef;
  if($self->chrom) { $chrom_id = $self->chrom_id; }

  my $sql = "UPDATE feature SET primary_name=?, chrom_id=?, chrom_start=?, chrom_end=?, strand=? WHERE feature_id=?";
  $self->database->execute_sql($sql,

lib/EEDB/Metadata.pm  view on Meta::CPAN

  $sth->finish;
  if($dbID) {
    $self->primary_id($dbID);
    $self->database($db);
    return $self;
  } else {
    return undef;
  }
}

sub update {
  #use with extreme caution!!!! I should not even include it
  my $self = shift;
  my $sql = "UPDATE metadata set data_type=?, data=? where metadata_id=?";
  $self->database->execute_sql($sql, $self->type, $self->data, $self->id);
}

sub check_exists_db {
  my $self = shift;
  my $db   = shift;
  

lib/EEDB/Tools/MultiLoader.pm  view on Meta::CPAN

                      foreach my $feature (@feature_array) {
                         #
                         # do some metadata additions here
                         #
                         $multiLoad->update_feature_metadata($feature);
                      }
                      $multiLoad->update_feature_metadata(); #to flush the queues
                      
=cut

sub update_feature_metadata {
  my $self = shift;
  my $feature = shift;
    
  if(defined($feature)) {
    if($feature->database->url ne $self->database->url) { return; }
  
    #first queue up the metadata 
    my $mdata_list = $feature->metadataset->metadata_list;
    my $mdata_count = 0;
    foreach my $mdata (@$mdata_list) {

scripts/eedb_sync_entrezgene.pl  view on Meta::CPAN

  exit(1);
}


##################################################################
#
# new XML webservice based mathods
#
##################################################################

sub update_from_webservice {
  my $url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?".
            "db=gene&retmax=100000";
  $url .= sprintf("&term=%d[taxid]%%20AND%%20gene_all[filter]", $assembly->taxon_id);
  printf("URL: %s\n", $url);
  my $tpp = XML::TreePP->new();
  my $tree = $tpp->parsehttp( GET => $url );
  #print $tree, "\n";

  my $search_count = $tree->{'eSearchResult'}->{'Count'};
  printf("search returned %d genes\n", $search_count);