[Bio] / Sprout / SproutLoad.pm Repository:
ViewVC logotype

Diff of /Sprout/SproutLoad.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.21, Sat Nov 12 03:42:48 2005 UTC revision 1.48, Fri Jul 7 00:24:16 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the NMPDR subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for the NMPDR file.
142                for my $sub (@subs) {
143                    if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 171  Line 182 
182      return $retVal;      return $retVal;
183  }  }
184    
185    =head3 LoadOnly
186    
187    C<< my $flag = $spl->LoadOnly; >>
188    
189    Return TRUE if we are in load-only mode, else FALSE.
190    
191    =cut
192    
193    sub LoadOnly {
194        my ($self) = @_;
195        return $self->{options}->{loadOnly};
196    }
197    
198    =head3 PrimaryOnly
199    
200    C<< my $flag = $spl->PrimaryOnly; >>
201    
202    Return TRUE if only the main entity is to be loaded, else FALSE.
203    
204    =cut
205    
206    sub PrimaryOnly {
207        my ($self) = @_;
208        return $self->{options}->{primaryOnly};
209    }
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
213  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 235 
235    
236  =back  =back
237    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
238  =cut  =cut
239  #: Return Type $%;  #: Return Type $%;
240  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 245 
245      # Get the genome count.      # Get the genome count.
246      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
249      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254        if ($self->{options}->{loadOnly}) {
255            Trace("Loading from existing files.") if T(2);
256        } else {
257            Trace("Generating genome data.") if T(2);
258      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
259      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
260          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
261          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
262          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
263          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
264          # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
         # the genome ID to the strain. In some cases this is the totality of the strain name.  
265          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267          # Get the full taxonomy.          # Get the full taxonomy.
268          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
269          # Output the genome record.          # Output the genome record.
# Line 268  Line 299 
299              }              }
300          }          }
301      }      }
302        }
303      # Finish the loads.      # Finish the loads.
304      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
305      # Return the result.      # Return the result.
# Line 311  Line 343 
343      my $genomeCount = (keys %{$genomeFilter});      my $genomeCount = (keys %{$genomeFilter});
344      my $featureCount = $genomeCount * 4000;      my $featureCount = $genomeCount * 4000;
345      # Start the loads.      # Start the loads.
346      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
347      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
348      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
349      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
350      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
351      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
352            Trace("Loading from existing files.") if T(2);
353        } else {
354            Trace("Generating coupling data.") if T(2);
355      # Loop through the genomes found.      # Loop through the genomes found.
356      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
357          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 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 389  Line 424 
424              }              }
425          }          }
426      }      }
427        }
428      # All done. Finish the load.      # All done. Finish the load.
429      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
430      return $retVal;      return $retVal;
# Line 410  Line 446 
446      FeatureTranslation      FeatureTranslation
447      FeatureUpstream      FeatureUpstream
448      IsLocatedIn      IsLocatedIn
449        HasFeature
450    
451  =over 4  =over 4
452    
# Line 426  Line 463 
463      my ($self) = @_;      my ($self) = @_;
464      # Get the FIG object.      # Get the FIG object.
465      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
466      # Get the table of genome IDs.      # Get the table of genome IDs.
467      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
468      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
469      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
470      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
471      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
472      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
473      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
474          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
475          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature');
         $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);  
     }  
476      # Get the maximum sequence size. We need this later for splitting up the      # Get the maximum sequence size. We need this later for splitting up the
477      # locations.      # locations.
478      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
479      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
480            Trace("Loading from existing files.") if T(2);
481        } else {
482            Trace("Generating feature data.") if T(2);
483      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
484      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
485          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
# Line 459  Line 493 
493              my ($featureID, $locations, undef, $type) = @{$featureData};              my ($featureID, $locations, undef, $type) = @{$featureData};
494              # Create the feature record.              # Create the feature record.
495              $loadFeature->Put($featureID, 1, $type);              $loadFeature->Put($featureID, 1, $type);
496                    # Link it to the parent genome.
497                    $loadHasFeature->Put($genomeID, $featureID, $type);
498              # Create the aliases.              # Create the aliases.
499              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
500                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
501              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
502                  # Get the links.                  # Get the links.
503                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
504                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 517 
517                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
518                      }                      }
519                  }                  }
             }  
520              # This part is the roughest. We need to relate the features to contig              # This part is the roughest. We need to relate the features to contig
521              # locations, and the locations must be split so that none of them exceed              # locations, and the locations must be split so that none of them exceed
522              # the maximum segment size. This simplifies the genes_in_region processing              # the maximum segment size. This simplifies the genes_in_region processing
# Line 512  Line 545 
545              }              }
546          }          }
547      }      }
548        }
549      # Finish the loads.      # Finish the loads.
550      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
551      return $retVal;      return $retVal;
# Line 548  Line 582 
582      my $fig = $self->{fig};      my $fig = $self->{fig};
583      # Get the table of genome IDs.      # Get the table of genome IDs.
584      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
585      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
586      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
587                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
588      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
589        } else {
590            Trace("Generating BBH data.") if T(2);
591      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
592      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
593          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
# Line 579  Line 613 
613              }              }
614          }          }
615      }      }
616        }
617      # Finish the loads.      # Finish the loads.
618      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
619      return $retVal;      return $retVal;
# Line 599  Line 634 
634  The following relations are loaded by this method.  The following relations are loaded by this method.
635    
636      Subsystem      Subsystem
637        SubsystemClass
638      Role      Role
639      RoleEC      RoleEC
640      SSCell      SSCell
# Line 639  Line 675 
675      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
676      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
677      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
     my $subsysCount = @subsysIDs;  
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
678      # Get the map list.      # Get the map list.
679      my @maps = $fig->all_maps;      my @maps = $fig->all_maps;
     my $mapCount = @maps;  
680      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
681      my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
682      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
683      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
684      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
685      my $loadRoleEC = $self->_TableLoader('RoleEC', $featureCount * 6);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
686      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $genomeCount * $featureCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
687      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
688      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
689      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
690      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
691      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
692      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
693      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
694      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $subsysCount * 50);      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
695      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $subsysCount * 50);      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
696      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $featureCount * $genomeCount);      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
697      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $featureCount * $genomeCount);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
698      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $subsysCount * 50);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
699      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $subsysCount * 50);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
700      # Create load objects for each of the tables we're loading.      my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
701      Trace("Beginning subsystem data load.") if T(2);      if ($self->{options}->{loadOnly}) {
702            Trace("Loading from existing files.") if T(2);
703        } else {
704            Trace("Generating subsystem data.") if T(2);
705      # This hash will contain the role for each EC. When we're done, this      # This hash will contain the role for each EC. When we're done, this
706      # information will be used to generate the Catalyzes table.      # information will be used to generate the Catalyzes table.
707      my %ecToRoles = ();      my %ecToRoles = ();
# Line 678  Line 713 
713      my ($genomeID, $roleID);      my ($genomeID, $roleID);
714      my %roleData = ();      my %roleData = ();
715      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
716          # Get the subsystem object.          # Get the subsystem object.
717          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
718                # Only proceed if the subsystem has a spreadsheet.
719                if (! $sub->{empty_ss}) {
720                    Trace("Creating subsystem $subsysID.") if T(3);
721                    $loadSubsystem->Add("subsystemIn");
722          # Create the subsystem record.          # Create the subsystem record.
723          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
724          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
725          $loadSubsystem->Put($subsysID, $curator, $notes);          $loadSubsystem->Put($subsysID, $curator, $notes);
726                    my $class = $fig->subsystem_classification($subsysID);
727                    if ($class) {
728                        $loadSubsystemClass->Put($subsysID, $class);
729                    }
730          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.          # Connect it to its roles. Each role is a column in the subsystem spreadsheet.
731          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
732              # Connect to this role.              # Connect to this role.
# Line 729  Line 770 
770                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
771                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
772                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
773                      my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
774                      # Only proceed if features exist.                      # Only proceed if features exist.
775                      if (@pegs > 0) {                      if (@pegs > 0) {
776                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
# Line 750  Line 791 
791                  if ($pegCount > 0) {                  if ($pegCount > 0) {
792                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
793                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                     # Partition the PEGs found into clusters.  
                     my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
794                      # Create a hash mapping PEG IDs to cluster numbers.                      # Create a hash mapping PEG IDs to cluster numbers.
795                      # We default to -1 for all of them.                      # We default to -1 for all of them.
796                      my %clusterOf = map { $_ => -1 } @pegsFound;                      my %clusterOf = map { $_ => -1 } @pegsFound;
797                                # Partition the PEGs found into clusters.
798                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
799                      for (my $i = 0; $i <= $#clusters; $i++) {                      for (my $i = 0; $i <= $#clusters; $i++) {
800                          my $subList = $clusters[$i];                          my $subList = $clusters[$i];
801                          for my $peg (@{$subList}) {                          for my $peg (@{$subList}) {
# Line 782  Line 823 
823              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
824              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
825              # Connect the subset to its roles.              # Connect the subset to its roles.
826              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
827              for my $roleID (@roles) {              for my $roleID (@roles) {
828                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
829              }              }
# Line 834  Line 875 
875              }              }
876          }          }
877      }      }
878            }
879        }
880      # Finish the load.      # Finish the load.
881      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
882      return $retVal;      return $retVal;
# Line 875  Line 918 
918      my $fig = $self->{fig};      my $fig = $self->{fig};
919      # Get the genome hash.      # Get the genome hash.
920      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
921      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
922      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
923      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
924      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
925            Trace("Loading from existing files.") if T(2);
926        } else {
927            Trace("Generating property data.") if T(2);
928      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
929      my %propertyKeys = ();      my %propertyKeys = ();
930      my $nextID = 1;      my $nextID = 1;
931      # Loop through the genomes.      # Loop through the genomes.
932      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
933          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
934                Trace("Generating properties for $genomeID.") if T(3);
935          # 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
936          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
937          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
938          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
939                my $featureCount = 0;
940                my $propertyCount = 0;
941          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
942          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
943              # 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
944              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
945              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
946                    if (scalar @attributeList) {
947                        $featureCount++;
948                    }
949              # Loop through the attributes.              # Loop through the attributes.
950              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
951                        $propertyCount++;
952                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
953                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
954                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 919  Line 970 
970                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
971              }              }
972          }          }
973                # Update the statistics.
974                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
975                $loadHasProperty->Add("featuresIn", $featureCount);
976                $loadHasProperty->Add("propertiesIn", $propertyCount);
977            }
978      }      }
979      # Finish the load.      # Finish the load.
980      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 959  Line 1015 
1015      my $fig = $self->{fig};      my $fig = $self->{fig};
1016      # Get the genome hash.      # Get the genome hash.
1017      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1018      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1019      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1020      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1021      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1022      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1023      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1024      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1025            Trace("Loading from existing files.") if T(2);
1026        } else {
1027            Trace("Generating annotation data.") if T(2);
1028      # 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
1029      # user records.      # user records.
1030      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 980  Line 1038 
1038      # Loop through the genomes.      # Loop through the genomes.
1039      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1040          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);  
1041              # Create a hash of timestamps. We use this to prevent duplicate time stamps              # Create a hash of timestamps. We use this to prevent duplicate time stamps
1042              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1043              my %seenTimestamps = ();              my %seenTimestamps = ();
1044              # Check for a functional assignment.              # Get the genome's annotations.
1045              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1046              if ($func) {              Trace("Processing annotations.") if T(2);
1047                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1048                  # assignment annotation for it.                  # Get the annotation tuple.
1049                  if (! FIG::hypo($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};  
1050                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1051                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1052                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1053                  # stop the substitution search.                  # stop the substitution search.
1054                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1019  Line 1061 
1061                      # 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
1062                      # the key is unique.                      # the key is unique.
1063                      my $keyStamp = $timestamp;                      my $keyStamp = $timestamp;
1064                      while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1065                          $keyStamp++;                          $keyStamp++;
1066                      }                      }
                     $seenTimestamps{$keyStamp} = 1;  
1067                      my $annotationID = "$peg:$keyStamp";                      my $annotationID = "$peg:$keyStamp";
1068                        $seenTimestamps{$annotationID} = 1;
1069                      # Insure the user exists.                      # Insure the user exists.
1070                      if (! $users{$user}) {                      if (! $users{$user}) {
1071                          $loadSproutUser->Put($user, "SEED user");                          $loadSproutUser->Put($user, "SEED user");
# Line 1081  Line 1123 
1123      my $fig = $self->{fig};      my $fig = $self->{fig};
1124      # Get the genome hash.      # Get the genome hash.
1125      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1126      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1127      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1128      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1129      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1130      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1131            Trace("Loading from existing files.") if T(2);
1132        } else {
1133            Trace("Generating annotation data.") if T(2);
1134      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1135      my %sourceURL = ();      my %sourceURL = ();
1136      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1116  Line 1160 
1160      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1161          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1162      }      }
1163        }
1164      # Finish the load.      # Finish the load.
1165      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1166      return $retVal;      return $retVal;
# Line 1155  Line 1200 
1200      my $fig = $self->{fig};      my $fig = $self->{fig};
1201      # Get the genome hash.      # Get the genome hash.
1202      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1203      # 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
1204      # it the key.      # it the key.
1205      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1206      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1207      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1208      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1209      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1210            Trace("Loading from existing files.") if T(2);
1211        } else {
1212            Trace("Generating external data.") if T(2);
1213      # 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.
1214      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");
1215      my $orgLine;      my $orgLine;
# Line 1192  Line 1239 
1239              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1240          }          }
1241      }      }
1242        }
1243      # Finish the load.      # Finish the load.
1244      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1245      return $retVal;      return $retVal;
# Line 1232  Line 1280 
1280      my ($self) = @_;      my ($self) = @_;
1281      # Get the FIG object.      # Get the FIG object.
1282      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1283      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1284      my $loadReaction = $self->_TableLoader('Reaction', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1285      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1286      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1287      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1288      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1289      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1290      Trace("Beginning reaction/compound data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1291            Trace("Loading from existing files.") if T(2);
1292        } else {
1293            Trace("Generating annotation data.") if T(2);
1294      # First we create the compounds.      # First we create the compounds.
1295      my @compounds = $fig->all_compounds();      my @compounds = $fig->all_compounds();
1296      for my $cid (@compounds) {      for my $cid (@compounds) {
# Line 1291  Line 1339 
1339              }              }
1340          }          }
1341      }      }
1342        }
1343      # Finish the load.      # Finish the load.
1344      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1345      return $retVal;      return $retVal;
# Line 1326  Line 1375 
1375      my $fig = $self->{fig};      my $fig = $self->{fig};
1376      # Get the genome hash.      # Get the genome hash.
1377      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1378      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1379      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1380      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1381            Trace("Loading from existing files.") if T(2);
1382        } else {
1383            Trace("Generating group data.") if T(2);
1384      # Loop through the genomes.      # Loop through the genomes.
1385      my $line;      my $line;
1386      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
# Line 1345  Line 1396 
1396          }          }
1397          close TMP;          close TMP;
1398      }      }
1399        }
1400        # Finish the load.
1401        my $retVal = $self->_FinishAll();
1402        return $retVal;
1403    }
1404    
1405    =head3 LoadSynonymData
1406    
1407    C<< my $stats = $spl->LoadSynonymData(); >>
1408    
1409    Load the synonym groups into Sprout.
1410    
1411    The following relations are loaded by this method.
1412    
1413        SynonymGroup
1414        IsSynonymGroupFor
1415    
1416    The source information for these relations is taken from the C<maps_to_id> method
1417    of the B<FIG> object. The process starts from the features, so it is possible
1418    that there will be duplicates in the SynonymGroup load file, since the relationship
1419    is one-to-many toward the features. The automatic sort on primary entity relations
1420    will fix this for us.
1421    
1422    =over 4
1423    
1424    =item RETURNS
1425    
1426    Returns a statistics object for the loads.
1427    
1428    =back
1429    
1430    =cut
1431    #: Return Type $%;
1432    sub LoadSynonymData {
1433        # Get this object instance.
1434        my ($self) = @_;
1435        # Get the FIG object.
1436        my $fig = $self->{fig};
1437        # Get the genome hash.
1438        my $genomeHash = $self->{genomes};
1439        # Create a load object for the table we're loading.
1440        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1441        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1442        if ($self->{options}->{loadOnly}) {
1443            Trace("Loading from existing files.") if T(2);
1444        } else {
1445            Trace("Generating synonym group data.") if T(2);
1446            # Loop through the genomes.
1447            for my $genomeID (sort keys %{$genomeHash}) {
1448                Trace("Processing $genomeID.") if T(3);
1449                # Get all of the features for this genome. The only method that does this is
1450                # all_features_detailed, which returns extra baggage that we discard.
1451                my $featureData = $fig->all_features_detailed($genomeID);
1452                my @fids = map { $_->[0] } @{$featureData};
1453                Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);
1454                # Loop through the feature IDs.
1455                for my $fid (@fids) {
1456                    # Get the group for this feature.
1457                    my $synonym = $fig->maps_to_id($fid);
1458                    # Only proceed if the synonym is a real group.
1459                    if ($synonym ne $fid) {
1460                        $loadSynonymGroup->Put($synonym);
1461                        $loadIsSynonymGroupFor->Put($synonym, $fid);
1462                    }
1463                }
1464            }
1465        }
1466      # Finish the load.      # Finish the load.
1467      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1468      return $retVal;      return $retVal;
1469  }  }
1470    
1471    
1472  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1473    
1474  =head3 TableLoader  =head3 TableLoader
# Line 1366  Line 1485 
1485    
1486  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1487    
1488  =item rowCount (optional)  =item ignore
1489    
1490  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1491    
1492  =item RETURN  =item RETURN
1493    
# Line 1380  Line 1499 
1499    
1500  sub _TableLoader {  sub _TableLoader {
1501      # Get the parameters.      # Get the parameters.
1502      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1503      # Create the load object.      # Create the load object.
1504      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1505                                   $ignore);
1506      # Cache it in the loader list.      # Cache it in the loader list.
1507      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1508      # Return it to the caller.      # Return it to the caller.
# Line 1416  Line 1536 
1536      my $retVal = Stats->new();      my $retVal = Stats->new();
1537      # Get the loader list.      # Get the loader list.
1538      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1539        # Create a hash to hold the statistics objects, keyed on relation name.
1540        my %loaderHash = ();
1541      # Loop through the list, finishing the loads. Note that if the finish fails, we die      # Loop through the list, finishing the loads. Note that if the finish fails, we die
1542      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads more restartable.
1543      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1544          # Trace the fact that we're cleaning up.          # Get the relation name.
1545          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1546          Trace("Finishing load for $relName.") if T(2);          # Check the ignore flag.
1547            if ($loader->Ignore) {
1548                Trace("Relation $relName not loaded.") if T(2);
1549            } else {
1550                # Here we really need to finish.
1551                Trace("Finishing $relName.") if T(2);
1552          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1553                $loaderHash{$relName} = $stats;
1554            }
1555        }
1556        # Now we loop through again, actually loading the tables. We want to finish before
1557        # loading so that if something goes wrong at this point, all the load files are usable
1558        # and we don't have to redo all that work.
1559        for my $relName (sort keys %loaderHash) {
1560            # Get the statistics for this relation.
1561            my $stats = $loaderHash{$relName};
1562            # Check for a database load.
1563          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1564              # Here we want to use the load file just created to load the database.              # Here we want to use the load file just created to load the database.
1565              Trace("Loading relation $relName.") if T(2);              Trace("Loading relation $relName.") if T(2);
# Line 1433  Line 1570 
1570          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
1571          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1572      }      }
1573        }
1574      # Return the load statistics.      # Return the load statistics.
1575      return $retVal;      return $retVal;
1576  }  }

Legend:
Removed from v.1.21  
changed lines
  Added in v.1.48

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3