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revision 1.21, Sat Nov 12 03:42:48 2005 UTC revision 1.34, Sat May 13 04:13:24 2006 UTC
# Line 80  Line 80 
80  =item subsysFile  =item subsysFile
81    
82  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
83  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
84  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
85    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
86    
87  =item options  =item options
88    
# Line 132  Line 133 
133      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
134      my %subsystems = ();      my %subsystems = ();
135      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
136          # Here we want all the subsystems.          # Here we want all the NMPDR subsystems. First we get the whole list.
137          %subsystems = map { $_ => 1 } $fig->all_subsystems();          my @subs = $fig->all_subsystems();
138            # Loop through, checking for the NMPDR file.
139            for my $sub (@subs) {
140                if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
141                    $subsystems{$sub} = 1;
142                }
143            }
144      } else {      } else {
145          my $type = ref $subsysFile;          my $type = ref $subsysFile;
146          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 171  Line 178 
178      return $retVal;      return $retVal;
179  }  }
180    
181    =head3 LoadOnly
182    
183    C<< my $flag = $spl->LoadOnly; >>
184    
185    Return TRUE if we are in load-only mode, else FALSE.
186    
187    =cut
188    
189    sub LoadOnly {
190        my ($self) = @_;
191        return $self->{options}->{loadOnly};
192    }
193    
194    =head3 PrimaryOnly
195    
196    C<< my $flag = $spl->PrimaryOnly; >>
197    
198    Return TRUE if only the main entity is to be loaded, else FALSE.
199    
200    =cut
201    
202    sub PrimaryOnly {
203        my ($self) = @_;
204        return $self->{options}->{primaryOnly};
205    }
206    
207  =head3 LoadGenomeData  =head3 LoadGenomeData
208    
209  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 231 
231    
232  =back  =back
233    
 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.)  
   
234  =cut  =cut
235  #: Return Type $%;  #: Return Type $%;
236  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 241 
241      # Get the genome count.      # Get the genome count.
242      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
243      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
244      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
245      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
246      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
247      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
248      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
249      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
250        if ($self->{options}->{loadOnly}) {
251            Trace("Loading from existing files.") if T(2);
252        } else {
253            Trace("Generating genome data.") if T(2);
254      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
255      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
256          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
257          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
258          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
259          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
260          # 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.  
261          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
262          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
263          # Get the full taxonomy.          # Get the full taxonomy.
264          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
265          # Output the genome record.          # Output the genome record.
# Line 268  Line 295 
295              }              }
296          }          }
297      }      }
298        }
299      # Finish the loads.      # Finish the loads.
300      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
301      # Return the result.      # Return the result.
# Line 311  Line 339 
339      my $genomeCount = (keys %{$genomeFilter});      my $genomeCount = (keys %{$genomeFilter});
340      my $featureCount = $genomeCount * 4000;      my $featureCount = $genomeCount * 4000;
341      # Start the loads.      # Start the loads.
342      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
343      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
344      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
345      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
346      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
347      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
348            Trace("Loading from existing files.") if T(2);
349        } else {
350            Trace("Generating coupling data.") if T(2);
351      # Loop through the genomes found.      # Loop through the genomes found.
352      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
353          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 389  Line 420 
420              }              }
421          }          }
422      }      }
423        }
424      # All done. Finish the load.      # All done. Finish the load.
425      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
426      return $retVal;      return $retVal;
# Line 410  Line 442 
442      FeatureTranslation      FeatureTranslation
443      FeatureUpstream      FeatureUpstream
444      IsLocatedIn      IsLocatedIn
445        HasFeature
446    
447  =over 4  =over 4
448    
# Line 426  Line 459 
459      my ($self) = @_;      my ($self) = @_;
460      # Get the FIG object.      # Get the FIG object.
461      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
462      # Get the table of genome IDs.      # Get the table of genome IDs.
463      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
464      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
465      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
466      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
467      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
468      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
469      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
470          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
471          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature');
         $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);  
     }  
472      # 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
473      # locations.      # locations.
474      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
475      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
476            Trace("Loading from existing files.") if T(2);
477        } else {
478            Trace("Generating feature data.") if T(2);
479      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
480      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
481          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
# Line 459  Line 489 
489              my ($featureID, $locations, undef, $type) = @{$featureData};              my ($featureID, $locations, undef, $type) = @{$featureData};
490              # Create the feature record.              # Create the feature record.
491              $loadFeature->Put($featureID, 1, $type);              $loadFeature->Put($featureID, 1, $type);
492                    # Link it to the parent genome.
493                    $loadHasFeature->Put($genomeID, $featureID, $type);
494              # Create the aliases.              # Create the aliases.
495              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
496                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
497              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
498                  # Get the links.                  # Get the links.
499                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
500                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 513 
513                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
514                      }                      }
515                  }                  }
             }  
516              # 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
517              # 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
518              # 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 541 
541              }              }
542          }          }
543      }      }
544        }
545      # Finish the loads.      # Finish the loads.
546      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
547      return $retVal;      return $retVal;
# Line 548  Line 578 
578      my $fig = $self->{fig};      my $fig = $self->{fig};
579      # Get the table of genome IDs.      # Get the table of genome IDs.
580      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
581      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
582      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
583                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
584      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
585        } else {
586            Trace("Generating BBH data.") if T(2);
587      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
588      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
589          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
# Line 579  Line 609 
609              }              }
610          }          }
611      }      }
612        }
613      # Finish the loads.      # Finish the loads.
614      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
615      return $retVal;      return $retVal;
# Line 639  Line 670 
670      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
671      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
672      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
     my $subsysCount = @subsysIDs;  
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
673      # Get the map list.      # Get the map list.
674      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);  
675      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
676      Trace("Beginning subsystem data load.") if T(2);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
677        my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
678        my $loadSubsystem = $self->_TableLoader('Subsystem');
679        my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
680        my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
681        my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
682        my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
683        my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
684        my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
685        my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
686        my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
687        my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
688        my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
689        my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
690        my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
691        my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
692        my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
693        my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
694        my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
695        if ($self->{options}->{loadOnly}) {
696            Trace("Loading from existing files.") if T(2);
697        } else {
698            Trace("Generating subsystem data.") if T(2);
699      # 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
700      # information will be used to generate the Catalyzes table.      # information will be used to generate the Catalyzes table.
701      my %ecToRoles = ();      my %ecToRoles = ();
# Line 678  Line 707 
707      my ($genomeID, $roleID);      my ($genomeID, $roleID);
708      my %roleData = ();      my %roleData = ();
709      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
710          # Get the subsystem object.          # Get the subsystem object.
711          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
712                # Only proceed if the subsystem has a spreadsheet.
713                if (! $sub->{empty_ss}) {
714                    Trace("Creating subsystem $subsysID.") if T(3);
715                    $loadSubsystem->Add("subsystemIn");
716          # Create the subsystem record.          # Create the subsystem record.
717          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
718          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
# Line 782  Line 813 
813              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
814              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
815              # Connect the subset to its roles.              # Connect the subset to its roles.
816              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
817              for my $roleID (@roles) {              for my $roleID (@roles) {
818                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
819              }              }
# Line 834  Line 865 
865              }              }
866          }          }
867      }      }
868            }
869        }
870      # Finish the load.      # Finish the load.
871      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
872      return $retVal;      return $retVal;
# Line 875  Line 908 
908      my $fig = $self->{fig};      my $fig = $self->{fig};
909      # Get the genome hash.      # Get the genome hash.
910      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
911      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
912      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
913      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
914      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
915            Trace("Loading from existing files.") if T(2);
916        } else {
917            Trace("Generating property data.") if T(2);
918      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
919      my %propertyKeys = ();      my %propertyKeys = ();
920      my $nextID = 1;      my $nextID = 1;
921      # Loop through the genomes.      # Loop through the genomes.
922      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
923          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
924                Trace("Generating properties for $genomeID.") if T(3);
925          # 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
926          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
927          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
928          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
929                my $featureCount = 0;
930                my $propertyCount = 0;
931          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
932          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
933              # 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
934              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
935              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
936                    if (scalar @attributeList) {
937                        $featureCount++;
938                    }
939              # Loop through the attributes.              # Loop through the attributes.
940              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
941                        $propertyCount++;
942                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
943                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
944                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 919  Line 960 
960                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
961              }              }
962          }          }
963                # Update the statistics.
964                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
965                $loadHasProperty->Add("featuresIn", $featureCount);
966                $loadHasProperty->Add("propertiesIn", $propertyCount);
967            }
968      }      }
969      # Finish the load.      # Finish the load.
970      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 959  Line 1005 
1005      my $fig = $self->{fig};      my $fig = $self->{fig};
1006      # Get the genome hash.      # Get the genome hash.
1007      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1008      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1009      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1010      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1011      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1012      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1013      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1014      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1015            Trace("Loading from existing files.") if T(2);
1016        } else {
1017            Trace("Generating annotation data.") if T(2);
1018      # 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
1019      # user records.      # user records.
1020      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 987  Line 1035 
1035              # Create a hash of timestamps. We use this to prevent duplicate time stamps              # Create a hash of timestamps. We use this to prevent duplicate time stamps
1036              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1037              my %seenTimestamps = ();              my %seenTimestamps = ();
1038              # Check for a functional assignment.                  # Loop through the annotations.
             my $func = $fig->function_of($peg);  
             if ($func) {  
                 # If this is NOT a hypothetical assignment, we create an  
                 # assignment annotation for it.  
                 if (! FIG::hypo($peg)) {  
                     # Note that we double the slashes so that what goes into the database is  
                     # a new-line escape sequence rather than an actual new-line.  
                     $loadAnnotation->Put("$peg:$time", $time, "FIG\\nSet function to\\n$func");  
                     $loadIsTargetOfAnnotation->Put($peg, "$peg:$time");  
                     $loadMadeAnnotation->Put("FIG", "$peg:$time");  
                     # Denote we've seen this timestamp.  
                     $seenTimestamps{$time} = 1;  
                 }  
             }  
             # Now loop through the real annotations.  
1039              for my $tuple ($fig->feature_annotations($peg, "raw")) {              for my $tuple ($fig->feature_annotations($peg, "raw")) {
1040                  my ($fid, $timestamp, $user, $text) = @{$tuple};                  my ($fid, $timestamp, $user, $text) = @{$tuple};
1041                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
# Line 1041  Line 1074 
1074              }              }
1075          }          }
1076      }      }
1077        }
1078      # Finish the load.      # Finish the load.
1079      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1080      return $retVal;      return $retVal;
# Line 1081  Line 1115 
1115      my $fig = $self->{fig};      my $fig = $self->{fig};
1116      # Get the genome hash.      # Get the genome hash.
1117      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1118      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1119      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1120      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1121      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1122      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1123            Trace("Loading from existing files.") if T(2);
1124        } else {
1125            Trace("Generating annotation data.") if T(2);
1126      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1127      my %sourceURL = ();      my %sourceURL = ();
1128      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1116  Line 1152 
1152      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1153          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1154      }      }
1155        }
1156      # Finish the load.      # Finish the load.
1157      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1158      return $retVal;      return $retVal;
# Line 1155  Line 1192 
1192      my $fig = $self->{fig};      my $fig = $self->{fig};
1193      # Get the genome hash.      # Get the genome hash.
1194      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1195      # 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
1196      # it the key.      # it the key.
1197      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1198      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1199      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1200      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1201      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1202            Trace("Loading from existing files.") if T(2);
1203        } else {
1204            Trace("Generating external data.") if T(2);
1205      # 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.
1206      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");
1207      my $orgLine;      my $orgLine;
# Line 1192  Line 1231 
1231              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1232          }          }
1233      }      }
1234        }
1235      # Finish the load.      # Finish the load.
1236      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1237      return $retVal;      return $retVal;
# Line 1232  Line 1272 
1272      my ($self) = @_;      my ($self) = @_;
1273      # Get the FIG object.      # Get the FIG object.
1274      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1275      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1276      my $loadReaction = $self->_TableLoader('Reaction', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1277      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1278      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1279      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1280      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1281      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1282      Trace("Beginning reaction/compound data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1283            Trace("Loading from existing files.") if T(2);
1284        } else {
1285            Trace("Generating annotation data.") if T(2);
1286      # First we create the compounds.      # First we create the compounds.
1287      my @compounds = $fig->all_compounds();      my @compounds = $fig->all_compounds();
1288      for my $cid (@compounds) {      for my $cid (@compounds) {
# Line 1291  Line 1331 
1331              }              }
1332          }          }
1333      }      }
1334        }
1335      # Finish the load.      # Finish the load.
1336      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1337      return $retVal;      return $retVal;
# Line 1326  Line 1367 
1367      my $fig = $self->{fig};      my $fig = $self->{fig};
1368      # Get the genome hash.      # Get the genome hash.
1369      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1370      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1371      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1372      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1373            Trace("Loading from existing files.") if T(2);
1374        } else {
1375            Trace("Generating group data.") if T(2);
1376      # Loop through the genomes.      # Loop through the genomes.
1377      my $line;      my $line;
1378      for my $genomeID (keys %{$genomeHash}) {      for my $genomeID (keys %{$genomeHash}) {
# Line 1345  Line 1388 
1388          }          }
1389          close TMP;          close TMP;
1390      }      }
1391        }
1392      # Finish the load.      # Finish the load.
1393      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1394      return $retVal;      return $retVal;
# Line 1366  Line 1410 
1410    
1411  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1412    
1413  =item rowCount (optional)  =item ignore
1414    
1415  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1416    
1417  =item RETURN  =item RETURN
1418    
# Line 1380  Line 1424 
1424    
1425  sub _TableLoader {  sub _TableLoader {
1426      # Get the parameters.      # Get the parameters.
1427      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1428      # Create the load object.      # Create the load object.
1429      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1430                                   $ignore);
1431      # Cache it in the loader list.      # Cache it in the loader list.
1432      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1433      # Return it to the caller.      # Return it to the caller.
# Line 1419  Line 1464 
1464      # 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
1465      # ignominiously. At some future point, we want to make the loads restartable.      # ignominiously. At some future point, we want to make the loads restartable.
1466      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1467          # Trace the fact that we're cleaning up.          # Get the relation name.
1468          my $relName = $loader->RelName;          my $relName = $loader->RelName;
1469          Trace("Finishing load for $relName.") if T(2);          # Check the ignore flag.
1470            if ($loader->Ignore) {
1471                Trace("Relation $relName not loaded.") if T(2);
1472            } else {
1473                # Here we really need to finish.
1474                Trace("Finishing $relName.") if T(2);
1475          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1476          if ($self->{options}->{dbLoad}) {          if ($self->{options}->{dbLoad}) {
1477              # Here we want to use the load file just created to load the database.              # Here we want to use the load file just created to load the database.
# Line 1433  Line 1483 
1483          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
1484          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1485      }      }
1486        }
1487      # Return the load statistics.      # Return the load statistics.
1488      return $retVal;      return $retVal;
1489  }  }

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