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revision 1.18, Wed Oct 12 03:17:58 2005 UTC revision 1.68, Sun Sep 24 17:14:16 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 119  Line 120 
120                  # an omitted access code can be defaulted to 1.                  # an omitted access code can be defaulted to 1.
121                  for my $genomeLine (@genomeList) {                  for my $genomeLine (@genomeList) {
122                      my ($genomeID, $accessCode) = split("\t", $genomeLine);                      my ($genomeID, $accessCode) = split("\t", $genomeLine);
123                      if (undef $accessCode) {                          if (! defined($accessCode)) {
124                          $accessCode = 1;                          $accessCode = 1;
125                      }                      }
126                      $genomes{$genomeID} = $accessCode;                      $genomes{$genomeID} = $accessCode;
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the usable subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for usability.
142                for my $sub (@subs) {
143                    if ($fig->usable_subsystem($sub)) {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 171  Line 182 
182      return $retVal;      return $retVal;
183  }  }
184    
185    =head3 LoadOnly
186    
187    C<< my $flag = $spl->LoadOnly; >>
188    
189    Return TRUE if we are in load-only mode, else FALSE.
190    
191    =cut
192    
193    sub LoadOnly {
194        my ($self) = @_;
195        return $self->{options}->{loadOnly};
196    }
197    
198    =head3 PrimaryOnly
199    
200    C<< my $flag = $spl->PrimaryOnly; >>
201    
202    Return TRUE if only the main entity is to be loaded, else FALSE.
203    
204    =cut
205    
206    sub PrimaryOnly {
207        my ($self) = @_;
208        return $self->{options}->{primaryOnly};
209    }
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
213  C<< my $stats = $spl->LoadGenomeData(); >>  C<< my $stats = $spl->LoadGenomeData(); >>
# Line 198  Line 235 
235    
236  =back  =back
237    
 B<TO DO>  
   
 Real quality vectors instead of C<unknown> for everything.  
   
 GenomeGroup relation. (The original script took group information from the C<NMPDR> file  
 in each genome's main directory, but no such file exists anywhere in my version of the  
 data store.)  
   
238  =cut  =cut
239  #: Return Type $%;  #: Return Type $%;
240  sub LoadGenomeData {  sub LoadGenomeData {
# Line 216  Line 245 
245      # Get the genome count.      # Get the genome count.
246      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
     Trace("Beginning genome data load.") if T(2);  
248      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
249      my $loadGenome = $self->_TableLoader('Genome', $genomeCount);      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $genomeCount * 300);      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);
251      my $loadContig = $self->_TableLoader('Contig', $genomeCount * 300);      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $genomeCount * 60000);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);
253      my $loadSequence = $self->_TableLoader('Sequence', $genomeCount * 60000);      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);
254        if ($self->{options}->{loadOnly}) {
255            Trace("Loading from existing files.") if T(2);
256        } else {
257            Trace("Generating genome data.") if T(2);
258      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
259      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
260          Trace("Loading data for genome $genomeID.") if T(3);              Trace("Generating data for genome $genomeID.") if T(3);
261          $loadGenome->Add("genomeIn");          $loadGenome->Add("genomeIn");
262          # The access code comes in via the genome hash.          # The access code comes in via the genome hash.
263          my $accessCode = $genomeHash->{$genomeID};          my $accessCode = $genomeHash->{$genomeID};
264          # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
         # the genome ID to the strain. In some cases this is the totality of the strain name.  
265          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266          my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267          # Get the full taxonomy.          # Get the full taxonomy.
268          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
269                # Open the NMPDR group file for this genome.
270                my $group;
271                if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
272                    defined($group = <TMP>)) {
273                    # Clean the line ending.
274                    chomp $group;
275                } else {
276                    # No group, so use the default.
277                    $group = $FIG_Config::otherGroup;
278                }
279                close TMP;
280          # Output the genome record.          # Output the genome record.
281          $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,          $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,
282                           $species, $extra, $taxonomy);                               $group, $species, $extra, $taxonomy);
283          # Now we loop through each of the genome's contigs.          # Now we loop through each of the genome's contigs.
284          my @contigs = $fig->all_contigs($genomeID);          my @contigs = $fig->all_contigs($genomeID);
285          for my $contigID (@contigs) {          for my $contigID (@contigs) {
# Line 268  Line 310 
310              }              }
311          }          }
312      }      }
313        }
314      # Finish the loads.      # Finish the loads.
315      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
316      # Return the result.      # Return the result.
# Line 308  Line 351 
351      my $fig = $self->{fig};      my $fig = $self->{fig};
352      # Get the genome hash.      # Get the genome hash.
353      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
354      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
355      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
356      # Start the loads.      # Start the loads.
357      my $loadCoupling = $self->_TableLoader('Coupling', $featureCount * $genomeCount);      my $loadCoupling = $self->_TableLoader('Coupling');
358      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $featureCount * 8000);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
359      my $loadPCH = $self->_TableLoader('PCH', $featureCount * 2000);      my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);
360      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $featureCount * 2000);      my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);
361      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $featureCount * 8000);      my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);
362      Trace("Beginning coupling data load.") if T(2);      if ($self->{options}->{loadOnly}) {
363            Trace("Loading from existing files.") if T(2);
364        } else {
365            Trace("Generating coupling data.") if T(2);
366      # Loop through the genomes found.      # Loop through the genomes found.
367      for my $genome (sort keys %{$genomeFilter}) {      for my $genome (sort keys %{$genomeFilter}) {
368          Trace("Generating coupling data for $genome.") if T(3);          Trace("Generating coupling data for $genome.") if T(3);
# Line 340  Line 386 
386              for my $coupleData (@couplings) {              for my $coupleData (@couplings) {
387                  my ($peg2, $score) = @{$coupleData};                  my ($peg2, $score) = @{$coupleData};
388                  # Compute the coupling ID.                  # Compute the coupling ID.
389                  my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
390                  if (! exists $dupHash{$coupleID}) {                  if (! exists $dupHash{$coupleID}) {
391                      $loadCoupling->Add("couplingIn");                      $loadCoupling->Add("couplingIn");
392                      # Here we have a new coupling to store in the load files.                      # Here we have a new coupling to store in the load files.
# Line 376  Line 422 
422                          }                          }
423                      }                      }
424                      for my $evidenceID (keys %evidenceMap) {                      for my $evidenceID (keys %evidenceMap) {
425                                # Get the ID for this evidence.
426                                $pchID++;
427                          # Create the evidence record.                          # Create the evidence record.
428                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                          my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
429                          $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
430                          # Connect it to the coupling.                          # Connect it to the coupling.
431                          $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
432                          # Connect it to the features.                          # Connect it to the features.
433                          $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
434                          $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
435                            }
436                      }                      }
437                  }                  }
438              }              }
# Line 410  Line 459 
459      FeatureTranslation      FeatureTranslation
460      FeatureUpstream      FeatureUpstream
461      IsLocatedIn      IsLocatedIn
462        HasFeature
463    
464  =over 4  =over 4
465    
# Line 426  Line 476 
476      my ($self) = @_;      my ($self) = @_;
477      # Get the FIG object.      # Get the FIG object.
478      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Find out if this is a limited run.  
     my $limited = $self->{options}->{limitedFeatures};  
479      # Get the table of genome IDs.      # Get the table of genome IDs.
480      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
481      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
482      my $loadFeature = $self->_TableLoader('Feature', $featureCount);      my $loadFeature = $self->_TableLoader('Feature');
483      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $featureCount);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);
484      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias', $featureCount * 6);      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
485      my ($loadFeatureLink, $loadFeatureTranslation, $loadFeatureUpstream);      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
486      if (! $limited) {      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
487          $loadFeatureLink = $self->_TableLoader('FeatureLink', $featureCount * 10);      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
488          $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation', $featureCount);      my $loadHasFeature = $self->_TableLoader('HasFeature');
         $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream', $featureCount);  
     }  
489      # 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
490      # locations.      # locations.
491      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
492      Trace("Beginning feature data load.") if T(2);      if ($self->{options}->{loadOnly}) {
493            Trace("Loading from existing files.") if T(2);
494        } else {
495            Trace("Generating feature data.") if T(2);
496      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
497      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
498          Trace("Loading features for genome $genomeID.") if T(3);          Trace("Loading features for genome $genomeID.") if T(3);
499          $loadFeature->Add("genomeIn");          $loadFeature->Add("genomeIn");
500          # Get the feature list for this genome.          # Get the feature list for this genome.
501          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
502                # Sort and count the list.
503                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
504                my $count = scalar @featureTuples;
505                Trace("$count features found for genome $genomeID.") if T(3);
506                # Set up for our duplicate-feature check.
507                my $oldFeatureID = "";
508          # Loop through the features.          # Loop through the features.
509          for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
             $loadFeature->Add("featureIn");  
510              # Split the tuple.              # Split the tuple.
511              my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
512                    # Check for duplicates.
513                    if ($featureID eq $oldFeatureID) {
514                        Trace("Duplicate feature $featureID found.") if T(1);
515                    } else {
516                        $oldFeatureID = $featureID;
517                        # Count this feature.
518                        $loadFeature->Add("featureIn");
519                        # Get the functional assignment.
520                        my $assignment = $fig->function_of($featureID);
521              # Create the feature record.              # Create the feature record.
522              $loadFeature->Put($featureID, 1, $type);                      $loadFeature->Put($featureID, 1, $type, $assignment);
523                        # Link it to the parent genome.
524                        $loadHasFeature->Put($genomeID, $featureID, $type);
525              # Create the aliases.              # Create the aliases.
526              for my $alias ($fig->feature_aliases($featureID)) {              for my $alias ($fig->feature_aliases($featureID)) {
527                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);
528              }              }
             # The next stuff is for a full load only.  
             if (! $limited) {  
529                  # Get the links.                  # Get the links.
530                  my @links = $fig->fid_links($featureID);                  my @links = $fig->fid_links($featureID);
531                  for my $link (@links) {                  for my $link (@links) {
# Line 483  Line 544 
544                          $loadFeatureUpstream->Put($featureID, $upstream);                          $loadFeatureUpstream->Put($featureID, $upstream);
545                      }                      }
546                  }                  }
             }  
547              # 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
548              # 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
549              # 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 572 
572              }              }
573          }          }
574      }      }
575            }
576        }
577      # Finish the loads.      # Finish the loads.
578      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
579      return $retVal;      return $retVal;
# Line 548  Line 610 
610      my $fig = $self->{fig};      my $fig = $self->{fig};
611      # Get the table of genome IDs.      # Get the table of genome IDs.
612      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
     my $featureCount = $genomeCount * 4000;  
613      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
614      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf',      my $loadIsBidirectionalBestHitOf = $self->_TableLoader('IsBidirectionalBestHitOf');
615                                                             $featureCount * $genomeCount);      if ($self->{options}->{loadOnly}) {
616      Trace("Beginning BBH load.") if T(2);          Trace("Loading from existing files.") if T(2);
617        } else {
618            Trace("Generating BBH data.") if T(2);
619      # Now we loop through the genomes, generating the data for each one.      # Now we loop through the genomes, generating the data for each one.
620      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
621          $loadIsBidirectionalBestHitOf->Add("genomeIn");          $loadIsBidirectionalBestHitOf->Add("genomeIn");
622          Trace("Processing features for genome $genomeID.") if T(3);          Trace("Processing features for genome $genomeID.") if T(3);
623          # Get the feature list for this genome.          # Get the feature list for this genome.
624          my $features = $fig->all_features_detailed($genomeID);          my $features = $fig->all_features_detailed($genomeID);
625                # Count the BBHs we find.
626                my $bbhCount = 0;
627          # Loop through the features.          # Loop through the features.
628          for my $featureData (@{$features}) {          for my $featureData (@{$features}) {
629              # Split the tuple.              # Split the tuple.
# Line 575  Line 639 
639                  if ($genomeHash->{$targetGenomeID}) {                  if ($genomeHash->{$targetGenomeID}) {
640                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,                      $loadIsBidirectionalBestHitOf->Put($featureID, $targetID, $targetGenomeID,
641                                                         $score);                                                         $score);
642                            $bbhCount++;
643                        }
644                  }                  }
645              }              }
646                Trace("$bbhCount BBHs found for $genomeID.") if T(3);
647          }          }
648      }      }
649      # Finish the loads.      # Finish the loads.
# Line 599  Line 666 
666  The following relations are loaded by this method.  The following relations are loaded by this method.
667    
668      Subsystem      Subsystem
669        SubsystemClass
670      Role      Role
671        RoleEC
672      SSCell      SSCell
673      ContainsFeature      ContainsFeature
674      IsGenomeOf      IsGenomeOf
# Line 607  Line 676 
676      OccursInSubsystem      OccursInSubsystem
677      ParticipatesIn      ParticipatesIn
678      HasSSCell      HasSSCell
     Catalyzes  
     Reaction  
679      ConsistsOfRoles      ConsistsOfRoles
680      RoleSubset      RoleSubset
681      HasRoleSubset      HasRoleSubset
682      ConsistsOfGenomes      ConsistsOfGenomes
683      GenomeSubset      GenomeSubset
684      HasGenomeSubset      HasGenomeSubset
685        Catalyzes
686        Diagram
687        RoleOccursIn
688    
689  =over 4  =over 4
690    
# Line 624  Line 694 
694    
695  =back  =back
696    
 B<TO DO>  
   
 Generate RoleName table?  
   
697  =cut  =cut
698  #: Return Type $%;  #: Return Type $%;
699  sub LoadSubsystemData {  sub LoadSubsystemData {
# Line 641  Line 707 
707      # Get the subsystem hash. This lists the subsystems we'll process.      # Get the subsystem hash. This lists the subsystems we'll process.
708      my $subsysHash = $self->{subsystems};      my $subsysHash = $self->{subsystems};
709      my @subsysIDs = sort keys %{$subsysHash};      my @subsysIDs = sort keys %{$subsysHash};
710      my $subsysCount = @subsysIDs;      # Get the map list.
711      my $genomeCount = (keys %{$genomeHash});      my @maps = $fig->all_maps;
     my $featureCount = $genomeCount * 4000;  
712      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
713      my $loadSubsystem = $self->_TableLoader('Subsystem', $subsysCount);      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);
714      my $loadRole = $self->_TableLoader('Role', $featureCount * 6);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);
715      my $loadSSCell = $self->_TableLoader('SSCell', $featureCount * $genomeCount);      my $loadSubsystem = $self->_TableLoader('Subsystem');
716      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $featureCount * $subsysCount);      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);
717      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $featureCount * $genomeCount);      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);
718      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $featureCount * $genomeCount);      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);
719      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $featureCount * 6);      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);
720      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $subsysCount * $genomeCount);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);
721      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $featureCount * $genomeCount);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);
722      my $loadReaction = $self->_TableLoader('Reaction', $featureCount * $genomeCount);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);
723      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $featureCount * $genomeCount);      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);
724      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $subsysCount * 50);      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);
725      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $subsysCount * 50);      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);
726      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $featureCount * $genomeCount);      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);
727      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $featureCount * $genomeCount);      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);
728      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $subsysCount * 50);      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);
729      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $subsysCount * 50);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
730      Trace("Beginning subsystem data load.") if T(2);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
731      # The reaction hash will contain a list of reactions for each role. When we're done,      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
732      # a complicated sort and merge will be used to generate the Reaction and Catalyzes      my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
733      # tables.      if ($self->{options}->{loadOnly}) {
734      my %reactionsToRoles = ();          Trace("Loading from existing files.") if T(2);
735        } else {
736            Trace("Generating subsystem data.") if T(2);
737            # This hash will contain the role for each EC. When we're done, this
738            # information will be used to generate the Catalyzes table.
739            my %ecToRoles = ();
740      # Loop through the subsystems. Our first task will be to create the      # Loop through the subsystems. Our first task will be to create the
741      # roles. We do this by looping through the subsystems and creating a      # roles. We do this by looping through the subsystems and creating a
742      # role hash. The hash tracks each role ID so that we don't create      # role hash. The hash tracks each role ID so that we don't create
# Line 675  Line 745 
745      my ($genomeID, $roleID);      my ($genomeID, $roleID);
746      my %roleData = ();      my %roleData = ();
747      for my $subsysID (@subsysIDs) {      for my $subsysID (@subsysIDs) {
         Trace("Creating subsystem $subsysID.") if T(3);  
         $loadSubsystem->Add("subsystemIn");  
748          # Get the subsystem object.          # Get the subsystem object.
749          my $sub = $fig->get_subsystem($subsysID);          my $sub = $fig->get_subsystem($subsysID);
750          # Get its reaction hash.              # Only proceed if the subsystem has a spreadsheet.
751          my $reactionHash = $sub->get_reactions();              if (! $sub->{empty_ss}) {
752                    Trace("Creating subsystem $subsysID.") if T(3);
753                    $loadSubsystem->Add("subsystemIn");
754          # Create the subsystem record.          # Create the subsystem record.
755          my $curator = $sub->get_curator();          my $curator = $sub->get_curator();
756          my $notes = $sub->get_notes();          my $notes = $sub->get_notes();
757          $loadSubsystem->Put($subsysID, $curator, $notes);          $loadSubsystem->Put($subsysID, $curator, $notes);
758                    my $classList = $fig->subsystem_classification($subsysID);
759                    my @classes = @$classList;
760                    if (@classes) {
761                        for my $class (@classes) {
762                            $loadSubsystemClass->Put($subsysID, $class);
763                        }
764                    }
765          # 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.
766          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
767              # Connect to this role.              # Connect to this role.
# Line 697  Line 774 
774                  # Add the role.                  # Add the role.
775                  $loadRole->Put($roleID, $abbr);                  $loadRole->Put($roleID, $abbr);
776                  $roleData{$roleID} = 1;                  $roleData{$roleID} = 1;
777                  # Add the role's reactions.                          # Check for an EC number.
778                  my $reactions = $reactionHash->{$roleID};                          if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {
779                  for my $reactionID (@{$reactions}) {                              my $ec = $1;
780                      if (! exists $reactionsToRoles{$reactionID}) {                              $loadRoleEC->Put($roleID, $ec);
781                          # Here the reaction is brand-new, so we create its reaction                              $ecToRoles{$ec} = $roleID;
                         # record.  
                         $loadReaction->Put($reactionID, $fig->reversible($reactionID));  
                         # We also create a blank list for it in the reaction hash.  
                         $reactionsToRoles{$reactionID} = [];  
                     }  
                     # Add the role to the reaction's role list.  
                     push @{$reactionsToRoles{$reactionID}}, $roleID;  
782                  }                  }
783              }              }
784          }          }
# Line 735  Line 805 
805                  # part of the spreadsheet cell ID.                  # part of the spreadsheet cell ID.
806                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
807                      # Get the features in the spreadsheet cell for this genome and role.                      # Get the features in the spreadsheet cell for this genome and role.
808                      my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
809                      # Only proceed if features exist.                      # Only proceed if features exist.
810                      if (@pegs > 0) {                      if (@pegs > 0) {
811                          # Create the spreadsheet cell.                          # Create the spreadsheet cell.
# Line 756  Line 826 
826                  if ($pegCount > 0) {                  if ($pegCount > 0) {
827                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                      Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
828                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                      $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                     # Partition the PEGs found into clusters.  
                     my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
829                      # Create a hash mapping PEG IDs to cluster numbers.                      # Create a hash mapping PEG IDs to cluster numbers.
830                      # We default to -1 for all of them.                      # We default to -1 for all of them.
831                      my %clusterOf = map { $_ => -1 } @pegsFound;                      my %clusterOf = map { $_ => -1 } @pegsFound;
832                                # Partition the PEGs found into clusters.
833                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
834                      for (my $i = 0; $i <= $#clusters; $i++) {                      for (my $i = 0; $i <= $#clusters; $i++) {
835                          my $subList = $clusters[$i];                          my $subList = $clusters[$i];
836                          for my $peg (@{$subList}) {                          for my $peg (@{$subList}) {
# Line 788  Line 858 
858              # Connect the subset to the subsystem.              # Connect the subset to the subsystem.
859              $loadHasRoleSubset->Put($subsysID, $actualID);              $loadHasRoleSubset->Put($subsysID, $actualID);
860              # Connect the subset to its roles.              # Connect the subset to its roles.
861              my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
862              for my $roleID (@roles) {              for my $roleID (@roles) {
863                  $loadConsistsOfRoles->Put($actualID, $roleID);                  $loadConsistsOfRoles->Put($actualID, $roleID);
864              }              }
# Line 808  Line 878 
878              }              }
879          }          }
880      }      }
     # Before we leave, we must create the Catalyzes table. The data is all stored in  
     # "reactionToRoles" hash.  
     for my $reactionID (keys %reactionsToRoles) {  
         # Get this reaction's list of roles. We sort it so we can merge out duplicates.  
         my @roles = sort @{$reactionsToRoles{$reactionID}};  
         my $lastRole = "";  
         # Loop through the roles, creating catalyzation records.  
         for my $thisRole (@roles) {  
             if ($thisRole ne $lastRole) {  
                 $loadCatalyzes->Put($thisRole, $reactionID);  
             }  
         }  
     }  
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
881  }  }
882            # Now we loop through the diagrams. We need to create the diagram records
883  =head3 LoadDiagramData          # and link each diagram to its roles. Note that only roles which occur
884            # in subsystems (and therefore appear in the %ecToRoles hash) are
885  C<< my $stats = $spl->LoadDiagramData(); >>          # included.
886            for my $map (@maps) {
 Load the diagram data from FIG into Sprout.  
   
 Diagrams are used to organize functional roles. The diagram shows the  
 connections between chemicals that interact with a subsystem.  
   
 The following relations are loaded by this method.  
   
     Diagram  
     RoleOccursIn  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadDiagramData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the map list.  
     my @maps = $fig->all_maps;  
     my $mapCount = @maps;  
     my $genomeCount = (keys %{$self->{genomes}});  
     my $featureCount = $genomeCount * 4000;  
     # Create load objects for each of the tables we're loading.  
     my $loadDiagram = $self->_TableLoader('Diagram', $mapCount);  
     my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $featureCount * 6);  
     Trace("Beginning diagram data load.") if T(2);  
     # Loop through the diagrams.  
     for my $map ($fig->all_maps) {  
887          Trace("Loading diagram $map.") if T(3);          Trace("Loading diagram $map.") if T(3);
888          # Get the diagram's descriptive name.          # Get the diagram's descriptive name.
889          my $name = $fig->map_name($map);          my $name = $fig->map_name($map);
# Line 874  Line 892 
892          # A hash is used to prevent duplicates.          # A hash is used to prevent duplicates.
893          my %roleHash = ();          my %roleHash = ();
894          for my $role ($fig->map_to_ecs($map)) {          for my $role ($fig->map_to_ecs($map)) {
895              if (! $roleHash{$role}) {                  if (exists $ecToRoles{$role} && ! $roleHash{$role}) {
896                  $loadRoleOccursIn->Put($role, $map);                      $loadRoleOccursIn->Put($ecToRoles{$role}, $map);
897                  $roleHash{$role} = 1;                  $roleHash{$role} = 1;
898              }              }
899          }          }
900      }      }
901            # Before we leave, we must create the Catalyzes table. We start with the reactions,
902            # then use the "ecToRoles" table to convert EC numbers to role IDs.
903            my @reactions = $fig->all_reactions();
904            for my $reactionID (@reactions) {
905                # Get this reaction's list of roles. The results will be EC numbers.
906                my @roles = $fig->catalyzed_by($reactionID);
907                # Loop through the roles, creating catalyzation records.
908                for my $thisRole (@roles) {
909                    if (exists $ecToRoles{$thisRole}) {
910                        $loadCatalyzes->Put($ecToRoles{$thisRole}, $reactionID);
911                    }
912                }
913            }
914        }
915      # Finish the load.      # Finish the load.
916      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
917      return $retVal;      return $retVal;
# Line 921  Line 953 
953      my $fig = $self->{fig};      my $fig = $self->{fig};
954      # Get the genome hash.      # Get the genome hash.
955      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
956      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
957      my $loadProperty = $self->_TableLoader('Property', $genomeCount * 1500);      my $loadProperty = $self->_TableLoader('Property');
958      my $loadHasProperty = $self->_TableLoader('HasProperty', $genomeCount * 1500);      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);
959      Trace("Beginning property data load.") if T(2);      if ($self->{options}->{loadOnly}) {
960            Trace("Loading from existing files.") if T(2);
961        } else {
962            Trace("Generating property data.") if T(2);
963      # Create a hash for storing property IDs.      # Create a hash for storing property IDs.
964      my %propertyKeys = ();      my %propertyKeys = ();
965      my $nextID = 1;      my $nextID = 1;
966      # Loop through the genomes.      # Loop through the genomes.
967      for my $genomeID (keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
968          $loadProperty->Add("genomeIn");          $loadProperty->Add("genomeIn");
969                Trace("Generating properties for $genomeID.") if T(3);
970          # 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
971          # tuples returned by "all_features_detailed". We use "all_features_detailed"          # tuples returned by "all_features_detailed". We use "all_features_detailed"
972          # rather than "all_features" because we want all features regardless of type.          # rather than "all_features" because we want all features regardless of type.
973          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};          my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};
974                my $featureCount = 0;
975                my $propertyCount = 0;
976          # Loop through the features, creating HasProperty records.          # Loop through the features, creating HasProperty records.
977          for my $fid (@features) {          for my $fid (@features) {
             $loadProperty->Add("featureIn");  
978              # 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
979              # to insure we do not get any genome attributes.              # to insure we do not get any genome attributes.
980              my @attributeList = $fig->get_attributes($fid, '', '', '');              my @attributeList = $fig->get_attributes($fid, '', '', '');
981                    if (scalar @attributeList) {
982                        $featureCount++;
983                    }
984              # Loop through the attributes.              # Loop through the attributes.
985              for my $tuple (@attributeList) {              for my $tuple (@attributeList) {
986                        $propertyCount++;
987                  # Get this attribute value's data. Note that we throw away the FID,                  # Get this attribute value's data. Note that we throw away the FID,
988                  # since it will always be the same as the value if "$fid".                  # since it will always be the same as the value if "$fid".
989                  my (undef, $key, $value, $url) = @{$tuple};                  my (undef, $key, $value, $url) = @{$tuple};
# Line 965  Line 1005 
1005                  $loadHasProperty->Put($fid, $propertyID, $url);                  $loadHasProperty->Put($fid, $propertyID, $url);
1006              }              }
1007          }          }
1008                # Update the statistics.
1009                Trace("$propertyCount attributes processed for $featureCount features.") if T(3);
1010                $loadHasProperty->Add("featuresIn", $featureCount);
1011                $loadHasProperty->Add("propertiesIn", $propertyCount);
1012            }
1013      }      }
1014      # Finish the load.      # Finish the load.
1015      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1005  Line 1050 
1050      my $fig = $self->{fig};      my $fig = $self->{fig};
1051      # Get the genome hash.      # Get the genome hash.
1052      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1053      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1054      my $loadAnnotation = $self->_TableLoader('Annotation', $genomeCount * 4000);      my $loadAnnotation = $self->_TableLoader('Annotation');
1055      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $genomeCount * 4000);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);
1056      my $loadSproutUser = $self->_TableLoader('SproutUser', 100);      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);
1057      my $loadUserAccess = $self->_TableLoader('UserAccess', 1000);      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);
1058      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $genomeCount * 4000);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);
1059      Trace("Beginning annotation data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1060            Trace("Loading from existing files.") if T(2);
1061        } else {
1062            Trace("Generating annotation data.") if T(2);
1063      # 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
1064      # user records.      # user records.
1065      my %users = ( FIG => 1, master => 1 );      my %users = ( FIG => 1, master => 1 );
# Line 1026  Line 1073 
1073      # Loop through the genomes.      # Loop through the genomes.
1074      for my $genomeID (sort keys %{$genomeHash}) {      for my $genomeID (sort keys %{$genomeHash}) {
1075          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);  
1076              # 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
1077              # from showing up for a single PEG's annotations.              # from showing up for a single PEG's annotations.
1078              my %seenTimestamps = ();              my %seenTimestamps = ();
1079              # Check for a functional assignment.              # Get the genome's annotations.
1080              my $func = $fig->function_of($peg);              my @annotations = $fig->read_all_annotations($genomeID);
1081              if ($func) {              Trace("Processing annotations.") if T(2);
1082                  # If this is NOT a hypothetical assignment, we create an              for my $tuple (@annotations) {
1083                  # assignment annotation for it.                  # Get the annotation tuple.
1084                  if (! FIG::hypo($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};  
1085                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1086                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1087                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1088                  # stop the substitution search.                  # stop the substitution search.
1089                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1065  Line 1096 
1096                      # 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
1097                      # the key is unique.                      # the key is unique.
1098                      my $keyStamp = $timestamp;                      my $keyStamp = $timestamp;
1099                      while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1100                          $keyStamp++;                          $keyStamp++;
1101                      }                      }
                     $seenTimestamps{$keyStamp} = 1;  
1102                      my $annotationID = "$peg:$keyStamp";                      my $annotationID = "$peg:$keyStamp";
1103                        $seenTimestamps{$annotationID} = 1;
1104                      # Insure the user exists.                      # Insure the user exists.
1105                      if (! $users{$user}) {                      if (! $users{$user}) {
1106                          $loadSproutUser->Put($user, "SEED user");                          $loadSproutUser->Put($user, "SEED user");
# Line 1127  Line 1158 
1158      my $fig = $self->{fig};      my $fig = $self->{fig};
1159      # Get the genome hash.      # Get the genome hash.
1160      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1161      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1162      my $loadComesFrom = $self->_TableLoader('ComesFrom', $genomeCount * 4);      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);
1163      my $loadSource = $self->_TableLoader('Source', $genomeCount * 4);      my $loadSource = $self->_TableLoader('Source');
1164      my $loadSourceURL = $self->_TableLoader('SourceURL', $genomeCount * 8);      my $loadSourceURL = $self->_TableLoader('SourceURL');
1165      Trace("Beginning source data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1166            Trace("Loading from existing files.") if T(2);
1167        } else {
1168            Trace("Generating annotation data.") if T(2);
1169      # Create hashes to collect the Source information.      # Create hashes to collect the Source information.
1170      my %sourceURL = ();      my %sourceURL = ();
1171      my %sourceDesc = ();      my %sourceDesc = ();
# Line 1162  Line 1195 
1195      for my $sourceID (keys %sourceDesc) {      for my $sourceID (keys %sourceDesc) {
1196          $loadSource->Put($sourceID, $sourceDesc{$sourceID});          $loadSource->Put($sourceID, $sourceDesc{$sourceID});
1197      }      }
1198        }
1199      # Finish the load.      # Finish the load.
1200      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1201      return $retVal;      return $retVal;
# Line 1201  Line 1235 
1235      my $fig = $self->{fig};      my $fig = $self->{fig};
1236      # Get the genome hash.      # Get the genome hash.
1237      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1238      # 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
1239      # it the key.      # it the key.
1240      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});      my %speciesHash = map { $fig->genus_species($_) => $_ } (keys %{$genomeHash});
1241      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1242      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc', $genomeCount * 4000);      my $loadExternalAliasFunc = $self->_TableLoader('ExternalAliasFunc');
1243      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg', $genomeCount * 4000);      my $loadExternalAliasOrg = $self->_TableLoader('ExternalAliasOrg');
1244      Trace("Beginning external data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1245            Trace("Loading from existing files.") if T(2);
1246        } else {
1247            Trace("Generating external data.") if T(2);
1248      # 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.
1249      Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1250      my $orgLine;      my $orgLine;
1251      while (defined($orgLine = <ORGS>)) {      while (defined($orgLine = <ORGS>)) {
1252          # Clean the input line.          # Clean the input line.
# Line 1222  Line 1258 
1258      close ORGS;      close ORGS;
1259      # Now the function file.      # Now the function file.
1260      my $funcLine;      my $funcLine;
1261      Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1262      while (defined($funcLine = <FUNCS>)) {      while (defined($funcLine = <FUNCS>)) {
1263          # Clean the line ending.          # Clean the line ending.
1264          chomp $funcLine;          chomp $funcLine;
# Line 1238  Line 1274 
1274              $loadExternalAliasFunc->Put(@funcFields[0,1]);              $loadExternalAliasFunc->Put(@funcFields[0,1]);
1275          }          }
1276      }      }
1277        }
1278      # Finish the load.      # Finish the load.
1279      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1280      return $retVal;      return $retVal;
# Line 1254  Line 1291 
1291    
1292  The following relations are loaded by this method.  The following relations are loaded by this method.
1293    
1294        Reaction
1295      ReactionURL      ReactionURL
1296      Compound      Compound
1297      CompoundName      CompoundName
# Line 1277  Line 1315 
1315      my ($self) = @_;      my ($self) = @_;
1316      # Get the FIG object.      # Get the FIG object.
1317      my $fig = $self->{fig};      my $fig = $self->{fig};
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     my $genomeCount = (keys %{$genomeHash});  
1318      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1319      my $loadReactionURL = $self->_TableLoader('ReactionURL', $genomeCount * 4000);      my $loadReaction = $self->_TableLoader('Reaction');
1320      my $loadCompound = $self->_TableLoader('Compound', $genomeCount * 4000);      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);
1321      my $loadCompoundName = $self->_TableLoader('CompoundName', $genomeCount * 8000);      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);
1322      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $genomeCount * 4000);      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);
1323      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $genomeCount * 12000);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);
1324      Trace("Beginning reaction/compound data load.") if T(2);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);
1325      # Create a hash to remember the compounds we've generated in the compound table.      if ($self->{options}->{loadOnly}) {
1326      my %compoundHash = ();          Trace("Loading from existing files.") if T(2);
1327      # Loop through the reactions.      } else {
1328            Trace("Generating annotation data.") if T(2);
1329            # First we create the compounds.
1330            my @compounds = $fig->all_compounds();
1331            for my $cid (@compounds) {
1332                # Check for names.
1333                my @names = $fig->names_of_compound($cid);
1334                # Each name will be given a priority number, starting with 1.
1335                my $prio = 1;
1336                for my $name (@names) {
1337                    $loadCompoundName->Put($cid, $name, $prio++);
1338                }
1339                # Create the main compound record. Note that the first name
1340                # becomes the label.
1341                my $label = (@names > 0 ? $names[0] : $cid);
1342                $loadCompound->Put($cid, $label);
1343                # Check for a CAS ID.
1344                my $cas = $fig->cas($cid);
1345                if ($cas) {
1346                    $loadCompoundCAS->Put($cid, $cas);
1347                }
1348            }
1349            # All the compounds are set up, so we need to loop through the reactions next. First,
1350            # we initialize the discriminator index. This is a single integer used to insure
1351            # duplicate elements in a reaction are not accidentally collapsed.
1352            my $discrim = 0;
1353      my @reactions = $fig->all_reactions();      my @reactions = $fig->all_reactions();
1354      for my $reactionID (@reactions) {      for my $reactionID (@reactions) {
1355                # Create the reaction record.
1356                $loadReaction->Put($reactionID, $fig->reversible($reactionID));
1357          # Compute the reaction's URL.          # Compute the reaction's URL.
1358          my $url = HTML::reaction_link($reactionID);          my $url = HTML::reaction_link($reactionID);
1359          # Put it in the ReactionURL table.          # Put it in the ReactionURL table.
# Line 1300  Line 1362 
1362          # substrates first and then products.          # substrates first and then products.
1363          for my $product (0, 1) {          for my $product (0, 1) {
1364              # Get the compounds of the current type for the current reaction. FIG will              # Get the compounds of the current type for the current reaction. FIG will
1365              # give us 3-tuples: [ID, Stoichometry, main-flag]. At this time we do not                  # give us 3-tuples: [ID, stoichiometry, main-flag]. At this time we do not
1366              # have location data in SEED, so it defaults to the empty string.              # have location data in SEED, so it defaults to the empty string.
1367              my @compounds = $fig->reaction2comp($reactionID, $product);              my @compounds = $fig->reaction2comp($reactionID, $product);
1368              for my $compData (@compounds) {              for my $compData (@compounds) {
1369                  # Extract the compound data from the current tuple.                  # Extract the compound data from the current tuple.
1370                  my ($cid, $stoich, $main) = @{$compData};                  my ($cid, $stoich, $main) = @{$compData};
1371                  # Link the compound to the reaction.                  # Link the compound to the reaction.
1372                  $loadIsAComponentOf->Put($cid, $reactionID, "", $main, $product, $stoich);                      $loadIsAComponentOf->Put($cid, $reactionID, $discrim++, "", $main,
1373                  # If this is a new compound, we need to create its table entries.                                               $product, $stoich);
                 if (! exists $compoundHash{$cid}) {  
                     $compoundHash{$cid} = 1;  
                     # Create the main compound record and denote we've done it.  
                     $loadCompound->Put($cid);  
                     # Check for a CAS ID.  
                     my $cas = $fig->cas($cid);  
                     if ($cas) {  
                         $loadCompoundCAS->Put($cid, $cas);  
                     }  
                     # Check for names.  
                     my @names = $fig->names_of_compound($cid);  
                     # Each name will be given a priority number, starting with 1.  
                     my $prio = 0;  
                     for my $name (@names) {  
                         $loadCompoundName->Put($cid, $name, $prio++);  
                     }  
1374                  }                  }
1375              }              }
1376          }          }
# Line 1344  Line 1390 
1390    
1391      GenomeGroups      GenomeGroups
1392    
1393  There is no direct support for genome groups in FIG, so we access the SEED  Currently, we do not use groups. We used to use them for NMPDR groups,
1394    butThere is no direct support for genome groups in FIG, so we access the SEED
1395  files directly.  files directly.
1396    
1397  =over 4  =over 4
# Line 1364  Line 1411 
1411      my $fig = $self->{fig};      my $fig = $self->{fig};
1412      # Get the genome hash.      # Get the genome hash.
1413      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
     my $genomeCount = (keys %{$genomeHash});  
1414      # Create a load object for the table we're loading.      # Create a load object for the table we're loading.
1415      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups', $genomeCount * 4);      my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');
1416      Trace("Beginning group data load.") if T(2);      if ($self->{options}->{loadOnly}) {
1417            Trace("Loading from existing files.") if T(2);
1418        } else {
1419            Trace("Generating group data.") if T(2);
1420            # Currently there are no groups.
1421        }
1422        # Finish the load.
1423        my $retVal = $self->_FinishAll();
1424        return $retVal;
1425    }
1426    
1427    =head3 LoadSynonymData
1428    
1429    C<< my $stats = $spl->LoadSynonymData(); >>
1430    
1431    Load the synonym groups into Sprout.
1432    
1433    The following relations are loaded by this method.
1434    
1435        SynonymGroup
1436        IsSynonymGroupFor
1437    
1438    The source information for these relations is taken from the C<maps_to_id> method
1439    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1440    SQL against the FIG database.
1441    
1442    =over 4
1443    
1444    =item RETURNS
1445    
1446    Returns a statistics object for the loads.
1447    
1448    =back
1449    
1450    =cut
1451    #: Return Type $%;
1452    sub LoadSynonymData {
1453        # Get this object instance.
1454        my ($self) = @_;
1455        # Get the FIG object.
1456        my $fig = $self->{fig};
1457        # Get the genome hash.
1458        my $genomeHash = $self->{genomes};
1459        # Create a load object for the table we're loading.
1460        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1461        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1462        if ($self->{options}->{loadOnly}) {
1463            Trace("Loading from existing files.") if T(2);
1464        } else {
1465            Trace("Generating synonym group data.") if T(2);
1466            # Get the database handle.
1467            my $dbh = $fig->db_handle();
1468            # Ask for the synonyms.
1469            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1470            my $result = $sth->execute();
1471            if (! defined($result)) {
1472                Confess("Database error in Synonym load: " . $sth->errstr());
1473            } else {
1474                # Remember the current synonym.
1475                my $current_syn = "";
1476                # Count the features.
1477                my $featureCount = 0;
1478                # Loop through the synonym/peg pairs.
1479                while (my @row = $sth->fetchrow()) {
1480                    # Get the synonym ID and feature ID.
1481                    my ($syn_id, $peg) = @row;
1482                    # Insure it's for one of our genomes.
1483                    my $genomeID = FIG::genome_of($peg);
1484                    if (exists $genomeHash->{$genomeID}) {
1485                        # Verify the synonym.
1486                        if ($syn_id ne $current_syn) {
1487                            # It's new, so put it in the group table.
1488                            $loadSynonymGroup->Put($syn_id);
1489                            $current_syn = $syn_id;
1490                        }
1491                        # Connect the synonym to the peg.
1492                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1493                        # Count this feature.
1494                        $featureCount++;
1495                        if ($featureCount % 1000 == 0) {
1496                            Trace("$featureCount features processed.") if T(3);
1497                        }
1498                    }
1499                }
1500            }
1501        }
1502        # Finish the load.
1503        my $retVal = $self->_FinishAll();
1504        return $retVal;
1505    }
1506    
1507    =head3 LoadFamilyData
1508    
1509    C<< my $stats = $spl->LoadFamilyData(); >>
1510    
1511    Load the protein families into Sprout.
1512    
1513    The following relations are loaded by this method.
1514    
1515        Family
1516        IsFamilyForFeature
1517    
1518    The source information for these relations is taken from the C<families_for_protein>,
1519    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1520    
1521    =over 4
1522    
1523    =item RETURNS
1524    
1525    Returns a statistics object for the loads.
1526    
1527    =back
1528    
1529    =cut
1530    #: Return Type $%;
1531    sub LoadFamilyData {
1532        # Get this object instance.
1533        my ($self) = @_;
1534        # Get the FIG object.
1535        my $fig = $self->{fig};
1536        # Get the genome hash.
1537        my $genomeHash = $self->{genomes};
1538        # Create load objects for the tables we're loading.
1539        my $loadFamily = $self->_TableLoader('Family');
1540        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1541        if ($self->{options}->{loadOnly}) {
1542            Trace("Loading from existing files.") if T(2);
1543        } else {
1544            Trace("Generating family data.") if T(2);
1545            # Create a hash for the family IDs.
1546            my %familyHash = ();
1547      # Loop through the genomes.      # Loop through the genomes.
1548      my $line;          for my $genomeID (sort keys %{$genomeHash}) {
1549      for my $genomeID (keys %{$genomeHash}) {              Trace("Processing features for $genomeID.") if T(2);
1550          Trace("Processing $genomeID.") if T(3);              # Loop through this genome's PEGs.
1551          # Open the NMPDR group file for this genome.              for my $fid ($fig->all_features($genomeID, "peg")) {
1552          if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&                  $loadIsFamilyForFeature->Add("features", 1);
1553              defined($line = <TMP>)) {                  # Get this feature's families.
1554              # Clean the line ending.                  my @families = $fig->families_for_protein($fid);
1555              chomp $line;                  # Loop through the families, connecting them to the feature.
1556              # Add the group to the table. Note that there can only be one group                  for my $family (@families) {
1557              # per genome.                      $loadIsFamilyForFeature->Put($family, $fid);
1558              $loadGenomeGroups->Put($genomeID, $line);                      # If this is a new family, create a record for it.
1559                        if (! exists $familyHash{$family}) {
1560                            $familyHash{$family} = 1;
1561                            $loadFamily->Add("families", 1);
1562                            my $size = $fig->sz_family($family);
1563                            my $func = $fig->family_function($family);
1564                            $loadFamily->Put($family, $size, $func);
1565                        }
1566                    }
1567                }
1568          }          }
         close TMP;  
1569      }      }
1570      # Finish the load.      # Finish the load.
1571      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
# Line 1404  Line 1588 
1588    
1589  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1590    
1591  =item rowCount (optional)  =item ignore
1592    
1593  Estimated maximum number of rows in the table.  TRUE if the table should be ignored entirely, else FALSE.
1594    
1595  =item RETURN  =item RETURN
1596    
# Line 1418  Line 1602 
1602    
1603  sub _TableLoader {  sub _TableLoader {
1604      # Get the parameters.      # Get the parameters.
1605      my ($self, $tableName, $rowCount) = @_;      my ($self, $tableName, $ignore) = @_;
1606      # Create the load object.      # Create the load object.
1607      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $rowCount);      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,
1608                                   $ignore);
1609      # Cache it in the loader list.      # Cache it in the loader list.
1610      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1611      # Return it to the caller.      # Return it to the caller.
# Line 1454  Line 1639 
1639      my $retVal = Stats->new();      my $retVal = Stats->new();
1640      # Get the loader list.      # Get the loader list.
1641      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1642        # Create a hash to hold the statistics objects, keyed on relation name.
1643        my %loaderHash = ();
1644      # 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
1645      # 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.
1646      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1647            # Get the relation name.
1648            my $relName = $loader->RelName;
1649            # Check the ignore flag.
1650            if ($loader->Ignore) {
1651                Trace("Relation $relName not loaded.") if T(2);
1652            } else {
1653                # Here we really need to finish.
1654                Trace("Finishing $relName.") if T(2);
1655          my $stats = $loader->Finish();          my $stats = $loader->Finish();
1656                $loaderHash{$relName} = $stats;
1657            }
1658        }
1659        # Now we loop through again, actually loading the tables. We want to finish before
1660        # loading so that if something goes wrong at this point, all the load files are usable
1661        # and we don't have to redo all that work.
1662        for my $relName (sort keys %loaderHash) {
1663            # Get the statistics for this relation.
1664            my $stats = $loaderHash{$relName};
1665            # Check for a database load.
1666            if ($self->{options}->{dbLoad}) {
1667                # Here we want to use the load file just created to load the database.
1668                Trace("Loading relation $relName.") if T(2);
1669                my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
1670                # Accumulate the statistics from the DB load.
1671                $stats->Accumulate($newStats);
1672            }
1673          $retVal->Accumulate($stats);          $retVal->Accumulate($stats);
         my $relName = $loader->RelName;  
1674          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);          Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1675      }      }
1676      # Return the load statistics.      # Return the load statistics.

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