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revision 1.19, Thu Oct 20 09:34:09 2005 UTC revision 1.40, Thu Jun 8 15:37:32 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the NMPDR subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for the NMPDR file.
142                for my $sub (@subs) {
143                    if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 171  Line 182 
182      return $retVal;      return $retVal;
183  }  }
184    
185    =head3 LoadOnly
186    
187    C<< my $flag = $spl->LoadOnly; >>
188    
189    Return TRUE if we are in load-only mode, else FALSE.
190    
191    =cut
192    
193    sub LoadOnly {
194        my ($self) = @_;
195        return $self->{options}->{loadOnly};
196    }
197    
198    =head3 PrimaryOnly
199    
200    C<< my $flag = $spl->PrimaryOnly; >>
201    
202    Return TRUE if only the main entity is to be loaded, else FALSE.
203    
204    =cut
205    
206    sub PrimaryOnly {
207        my ($self) = @_;
208        return $self->{options}->{primaryOnly};
209    }
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
213  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 235 
235    
236  =back  =back
237    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
238  =cut  =cut
239  #: Return Type $%;  #: Return Type $%;
240  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 245 
245      # Get the genome count.      # Get the genome count.
246      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
249      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254        if ($self->{options}->{loadOnly}) {
255            Trace("Loading from existing files.") if T(2);
256        } else {
257            Trace("Generating genome data.") if T(2);
258      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
259      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
260          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
261          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
262          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
263          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
264          # 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.  
265          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267          # Get the full taxonomy.          # Get the full taxonomy.
268          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
269          # Output the genome record.          # Output the genome record.
# Line 268  Line 299 
299              }              }
300          }          }
301      }      }
302        }
303      # Finish the loads.      # Finish the loads.
304      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
305      # Return the result.      # Return the result.
# Line 311  Line 343 
343      my $genomeCount = (keys %{$genomeFilter});      my $genomeCount = (keys %{$genomeFilter});
344      my $featureCount = $genomeCount * 4000;      my $featureCount = $genomeCount * 4000;
345      # Start the loads.      # Start the loads.
346      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
347      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
348      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
349      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
350      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
351      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
352            Trace("Loading from existing files.") if T(2);
353        } else {
354            Trace("Generating coupling data.") if T(2);
355      # Loop through the genomes found.      # Loop through the genomes found.
356      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
357          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 389  Line 424 
424              }              }
425          }          }
426      }      }
427        }
428      # All done. Finish the load.      # All done. Finish the load.
429      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
430      return $retVal;      return $retVal;
# Line 410  Line 446 
446      FeatureTranslation      FeatureTranslation
447      FeatureUpstream      FeatureUpstream
448      IsLocatedIn      IsLocatedIn
449        HasFeature
450    
451  =over 4  =over 4
452    
# Line 426  Line 463 
463      my ($self) = @_;      my ($self) = @_;
464      # Get the FIG object.      # Get the FIG object.
465      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
466      # Get the table of genome IDs.      # Get the table of genome IDs.
467      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
468      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
469      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
470      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
471      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
472      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
473      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
474          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
475          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature');
         $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);  
     }  
476      # 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
477      # locations.      # locations.
478      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
479      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
480            Trace("Loading from existing files.") if T(2);
481        } else {
482            Trace("Generating feature data.") if T(2);
483      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
484      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
485          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
# Line 459  Line 493 
493              my ($featureID, $locations, undef, $type) = @{$featureData};              my ($featureID, $locations, undef, $type) = @{$featureData};
494              # Create the feature record.              # Create the feature record.
495              $loadFeature->Put($featureID, 1, $type);              $loadFeature->Put($featureID, 1, $type);
496                    # Link it to the parent genome.
497                    $loadHasFeature->Put($genomeID, $featureID, $type);
498              # Create the aliases.              # Create the aliases.
499              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
500                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
501              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
502                  # Get the links.                  # Get the links.
503                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
504                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 517 
517                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
518                      }                      }
519                  }                  }
             }  
520              # This part is the roughest. We need to relate the features to contig              # This part is the roughest. We need to relate the features to contig
521              # locations, and the locations must be split so that none of them exceed              # locations, and the locations must be split so that none of them exceed
522              # the maximum segment size. This simplifies the genes_in_region processing              # the maximum segment size. This simplifies the genes_in_region processing
# Line 512  Line 545 
545              }              }
546          }          }
547      }      }
548        }
549      # Finish the loads.      # Finish the loads.
550      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
551      return $retVal;      return $retVal;
# Line 548  Line 582 
582      my $fig = $self->{fig};      my $fig = $self->{fig};
583      # Get the table of genome IDs.      # Get the table of genome IDs.
584      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
585      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
586      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
587                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
588      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
589        } else {
590            Trace("Generating BBH data.") if T(2);
591      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
592      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
593          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
# Line 579  Line 613 
613              }              }
614          }          }
615      }      }
616        }
617      # Finish the loads.      # Finish the loads.
618      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
619      return $retVal;      return $retVal;
# Line 608  Line 643 
643      OccursInSubsystem      OccursInSubsystem
644      ParticipatesIn      ParticipatesIn
645      HasSSCell      HasSSCell
     Catalyzes  
     Reaction  
646      ConsistsOfRoles      ConsistsOfRoles
647      RoleSubset      RoleSubset
648      HasRoleSubset      HasRoleSubset
649      ConsistsOfGenomes      ConsistsOfGenomes
650      GenomeSubset      GenomeSubset
651      HasGenomeSubset      HasGenomeSubset
652        Catalyzes
653        Diagram
654        RoleOccursIn
655    
656  =over 4  =over 4
657    
# Line 638  Line 674 
674      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
675      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
676      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
677      my $subsysCount = @subsysIDs;      # Get the map list.
678      my $genomeCount = (keys %{$genomeHash});      my @maps = $fig->all_maps;
     my $featureCount = $genomeCount * 4000;  
679      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
680      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
681      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
682      my $loadRoleEC = $self->_TableLoader('RoleEC', $featureCount * 6);      my $loadSubsystem = $self->_TableLoader('Subsystem');
683      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
684      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
685      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
686      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
687      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
688      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
689      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
690      my $loadReaction = $self->_TableLoader('Reaction', $featureCount * $genomeCount);      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
691      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $featureCount * $genomeCount);      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
692      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $subsysCount * 50);      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
693      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $subsysCount * 50);      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
694      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $featureCount * $genomeCount);      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
695      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $featureCount * $genomeCount);      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
696      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $subsysCount * 50);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
697      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $subsysCount * 50);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
698      Trace("Beginning subsystem data load.") if T(2);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
699      # The reaction hash will contain a list of reactions for each role. When we're done,      if ($self->{options}->{loadOnly}) {
700      # a complicated sort and merge will be used to generate the Reaction and Catalyzes          Trace("Loading from existing files.") if T(2);
701      # tables.      } else {
702      my %reactionsToRoles = ();          Trace("Generating subsystem data.") if T(2);
703            # This hash will contain the role for each EC. When we're done, this
704            # information will be used to generate the Catalyzes table.
705            my %ecToRoles = ();
706      # Loop through the subsystems. Our first task will be to create the      # Loop through the subsystems. Our first task will be to create the
707      # roles. We do this by looping through the subsystems and creating a      # roles. We do this by looping through the subsystems and creating a
708      # role hash. The hash tracks each role ID so that we don't create      # role hash. The hash tracks each role ID so that we don't create
# Line 673  Line 711 
711      my ($genomeID, $roleID);      my ($genomeID, $roleID);
712      my %roleData = ();      my %roleData = ();
713      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
714          # Get the subsystem object.          # Get the subsystem object.
715          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
716          # Get its reaction hash.              # Only proceed if the subsystem has a spreadsheet.
717          my $reactionHash = $sub->get_reactions();              if (! $sub->{empty_ss}) {
718                    Trace("Creating subsystem $subsysID.") if T(3);
719                    $loadSubsystem->Add("subsystemIn");
720          # Create the subsystem record.          # Create the subsystem record.
721          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
722          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
# Line 697  Line 735 
735                  $roleData{$roleID} = 1;                  $roleData{$roleID} = 1;
736                  # Check for an EC number.                  # Check for an EC number.
737                  if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {                  if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {
738                      $loadRoleEC->Put($roleID, $1);                              my $ec = $1;
739                  }                              $loadRoleEC->Put($roleID, $ec);
740                  # Add the role's reactions.                              $ecToRoles{$ec} = $roleID;
                 my $reactions = $reactionHash->{$roleID};  
                 for my $reactionID (@{$reactions}) {  
                     if (! exists $reactionsToRoles{$reactionID}) {  
                         # Here the reaction is brand-new, so we create its reaction  
                         # record.  
                         $loadReaction->Put($reactionID, $fig->reversible($reactionID));  
                         # We also create a blank list for it in the reaction hash.  
                         $reactionsToRoles{$reactionID} = [];  
                     }  
                     # Add the role to the reaction's role list.  
                     push @{$reactionsToRoles{$reactionID}}, $roleID;  
741                  }                  }
742              }              }
743          }          }
# Line 737  Line 764 
764                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
765                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
766                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
767                      my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
768                      # Only proceed if features exist.                      # Only proceed if features exist.
769                      if (@pegs > 0) {                      if (@pegs > 0) {
770                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
# Line 790  Line 817 
817              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
818              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
819              # Connect the subset to its roles.              # Connect the subset to its roles.
820              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
821              for my $roleID (@roles) {              for my $roleID (@roles) {
822                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
823              }              }
# Line 810  Line 837 
837              }              }
838          }          }
839      }      }
840      # Before we leave, we must create the Catalyzes table. The data is all stored in              # Now we loop through the diagrams. We need to create the diagram records
841      # "reactionToRoles" hash.              # and link each diagram to its roles. Note that only roles which occur
842      for my $reactionID (keys %reactionsToRoles) {              # in subsystems (and therefore appear in the %ecToRoles hash) are
843          # Get this reaction's list of roles. We sort it so we can merge out duplicates.              # included.
844          my @roles = sort @{$reactionsToRoles{$reactionID}};              for my $map (@maps) {
         my $lastRole = "";  
         # Loop through the roles, creating catalyzation records.  
         for my $thisRole (@roles) {  
             if ($thisRole ne $lastRole) {  
                 $loadCatalyzes->Put($thisRole, $reactionID);  
             }  
         }  
     }  
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
 =head3 LoadDiagramData  
   
 C<< my $stats = $spl->LoadDiagramData(); >>  
   
 Load the diagram data from FIG into Sprout.  
   
 Diagrams are used to organize functional roles. The diagram shows the  
 connections between chemicals that interact with a subsystem.  
   
 The following relations are loaded by this method.  
   
     Diagram  
     RoleOccursIn  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadDiagramData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the map list.  
     my @maps = $fig->all_maps;  
     my $mapCount = @maps;  
     my $genomeCount = (keys %{$self->{genomes}});  
     my $featureCount = $genomeCount * 4000;  
     # Create load objects for each of the tables we're loading.  
     my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);  
     my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);  
     Trace("Beginning diagram data load.") if T(2);  
     # Loop through the diagrams.  
     for my $map ($fig->all_maps) {  
845          Trace("Loading diagram $map.") if T(3);          Trace("Loading diagram $map.") if T(3);
846          # Get the diagram's descriptive name.          # Get the diagram's descriptive name.
847          my $name = $fig->map_name($map);          my $name = $fig->map_name($map);
# Line 876  Line 850 
850          # A hash is used to prevent duplicates.          # A hash is used to prevent duplicates.
851          my %roleHash = ();          my %roleHash = ();
852          for my $role ($fig->map_to_ecs($map)) {          for my $role ($fig->map_to_ecs($map)) {
853              if (! $roleHash{$role}) {                      if (exists $ecToRoles{$role} && ! $roleHash{$role}) {
854                  $loadRoleOccursIn->Put($role, $map);                          $loadRoleOccursIn->Put($ecToRoles{$role}, $map);
855                  $roleHash{$role} = 1;                  $roleHash{$role} = 1;
856              }              }
857          }          }
858      }      }
859                # Before we leave, we must create the Catalyzes table. We start with the reactions,
860                # then use the "ecToRoles" table to convert EC numbers to role IDs.
861                my @reactions = $fig->all_reactions();
862                for my $reactionID (@reactions) {
863                    # Get this reaction's list of roles. The results will be EC numbers.
864                    my @roles = $fig->catalyzed_by($reactionID);
865                    # Loop through the roles, creating catalyzation records.
866                    for my $thisRole (@roles) {
867                        if (exists $ecToRoles{$thisRole}) {
868                            $loadCatalyzes->Put($ecToRoles{$thisRole}, $reactionID);
869                        }
870                    }
871                }
872            }
873        }
874      # Finish the load.      # Finish the load.
875      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
876      return $retVal;      return $retVal;
# Line 923  Line 912 
912      my $fig = $self->{fig};      my $fig = $self->{fig};
913      # Get the genome hash.      # Get the genome hash.
914      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
915      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
916      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
917      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
918      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
919            Trace("Loading from existing files.") if T(2);
920        } else {
921            Trace("Generating property data.") if T(2);
922      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
923      my %propertyKeys = ();      my %propertyKeys = ();
924      my $nextID = 1;      my $nextID = 1;
925      # Loop through the genomes.      # Loop through the genomes.
926      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
927          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
928                Trace("Generating properties for $genomeID.") if T(3);
929          # Get the genome's features. The feature ID is the first field in the          # Get the genome's features. The feature ID is the first field in the
930          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
931          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
932          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
933                my $featureCount = 0;
934                my $propertyCount = 0;
935          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
936          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
937              # Get all attributes for this feature. We do this one feature at a time              # Get all attributes for this feature. We do this one feature at a time
938              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
939              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
940                    if (scalar @attributeList) {
941                        $featureCount++;
942                    }
943              # Loop through the attributes.              # Loop through the attributes.
944              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
945                        $propertyCount++;
946                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
947                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
948                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 967  Line 964 
964                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
965              }              }
966          }          }
967                # Update the statistics.
968                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
969                $loadHasProperty->Add("featuresIn", $featureCount);
970                $loadHasProperty->Add("propertiesIn", $propertyCount);
971            }
972      }      }
973      # Finish the load.      # Finish the load.
974      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1007  Line 1009 
1009      my $fig = $self->{fig};      my $fig = $self->{fig};
1010      # Get the genome hash.      # Get the genome hash.
1011      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1012      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1013      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1014      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1015      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1016      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1017      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1018      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1019            Trace("Loading from existing files.") if T(2);
1020        } else {
1021            Trace("Generating annotation data.") if T(2);
1022      # Create a hash of user names. We'll use this to prevent us from generating duplicate      # Create a hash of user names. We'll use this to prevent us from generating duplicate
1023      # user records.      # user records.
1024      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 1028  Line 1032 
1032      # Loop through the genomes.      # Loop through the genomes.
1033      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1034          Trace("Processing $genomeID.") if T(3);          Trace("Processing $genomeID.") if T(3);
         # Get the genome's PEGs.  
         my @pegs = $fig->pegs_of($genomeID);  
         for my $peg (@pegs) {  
             Trace("Processing $peg.") if T(4);  
1035              # Create a hash of timestamps. We use this to prevent duplicate time stamps              # Create a hash of timestamps. We use this to prevent duplicate time stamps
1036              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1037              my %seenTimestamps = ();              my %seenTimestamps = ();
1038              # Check for a functional assignment.              # Get the genome's annotations.
1039              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1040              if ($func) {              Trace("Processing annotations.") if T(2);
1041                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1042                  # assignment annotation for it.                  # Get the annotation tuple.
1043                  if (! FIG::hypo($peg)) {                  my ($peg, $timestamp, $user, $text) = @{$tuple};
                     # Note that we double the slashes so that what goes into the database is  
                     # a new-line escape sequence rather than an actual new-line.  
                     $loadAnnotation->Put("$peg:$time", $time, "FIG\\nSet function to\\n$func");  
                     $loadIsTargetOfAnnotation->Put($peg, "$peg:$time");  
                     $loadMadeAnnotation->Put("FIG", "$peg:$time");  
                     # Denote we've seen this timestamp.  
                     $seenTimestamps{$time} = 1;  
                 }  
             }  
             # Now loop through the real annotations.  
             for my $tuple ($fig->feature_annotations($peg, "raw")) {  
                 my ($fid, $timestamp, $user, $text) = @{$tuple};  
1044                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1045                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "s"
1046                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
# Line 1067  Line 1055 
1055                      # Here it's a number. We need to insure the one we use to form                      # Here it's a number. We need to insure the one we use to form
1056                      # the key is unique.                      # the key is unique.
1057                      my $keyStamp = $timestamp;                      my $keyStamp = $timestamp;
1058                      while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1059                          $keyStamp++;                          $keyStamp++;
1060                      }                      }
                     $seenTimestamps{$keyStamp} = 1;  
1061                      my $annotationID = "$peg:$keyStamp";                      my $annotationID = "$peg:$keyStamp";
1062                        $seenTimestamps{$annotationID} = 1;
1063                      # Insure the user exists.                      # Insure the user exists.
1064                      if (! $users{$user}) {                      if (! $users{$user}) {
1065                          $loadSproutUser->Put($user, "SEED user");                          $loadSproutUser->Put($user, "SEED user");
# Line 1129  Line 1117 
1117      my $fig = $self->{fig};      my $fig = $self->{fig};
1118      # Get the genome hash.      # Get the genome hash.
1119      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1120      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1121      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1122      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1123      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1124      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1125            Trace("Loading from existing files.") if T(2);
1126        } else {
1127            Trace("Generating annotation data.") if T(2);
1128      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1129      my %sourceURL = ();      my %sourceURL = ();
1130      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1164  Line 1154 
1154      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1155          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1156      }      }
1157        }
1158      # Finish the load.      # Finish the load.
1159      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1160      return $retVal;      return $retVal;
# Line 1203  Line 1194 
1194      my $fig = $self->{fig};      my $fig = $self->{fig};
1195      # Get the genome hash.      # Get the genome hash.
1196      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1197      # Convert the genome hash. We'll get the genus and species for each genome and make      # Convert the genome hash. We'll get the genus and species for each genome and make
1198      # it the key.      # it the key.
1199      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1200      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1201      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1202      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1203      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1204            Trace("Loading from existing files.") if T(2);
1205        } else {
1206            Trace("Generating external data.") if T(2);
1207      # We loop through the files one at a time. First, the organism file.      # We loop through the files one at a time. First, the organism file.
1208      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");
1209      my $orgLine;      my $orgLine;
# Line 1240  Line 1233 
1233              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1234          }          }
1235      }      }
1236        }
1237      # Finish the load.      # Finish the load.
1238      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1239      return $retVal;      return $retVal;
# Line 1256  Line 1250 
1250    
1251  The following relations are loaded by this method.  The following relations are loaded by this method.
1252    
1253        Reaction
1254      ReactionURL      ReactionURL
1255      Compound      Compound
1256      CompoundName      CompoundName
# Line 1279  Line 1274 
1274      my ($self) = @_;      my ($self) = @_;
1275      # Get the FIG object.      # Get the FIG object.
1276      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1277      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1278      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1279      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1280      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1281      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1282      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1283      Trace("Beginning reaction/compound data load.") if T(2);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1284      # Create a hash to remember the compounds we've generated in the compound table.      if ($self->{options}->{loadOnly}) {
1285      my %compoundHash = ();          Trace("Loading from existing files.") if T(2);
1286      # Loop through the reactions.      } else {
1287            Trace("Generating annotation data.") if T(2);
1288            # First we create the compounds.
1289            my @compounds = $fig->all_compounds();
1290            for my $cid (@compounds) {
1291                # Check for names.
1292                my @names = $fig->names_of_compound($cid);
1293                # Each name will be given a priority number, starting with 1.
1294                my $prio = 1;
1295                for my $name (@names) {
1296                    $loadCompoundName->Put($cid, $name, $prio++);
1297                }
1298                # Create the main compound record. Note that the first name
1299                # becomes the label.
1300                my $label = (@names > 0 ? $names[0] : $cid);
1301                $loadCompound->Put($cid, $label);
1302                # Check for a CAS ID.
1303                my $cas = $fig->cas($cid);
1304                if ($cas) {
1305                    $loadCompoundCAS->Put($cid, $cas);
1306                }
1307            }
1308            # All the compounds are set up, so we need to loop through the reactions next. First,
1309            # we initialize the discriminator index. This is a single integer used to insure
1310            # duplicate elements in a reaction are not accidentally collapsed.
1311            my $discrim = 0;
1312      my @reactions = $fig->all_reactions();      my @reactions = $fig->all_reactions();
1313      for my $reactionID (@reactions) {      for my $reactionID (@reactions) {
1314                # Create the reaction record.
1315                $loadReaction->Put($reactionID, $fig->reversible($reactionID));
1316          # Compute the reaction's URL.          # Compute the reaction's URL.
1317          my $url = HTML::reaction_link($reactionID);          my $url = HTML::reaction_link($reactionID);
1318          # Put it in the ReactionURL table.          # Put it in the ReactionURL table.
# Line 1302  Line 1321 
1321          # substrates first and then products.          # substrates first and then products.
1322          for my $product (0, 1) {          for my $product (0, 1) {
1323              # Get the compounds of the current type for the current reaction. FIG will              # Get the compounds of the current type for the current reaction. FIG will
1324              # give us 3-tuples: [ID, Stoichometry, main-flag]. At this time we do not                  # give us 3-tuples: [ID, stoichiometry, main-flag]. At this time we do not
1325              # have location data in SEED, so it defaults to the empty string.              # have location data in SEED, so it defaults to the empty string.
1326              my @compounds = $fig->reaction2comp($reactionID, $product);              my @compounds = $fig->reaction2comp($reactionID, $product);
1327              for my $compData (@compounds) {              for my $compData (@compounds) {
1328                  # Extract the compound data from the current tuple.                  # Extract the compound data from the current tuple.
1329                  my ($cid, $stoich, $main) = @{$compData};                  my ($cid, $stoich, $main) = @{$compData};
1330                  # Link the compound to the reaction.                  # Link the compound to the reaction.
1331                  $loadIsAComponentOf->Put($cid, $reactionID, "", $main, $product, $stoich);                      $loadIsAComponentOf->Put($cid, $reactionID, $discrim++, "", $main,
1332                  # If this is a new compound, we need to create its table entries.                                               $product, $stoich);
                 if (! exists $compoundHash{$cid}) {  
                     $compoundHash{$cid} = 1;  
                     # Create the main compound record and denote we've done it.  
                     $loadCompound->Put($cid);  
                     # Check for a CAS ID.  
                     my $cas = $fig->cas($cid);  
                     if ($cas) {  
                         $loadCompoundCAS->Put($cid, $cas);  
                     }  
                     # Check for names.  
                     my @names = $fig->names_of_compound($cid);  
                     # Each name will be given a priority number, starting with 1.  
                     my $prio = 0;  
                     for my $name (@names) {  
                         $loadCompoundName->Put($cid, $name, $prio++);  
                     }  
1333                  }                  }
1334              }              }
1335          }          }
# Line 1366  Line 1369 
1369      my $fig = $self->{fig};      my $fig = $self->{fig};
1370      # Get the genome hash.      # Get the genome hash.
1371      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1372      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1373      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1374      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1375            Trace("Loading from existing files.") if T(2);
1376        } else {
1377            Trace("Generating group data.") if T(2);
1378      # Loop through the genomes.      # Loop through the genomes.
1379      my $line;      my $line;
1380      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
# Line 1385  Line 1390 
1390          }          }
1391          close TMP;          close TMP;
1392      }      }
1393        }
1394      # Finish the load.      # Finish the load.
1395      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1396      return $retVal;      return $retVal;
# Line 1406  Line 1412 
1412    
1413  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1414    
1415  =item rowCount (optional)  =item ignore
1416    
1417  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1418    
1419  =item RETURN  =item RETURN
1420    
# Line 1420  Line 1426 
1426    
1427  sub _TableLoader {  sub _TableLoader {
1428      # Get the parameters.      # Get the parameters.
1429      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1430      # Create the load object.      # Create the load object.
1431      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1432                                   $ignore);
1433      # Cache it in the loader list.      # Cache it in the loader list.
1434      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1435      # Return it to the caller.      # Return it to the caller.
# Line 1459  Line 1466 
1466      # 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
1467      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads restartable.
1468      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1469          # Trace the fact that we're cleaning up.          # Get the relation name.
1470          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1471          Trace("Finishing load for $relName.") if T(2);          # Check the ignore flag.
1472            if ($loader->Ignore) {
1473                Trace("Relation $relName not loaded.") if T(2);
1474            } else {
1475                # Here we really need to finish.
1476                Trace("Finishing $relName.") if T(2);
1477          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1478          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1479              # 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.
# Line 1473  Line 1485 
1485          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
1486          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1487      }      }
1488        }
1489      # Return the load statistics.      # Return the load statistics.
1490      return $retVal;      return $retVal;
1491  }  }

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