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revision 1.15, Fri Sep 16 04:12:05 2005 UTC revision 1.36, Fri May 19 07:26:17 2006 UTC
# Line 10  Line 10 
10      use Sprout;      use Sprout;
11      use Stats;      use Stats;
12      use BasicLocation;      use BasicLocation;
13        use HTML;
14    
15  =head1 Sprout Load Methods  =head1 Sprout Load Methods
16    
# Line 79  Line 80 
80  =item subsysFile  =item subsysFile
81    
82  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
83  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
84  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>
85    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
86    
87  =item options  =item options
88    
# Line 93  Line 95 
95  sub new {  sub new {
96      # Get the parameters.      # Get the parameters.
97      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
98      # Load the list of genomes into a hash.      # Create the genome hash.
99      my %genomes;      my %genomes = ();
100        # We only need it if load-only is NOT specified.
101        if (! $options->{loadOnly}) {
102      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
103          # 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.
104          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 128  Line 132 
132              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
133          }          }
134      }      }
135        }
136      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
137      my %subsystems = ();      my %subsystems = ();
138        # We only need it if load-only is NOT specified.
139        if (! $options->{loadOnly}) {
140      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
141          # Here we want all the subsystems.              # Here we want all the NMPDR subsystems. First we get the whole list.
142          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
143                # Loop through, checking for the NMPDR file.
144                for my $sub (@subs) {
145                    if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
146                        $subsystems{$sub} = 1;
147                    }
148                }
149      } else {      } else {
150          my $type = ref $subsysFile;          my $type = ref $subsysFile;
151          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 152  Line 165 
165              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
166          }          }
167      }      }
168        }
169      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
170      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
171      # Create the Sprout load object.      # Create the Sprout load object.
# Line 170  Line 184 
184      return $retVal;      return $retVal;
185  }  }
186    
187    =head3 LoadOnly
188    
189    C<< my $flag = $spl->LoadOnly; >>
190    
191    Return TRUE if we are in load-only mode, else FALSE.
192    
193    =cut
194    
195    sub LoadOnly {
196        my ($self) = @_;
197        return $self->{options}->{loadOnly};
198    }
199    
200    =head3 PrimaryOnly
201    
202    C<< my $flag = $spl->PrimaryOnly; >>
203    
204    Return TRUE if only the main entity is to be loaded, else FALSE.
205    
206    =cut
207    
208    sub PrimaryOnly {
209        my ($self) = @_;
210        return $self->{options}->{primaryOnly};
211    }
212    
213  =head3 LoadGenomeData  =head3 LoadGenomeData
214    
215  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 197  Line 237 
237    
238  =back  =back
239    
 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.)  
   
240  =cut  =cut
241  #: Return Type $%;  #: Return Type $%;
242  sub LoadGenomeData {  sub LoadGenomeData {
# Line 215  Line 247 
247      # Get the genome count.      # Get the genome count.
248      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
249      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
250      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
251      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
252      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
253      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
254      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
255      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
256        if ($self->{options}->{loadOnly}) {
257            Trace("Loading from existing files.") if T(2);
258        } else {
259            Trace("Generating genome data.") if T(2);
260      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
261      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
262          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
263          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
264          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
265          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
266          # 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.  
267          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
268          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
269          # Get the full taxonomy.          # Get the full taxonomy.
270          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
271          # Output the genome record.          # Output the genome record.
# Line 267  Line 301 
301              }              }
302          }          }
303      }      }
304        }
305      # Finish the loads.      # Finish the loads.
306      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
307      # Return the result.      # Return the result.
# Line 310  Line 345 
345      my $genomeCount = (keys %{$genomeFilter});      my $genomeCount = (keys %{$genomeFilter});
346      my $featureCount = $genomeCount * 4000;      my $featureCount = $genomeCount * 4000;
347      # Start the loads.      # Start the loads.
348      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
349      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
350      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
351      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
352      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
353      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
354            Trace("Loading from existing files.") if T(2);
355        } else {
356            Trace("Generating coupling data.") if T(2);
357      # Loop through the genomes found.      # Loop through the genomes found.
358      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
359          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 367  Line 405 
405                              # We store this evidence in the hash if the usage                              # We store this evidence in the hash if the usage
406                              # is nonzero or no prior evidence has been found. This                              # is nonzero or no prior evidence has been found. This
407                              # insures that if there is duplicate evidence, we                              # insures that if there is duplicate evidence, we
408                              # at least keep the meaningful ones. Only evidence is                                  # at least keep the meaningful ones. Only evidence in
409                              # the hash makes it to the output.                              # the hash makes it to the output.
410                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {
411                                  $evidenceMap{$evidenceKey} = $evidenceData;                                  $evidenceMap{$evidenceKey} = $evidenceData;
# Line 382  Line 420 
420                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);
421                          # Connect it to the features.                          # Connect it to the features.
422                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);
423                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 1);                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);
424                            }
425                      }                      }
426                  }                  }
427              }              }
# Line 409  Line 448 
448      FeatureTranslation      FeatureTranslation
449      FeatureUpstream      FeatureUpstream
450      IsLocatedIn      IsLocatedIn
451        HasFeature
452    
453  =over 4  =over 4
454    
# Line 425  Line 465 
465      my ($self) = @_;      my ($self) = @_;
466      # Get the FIG object.      # Get the FIG object.
467      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
468      # Get the table of genome IDs.      # Get the table of genome IDs.
469      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
470      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
471      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
472      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
473      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
474      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
475      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
476          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
477          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature');
         $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);  
     }  
478      # 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
479      # locations.      # locations.
480      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
481      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
482            Trace("Loading from existing files.") if T(2);
483        } else {
484            Trace("Generating feature data.") if T(2);
485      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
486      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
487          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
# Line 458  Line 495 
495              my ($featureID, $locations, undef, $type) = @{$featureData};              my ($featureID, $locations, undef, $type) = @{$featureData};
496              # Create the feature record.              # Create the feature record.
497              $loadFeature->Put($featureID, 1, $type);              $loadFeature->Put($featureID, 1, $type);
498                    # Link it to the parent genome.
499                    $loadHasFeature->Put($genomeID, $featureID, $type);
500              # Create the aliases.              # Create the aliases.
501              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
502                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
503              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
504                  # Get the links.                  # Get the links.
505                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
506                  for my $link (@links) {                  for my $link (@links) {
# Line 482  Line 519 
519                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
520                      }                      }
521                  }                  }
             }  
522              # 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
523              # 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
524              # the maximum segment size. This simplifies the genes_in_region processing              # the maximum segment size. This simplifies the genes_in_region processing
# Line 511  Line 547 
547              }              }
548          }          }
549      }      }
550        }
551      # Finish the loads.      # Finish the loads.
552      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
553      return $retVal;      return $retVal;
# Line 547  Line 584 
584      my $fig = $self->{fig};      my $fig = $self->{fig};
585      # Get the table of genome IDs.      # Get the table of genome IDs.
586      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
587      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
588      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
589                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
590      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
591        } else {
592            Trace("Generating BBH data.") if T(2);
593      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
594      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
595          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
# Line 578  Line 615 
615              }              }
616          }          }
617      }      }
618        }
619      # Finish the loads.      # Finish the loads.
620      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
621      return $retVal;      return $retVal;
# Line 599  Line 637 
637    
638      Subsystem      Subsystem
639      Role      Role
640        RoleEC
641      SSCell      SSCell
642      ContainsFeature      ContainsFeature
643      IsGenomeOf      IsGenomeOf
# Line 606  Line 645 
645      OccursInSubsystem      OccursInSubsystem
646      ParticipatesIn      ParticipatesIn
647      HasSSCell      HasSSCell
648        ConsistsOfRoles
649        RoleSubset
650        HasRoleSubset
651        ConsistsOfGenomes
652        GenomeSubset
653        HasGenomeSubset
654        Catalyzes
655        Diagram
656        RoleOccursIn
657    
658  =over 4  =over 4
659    
# Line 615  Line 663 
663    
664  =back  =back
665    
 B<TO DO>  
   
 Generate RoleName table?  
   
666  =cut  =cut
667  #: Return Type $%;  #: Return Type $%;
668  sub LoadSubsystemData {  sub LoadSubsystemData {
# Line 632  Line 676 
676      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
677      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
678      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
679      my $subsysCount = @subsysIDs;      # Get the map list.
680      my $genomeCount = (keys %{$genomeHash});      my @maps = $fig->all_maps;
     my $featureCount = $genomeCount * 4000;  
681      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
682      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
683      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
684      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
685      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
686      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
687      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
688      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
689      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
690      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
691      Trace("Beginning subsystem data load.") if T(2);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
692        my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
693        my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
694        my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
695        my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
696        my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
697        my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
698        my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
699        my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
700        my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
701        if ($self->{options}->{loadOnly}) {
702            Trace("Loading from existing files.") if T(2);
703        } else {
704            Trace("Generating subsystem data.") if T(2);
705            # This hash will contain the role for each EC. When we're done, this
706            # information will be used to generate the Catalyzes table.
707            my %ecToRoles = ();
708      # Loop through the subsystems. Our first task will be to create the      # Loop through the subsystems. Our first task will be to create the
709      # roles. We do this by looping through the subsystems and creating a      # roles. We do this by looping through the subsystems and creating a
710      # 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
711      # duplicates. As we move along, we'll connect the roles and subsystems.          # duplicates. As we move along, we'll connect the roles and subsystems
712            # and memorize up the reactions.
713      my ($genomeID, $roleID);      my ($genomeID, $roleID);
714      my %roleData = ();      my %roleData = ();
715      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
716                # Get the subsystem object.
717                my $sub = $fig->get_subsystem($subsysID);
718                # Only proceed if the subsystem has a spreadsheet.
719                if (! $sub->{empty_ss}) {
720          Trace("Creating subsystem $subsysID.") if T(3);          Trace("Creating subsystem $subsysID.") if T(3);
721          $loadSubsystem->Add("subsystemIn");          $loadSubsystem->Add("subsystemIn");
722          # Create the subsystem record.          # Create the subsystem record.
723          $loadSubsystem->Put($subsysID);                  my $curator = $sub->get_curator();
724          # Get the subsystem object.                  my $notes = $sub->get_notes();
725          my $sub = $fig->get_subsystem($subsysID);                  $loadSubsystem->Put($subsysID, $curator, $notes);
726          # Connect it to its roles.                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
727          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
728                        # Connect to this role.
729              $loadOccursInSubsystem->Add("roleIn");              $loadOccursInSubsystem->Add("roleIn");
730              $loadOccursInSubsystem->Put($roleID, $subsysID);                      $loadOccursInSubsystem->Put($roleID, $subsysID, $col);
731                        # If it's a new role, add it to the role table.
732              if (! exists $roleData{$roleID}) {              if (! exists $roleData{$roleID}) {
733                  $loadRole->Put($roleID);                          # Get the role's abbreviation.
734                            my $abbr = $sub->get_role_abbr($col);
735                            # Add the role.
736                            $loadRole->Put($roleID, $abbr);
737                  $roleData{$roleID} = 1;                  $roleData{$roleID} = 1;
738                            # Check for an EC number.
739                            if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {
740                                my $ec = $1;
741                                $loadRoleEC->Put($roleID, $ec);
742                                $ecToRoles{$ec} = $roleID;
743                            }
744              }              }
745          }          }
746          # Now we create the spreadsheet for the subsystem by matching roles to          # Now we create the spreadsheet for the subsystem by matching roles to
# Line 678  Line 753 
753                  # Count the PEGs and cells found for verification purposes.                  # Count the PEGs and cells found for verification purposes.
754                  my $pegCount = 0;                  my $pegCount = 0;
755                  my $cellCount = 0;                  my $cellCount = 0;
756                            # Create a list for the PEGs we find. This list will be used
757                            # to generate cluster numbers.
758                            my @pegsFound = ();
759                            # Create a hash that maps spreadsheet IDs to PEGs. We will
760                            # use this to generate the ContainsFeature data after we have
761                            # the cluster numbers.
762                            my %cellPegs = ();
763                            # Get the genome's variant code for this subsystem.
764                            my $variantCode = $sub->get_variant_code($row);
765                  # Loop through the subsystem's roles. We use an index because it is                  # Loop through the subsystem's roles. We use an index because it is
766                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
767                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
# Line 692  Line 776 
776                          $loadIsGenomeOf->Put($genomeID, $cellID);                          $loadIsGenomeOf->Put($genomeID, $cellID);
777                          $loadIsRoleOf->Put($roleID, $cellID);                          $loadIsRoleOf->Put($roleID, $cellID);
778                          $loadHasSSCell->Put($subsysID, $cellID);                          $loadHasSSCell->Put($subsysID, $cellID);
779                          # Attach the features to it.                                  # Remember its features.
780                          for my $pegID (@pegs) {                                  push @pegsFound, @pegs;
781                              $loadContainsFeature->Put($cellID, $pegID);                                  $cellPegs{$cellID} = \@pegs;
782                              $pegCount++;                                  $pegCount += @pegs;
                         }  
783                      }                      }
784                  }                  }
785                  # If we found some cells for this genome, denote it participates in the                          # If we found some cells for this genome, we need to compute clusters and
786                  # subsystem.                          # denote it participates in the subsystem.
787                  if ($pegCount > 0) {                  if ($pegCount > 0) {
788                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
789                      $loadParticipatesIn->Put($genomeID, $subsysID);                              $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
790                                # Partition the PEGs found into clusters.
791                                my @clusters = $fig->compute_clusters(\@pegsFound, $sub);
792                                # Create a hash mapping PEG IDs to cluster numbers.
793                                # We default to -1 for all of them.
794                                my %clusterOf = map { $_ => -1 } @pegsFound;
795                                for (my $i = 0; $i <= $#clusters; $i++) {
796                                    my $subList = $clusters[$i];
797                                    for my $peg (@{$subList}) {
798                                        $clusterOf{$peg} = $i;
799                                    }
800                                }
801                                # Create the ContainsFeature data.
802                                for my $cellID (keys %cellPegs) {
803                                    my $cellList = $cellPegs{$cellID};
804                                    for my $cellPeg (@$cellList) {
805                                        $loadContainsFeature->Put($cellID, $cellPeg, $clusterOf{$cellPeg});
806                  }                  }
807              }              }
808          }          }
809      }      }
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
810  }  }
811                    # Now we need to generate the subsets. The subset names must be concatenated to
812  =head3 LoadDiagramData                  # the subsystem name to make them unique keys. There are two types of subsets:
813                    # genome subsets and role subsets. We do the role subsets first.
814  C<< my $stats = $spl->LoadDiagramData(); >>                  my @subsetNames = $sub->get_subset_names();
815                    for my $subsetID (@subsetNames) {
816  Load the diagram data from FIG into Sprout.                      # Create the subset record.
817                        my $actualID = "$subsysID:$subsetID";
818  Diagrams are used to organize functional roles. The diagram shows the                      $loadRoleSubset->Put($actualID);
819  connections between chemicals that interact with a subsystem.                      # Connect the subset to the subsystem.
820                        $loadHasRoleSubset->Put($subsysID, $actualID);
821  The following relations are loaded by this method.                      # Connect the subset to its roles.
822                        my @roles = $sub->get_subsetC_roles($subsetID);
823      Diagram                      for my $roleID (@roles) {
824      RoleOccursIn                          $loadConsistsOfRoles->Put($actualID, $roleID);
825                        }
826  =over 4                  }
827                    # Next the genome subsets.
828  =item RETURNS                  @subsetNames = $sub->get_subset_namesR();
829                    for my $subsetID (@subsetNames) {
830  Returns a statistics object for the loads.                      # Create the subset record.
831                        my $actualID = "$subsysID:$subsetID";
832  =back                      $loadGenomeSubset->Put($actualID);
833                        # Connect the subset to the subsystem.
834  =cut                      $loadHasGenomeSubset->Put($subsysID, $actualID);
835  #: Return Type $%;                      # Connect the subset to its genomes.
836  sub LoadDiagramData {                      my @genomes = $sub->get_subsetR($subsetID);
837      # Get this object instance.                      for my $genomeID (@genomes) {
838      my ($self) = @_;                          $loadConsistsOfGenomes->Put($actualID, $genomeID);
839      # Get the FIG object.                      }
840      my $fig = $self->{fig};                  }
841      # Get the map list.              }
842      my @maps = $fig->all_maps;              # Now we loop through the diagrams. We need to create the diagram records
843      my $mapCount = @maps;              # and link each diagram to its roles. Note that only roles which occur
844      my $genomeCount = (keys %{$self->{genomes}});              # in subsystems (and therefore appear in the %ecToRoles hash) are
845      my $featureCount = $genomeCount * 4000;              # included.
846      # Create load objects for each of the tables we're loading.              for my $map (@maps) {
     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) {  
847          Trace("Loading diagram $map.") if T(3);          Trace("Loading diagram $map.") if T(3);
848          # Get the diagram's descriptive name.          # Get the diagram's descriptive name.
849          my $name = $fig->map_name($map);          my $name = $fig->map_name($map);
# Line 761  Line 852 
852          # A hash is used to prevent duplicates.          # A hash is used to prevent duplicates.
853          my %roleHash = ();          my %roleHash = ();
854          for my $role ($fig->map_to_ecs($map)) {          for my $role ($fig->map_to_ecs($map)) {
855              if (! $roleHash{$role}) {                      if (exists $ecToRoles{$role} && ! $roleHash{$role}) {
856                  $loadRoleOccursIn->Put($role, $map);                          $loadRoleOccursIn->Put($ecToRoles{$role}, $map);
857                  $roleHash{$role} = 1;                  $roleHash{$role} = 1;
858              }              }
859          }          }
860      }      }
861                # Before we leave, we must create the Catalyzes table. We start with the reactions,
862                # then use the "ecToRoles" table to convert EC numbers to role IDs.
863                my @reactions = $fig->all_reactions();
864                for my $reactionID (@reactions) {
865                    # Get this reaction's list of roles. The results will be EC numbers.
866                    my @roles = $fig->catalyzed_by($reactionID);
867                    # Loop through the roles, creating catalyzation records.
868                    for my $thisRole (@roles) {
869                        if (exists $ecToRoles{$thisRole}) {
870                            $loadCatalyzes->Put($ecToRoles{$thisRole}, $reactionID);
871                        }
872                    }
873                }
874            }
875        }
876      # Finish the load.      # Finish the load.
877      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
878      return $retVal;      return $retVal;
# Line 808  Line 914 
914      my $fig = $self->{fig};      my $fig = $self->{fig};
915      # Get the genome hash.      # Get the genome hash.
916      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
917      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
918      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
919      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
920      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
921            Trace("Loading from existing files.") if T(2);
922        } else {
923            Trace("Generating property data.") if T(2);
924      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
925      my %propertyKeys = ();      my %propertyKeys = ();
926      my $nextID = 1;      my $nextID = 1;
927      # Loop through the genomes.      # Loop through the genomes.
928      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
929          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
930                Trace("Generating properties for $genomeID.") if T(3);
931          # 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
932          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
933          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
934          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
935                my $featureCount = 0;
936                my $propertyCount = 0;
937          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
938          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
939              # 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
940              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
941              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
942                    if (scalar @attributeList) {
943                        $featureCount++;
944                    }
945              # Loop through the attributes.              # Loop through the attributes.
946              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
947                        $propertyCount++;
948                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
949                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
950                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 852  Line 966 
966                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
967              }              }
968          }          }
969                # Update the statistics.
970                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
971                $loadHasProperty->Add("featuresIn", $featureCount);
972                $loadHasProperty->Add("propertiesIn", $propertyCount);
973            }
974      }      }
975      # Finish the load.      # Finish the load.
976      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 892  Line 1011 
1011      my $fig = $self->{fig};      my $fig = $self->{fig};
1012      # Get the genome hash.      # Get the genome hash.
1013      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1014      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1015      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1016      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1017      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1018      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1019      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1020      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1021            Trace("Loading from existing files.") if T(2);
1022        } else {
1023            Trace("Generating annotation data.") if T(2);
1024      # 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
1025      # user records.      # user records.
1026      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 913  Line 1034 
1034      # Loop through the genomes.      # Loop through the genomes.
1035      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1036          Trace("Processing $genomeID.") if T(3);          Trace("Processing $genomeID.") if T(3);
1037          # Get the genome's PEGs.              # Get the genome's annotations.
1038          my @pegs = $fig->pegs_of($genomeID);              my @annotations = $fig->read_all_annotations($genomeID);
1039          for my $peg (@pegs) {              Trace("Processing annotations.") if T(2);
1040              Trace("Processing $peg.") if T(4);              for my $tuple (@annotations) {
1041              # 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
1042              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1043              my %seenTimestamps = ();              my %seenTimestamps = ();
1044              # Check for a functional assignment.                  # Get the annotation tuple.
1045              my $func = $fig->function_of($peg);                  my ($peg, $timestamp, $user, $text) = @{$tuple};
             if ($func) {  
                 # If this is NOT a hypothetical assignment, we create an  
                 # assignment annotation for it.  
                 if (! FIG::hypo($peg)) {  
                     # 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};  
1046                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1047                      # and "\t" and "\n" are escaped. Note we use the "s"                      # and "\t" and "\n" are escaped. Note we use the "s"
1048                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
# Line 948  Line 1054 
1054                      $text =~ s/Set master function/Set FIG function/s;                      $text =~ s/Set master function/Set FIG function/s;
1055                      # Insure the time stamp is valid.                      # Insure the time stamp is valid.
1056                      if ($timestamp =~ /^\d+$/) {                      if ($timestamp =~ /^\d+$/) {
1057                          # Here it's a number. We need to insure it's unique.                      # Here it's a number. We need to insure the one we use to form
1058                          while ($seenTimestamps{$timestamp}) {                      # the key is unique.
1059                              $timestamp++;                      my $keyStamp = $timestamp;
1060                        while ($seenTimestamps{"$peg:$keyStamp"}) {
1061                            $keyStamp++;
1062                          }                          }
1063                          $seenTimestamps{$timestamp} = 1;                      my $annotationID = "$peg:$keyStamp";
1064                          my $annotationID = "$peg:$timestamp";                      $seenTimestamps{$annotationID} = 1;
1065                          # Insure the user exists.                          # Insure the user exists.
1066                          if (! $users{$user}) {                          if (! $users{$user}) {
1067                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 961  Line 1069 
1069                              $users{$user} = 1;                              $users{$user} = 1;
1070                          }                          }
1071                          # Generate the annotation.                          # Generate the annotation.
1072                          $loadAnnotation->Put($annotationID, $timestamp, "$user\\n$text");                      $loadAnnotation->Put($annotationID, $timestamp, $text);
1073                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);
1074                          $loadMadeAnnotation->Put($user, $annotationID);                          $loadMadeAnnotation->Put($user, $annotationID);
1075                      } else {                      } else {
# Line 971  Line 1079 
1079                  }                  }
1080              }              }
1081          }          }
     }  
1082      # Finish the load.      # Finish the load.
1083      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1084      return $retVal;      return $retVal;
# Line 1012  Line 1119 
1119      my $fig = $self->{fig};      my $fig = $self->{fig};
1120      # Get the genome hash.      # Get the genome hash.
1121      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1122      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1123      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1124      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1125      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1126      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1127            Trace("Loading from existing files.") if T(2);
1128        } else {
1129            Trace("Generating annotation data.") if T(2);
1130      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1131      my %sourceURL = ();      my %sourceURL = ();
1132      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1031  Line 1140 
1140              chomp $line;              chomp $line;
1141              my($sourceID, $desc, $url) = split(/\t/,$line);              my($sourceID, $desc, $url) = split(/\t/,$line);
1142              $loadComesFrom->Put($genomeID, $sourceID);              $loadComesFrom->Put($genomeID, $sourceID);
1143              if ($url && ! exists $sourceURL{$genomeID}) {                  if ($url && ! exists $sourceURL{$sourceID}) {
1144                  $loadSourceURL->Put($sourceID, $url);                  $loadSourceURL->Put($sourceID, $url);
1145                  $sourceURL{$sourceID} = 1;                  $sourceURL{$sourceID} = 1;
1146              }              }
1147              if ($desc && ! exists $sourceDesc{$sourceID}) {                  if ($desc) {
1148                  $loadSource->Put($sourceID, $desc);                      $sourceDesc{$sourceID} = $desc;
1149                  $sourceDesc{$sourceID} = 1;                  } elsif (! exists $sourceDesc{$sourceID}) {
1150                        $sourceDesc{$sourceID} = $sourceID;
1151              }              }
1152          }          }
1153          close TMP;          close TMP;
1154      }      }
1155            # Write the source descriptions.
1156            for my $sourceID (keys %sourceDesc) {
1157                $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1158            }
1159        }
1160      # Finish the load.      # Finish the load.
1161      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1162      return $retVal;      return $retVal;
# Line 1081  Line 1196 
1196      my $fig = $self->{fig};      my $fig = $self->{fig};
1197      # Get the genome hash.      # Get the genome hash.
1198      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1199      # 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
1200      # it the key.      # it the key.
1201      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1202      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1203      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1204      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1205      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1206            Trace("Loading from existing files.") if T(2);
1207        } else {
1208            Trace("Generating external data.") if T(2);
1209      # 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.
1210      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");
1211      my $orgLine;      my $orgLine;
# Line 1118  Line 1235 
1235              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1236          }          }
1237      }      }
1238        }
1239        # Finish the load.
1240        my $retVal = $self->_FinishAll();
1241        return $retVal;
1242    }
1243    
1244    
1245    =head3 LoadReactionData
1246    
1247    C<< my $stats = $spl->LoadReactionData(); >>
1248    
1249    Load the reaction data from FIG into Sprout.
1250    
1251    Reaction data connects reactions to the compounds that participate in them.
1252    
1253    The following relations are loaded by this method.
1254    
1255        Reaction
1256        ReactionURL
1257        Compound
1258        CompoundName
1259        CompoundCAS
1260        IsAComponentOf
1261    
1262    This method proceeds reaction by reaction rather than genome by genome.
1263    
1264    =over 4
1265    
1266    =item RETURNS
1267    
1268    Returns a statistics object for the loads.
1269    
1270    =back
1271    
1272    =cut
1273    #: Return Type $%;
1274    sub LoadReactionData {
1275        # Get this object instance.
1276        my ($self) = @_;
1277        # Get the FIG object.
1278        my $fig = $self->{fig};
1279        # Create load objects for each of the tables we're loading.
1280        my $loadReaction = $self->_TableLoader('Reaction');
1281        my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1282        my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1283        my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1284        my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1285        my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1286        if ($self->{options}->{loadOnly}) {
1287            Trace("Loading from existing files.") if T(2);
1288        } else {
1289            Trace("Generating annotation data.") if T(2);
1290            # First we create the compounds.
1291            my @compounds = $fig->all_compounds();
1292            for my $cid (@compounds) {
1293                # Check for names.
1294                my @names = $fig->names_of_compound($cid);
1295                # Each name will be given a priority number, starting with 1.
1296                my $prio = 1;
1297                for my $name (@names) {
1298                    $loadCompoundName->Put($cid, $name, $prio++);
1299                }
1300                # Create the main compound record. Note that the first name
1301                # becomes the label.
1302                my $label = (@names > 0 ? $names[0] : $cid);
1303                $loadCompound->Put($cid, $label);
1304                # Check for a CAS ID.
1305                my $cas = $fig->cas($cid);
1306                if ($cas) {
1307                    $loadCompoundCAS->Put($cid, $cas);
1308                }
1309            }
1310            # All the compounds are set up, so we need to loop through the reactions next. First,
1311            # we initialize the discriminator index. This is a single integer used to insure
1312            # duplicate elements in a reaction are not accidentally collapsed.
1313            my $discrim = 0;
1314            my @reactions = $fig->all_reactions();
1315            for my $reactionID (@reactions) {
1316                # Create the reaction record.
1317                $loadReaction->Put($reactionID, $fig->reversible($reactionID));
1318                # Compute the reaction's URL.
1319                my $url = HTML::reaction_link($reactionID);
1320                # Put it in the ReactionURL table.
1321                $loadReactionURL->Put($reactionID, $url);
1322                # Now we need all of the reaction's compounds. We get these in two phases,
1323                # substrates first and then products.
1324                for my $product (0, 1) {
1325                    # Get the compounds of the current type for the current reaction. FIG will
1326                    # give us 3-tuples: [ID, stoichiometry, main-flag]. At this time we do not
1327                    # have location data in SEED, so it defaults to the empty string.
1328                    my @compounds = $fig->reaction2comp($reactionID, $product);
1329                    for my $compData (@compounds) {
1330                        # Extract the compound data from the current tuple.
1331                        my ($cid, $stoich, $main) = @{$compData};
1332                        # Link the compound to the reaction.
1333                        $loadIsAComponentOf->Put($cid, $reactionID, $discrim++, "", $main,
1334                                                 $product, $stoich);
1335                    }
1336                }
1337            }
1338        }
1339      # Finish the load.      # Finish the load.
1340      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1341      return $retVal;      return $retVal;
# Line 1153  Line 1371 
1371      my $fig = $self->{fig};      my $fig = $self->{fig};
1372      # Get the genome hash.      # Get the genome hash.
1373      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1374      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1375      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1376      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1377            Trace("Loading from existing files.") if T(2);
1378        } else {
1379            Trace("Generating group data.") if T(2);
1380      # Loop through the genomes.      # Loop through the genomes.
1381      my $line;      my $line;
1382      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
# Line 1172  Line 1392 
1392          }          }
1393          close TMP;          close TMP;
1394      }      }
1395        }
1396      # Finish the load.      # Finish the load.
1397      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1398      return $retVal;      return $retVal;
# Line 1193  Line 1414 
1414    
1415  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1416    
1417  =item rowCount (optional)  =item ignore
1418    
1419  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1420    
1421  =item RETURN  =item RETURN
1422    
# Line 1207  Line 1428 
1428    
1429  sub _TableLoader {  sub _TableLoader {
1430      # Get the parameters.      # Get the parameters.
1431      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1432      # Create the load object.      # Create the load object.
1433      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1434                                   $ignore);
1435      # Cache it in the loader list.      # Cache it in the loader list.
1436      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1437      # Return it to the caller.      # Return it to the caller.
# Line 1246  Line 1468 
1468      # 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
1469      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads restartable.
1470      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1471            # Get the relation name.
1472            my $relName = $loader->RelName;
1473            # Check the ignore flag.
1474            if ($loader->Ignore) {
1475                Trace("Relation $relName not loaded.") if T(2);
1476            } else {
1477                # Here we really need to finish.
1478                Trace("Finishing $relName.") if T(2);
1479          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1480                if ($self->{options}->{dbLoad}) {
1481                    # Here we want to use the load file just created to load the database.
1482                    Trace("Loading relation $relName.") if T(2);
1483                    my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
1484                    # Accumulate the statistics from the DB load.
1485                    $stats->Accumulate($newStats);
1486                }
1487          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
         my $relName = $loader->RelName;  
1488          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1489      }      }
1490        }
1491      # Return the load statistics.      # Return the load statistics.
1492      return $retVal;      return $retVal;
1493  }  }

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