Bio-EnsEMBL

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lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm  view on Meta::CPAN

  if(!$seq_region_id) {
    throw('Feature is associated with seq_region which is not in this DB.');
  }

  return ($feature, $seq_region_id);
}


# The same function as _pre_store
# This one is used to store user uploaded features in XXX_userdata db

sub _pre_store_userdata {
  my $self    = shift;
  my $feature = shift;

  if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
    throw('Expected Feature argument.');
  }

  my $slice = $feature->slice();

lib/Bio/EnsEMBL/IdMapping/Archiver.pm  view on Meta::CPAN

  # dump existing archive tables to file
  my $num_entries =
    $archiver->dump_table_to_file( 'source', 'gene_archive',
    'gene_archive_existing.txt', 1 );

=head1 DESCRIPTION

This module creates the gene_archive and peptide_archive
tables. Data is written to a file as tab-delimited text for
loading into a MySQL database (this can be done manually, or using
StableIdmapper->upload_file_into_table()).

An archive entry for a given source gene is created if no target
gene exists, or if any of its transcripts or their translations
changed. Non-coding transcripts only have an entry in gene_archive (i.e.
without a corresponding peptide_archive entry).

=head1 METHODS

  create_archive
  dump_gene

lib/Bio/EnsEMBL/IdMapping/BaseObject.pm  view on Meta::CPAN

This isn't very clean OO design but it's efficient and easy to use...

=head1 METHODS

  new
  get_filehandle
  file_exists
  fetch_value_from_db
  dump_table_to_file
  upload_file_into_table
  logger
  conf
  cache

=cut


package Bio::EnsEMBL::IdMapping::BaseObject;
$Bio::EnsEMBL::IdMapping::BaseObject::VERSION = '114.0.0';
use strict;

lib/Bio/EnsEMBL/IdMapping/BaseObject.pm  view on Meta::CPAN

    print $fh join("\t", @row);
    print $fh "\n";
  }

  $sth->finish;
  
  return $i;
}


=head2 upload_file_into_table

  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to upload the data to
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $no_check_empty - don't check if table is empty
  Example     : my $rows_uploaded = $object->upload_file_into_table('target',
                  'stable_id_event', 'stable_id_event_new.txt');
  Description : Uploads a tab-delimited data file into a db table. The data file
                will be taken from a subdirectory 'tables' under your configured
                basedir. If the db table isn't empty and $no_check_empty isn't
                set, no data is uploaded (and a warning is issued).
  Return type : Int - the number of rows uploaded
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub upload_file_into_table {
  my $self           = shift;
  my $dbtype         = shift;
  my $table          = shift;
  my $filename       = shift;
  my $no_check_empty = shift;

  # argument check
  unless ( ( $dbtype eq 'source' ) or ( $dbtype eq 'target' ) ) {
    throw("Missing or unknown db type: $dbtype.");
  }
  throw("Need a table name.") unless ($table);
  throw("Need a filename.")   unless ($filename);

  # sanity check for dry run
  if ( $self->conf->param('dry_run') ) {
    $self->logger->warning(
                       "dry_run - skipping db upload for $filename.\n");
    return;
  }

  my $file =
    join( '/', $self->conf->param('basedir'), 'tables', $filename );
  my $r = 0;

  if ( -s $file ) {

    $self->logger->debug( "$file -> $table\n", 1 );

lib/Bio/EnsEMBL/IdMapping/BaseObject.pm  view on Meta::CPAN

        if ($idtable) {
          $self->logger->warning(
                               "Table $table contains $c stable IDs.\n",
                               1 );
        }
        else {
          $self->logger->warning(
                          "Table $table not empty: found $c entries.\n",
                          1 );
        }
        $self->logger->info( "Data not uploaded!\n", 1 );
        return $r;
      }
    } ## end unless ($no_check_empty)

    # now upload the data
    if ($idtable) {
      # Create a temporary table, upload the data into it, and then
      # update the main table.
      $dbh->do(
        qq( CREATE TABLE stable_id_$$ (  object_id INTEGER UNSIGNED,
                                             stable_id VARCHAR(255),
                                             version SMALLINT UNSIGNED,
                                             created_date DATETIME,
                                             modified_date DATETIME,
                                             PRIMARY KEY(object_id) ) )
      );

lib/Bio/EnsEMBL/IdMapping/BaseObject.pm  view on Meta::CPAN

      $dbh->do(qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE $table));
    }
    $dbh->do(qq(OPTIMIZE TABLE $table));

  } ## end if ( -s $file )
  else {
    $self->logger->warning( "No data found in file $filename.\n", 1 );
  }

  return $r;
} ## end sub upload_file_into_table


=head2 logger

  Arg[1]      : (optional) Bio::EnsEMBL::Utils::Logger - the logger to set
  Example     : $object->logger->info("Starting ID mapping.\n");
  Description : Getter/setter for logger object
  Return type : Bio::EnsEMBL::Utils::Logger
  Exceptions  : none
  Caller      : constructor

lib/Bio/EnsEMBL/IdMapping/Cache.pm  view on Meta::CPAN

sub check_db_write_permissions {
  my $self = shift;
  my $dbtype = shift;
  
  # skip this check if db connection failed (this prevents re-throwing
  # exceptions).
  return 1 unless ($self->{'_db_conn_ok'}->{$dbtype});
  
  my $err = 0;

  unless ($self->do_upload) {
    $self->logger->debug("No uploads, so write permission on $dbtype db not required.\n");
    return $err;
  }

  my %privs = %{ $self->get_db_privs($dbtype) };

  unless ($privs{'INSERT'} or $privs{'ALL PRIVILEGES'}) {
    $self->logger->warning("User doesn't have write permission on $dbtype db.\n");
    $err++;
  } else {
    $self->logger->debug("Write permission on $dbtype db ok.\n");
  }

  return $err;
}


sub do_upload {
  my $self = shift;

  if ($self->conf->param('dry_run') or
    ! ($self->conf->param('upload_events') or
       $self->conf->param('upload_stable_ids') or
       $self->conf->param('upload_archive'))) {
    return 0;
  } else {
    return 1;
  }
}   


sub get_db_privs {
  my ( $self, $dbtype ) = @_;

lib/Bio/EnsEMBL/IdMapping/Cache.pm  view on Meta::CPAN

  my $self = shift;
  my $dbtype = shift;
  
  # skip this check if db connection failed (this prevents re-throwing
  # exceptions).
  return 1 unless ($self->{'_db_conn_ok'}->{$dbtype});
  
  my $err = 0;
  my $c = 0;

  if ($self->conf->param('no_check_empty_tables') or !$self->do_upload) {
    $self->logger->debug("Won't check for empty stable ID and archive tables in $dbtype db.\n");
    return $err;
  }

  eval {
    my @tables =
      qw(
      gene_stable_id
      transcript_stable_id
      translation_stable_id

lib/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm  view on Meta::CPAN

    
    if ($self->file_exists($filename, 'stats')) {
      print $fh $self->read_from_file($filename, 'stats');
      print $fh "\n\n";
    } else {
      print $fh "No mapping stats found for $type.\n\n";
    }
  }

  #
  # db uploads
  #
  my @uploads = (
    ['stable_ids'  => 'Stable IDs'],
    ['events'      => 'Stable ID events and mapping session'],
    ['archive'     => 'Gene and peptide archive'],
  );
  
  my $fmt1 = "%-40s%-20s\n";

  print $fh qq(Data uploaded to db:\n);
  print $fh qq(====================\n\n);

  if ($self->conf->param('dry_run')) {
   
    print $fh "None (dry run).\n";
  
  } else {
  
    foreach my $u (@uploads) {
      my $uploaded = 'no';
      $uploaded = 'yes' if ($self->conf->is_true("upload_".$u->[0]));
      print $fh sprintf($fmt1, $u->[1], $uploaded);
    }
    
  }

  print $fh "\n";

  #
  # stats and clicklist
  #
  my @output = (
    ['stats'    => 'statistics (including clicklists of deleted IDs)'],
    ['debug'    => 'detailed mapping output for debugging'],
    ['tables'   => 'data files for db upload'],
  );
  
  my $fmt2 = "%-20s%-50s\n";

  print $fh qq(\nOutput directories:\n);
  print $fh qq(===================\n\n);

  print $fh sprintf($fmt2, qw(DIRECTORY DESCRIPTION));
  print $fh ('-'x72), "\n";

lib/Bio/EnsEMBL/Registry.pm  view on Meta::CPAN

            $species, $species_id, $multidb );
        }
      }
    } ## end foreach my $multidb (@multi_dbs)
  }

  if(!$core_like_dbs_found && $verbose) {
    print("No core-like databases found. Check your DB_VERSION (used '$software_version')\n");
  }  

  # User upload DBs

  my @userupload_dbs = grep { /_userdata$/ } @dbnames;
  if (!$ignore_multi) {
    for my $userupload_db (@userupload_dbs) {
      if ( index( $userupload_db, 'collection' ) != -1 ) {
        # Skip multi-species databases.
        next;
      }
  
      my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ );
      my $dba =
        Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                           -group        => "userupload",
                                           -species      => $species.$species_suffix,
                                           -host         => $host,
                                           -user         => $user,
                                           -pass         => $pass,
                                           -port         => $port,
                                           -wait_timeout => $wait_timeout,
                                           -dbname   => $userupload_db,
                                           -no_cache => $no_cache );
  
      if ($verbose) {
        printf( "%s loaded\n", $userupload_db );
      }
    }
  }

  # Register multi-species userupload databases.
  my @userdata_multidbs = grep { /^.+_collection_userdata$/ } @dbnames;

  if (!$ignore_multi) {
    foreach my $multidb (@userdata_multidbs) {
      my $sth = $dbh->prepare(
        sprintf(
          "SELECT species_id, meta_value FROM %s.meta "
            . "WHERE meta_key = 'species.db_name'",
          $dbh->quote_identifier($multidb) ) );
  
      $sth->execute();
  
      my ( $species_id, $species );
      $sth->bind_columns( \( $species_id, $species ) );
  
      while ( $sth->fetch() ) {
        my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
          -group           => "userupload",
          -species         => $species.$species_suffix,
          -species_id      => $species_id,
          -multispecies_db => 1,
          -host            => $host,
          -user            => $user,
          -pass            => $pass,
          -port            => $port,
          -dbname          => $multidb,
          -wait_timeout    => $wait_timeout,
          -no_cache        => $no_cache

lib/Bio/EnsEMBL/Utils/ConfParser.pm  view on Meta::CPAN

    return $self->{'_param'}->{$name};
  } else {
    return undef;
  }
}


=head2 is_true

  Arg[1]      : Parameter name
  Example     : unless ($conf->is_true('upload')) {
                  print "Won't upload data.\n";
                  next;
                }
  Description : Checks whether a param value is set to 'true', which is defined
                here as TRUE (in the Perl sense) but not the string 'no'.
  Return type : Boolean
  Exceptions  : thrown if no parameter name is supplied
  Caller      : general
  Status      : At Risk
              : under development