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revision 1.15, Fri Sep 16 04:12:05 2005 UTC revision 1.40, Thu Jun 8 15:37:32 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 29  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 79  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 93  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 = $fig->genomes(1);
# Line 128  Line 130 
130              Confess("Invalid genome parameter ($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 ($type eq 'ARRAY') {
# Line 152  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 161  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 170  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 197  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 215  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 267  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 310  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 $genome.") if T(3);
# Line 367  Line 403 
403                              # We store this evidence in the hash if the usage                              # We store this evidence in the hash if the usage
404                              # is nonzero or no prior evidence has been found. This                              # is nonzero or no prior evidence has been found. This
405                              # insures that if there is duplicate evidence, we                              # insures that if there is duplicate evidence, we
406                              # at least keep the meaningful ones. Only evidence is                                  # at least keep the meaningful ones. Only evidence in
407                              # the hash makes it to the output.                              # the hash makes it to the output.
408                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {                              if ($usage || ! exists $evidenceMap{$evidenceKey}) {
409                                  $evidenceMap{$evidenceKey} = $evidenceData;                                  $evidenceMap{$evidenceKey} = $evidenceData;
# Line 382  Line 418 
418                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);
419                          # Connect it to the features.                          # Connect it to the features.
420                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);
421                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 1);                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);
422                            }
423                      }                      }
424                  }                  }
425              }              }
# Line 409  Line 446 
446      FeatureTranslation      FeatureTranslation
447      FeatureUpstream      FeatureUpstream
448      IsLocatedIn      IsLocatedIn
449        HasFeature
450    
451  =over 4  =over 4
452    
# Line 425  Line 463 
463      my ($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 $genomeID.") if T(3);
# Line 458  Line 493 
493              my ($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 482  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 511  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 547  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 578  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 599  Line 635 
635    
636      Subsystem      Subsystem
637      Role      Role
638        RoleEC
639      SSCell      SSCell
640      ContainsFeature      ContainsFeature
641      IsGenomeOf      IsGenomeOf
# Line 606  Line 643 
643      OccursInSubsystem      OccursInSubsystem
644      ParticipatesIn      ParticipatesIn
645      HasSSCell      HasSSCell
646        ConsistsOfRoles
647        RoleSubset
648        HasRoleSubset
649        ConsistsOfGenomes
650        GenomeSubset
651        HasGenomeSubset
652        Catalyzes
653        Diagram
654        RoleOccursIn
655    
656  =over 4  =over 4
657    
# Line 615  Line 661 
661    
662  =back  =back
663    
 B<TO DO>  
   
 Generate RoleName table?  
   
664  =cut  =cut
665  #: Return Type $%;  #: Return Type $%;
666  sub LoadSubsystemData {  sub LoadSubsystemData {
# Line 632  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 $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
683      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
684      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
685      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
686      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
687      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
688      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
689      Trace("Beginning subsystem data load.") if T(2);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
690        my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
691        my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
692        my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
693        my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
694        my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
695        my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
696        my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
697        my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
698        my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
699        if ($self->{options}->{loadOnly}) {
700            Trace("Loading from existing files.") if T(2);
701        } else {
702            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
709      # duplicates. As we move along, we'll connect the roles and subsystems.          # duplicates. As we move along, we'll connect the roles and subsystems
710            # and memorize up the reactions.
711      my ($genomeID, $roleID);      my ($genomeID, $roleID);
712      my %roleData = ();      my %roleData = ();
713      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
714                # Get the subsystem object.
715                my $sub = $fig->get_subsystem($subsysID);
716                # Only proceed if the subsystem has a spreadsheet.
717                if (! $sub->{empty_ss}) {
718          Trace("Creating subsystem $subsysID.") if T(3);          Trace("Creating subsystem $subsysID.") if T(3);
719          $loadSubsystem->Add("subsystemIn");          $loadSubsystem->Add("subsystemIn");
720          # Create the subsystem record.          # Create the subsystem record.
721          $loadSubsystem->Put($subsysID);                  my $curator = $sub->get_curator();
722          # Get the subsystem object.                  my $notes = $sub->get_notes();
723          my $sub = $fig->get_subsystem($subsysID);                  $loadSubsystem->Put($subsysID, $curator, $notes);
724          # Connect it to its roles.                  # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
725          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
726                        # Connect to this role.
727              $loadOccursInSubsystem->Add("roleIn");              $loadOccursInSubsystem->Add("roleIn");
728              $loadOccursInSubsystem->Put($roleID, $subsysID);                      $loadOccursInSubsystem->Put($roleID, $subsysID, $col);
729                        # If it's a new role, add it to the role table.
730              if (! exists $roleData{$roleID}) {              if (! exists $roleData{$roleID}) {
731                  $loadRole->Put($roleID);                          # Get the role's abbreviation.
732                            my $abbr = $sub->get_role_abbr($col);
733                            # Add the role.
734                            $loadRole->Put($roleID, $abbr);
735                  $roleData{$roleID} = 1;                  $roleData{$roleID} = 1;
736                            # Check for an EC number.
737                            if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {
738                                my $ec = $1;
739                                $loadRoleEC->Put($roleID, $ec);
740                                $ecToRoles{$ec} = $roleID;
741                            }
742              }              }
743          }          }
744          # 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 751 
751                  # Count the PEGs and cells found for verification purposes.                  # Count the PEGs and cells found for verification purposes.
752                  my $pegCount = 0;                  my $pegCount = 0;
753                  my $cellCount = 0;                  my $cellCount = 0;
754                            # Create a list for the PEGs we find. This list will be used
755                            # to generate cluster numbers.
756                            my @pegsFound = ();
757                            # Create a hash that maps spreadsheet IDs to PEGs. We will
758                            # use this to generate the ContainsFeature data after we have
759                            # the cluster numbers.
760                            my %cellPegs = ();
761                            # Get the genome's variant code for this subsystem.
762                            my $variantCode = $sub->get_variant_code($row);
763                  # 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
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 692  Line 774 
774                          $loadIsGenomeOf->Put($genomeID, $cellID);                          $loadIsGenomeOf->Put($genomeID, $cellID);
775                          $loadIsRoleOf->Put($roleID, $cellID);                          $loadIsRoleOf->Put($roleID, $cellID);
776                          $loadHasSSCell->Put($subsysID, $cellID);                          $loadHasSSCell->Put($subsysID, $cellID);
777                          # Attach the features to it.                                  # Remember its features.
778                          for my $pegID (@pegs) {                                  push @pegsFound, @pegs;
779                              $loadContainsFeature->Put($cellID, $pegID);                                  $cellPegs{$cellID} = \@pegs;
780                              $pegCount++;                                  $pegCount += @pegs;
781                          }                          }
782                      }                      }
783                  }                          # If we found some cells for this genome, we need to compute clusters and
784                  # If we found some cells for this genome, denote it participates in the                          # denote it participates in the subsystem.
                 # subsystem.  
785                  if ($pegCount > 0) {                  if ($pegCount > 0) {
786                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
787                      $loadParticipatesIn->Put($genomeID, $subsysID);                              $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
788                                # Partition the PEGs found into clusters.
789                                my @clusters = $fig->compute_clusters(\@pegsFound, $sub);
790                                # Create a hash mapping PEG IDs to cluster numbers.
791                                # We default to -1 for all of them.
792                                my %clusterOf = map { $_ => -1 } @pegsFound;
793                                for (my $i = 0; $i <= $#clusters; $i++) {
794                                    my $subList = $clusters[$i];
795                                    for my $peg (@{$subList}) {
796                                        $clusterOf{$peg} = $i;
797                                    }
798                                }
799                                # Create the ContainsFeature data.
800                                for my $cellID (keys %cellPegs) {
801                                    my $cellList = $cellPegs{$cellID};
802                                    for my $cellPeg (@$cellList) {
803                                        $loadContainsFeature->Put($cellID, $cellPeg, $clusterOf{$cellPeg});
804                  }                  }
805              }              }
806          }          }
807      }      }
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
808  }  }
809                    # Now we need to generate the subsets. The subset names must be concatenated to
810  =head3 LoadDiagramData                  # the subsystem name to make them unique keys. There are two types of subsets:
811                    # genome subsets and role subsets. We do the role subsets first.
812  C<< my $stats = $spl->LoadDiagramData(); >>                  my @subsetNames = $sub->get_subset_names();
813                    for my $subsetID (@subsetNames) {
814  Load the diagram data from FIG into Sprout.                      # Create the subset record.
815                        my $actualID = "$subsysID:$subsetID";
816  Diagrams are used to organize functional roles. The diagram shows the                      $loadRoleSubset->Put($actualID);
817  connections between chemicals that interact with a subsystem.                      # Connect the subset to the subsystem.
818                        $loadHasRoleSubset->Put($subsysID, $actualID);
819  The following relations are loaded by this method.                      # Connect the subset to its roles.
820                        my @roles = $sub->get_subsetC_roles($subsetID);
821      Diagram                      for my $roleID (@roles) {
822      RoleOccursIn                          $loadConsistsOfRoles->Put($actualID, $roleID);
823                        }
824  =over 4                  }
825                    # Next the genome subsets.
826  =item RETURNS                  @subsetNames = $sub->get_subset_namesR();
827                    for my $subsetID (@subsetNames) {
828  Returns a statistics object for the loads.                      # Create the subset record.
829                        my $actualID = "$subsysID:$subsetID";
830  =back                      $loadGenomeSubset->Put($actualID);
831                        # Connect the subset to the subsystem.
832  =cut                      $loadHasGenomeSubset->Put($subsysID, $actualID);
833  #: Return Type $%;                      # Connect the subset to its genomes.
834  sub LoadDiagramData {                      my @genomes = $sub->get_subsetR($subsetID);
835      # Get this object instance.                      for my $genomeID (@genomes) {
836      my ($self) = @_;                          $loadConsistsOfGenomes->Put($actualID, $genomeID);
837      # Get the FIG object.                      }
838      my $fig = $self->{fig};                  }
839      # Get the map list.              }
840      my @maps = $fig->all_maps;              # Now we loop through the diagrams. We need to create the diagram records
841      my $mapCount = @maps;              # and link each diagram to its roles. Note that only roles which occur
842      my $genomeCount = (keys %{$self->{genomes}});              # in subsystems (and therefore appear in the %ecToRoles hash) are
843      my $featureCount = $genomeCount * 4000;              # included.
844      # 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) {  
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 761  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 808  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 852  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 892  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 913  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 948  Line 1052 
1052                      $text =~ s/Set master function/Set FIG function/s;                      $text =~ s/Set master function/Set FIG function/s;
1053                      # Insure the time stamp is valid.                      # Insure the time stamp is valid.
1054                      if ($timestamp =~ /^\d+$/) {                      if ($timestamp =~ /^\d+$/) {
1055                          # Here it's a number. We need to insure it's unique.                      # Here it's a number. We need to insure the one we use to form
1056                          while ($seenTimestamps{$timestamp}) {                      # the key is unique.
1057                              $timestamp++;                      my $keyStamp = $timestamp;
1058                        while ($seenTimestamps{"$peg:$keyStamp"}) {
1059                            $keyStamp++;
1060                          }                          }
1061                          $seenTimestamps{$timestamp} = 1;                      my $annotationID = "$peg:$keyStamp";
1062                          my $annotationID = "$peg:$timestamp";                      $seenTimestamps{$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 961  Line 1067 
1067                              $users{$user} = 1;                              $users{$user} = 1;
1068                          }                          }
1069                          # Generate the annotation.                          # Generate the annotation.
1070                          $loadAnnotation->Put($annotationID, $timestamp, "$user\\n$text");                      $loadAnnotation->Put($annotationID, $timestamp, $text);
1071                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);                          $loadIsTargetOfAnnotation->Put($peg, $annotationID);
1072                          $loadMadeAnnotation->Put($user, $annotationID);                          $loadMadeAnnotation->Put($user, $annotationID);
1073                      } else {                      } else {
# Line 971  Line 1077 
1077                  }                  }
1078              }              }
1079          }          }
     }  
1080      # Finish the load.      # Finish the load.
1081      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1082      return $retVal;      return $retVal;
# Line 1012  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 1031  Line 1138 
1138              chomp $line;              chomp $line;
1139              my($sourceID, $desc, $url) = split(/\t/,$line);              my($sourceID, $desc, $url) = split(/\t/,$line);
1140              $loadComesFrom->Put($genomeID, $sourceID);              $loadComesFrom->Put($genomeID, $sourceID);
1141              if ($url && ! exists $sourceURL{$genomeID}) {                  if ($url && ! exists $sourceURL{$sourceID}) {
1142                  $loadSourceURL->Put($sourceID, $url);                  $loadSourceURL->Put($sourceID, $url);
1143                  $sourceURL{$sourceID} = 1;                  $sourceURL{$sourceID} = 1;
1144              }              }
1145              if ($desc && ! exists $sourceDesc{$sourceID}) {                  if ($desc) {
1146                  $loadSource->Put($sourceID, $desc);                      $sourceDesc{$sourceID} = $desc;
1147                  $sourceDesc{$sourceID} = 1;                  } elsif (! exists $sourceDesc{$sourceID}) {
1148                        $sourceDesc{$sourceID} = $sourceID;
1149              }              }
1150          }          }
1151          close TMP;          close TMP;
1152      }      }
1153            # Write the source descriptions.
1154            for my $sourceID (keys %sourceDesc) {
1155                $loadSource->Put($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 1081  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 1118  Line 1233 
1233              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1234          }          }
1235      }      }
1236        }
1237        # Finish the load.
1238        my $retVal = $self->_FinishAll();
1239        return $retVal;
1240    }
1241    
1242    
1243    =head3 LoadReactionData
1244    
1245    C<< my $stats = $spl->LoadReactionData(); >>
1246    
1247    Load the reaction data from FIG into Sprout.
1248    
1249    Reaction data connects reactions to the compounds that participate in them.
1250    
1251    The following relations are loaded by this method.
1252    
1253        Reaction
1254        ReactionURL
1255        Compound
1256        CompoundName
1257        CompoundCAS
1258        IsAComponentOf
1259    
1260    This method proceeds reaction by reaction rather than genome by genome.
1261    
1262    =over 4
1263    
1264    =item RETURNS
1265    
1266    Returns a statistics object for the loads.
1267    
1268    =back
1269    
1270    =cut
1271    #: Return Type $%;
1272    sub LoadReactionData {
1273        # Get this object instance.
1274        my ($self) = @_;
1275        # Get the FIG object.
1276        my $fig = $self->{fig};
1277        # Create load objects for each of the tables we're loading.
1278        my $loadReaction = $self->_TableLoader('Reaction');
1279        my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1280        my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1281        my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1282        my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1283        my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1284        if ($self->{options}->{loadOnly}) {
1285            Trace("Loading from existing files.") if T(2);
1286        } 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();
1313            for my $reactionID (@reactions) {
1314                # Create the reaction record.
1315                $loadReaction->Put($reactionID, $fig->reversible($reactionID));
1316                # Compute the reaction's URL.
1317                my $url = HTML::reaction_link($reactionID);
1318                # Put it in the ReactionURL table.
1319                $loadReactionURL->Put($reactionID, $url);
1320                # Now we need all of the reaction's compounds. We get these in two phases,
1321                # substrates first and then products.
1322                for my $product (0, 1) {
1323                    # Get the compounds of the current type for the current reaction. FIG will
1324                    # 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.
1326                    my @compounds = $fig->reaction2comp($reactionID, $product);
1327                    for my $compData (@compounds) {
1328                        # Extract the compound data from the current tuple.
1329                        my ($cid, $stoich, $main) = @{$compData};
1330                        # Link the compound to the reaction.
1331                        $loadIsAComponentOf->Put($cid, $reactionID, $discrim++, "", $main,
1332                                                 $product, $stoich);
1333                    }
1334                }
1335            }
1336        }
1337      # Finish the load.      # Finish the load.
1338      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1339      return $retVal;      return $retVal;
# Line 1153  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 1172  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 $retVal;
# Line 1193  Line 1412 
1412    
1413  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1414    
1415  =item rowCount (optional)  =item ignore
1416    
1417  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1418    
1419  =item RETURN  =item RETURN
1420    
# Line 1207  Line 1426 
1426    
1427  sub _TableLoader {  sub _TableLoader {
1428      # Get the parameters.      # Get the parameters.
1429      my ($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 1246  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            # Get the relation name.
1470            my $relName = $loader->RelName;
1471            # Check the ignore flag.
1472            if ($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}) {
1479                    # Here we want to use the load file just created to load the database.
1480                    Trace("Loading relation $relName.") if T(2);
1481                    my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
1482                    # Accumulate the statistics from the DB load.
1483                    $stats->Accumulate($newStats);
1484                }
1485          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
         my $relName = $loader->RelName;  
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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