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revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.33, Sat May 13 04:11:23 2006 UTC
# Line 132  Line 132 
132      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
133      my %subsystems = ();      my %subsystems = ();
134      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
135          # Here we want all the subsystems.          # Here we want all the NMPDR subsystems. First we get the whole list.
136          %subsystems = map { $_ => 1 } $fig->all_subsystems();          my @subs = $fig->all_subsystems();
137            # Loop through, checking for the NMPDR file.
138            for my $sub (@subs) {
139                if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
140                    $subsystems{$sub} = 1;
141                }
142            }
143      } else {      } else {
144          my $type = ref $subsysFile;          my $type = ref $subsysFile;
145          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 250  Line 256 
256              $loadGenome->Add("genomeIn");              $loadGenome->Add("genomeIn");
257              # The access code comes in via the genome hash.              # The access code comes in via the genome hash.
258              my $accessCode = $genomeHash->{$genomeID};              my $accessCode = $genomeHash->{$genomeID};
259              # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
             # the genome ID to the strain. In some cases this is the totality of the strain name.  
260              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
261              my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
262              # Get the full taxonomy.              # Get the full taxonomy.
263              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
264              # Output the genome record.              # Output the genome record.
# Line 436  Line 441 
441      FeatureTranslation      FeatureTranslation
442      FeatureUpstream      FeatureUpstream
443      IsLocatedIn      IsLocatedIn
444        HasFeature
445    
446  =over 4  =over 4
447    
# Line 461  Line 467 
467      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
468      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
469      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
470        my $loadHasFeature = $self->_TableLoader('HasFeature');
471      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
472      # locations.      # locations.
473      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 481  Line 488 
488                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureData};
489                  # Create the feature record.                  # Create the feature record.
490                  $loadFeature->Put($featureID, 1, $type);                  $loadFeature->Put($featureID, 1, $type);
491                    # Link it to the parent genome.
492                    $loadHasFeature->Put($genomeID, $featureID, $type);
493                  # Create the aliases.                  # Create the aliases.
494                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
495                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 697  Line 706 
706          my ($genomeID, $roleID);          my ($genomeID, $roleID);
707          my %roleData = ();          my %roleData = ();
708          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
709              # Get the subsystem object.              # Get the subsystem object.
710              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
711                # Only proceed if the subsystem has a spreadsheet.
712                if (! $sub->{empty_ss}) {
713                    Trace("Creating subsystem $subsysID.") if T(3);
714                    $loadSubsystem->Add("subsystemIn");
715              # Create the subsystem record.              # Create the subsystem record.
716              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
717              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
# Line 801  Line 812 
812                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
813                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
814                  # Connect the subset to its roles.                  # Connect the subset to its roles.
815                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
816                  for my $roleID (@roles) {                  for my $roleID (@roles) {
817                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
818                  }                  }
# Line 854  Line 865 
865              }              }
866          }          }
867      }      }
868        }
869      # Finish the load.      # Finish the load.
870      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
871      return $retVal;      return $retVal;
# Line 1460  Line 1472 
1472              # Here we really need to finish.              # Here we really need to finish.
1473              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1474              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1475              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              if ($self->{options}->{dbLoad}) {
1476                  # Here we want to use the load file just created to load the database.                  # Here we want to use the load file just created to load the database.
1477                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
1478                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
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