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revision 1.21, Sat Nov 12 03:42:48 2005 UTC revision 1.67, Tue Sep 19 00:11:12 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 119  Line 120 
120                  # an omitted access code can be defaulted to 1.                  # an omitted access code can be defaulted to 1.
121                  for my $genomeLine (@genomeList) {                  for my $genomeLine (@genomeList) {
122                      my ($genomeID, $accessCode) = split("\t", $genomeLine);                      my ($genomeID, $accessCode) = split("\t", $genomeLine);
123                      if (undef $accessCode) {                          if (! defined($accessCode)) {
124                          $accessCode = 1;                          $accessCode = 1;
125                      }                      }
126                      $genomes{$genomeID} = $accessCode;                      $genomes{$genomeID} = $accessCode;
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 171  Line 182 
182      return $retVal;      return $retVal;
183  }  }
184    
185    =head3 LoadOnly
186    
187    C<< my $flag = $spl->LoadOnly; >>
188    
189    Return TRUE if we are in load-only mode, else FALSE.
190    
191    =cut
192    
193    sub LoadOnly {
194        my ($self) = @_;
195        return $self->{options}->{loadOnly};
196    }
197    
198    =head3 PrimaryOnly
199    
200    C<< my $flag = $spl->PrimaryOnly; >>
201    
202    Return TRUE if only the main entity is to be loaded, else FALSE.
203    
204    =cut
205    
206    sub PrimaryOnly {
207        my ($self) = @_;
208        return $self->{options}->{primaryOnly};
209    }
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
213  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 235 
235    
236  =back  =back
237    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
238  =cut  =cut
239  #: Return Type $%;  #: Return Type $%;
240  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 245 
245      # Get the genome count.      # Get the genome count.
246      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
249      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254        if ($self->{options}->{loadOnly}) {
255            Trace("Loading from existing files.") if T(2);
256        } else {
257            Trace("Generating genome data.") if T(2);
258      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
259      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
260          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
261          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
262          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
263          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
264          # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
         # the genome ID to the strain. In some cases this is the totality of the strain name.  
265          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267          # Get the full taxonomy.          # Get the full taxonomy.
268          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
269          # Output the genome record.          # Output the genome record.
# Line 268  Line 299 
299              }              }
300          }          }
301      }      }
302        }
303      # Finish the loads.      # Finish the loads.
304      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
305      # Return the result.      # Return the result.
# Line 308  Line 340 
340      my $fig = $self->{fig};      my $fig = $self->{fig};
341      # Get the genome hash.      # Get the genome hash.
342      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
343      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
344      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
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 340  Line 375 
375              for my $coupleData (@couplings) {              for my $coupleData (@couplings) {
376                  my ($peg2, $score) = @{$coupleData};                  my ($peg2, $score) = @{$coupleData};
377                  # Compute the coupling ID.                  # Compute the coupling ID.
378                  my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
379                  if (! exists $dupHash{$coupleID}) {                  if (! exists $dupHash{$coupleID}) {
380                      $loadCoupling->Add("couplingIn");                      $loadCoupling->Add("couplingIn");
381                      # Here we have a new coupling to store in the load files.                      # Here we have a new coupling to store in the load files.
# Line 376  Line 411 
411                          }                          }
412                      }                      }
413                      for my $evidenceID (keys %evidenceMap) {                      for my $evidenceID (keys %evidenceMap) {
414                                # Get the ID for this evidence.
415                                $pchID++;
416                          # Create the evidence record.                          # Create the evidence record.
417                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
418                          $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
419                          # Connect it to the coupling.                          # Connect it to the coupling.
420                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
421                          # Connect it to the features.                          # Connect it to the features.
422                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
423                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
424                            }
425                      }                      }
426                  }                  }
427              }              }
# Line 410  Line 448 
448      FeatureTranslation      FeatureTranslation
449      FeatureUpstream      FeatureUpstream
450      IsLocatedIn      IsLocatedIn
451        HasFeature
452    
453  =over 4  =over 4
454    
# Line 426  Line 465 
465      my ($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);
488          $loadFeature->Add("genomeIn");          $loadFeature->Add("genomeIn");
489          # Get the feature list for this genome.          # Get the feature list for this genome.
490          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
491                # Sort and count the list.
492                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
493                my $count = scalar @featureTuples;
494                Trace("$count features found for genome $genomeID.") if T(3);
495                # Set up for our duplicate-feature check.
496                my $oldFeatureID = "";
497          # Loop through the features.          # Loop through the features.
498          for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
             $loadFeature->Add("featureIn");  
499              # Split the tuple.              # Split the tuple.
500              my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
501                    # Check for duplicates.
502                    if ($featureID eq $oldFeatureID) {
503                        Trace("Duplicate feature $featureID found.") if T(1);
504                    } else {
505                        $oldFeatureID = $featureID;
506                        # Count this feature.
507                        $loadFeature->Add("featureIn");
508                        # Get the functional assignment.
509                        my $assignment = $fig->function_of($featureID);
510              # Create the feature record.              # Create the feature record.
511              $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
512                        # Link it to the parent genome.
513                        $loadHasFeature->Put($genomeID, $featureID, $type);
514              # Create the aliases.              # Create the aliases.
515              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
516                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
517              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
518                  # Get the links.                  # Get the links.
519                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
520                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 533 
533                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
534                      }                      }
535                  }                  }
             }  
536              # 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
537              # 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
538              # the maximum segment size. This simplifies the genes_in_region processing              # the maximum segment size. This simplifies the genes_in_region processing
# Line 512  Line 561 
561              }              }
562          }          }
563      }      }
564            }
565        }
566      # Finish the loads.      # Finish the loads.
567      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
568      return $retVal;      return $retVal;
# Line 548  Line 599 
599      my $fig = $self->{fig};      my $fig = $self->{fig};
600      # Get the table of genome IDs.      # Get the table of genome IDs.
601      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
602      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
603      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
604                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
605      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
606        } else {
607            Trace("Generating BBH data.") if T(2);
608      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
609      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
610          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
611          Trace("Processing features for genome $genomeID.") if T(3);          Trace("Processing features for genome $genomeID.") if T(3);
612          # Get the feature list for this genome.          # Get the feature list for this genome.
613          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
614                # Count the BBHs we find.
615                my $bbhCount = 0;
616          # Loop through the features.          # Loop through the features.
617          for my $featureData (@{$features}) {          for my $featureData (@{$features}) {
618              # Split the tuple.              # Split the tuple.
# Line 575  Line 628 
628                  if ($genomeHash->{$targetGenomeID}) {                  if ($genomeHash->{$targetGenomeID}) {
629                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
630                                                         $score);                                                         $score);
631                            $bbhCount++;
632                        }
633                  }                  }
634              }              }
635                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
636          }          }
637      }      }
638      # Finish the loads.      # Finish the loads.
# Line 599  Line 655 
655  The following relations are loaded by this method.  The following relations are loaded by this method.
656    
657      Subsystem      Subsystem
658        SubsystemClass
659      Role      Role
660      RoleEC      RoleEC
661      SSCell      SSCell
# Line 639  Line 696 
696      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
697      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
698      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
     my $subsysCount = @subsysIDs;  
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
699      # Get the map list.      # Get the map list.
700      my @maps = $fig->all_maps;      my @maps = $fig->all_maps;
     my $mapCount = @maps;  
     # Create load objects for each of the tables we're loading.  
     my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);  
     my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);  
     my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);  
     my $loadRole = $self->_TableLoader('Role', $featureCount * 6);  
     my $loadRoleEC = $self->_TableLoader('RoleEC', $featureCount * 6);  
     my $loadCatalyzes = $self->_TableLoader('Catalyzes', $genomeCount * $featureCount);  
     my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);  
     my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);  
     my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);  
     my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);  
     my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);  
     my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);  
     my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);  
     my $loadRoleSubset = $self->_TableLoader('RoleSubset', $subsysCount * 50);  
     my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $subsysCount * 50);  
     my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $featureCount * $genomeCount);  
     my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $featureCount * $genomeCount);  
     my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $subsysCount * 50);  
     my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $subsysCount * 50);  
701      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
702      Trace("Beginning subsystem data load.") if T(2);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
703        my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
704        my $loadSubsystem = $self->_TableLoader('Subsystem');
705        my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
706        my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
707        my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
708        my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
709        my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
710        my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
711        my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
712        my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
713        my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
714        my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
715        my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
716        my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
717        my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
718        my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
719        my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
720        my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
721        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
722        if ($self->{options}->{loadOnly}) {
723            Trace("Loading from existing files.") if T(2);
724        } else {
725            Trace("Generating subsystem data.") if T(2);
726      # This hash will contain the role for each EC. When we're done, this      # This hash will contain the role for each EC. When we're done, this
727      # information will be used to generate the Catalyzes table.      # information will be used to generate the Catalyzes table.
728      my %ecToRoles = ();      my %ecToRoles = ();
# Line 678  Line 734 
734      my ($genomeID, $roleID);      my ($genomeID, $roleID);
735      my %roleData = ();      my %roleData = ();
736      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
737          # Get the subsystem object.          # Get the subsystem object.
738          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
739                # Only proceed if the subsystem has a spreadsheet.
740                if (! $sub->{empty_ss}) {
741                    Trace("Creating subsystem $subsysID.") if T(3);
742                    $loadSubsystem->Add("subsystemIn");
743          # Create the subsystem record.          # Create the subsystem record.
744          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
745          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
746          $loadSubsystem->Put($subsysID, $curator, $notes);          $loadSubsystem->Put($subsysID, $curator, $notes);
747                    my $classList = $fig->subsystem_classification($subsysID);
748                    my @classes = @$classList;
749                    if (@classes) {
750                        for my $class (@classes) {
751                            $loadSubsystemClass->Put($subsysID, $class);
752                        }
753                    }
754          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
755          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
756              # Connect to this role.              # Connect to this role.
# Line 729  Line 794 
794                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
795                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
796                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
797                      my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
798                      # Only proceed if features exist.                      # Only proceed if features exist.
799                      if (@pegs > 0) {                      if (@pegs > 0) {
800                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
# Line 750  Line 815 
815                  if ($pegCount > 0) {                  if ($pegCount > 0) {
816                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
817                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                     # Partition the PEGs found into clusters.  
                     my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
818                      # Create a hash mapping PEG IDs to cluster numbers.                      # Create a hash mapping PEG IDs to cluster numbers.
819                      # We default to -1 for all of them.                      # We default to -1 for all of them.
820                      my %clusterOf = map { $_ => -1 } @pegsFound;                      my %clusterOf = map { $_ => -1 } @pegsFound;
821                                # Partition the PEGs found into clusters.
822                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
823                      for (my $i = 0; $i <= $#clusters; $i++) {                      for (my $i = 0; $i <= $#clusters; $i++) {
824                          my $subList = $clusters[$i];                          my $subList = $clusters[$i];
825                          for my $peg (@{$subList}) {                          for my $peg (@{$subList}) {
# Line 782  Line 847 
847              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
848              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
849              # Connect the subset to its roles.              # Connect the subset to its roles.
850              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
851              for my $roleID (@roles) {              for my $roleID (@roles) {
852                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
853              }              }
# Line 802  Line 867 
867              }              }
868          }          }
869      }      }
870            }
871      # Now we loop through the diagrams. We need to create the diagram records      # Now we loop through the diagrams. We need to create the diagram records
872      # and link each diagram to its roles. Note that only roles which occur      # and link each diagram to its roles. Note that only roles which occur
873      # in subsystems (and therefore appear in the %ecToRoles hash) are      # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 834  Line 900 
900              }              }
901          }          }
902      }      }
903        }
904      # Finish the load.      # Finish the load.
905      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
906      return $retVal;      return $retVal;
# Line 875  Line 942 
942      my $fig = $self->{fig};      my $fig = $self->{fig};
943      # Get the genome hash.      # Get the genome hash.
944      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
945      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
946      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
947      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
948      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
949            Trace("Loading from existing files.") if T(2);
950        } else {
951            Trace("Generating property data.") if T(2);
952      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
953      my %propertyKeys = ();      my %propertyKeys = ();
954      my $nextID = 1;      my $nextID = 1;
955      # Loop through the genomes.      # Loop through the genomes.
956      for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
957          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
958                Trace("Generating properties for $genomeID.") if T(3);
959          # 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
960          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
961          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
962          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
963                my $featureCount = 0;
964                my $propertyCount = 0;
965          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
966          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
967              # 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
968              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
969              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
970                    if (scalar @attributeList) {
971                        $featureCount++;
972                    }
973              # Loop through the attributes.              # Loop through the attributes.
974              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
975                        $propertyCount++;
976                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
977                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
978                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 919  Line 994 
994                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
995              }              }
996          }          }
997                # Update the statistics.
998                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
999                $loadHasProperty->Add("featuresIn", $featureCount);
1000                $loadHasProperty->Add("propertiesIn", $propertyCount);
1001            }
1002      }      }
1003      # Finish the load.      # Finish the load.
1004      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 959  Line 1039 
1039      my $fig = $self->{fig};      my $fig = $self->{fig};
1040      # Get the genome hash.      # Get the genome hash.
1041      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1042      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1043      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1044      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1045      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1046      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1047      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1048      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1049            Trace("Loading from existing files.") if T(2);
1050        } else {
1051            Trace("Generating annotation data.") if T(2);
1052      # 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
1053      # user records.      # user records.
1054      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 980  Line 1062 
1062      # Loop through the genomes.      # Loop through the genomes.
1063      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1064          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);  
1065              # 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
1066              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1067              my %seenTimestamps = ();              my %seenTimestamps = ();
1068              # Check for a functional assignment.              # Get the genome's annotations.
1069              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1070              if ($func) {              Trace("Processing annotations.") if T(2);
1071                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1072                  # assignment annotation for it.                  # Get the annotation tuple.
1073                  if (! FIG::hypo($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};  
1074                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1075                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1076                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1077                  # stop the substitution search.                  # stop the substitution search.
1078                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1019  Line 1085 
1085                      # Here it's a number. We need to insure the one we use to form                      # Here it's a number. We need to insure the one we use to form
1086                      # the key is unique.                      # the key is unique.
1087                      my $keyStamp = $timestamp;                      my $keyStamp = $timestamp;
1088                      while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1089                          $keyStamp++;                          $keyStamp++;
1090                      }                      }
                     $seenTimestamps{$keyStamp} = 1;  
1091                      my $annotationID = "$peg:$keyStamp";                      my $annotationID = "$peg:$keyStamp";
1092                        $seenTimestamps{$annotationID} = 1;
1093                      # Insure the user exists.                      # Insure the user exists.
1094                      if (! $users{$user}) {                      if (! $users{$user}) {
1095                          $loadSproutUser->Put($user, "SEED user");                          $loadSproutUser->Put($user, "SEED user");
# Line 1081  Line 1147 
1147      my $fig = $self->{fig};      my $fig = $self->{fig};
1148      # Get the genome hash.      # Get the genome hash.
1149      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1150      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1151      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1152      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1153      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1154      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1155            Trace("Loading from existing files.") if T(2);
1156        } else {
1157            Trace("Generating annotation data.") if T(2);
1158      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1159      my %sourceURL = ();      my %sourceURL = ();
1160      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1116  Line 1184 
1184      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1185          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1186      }      }
1187        }
1188      # Finish the load.      # Finish the load.
1189      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1190      return $retVal;      return $retVal;
# Line 1155  Line 1224 
1224      my $fig = $self->{fig};      my $fig = $self->{fig};
1225      # Get the genome hash.      # Get the genome hash.
1226      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1227      # 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
1228      # it the key.      # it the key.
1229      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1230      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1231      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1232      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1233      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1234            Trace("Loading from existing files.") if T(2);
1235        } else {
1236            Trace("Generating external data.") if T(2);
1237      # 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.
1238      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1239      my $orgLine;      my $orgLine;
1240      while (defined($orgLine = <ORGS>)) {      while (defined($orgLine = <ORGS>)) {
1241          # Clean the input line.          # Clean the input line.
# Line 1176  Line 1247 
1247      close ORGS;      close ORGS;
1248      # Now the function file.      # Now the function file.
1249      my $funcLine;      my $funcLine;
1250      Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1251      while (defined($funcLine = <FUNCS>)) {      while (defined($funcLine = <FUNCS>)) {
1252          # Clean the line ending.          # Clean the line ending.
1253          chomp $funcLine;          chomp $funcLine;
# Line 1192  Line 1263 
1263              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1264          }          }
1265      }      }
1266        }
1267      # Finish the load.      # Finish the load.
1268      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1269      return $retVal;      return $retVal;
# Line 1232  Line 1304 
1304      my ($self) = @_;      my ($self) = @_;
1305      # Get the FIG object.      # Get the FIG object.
1306      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1307      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1308      my $loadReaction = $self->_TableLoader('Reaction', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1309      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1310      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1311      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1312      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1313      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1314      Trace("Beginning reaction/compound data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1315            Trace("Loading from existing files.") if T(2);
1316        } else {
1317            Trace("Generating annotation data.") if T(2);
1318      # First we create the compounds.      # First we create the compounds.
1319      my @compounds = $fig->all_compounds();      my @compounds = $fig->all_compounds();
1320      for my $cid (@compounds) {      for my $cid (@compounds) {
# Line 1291  Line 1363 
1363              }              }
1364          }          }
1365      }      }
1366        }
1367      # Finish the load.      # Finish the load.
1368      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1369      return $retVal;      return $retVal;
# Line 1326  Line 1399 
1399      my $fig = $self->{fig};      my $fig = $self->{fig};
1400      # Get the genome hash.      # Get the genome hash.
1401      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1402      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1403      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1404      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1405            Trace("Loading from existing files.") if T(2);
1406        } else {
1407            Trace("Generating group data.") if T(2);
1408      # Loop through the genomes.      # Loop through the genomes.
1409      my $line;      my $line;
1410      for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1411          Trace("Processing $genomeID.") if T(3);          Trace("Processing $genomeID.") if T(3);
1412          # Open the NMPDR group file for this genome.          # Open the NMPDR group file for this genome.
1413          if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&          if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
# Line 1345  Line 1420 
1420          }          }
1421          close TMP;          close TMP;
1422      }      }
1423        }
1424        # Finish the load.
1425        my $retVal = $self->_FinishAll();
1426        return $retVal;
1427    }
1428    
1429    =head3 LoadSynonymData
1430    
1431    C<< my $stats = $spl->LoadSynonymData(); >>
1432    
1433    Load the synonym groups into Sprout.
1434    
1435    The following relations are loaded by this method.
1436    
1437        SynonymGroup
1438        IsSynonymGroupFor
1439    
1440    The source information for these relations is taken from the C<maps_to_id> method
1441    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1442    SQL against the FIG database.
1443    
1444    =over 4
1445    
1446    =item RETURNS
1447    
1448    Returns a statistics object for the loads.
1449    
1450    =back
1451    
1452    =cut
1453    #: Return Type $%;
1454    sub LoadSynonymData {
1455        # Get this object instance.
1456        my ($self) = @_;
1457        # Get the FIG object.
1458        my $fig = $self->{fig};
1459        # Get the genome hash.
1460        my $genomeHash = $self->{genomes};
1461        # Create a load object for the table we're loading.
1462        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1463        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1464        if ($self->{options}->{loadOnly}) {
1465            Trace("Loading from existing files.") if T(2);
1466        } else {
1467            Trace("Generating synonym group data.") if T(2);
1468            # Get the database handle.
1469            my $dbh = $fig->db_handle();
1470            # Ask for the synonyms.
1471            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1472            my $result = $sth->execute();
1473            if (! defined($result)) {
1474                Confess("Database error in Synonym load: " . $sth->errstr());
1475            } else {
1476                # Remember the current synonym.
1477                my $current_syn = "";
1478                # Count the features.
1479                my $featureCount = 0;
1480                # Loop through the synonym/peg pairs.
1481                while (my @row = $sth->fetchrow()) {
1482                    # Get the synonym ID and feature ID.
1483                    my ($syn_id, $peg) = @row;
1484                    # Insure it's for one of our genomes.
1485                    my $genomeID = FIG::genome_of($peg);
1486                    if (exists $genomeHash->{$genomeID}) {
1487                        # Verify the synonym.
1488                        if ($syn_id ne $current_syn) {
1489                            # It's new, so put it in the group table.
1490                            $loadSynonymGroup->Put($syn_id);
1491                            $current_syn = $syn_id;
1492                        }
1493                        # Connect the synonym to the peg.
1494                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1495                        # Count this feature.
1496                        $featureCount++;
1497                        if ($featureCount % 1000 == 0) {
1498                            Trace("$featureCount features processed.") if T(3);
1499                        }
1500                    }
1501                }
1502            }
1503        }
1504        # Finish the load.
1505        my $retVal = $self->_FinishAll();
1506        return $retVal;
1507    }
1508    
1509    =head3 LoadFamilyData
1510    
1511    C<< my $stats = $spl->LoadFamilyData(); >>
1512    
1513    Load the protein families into Sprout.
1514    
1515    The following relations are loaded by this method.
1516    
1517        Family
1518        IsFamilyForFeature
1519    
1520    The source information for these relations is taken from the C<families_for_protein>,
1521    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1522    
1523    =over 4
1524    
1525    =item RETURNS
1526    
1527    Returns a statistics object for the loads.
1528    
1529    =back
1530    
1531    =cut
1532    #: Return Type $%;
1533    sub LoadFamilyData {
1534        # Get this object instance.
1535        my ($self) = @_;
1536        # Get the FIG object.
1537        my $fig = $self->{fig};
1538        # Get the genome hash.
1539        my $genomeHash = $self->{genomes};
1540        # Create load objects for the tables we're loading.
1541        my $loadFamily = $self->_TableLoader('Family');
1542        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1543        if ($self->{options}->{loadOnly}) {
1544            Trace("Loading from existing files.") if T(2);
1545        } else {
1546            Trace("Generating family data.") if T(2);
1547            # Create a hash for the family IDs.
1548            my %familyHash = ();
1549            # Loop through the genomes.
1550            for my $genomeID (sort keys %{$genomeHash}) {
1551                Trace("Processing features for $genomeID.") if T(2);
1552                # Loop through this genome's PEGs.
1553                for my $fid ($fig->all_features($genomeID, "peg")) {
1554                    $loadIsFamilyForFeature->Add("features", 1);
1555                    # Get this feature's families.
1556                    my @families = $fig->families_for_protein($fid);
1557                    # Loop through the families, connecting them to the feature.
1558                    for my $family (@families) {
1559                        $loadIsFamilyForFeature->Put($family, $fid);
1560                        # If this is a new family, create a record for it.
1561                        if (! exists $familyHash{$family}) {
1562                            $familyHash{$family} = 1;
1563                            $loadFamily->Add("families", 1);
1564                            my $size = $fig->sz_family($family);
1565                            my $func = $fig->family_function($family);
1566                            $loadFamily->Put($family, $size, $func);
1567                        }
1568                    }
1569                }
1570            }
1571        }
1572      # Finish the load.      # Finish the load.
1573      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1574      return $retVal;      return $retVal;
# Line 1366  Line 1590 
1590    
1591  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1592    
1593  =item rowCount (optional)  =item ignore
1594    
1595  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1596    
1597  =item RETURN  =item RETURN
1598    
# Line 1380  Line 1604 
1604    
1605  sub _TableLoader {  sub _TableLoader {
1606      # Get the parameters.      # Get the parameters.
1607      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1608      # Create the load object.      # Create the load object.
1609      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1610                                   $ignore);
1611      # Cache it in the loader list.      # Cache it in the loader list.
1612      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1613      # Return it to the caller.      # Return it to the caller.
# Line 1416  Line 1641 
1641      my $retVal = Stats->new();      my $retVal = Stats->new();
1642      # Get the loader list.      # Get the loader list.
1643      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1644        # Create a hash to hold the statistics objects, keyed on relation name.
1645        my %loaderHash = ();
1646      # 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
1647      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1648      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1649          # Trace the fact that we're cleaning up.          # Get the relation name.
1650          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1651          Trace("Finishing load for $relName.") if T(2);          # Check the ignore flag.
1652            if ($loader->Ignore) {
1653                Trace("Relation $relName not loaded.") if T(2);
1654            } else {
1655                # Here we really need to finish.
1656                Trace("Finishing $relName.") if T(2);
1657          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1658                $loaderHash{$relName} = $stats;
1659            }
1660        }
1661        # Now we loop through again, actually loading the tables. We want to finish before
1662        # loading so that if something goes wrong at this point, all the load files are usable
1663        # and we don't have to redo all that work.
1664        for my $relName (sort keys %loaderHash) {
1665            # Get the statistics for this relation.
1666            my $stats = $loaderHash{$relName};
1667            # Check for a database load.
1668          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1669              # Here we want to use the load file just created to load the database.              # Here we want to use the load file just created to load the database.
1670              Trace("Loading relation $relName.") if T(2);              Trace("Loading relation $relName.") if T(2);

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