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revision 1.41, Thu Jun 8 19:43:34 2006 UTC revision 1.48, Fri Jul 7 00:24:16 2006 UTC
# Line 375  Line 375 
375                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
376                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
377                      # Compute the coupling ID.                      # Compute the coupling ID.
378                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
379                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
380                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
381                          # Here we have a new coupling to store in the load files.                          # Here we have a new coupling to store in the load files.
# Line 634  Line 634 
634  The following relations are loaded by this method.  The following relations are loaded by this method.
635    
636      Subsystem      Subsystem
637        SubsystemClass
638      Role      Role
639      RoleEC      RoleEC
640      SSCell      SSCell
# Line 696  Line 697 
697      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
698      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
699      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
700        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
701      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
702          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
703      } else {      } else {
# Line 721  Line 723 
723                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
724                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
725                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
726                    my $class = $fig->subsystem_classification($subsysID);
727                    if ($class) {
728                        $loadSubsystemClass->Put($subsysID, $class);
729                    }
730                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
731                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
732                      # Connect to this role.                      # Connect to this role.
# Line 1042  Line 1048 
1048                  # Get the annotation tuple.                  # Get the annotation tuple.
1049                  my ($peg, $timestamp, $user, $text) = @{$tuple};                  my ($peg, $timestamp, $user, $text) = @{$tuple};
1050                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1051                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1052                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1053                  # stop the substitution search.                  # stop the substitution search.
1054                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1396  Line 1402 
1402      return $retVal;      return $retVal;
1403  }  }
1404    
1405    =head3 LoadSynonymData
1406    
1407    C<< my $stats = $spl->LoadSynonymData(); >>
1408    
1409    Load the synonym groups into Sprout.
1410    
1411    The following relations are loaded by this method.
1412    
1413        SynonymGroup
1414        IsSynonymGroupFor
1415    
1416    The source information for these relations is taken from the C<maps_to_id> method
1417    of the B<FIG> object. The process starts from the features, so it is possible
1418    that there will be duplicates in the SynonymGroup load file, since the relationship
1419    is one-to-many toward the features. The automatic sort on primary entity relations
1420    will fix this for us.
1421    
1422    =over 4
1423    
1424    =item RETURNS
1425    
1426    Returns a statistics object for the loads.
1427    
1428    =back
1429    
1430    =cut
1431    #: Return Type $%;
1432    sub LoadSynonymData {
1433        # Get this object instance.
1434        my ($self) = @_;
1435        # Get the FIG object.
1436        my $fig = $self->{fig};
1437        # Get the genome hash.
1438        my $genomeHash = $self->{genomes};
1439        # Create a load object for the table we're loading.
1440        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1441        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1442        if ($self->{options}->{loadOnly}) {
1443            Trace("Loading from existing files.") if T(2);
1444        } else {
1445            Trace("Generating synonym group data.") if T(2);
1446            # Loop through the genomes.
1447            for my $genomeID (sort keys %{$genomeHash}) {
1448                Trace("Processing $genomeID.") if T(3);
1449                # Get all of the features for this genome. The only method that does this is
1450                # all_features_detailed, which returns extra baggage that we discard.
1451                my $featureData = $fig->all_features_detailed($genomeID);
1452                my @fids = map { $_->[0] } @{$featureData};
1453                Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);
1454                # Loop through the feature IDs.
1455                for my $fid (@fids) {
1456                    # Get the group for this feature.
1457                    my $synonym = $fig->maps_to_id($fid);
1458                    # Only proceed if the synonym is a real group.
1459                    if ($synonym ne $fid) {
1460                        $loadSynonymGroup->Put($synonym);
1461                        $loadIsSynonymGroupFor->Put($synonym, $fid);
1462                    }
1463                }
1464            }
1465        }
1466        # Finish the load.
1467        my $retVal = $self->_FinishAll();
1468        return $retVal;
1469    }
1470    
1471    
1472  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1473    
1474  =head3 TableLoader  =head3 TableLoader
# Line 1463  Line 1536 
1536      my $retVal = Stats->new();      my $retVal = Stats->new();
1537      # Get the loader list.      # Get the loader list.
1538      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1539        # Create a hash to hold the statistics objects, keyed on relation name.
1540        my %loaderHash = ();
1541      # Loop through the list, finishing the loads. Note that if the finish fails, we die      # Loop through the list, finishing the loads. Note that if the finish fails, we die
1542      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1543      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1544          # Get the relation name.          # Get the relation name.
1545          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1475  Line 1550 
1550              # Here we really need to finish.              # Here we really need to finish.
1551              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1552              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1553                $loaderHash{$relName} = $stats;
1554            }
1555        }
1556        # Now we loop through again, actually loading the tables. We want to finish before
1557        # loading so that if something goes wrong at this point, all the load files are usable
1558        # and we don't have to redo all that work.
1559        for my $relName (sort keys %loaderHash) {
1560            # Get the statistics for this relation.
1561            my $stats = $loaderHash{$relName};
1562            # Check for a database load.
1563              if ($self->{options}->{dbLoad}) {              if ($self->{options}->{dbLoad}) {
1564                  # 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.
1565                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);

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