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revision 1.76, Fri Nov 3 00:43:22 2006 UTC revision 1.87, Mon Sep 10 18:16:54 2007 UTC
# Line 7  Line 7 
7      use PageBuilder;      use PageBuilder;
8      use ERDBLoad;      use ERDBLoad;
9      use FIG;      use FIG;
10        use FIGRules;
11      use Sprout;      use Sprout;
12      use Stats;      use Stats;
13      use BasicLocation;      use BasicLocation;
# Line 167  Line 168 
168          for my $subsystem (keys %subsystems) {          for my $subsystem (keys %subsystems) {
169              my $name = $subsystem;              my $name = $subsystem;
170              $name =~ s/_/ /g;              $name =~ s/_/ /g;
171              my $classes = $fig->subsystem_classification($subsystem);  #            my $classes = $fig->subsystem_classification($subsystem);
172              $name .= " " . join(" ", @{$classes});  #            $name .= " " . join(" ", @{$classes});
173              $subsystems{$subsystem} = $name;              $subsystems{$subsystem} = $name;
174          }          }
175      }      }
176        # Get the list of NMPDR-oriented attribute keys.
177        my @propKeys = $fig->get_group_keys("NMPDR");
178      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
179      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
180      # Create the Sprout load object.      # Create the Sprout load object.
# Line 183  Line 186 
186                    loadDirectory => $directory,                    loadDirectory => $directory,
187                    erdb => $sprout,                    erdb => $sprout,
188                    loaders => [],                    loaders => [],
189                    options => $options                    options => $options,
190                      propKeys => \@propKeys,
191                   };                   };
192      # Bless and return it.      # Bless and return it.
193      bless $retVal, $class;      bless $retVal, $class;
# Line 203  Line 207 
207      return $self->{options}->{loadOnly};      return $self->{options}->{loadOnly};
208  }  }
209    
 =head3 PrimaryOnly  
   
 C<< my $flag = $spl->PrimaryOnly; >>  
   
 Return TRUE if only the main entity is to be loaded, else FALSE.  
   
 =cut  
   
 sub PrimaryOnly {  
     my ($self) = @_;  
     return $self->{options}->{primaryOnly};  
 }  
210    
211  =head3 LoadGenomeData  =head3 LoadGenomeData
212    
# Line 255  Line 247 
247      my $genomeCount = (keys %{$genomeHash});      my $genomeCount = (keys %{$genomeHash});
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');      my $loadGenome = $self->_TableLoader('Genome');
250      my $loadHasContig = $self->_TableLoader('HasContig', $self->PrimaryOnly);      my $loadHasContig = $self->_TableLoader('HasContig');
251      my $loadContig = $self->_TableLoader('Contig', $self->PrimaryOnly);      my $loadContig = $self->_TableLoader('Contig');
252      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf', $self->PrimaryOnly);      my $loadIsMadeUpOf = $self->_TableLoader('IsMadeUpOf');
253      my $loadSequence = $self->_TableLoader('Sequence', $self->PrimaryOnly);      my $loadSequence = $self->_TableLoader('Sequence');
254      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
255          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
256      } else {      } else {
# Line 274  Line 266 
266              my $extra = join " ", @extraData;              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                # Get the version. If no version is specified, we default to the genome ID by itself.
270                my $version = $fig->genome_version($genomeID);
271                if (! defined($version)) {
272                    $version = $genomeID;
273                }
274                # Get the DNA size.
275                my $dnaSize = $fig->genome_szdna($genomeID);
276              # Open the NMPDR group file for this genome.              # Open the NMPDR group file for this genome.
277              my $group;              my $group;
278              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
# Line 286  Line 285 
285              }              }
286              close TMP;              close TMP;
287              # Output the genome record.              # Output the genome record.
288              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID),
289                               $group, $species, $extra, $taxonomy);                               $dnaSize, $genus, $group, $species, $extra, $version, $taxonomy);
290              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
291              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
292              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 325  Line 324 
324      return $retVal;      return $retVal;
325  }  }
326    
 =head3 LoadCouplingData  
   
 C<< my $stats = $spl->LoadCouplingData(); >>  
   
 Load the coupling and evidence data from FIG into Sprout.  
   
 The coupling data specifies which genome features are functionally coupled. The  
 evidence data explains why the coupling is functional.  
   
 The following relations are loaded by this method.  
   
     Coupling  
     IsEvidencedBy  
     PCH  
     ParticipatesInCoupling  
     UsesAsEvidence  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadCouplingData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the genome hash.  
     my $genomeFilter = $self->{genomes};  
     # Set up an ID counter for the PCHs.  
     my $pchID = 0;  
     # Start the loads.  
     my $loadCoupling = $self->_TableLoader('Coupling');  
     my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);  
     my $loadPCH = $self->_TableLoader('PCH', $self->PrimaryOnly);  
     my $loadParticipatesInCoupling = $self->_TableLoader('ParticipatesInCoupling', $self->PrimaryOnly);  
     my $loadUsesAsEvidence = $self->_TableLoader('UsesAsEvidence', $self->PrimaryOnly);  
     if ($self->{options}->{loadOnly}) {  
         Trace("Loading from existing files.") if T(2);  
     } else {  
         Trace("Generating coupling data.") if T(2);  
         # Loop through the genomes found.  
         for my $genome (sort keys %{$genomeFilter}) {  
             Trace("Generating coupling data for $genome.") if T(3);  
             $loadCoupling->Add("genomeIn");  
             # Create a hash table for holding coupled pairs. We use this to prevent  
             # duplicates. For example, if A is coupled to B, we don't want to also  
             # assert that B is coupled to A, because we already know it. Fortunately,  
             # all couplings occur within a genome, so we can keep the hash table  
             # size reasonably small.  
             my %dupHash = ();  
             # Get all of the genome's PEGs.  
             my @pegs = $fig->pegs_of($genome);  
             # Loop through the PEGs.  
             for my $peg1 (@pegs) {  
                 $loadCoupling->Add("pegIn");  
                 Trace("Processing PEG $peg1 for $genome.") if T(4);  
                 # Get a list of the coupled PEGs.  
                 my @couplings = $fig->coupled_to($peg1);  
                 # For each coupled PEG, we need to verify that a coupling already  
                 # exists. If not, we have to create one.  
                 for my $coupleData (@couplings) {  
                     my ($peg2, $score) = @{$coupleData};  
                     # Compute the coupling ID.  
                     my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);  
                     if (! exists $dupHash{$coupleID}) {  
                         $loadCoupling->Add("couplingIn");  
                         # Here we have a new coupling to store in the load files.  
                         Trace("Storing coupling ($coupleID) with score $score.") if T(4);  
                         # Ensure we don't do this again.  
                         $dupHash{$coupleID} = $score;  
                         # Write the coupling record.  
                         $loadCoupling->Put($coupleID, $score);  
                         # Connect it to the coupled PEGs.  
                         $loadParticipatesInCoupling->Put($peg1, $coupleID, 1);  
                         $loadParticipatesInCoupling->Put($peg2, $coupleID, 2);  
                         # Get the evidence for this coupling.  
                         my @evidence = $fig->coupling_evidence($peg1, $peg2);  
                         # Organize the evidence into a hash table.  
                         my %evidenceMap = ();  
                         # Process each evidence item.  
                         for my $evidenceData (@evidence) {  
                             $loadPCH->Add("evidenceIn");  
                             my ($peg3, $peg4, $usage) = @{$evidenceData};  
                             # Only proceed if the evidence is from a Sprout  
                             # genome.  
                             if ($genomeFilter->{$fig->genome_of($peg3)}) {  
                                 $loadUsesAsEvidence->Add("evidenceChosen");  
                                 my $evidenceKey = "$coupleID $peg3 $peg4";  
                                 # We store this evidence in the hash if the usage  
                                 # is nonzero or no prior evidence has been found. This  
                                 # insures that if there is duplicate evidence, we  
                                 # at least keep the meaningful ones. Only evidence in  
                                 # the hash makes it to the output.  
                                 if ($usage || ! exists $evidenceMap{$evidenceKey}) {  
                                     $evidenceMap{$evidenceKey} = $evidenceData;  
                                 }  
                             }  
                         }  
                         for my $evidenceID (keys %evidenceMap) {  
                             # Get the ID for this evidence.  
                             $pchID++;  
                             # Create the evidence record.  
                             my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};  
                             $loadPCH->Put($pchID, $usage);  
                             # Connect it to the coupling.  
                             $loadIsEvidencedBy->Put($coupleID, $pchID);  
                             # Connect it to the features.  
                             $loadUsesAsEvidence->Put($pchID, $peg3, 1);  
                             $loadUsesAsEvidence->Put($pchID, $peg4, 2);  
                         }  
                     }  
                 }  
             }  
         }  
     }  
     # All done. Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
327  =head3 LoadFeatureData  =head3 LoadFeatureData
328    
329  C<< my $stats = $spl->LoadFeatureData(); >>  C<< my $stats = $spl->LoadFeatureData(); >>
# Line 463  Line 336 
336    
337      Feature      Feature
338      FeatureAlias      FeatureAlias
339        IsAliasOf
340      FeatureLink      FeatureLink
341      FeatureTranslation      FeatureTranslation
342      FeatureUpstream      FeatureUpstream
# Line 472  Line 346 
346      FeatureEssential      FeatureEssential
347      FeatureVirulent      FeatureVirulent
348      FeatureIEDB      FeatureIEDB
349        CDD
350        IsPresentOnProteinOf
351    
352  =over 4  =over 4
353    
# Line 493  Line 369 
369      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
370      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
371      my $loadFeature = $self->_TableLoader('Feature');      my $loadFeature = $self->_TableLoader('Feature');
372      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn', $self->PrimaryOnly);      my $loadIsLocatedIn = $self->_TableLoader('IsLocatedIn');
373      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');      my $loadFeatureAlias = $self->_TableLoader('FeatureAlias');
374        my $loadIsAliasOf = $self->_TableLoader('IsAliasOf');
375      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
376      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
377      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
378      my $loadHasFeature = $self->_TableLoader('HasFeature', $self->PrimaryOnly);      my $loadHasFeature = $self->_TableLoader('HasFeature');
379      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem', $self->PrimaryOnly);      my $loadHasRoleInSubsystem = $self->_TableLoader('HasRoleInSubsystem');
380      my $loadFeatureEssential = $self->_TableLoader('FeatureEssential');      my $loadFeatureEssential = $self->_TableLoader('FeatureEssential');
381      my $loadFeatureVirulent = $self->_TableLoader('FeatureVirulent');      my $loadFeatureVirulent = $self->_TableLoader('FeatureVirulent');
382      my $loadFeatureIEDB = $self->_TableLoader('FeatureIEDB');      my $loadFeatureIEDB = $self->_TableLoader('FeatureIEDB');
383        my $loadCDD = $self->_TableLoader('CDD');
384        my $loadIsPresentOnProteinOf = $self->_TableLoader('IsPresentOnProteinOf');
385      # Get the subsystem hash.      # Get the subsystem hash.
386      my $subHash = $self->{subsystems};      my $subHash = $self->{subsystems};
387        # Get the property keys.
388        my $propKeys = $self->{propKeys};
389        # Create a hashes to hold CDD and alias values.
390        my %CDD = ();
391        my %alias = ();
392      # 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
393      # locations.      # locations.
394      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 517  Line 401 
401              Trace("Loading features for genome $genomeID.") if T(3);              Trace("Loading features for genome $genomeID.") if T(3);
402              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
403              # Get the feature list for this genome.              # Get the feature list for this genome.
404              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed_fast($genomeID);
405              # Sort and count the list.              # Sort and count the list.
406              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
407              my $count = scalar @featureTuples;              my $count = scalar @featureTuples;
408                my @fids = map { $_->[0] } @featureTuples;
409              Trace("$count features found for genome $genomeID.") if T(3);              Trace("$count features found for genome $genomeID.") if T(3);
410                # Get the attributes for this genome and put them in a hash by feature ID.
411                my $attributes = GetGenomeAttributes($fig, $genomeID, \@fids, $propKeys);
412              # Set up for our duplicate-feature check.              # Set up for our duplicate-feature check.
413              my $oldFeatureID = "";              my $oldFeatureID = "";
414              # Loop through the features.              # Loop through the features.
415              for my $featureTuple (@featureTuples) {              for my $featureTuple (@featureTuples) {
416                  # Split the tuple.                  # Split the tuple.
417                  my ($featureID, $locations, undef, $type) = @{$featureTuple};                  my ($featureID, $locations, undef, $type, $minloc, $maxloc, $assignment, $user, $quality) = @{$featureTuple};
418                  # Check for duplicates.                  # Check for duplicates.
419                  if ($featureID eq $oldFeatureID) {                  if ($featureID eq $oldFeatureID) {
420                      Trace("Duplicate feature $featureID found.") if T(1);                      Trace("Duplicate feature $featureID found.") if T(1);
# Line 535  Line 422 
422                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
423                      # Count this feature.                      # Count this feature.
424                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
425                        # Fix the quality. It is almost always a space, but some odd stuff might sneak through, and the
426                        # Sprout database requires a single character.
427                        if (! defined($quality) || $quality eq "") {
428                            $quality = " ";
429                        }
430                      # Begin building the keywords. We start with the genome ID, the                      # Begin building the keywords. We start with the genome ID, the
431                      # feature ID, and the organism name.                      # feature ID, the taxonomy, and the organism name.
432                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID));                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID),
433                      # Get the functional assignment and aliases. This                                      $fig->taxonomy_of($genomeID));
                     # depends on the feature type.  
                     my $assignment;  
                     if ($type eq "peg") {  
                         $assignment = $fig->function_of($featureID);  
434                          # Create the aliases.                          # Create the aliases.
435                          for my $alias ($fig->feature_aliases($featureID)) {                          for my $alias ($fig->feature_aliases($featureID)) {
436                              $loadFeatureAlias->Put($featureID, $alias);                          #Connect this alias to this feature.
437                            $loadIsAliasOf->Put($alias, $featureID);
438                              push @keywords, $alias;                              push @keywords, $alias;
439                            # If this is a locus tag, also add its natural form as a keyword.
440                            my $naturalName = AliasAnalysis::Type(LocusTag => $alias);
441                            if ($naturalName) {
442                                push @keywords, $naturalName;
443                            }
444                            # If this is the first time for the specified alias, create its
445                            # alias record.
446                            if (! exists $alias{$alias}) {
447                                $loadFeatureAlias->Put($alias);
448                                $alias{$alias} = 1;
449                          }                          }
                     } else {  
                         # For other types, the assignment is the first (and ONLY) alias.  
                         ($assignment) = $fig->feature_aliases($featureID);  
450                      }                      }
451                      Trace("Assignment for $featureID is: $assignment") if T(4);                      Trace("Assignment for $featureID is: $assignment") if T(4);
452                      # Break the assignment into words and shove it onto the                      # Break the assignment into words and shove it onto the
# Line 578  Line 474 
474                      }                      }
475                      # Now we need to find the subsystems this feature participates in.                      # Now we need to find the subsystems this feature participates in.
476                      # We also add the subsystems to the keyword list. Before we do that,                      # We also add the subsystems to the keyword list. Before we do that,
477                      # we must convert underscores to spaces and tack on the classifications.                      # we must convert underscores to spaces.
478                      my @subsystems = $fig->peg_to_subsystems($featureID);                      my @subsystems = $fig->peg_to_subsystems($featureID);
479                      for my $subsystem (@subsystems) {                      for my $subsystem (@subsystems) {
480                          # Only proceed if we like this subsystem.                          # Only proceed if we like this subsystem.
# Line 607  Line 503 
503                      # [name, value, value with URL]. (We don't need the PEG, since                      # [name, value, value with URL]. (We don't need the PEG, since
504                      # we already know it.)                      # we already know it.)
505                      my @attributes = map { [$_->[1], $_->[2], Tracer::CombineURL($_->[2], $_->[3])] }                      my @attributes = map { [$_->[1], $_->[2], Tracer::CombineURL($_->[2], $_->[3])] }
506                                           $fig->get_attributes($featureID);                                           @{$attributes->{$featureID}};
507                      # Now we process each of the special attributes.                      # Now we process each of the special attributes.
508                      if (SpecialAttribute($featureID, \@attributes,                      if (SpecialAttribute($featureID, \@attributes,
509                                           1, 2, '^(essential|potential_essential)$',                                           1, [0,2], '^(essential|potential_essential)$',
510                                           $loadFeatureEssential)) {                                           $loadFeatureEssential)) {
511                          push @keywords, 'essential';                          push @keywords, 'essential';
512                          $loadFeature->Add('essential');                          $loadFeature->Add('essential');
513                      }                      }
514                      if (SpecialAttribute($featureID, \@attributes,                      if (SpecialAttribute($featureID, \@attributes,
515                                           0, 2, '^virulen',                                           0, [2], '^virulen',
516                                           $loadFeatureVirulent)) {                                           $loadFeatureVirulent)) {
517                          push @keywords, 'virulent';                          push @keywords, 'virulent';
518                          $loadFeature->Add('virulent');                          $loadFeature->Add('virulent');
519                      }                      }
520                      if (SpecialAttribute($featureID, \@attributes,                      if (SpecialAttribute($featureID, \@attributes,
521                                           0, 2, '^iedb_',                                           0, [0,2], '^iedb_',
522                                           $loadFeatureIEDB)) {                                           $loadFeatureIEDB)) {
523                          push @keywords, 'iedb';                          push @keywords, 'iedb';
524                          $loadFeature->Add('iedb');                          $loadFeature->Add('iedb');
525                      }                      }
526                        # Now we have some other attributes we need to process. Currently,
527                        # this is CDD and CELLO, but we expect the number to increase.
528                        my %attributeHash = ();
529                        for my $attrRow (@{$attributes->{$featureID}}) {
530                            my (undef, $key, @values) = @{$attrRow};
531                            $key =~ /^([^:]+)::(.+)/;
532                            if (exists $attributeHash{$1}) {
533                                $attributeHash{$1}->{$2} = \@values;
534                            } else {
535                                $attributeHash{$1} = {$2 => \@values};
536                            }
537                        }
538                        my $celloValue = "unknown";
539                        # Pull in the CELLO attribute. There will never be more than one.
540                        # If we have one, it's a feature attribute AND a keyword.
541                        my @celloData = keys %{$attributeHash{CELLO}};
542                        if (@celloData) {
543                            $celloValue = $celloData[0];
544                            push @keywords, $celloValue;
545                        }
546                        # Now we handle CDD. This is a bit more complicated, because
547                        # there are multiple CDDs per protein.
548                        if (exists $attributeHash{CDD}) {
549                            # Get the hash of CDD IDs to scores for this feature. We
550                            # already know it exists because of the above IF.
551                            my $cddHash = $attributeHash{CDD};
552                            my @cddData = sort keys %{$cddHash};
553                            for my $cdd (@cddData) {
554                                # Extract the score for this CDD and decode it.
555                                my ($codeScore) = split(/\s*,\s*/, $cddHash->{$cdd}->[0]);
556                                my $realScore = FIGRules::DecodeScore($codeScore);
557                                # Create the connection.
558                                $loadIsPresentOnProteinOf->Put($cdd, $featureID, $realScore);
559                                # If this CDD does not yet exist, create its record.
560                                if (! exists $CDD{$cdd}) {
561                                    $CDD{$cdd} = 1;
562                                    $loadCDD->Put($cdd);
563                                }
564                            }
565                        }
566                      # Now we need to bust up hyphenated words in the keyword                      # Now we need to bust up hyphenated words in the keyword
567                      # list.                      # list. We keep them separate and put them at the end so
568                        # the original word order is available.
569                      my $keywordString = "";                      my $keywordString = "";
570                        my $bustedString = "";
571                      for my $keyword (@keywords) {                      for my $keyword (@keywords) {
572                          if (length $keyword >= 4) {                          if (length $keyword >= 3) {
573                              $keywordString .= " $keyword";                              $keywordString .= " $keyword";
574                              if ($keyword =~ /-/) {                              if ($keyword =~ /-/) {
575                                  my @words = grep { length($_) >= 4 } split /-/, $keyword;                                  my @words = split /-/, $keyword;
576                                  $keywordString .= join(" ", "", @words);                                  $bustedString .= join(" ", "", @words);
577                              }                              }
578                          }                          }
579                      }                      }
580                        $keywordString .= $bustedString;
581                        # Get rid of annoying punctuation.
582                        $keywordString =~ s/[();]//g;
583                      # Clean the keyword list.                      # Clean the keyword list.
584                      my $cleanWords = $sprout->CleanKeywords($keywordString);                      my $cleanWords = $sprout->CleanKeywords($keywordString);
585                      Trace("Keyword string for $featureID: $cleanWords") if T(4);                      Trace("Keyword string for $featureID: $cleanWords") if T(4);
586                      # Create the feature record.                      # Now we need to process the feature's locations. First, we split them up.
587                      $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);                      my @locationList = split /\s*,\s*/, $locations;
588                        # Next, we convert them to Sprout location objects.
589                        my @locObjectList = map { BasicLocation->new("$genomeID:$_") } @locationList;
590                      # 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
591                      # 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
592                      # the maximum segment size. This simplifies the genes_in_region processing                      # the maximum segment size. This simplifies the genes_in_region processing
593                      # for Sprout.                      # for Sprout. To start, we create the location position indicator.
                     my @locationList = split /\s*,\s*/, $locations;  
                     # Create the location position indicator.  
594                      my $i = 1;                      my $i = 1;
595                      # Loop through the locations.                      # Loop through the locations.
596                      for my $location (@locationList) {                      for my $locObject (@locObjectList) {
597                          # Parse the location.                          # Split this location into a list of chunks.
                         my $locObject = BasicLocation->new("$genomeID:$location");  
                         # Split it into a list of chunks.  
598                          my @locOList = ();                          my @locOList = ();
599                          while (my $peeling = $locObject->Peel($chunkSize)) {                          while (my $peeling = $locObject->Peel($chunkSize)) {
600                              $loadIsLocatedIn->Add("peeling");                              $loadIsLocatedIn->Add("peeling");
# Line 670  Line 609 
609                              $i++;                              $i++;
610                          }                          }
611                      }                      }
612                        # Finally, reassemble the location objects into a list of Sprout location strings.
613                        $locations = join(", ", map { $_->String } @locObjectList);
614                        # Create the feature record.
615                        $loadFeature->Put($featureID, 1, $user, $quality, $celloValue, $type, $assignment, $cleanWords, $locations);
616                  }                  }
617              }              }
618          }          }
# Line 697  Line 640 
640      SubsystemClass      SubsystemClass
641      Role      Role
642      RoleEC      RoleEC
643        IsIdentifiedByEC
644      SSCell      SSCell
645      ContainsFeature      ContainsFeature
646      IsGenomeOf      IsGenomeOf
# Line 738  Line 682 
682      # Get the map list.      # Get the map list.
683      my @maps = $fig->all_maps;      my @maps = $fig->all_maps;
684      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
685      my $loadDiagram = $self->_TableLoader('Diagram', $self->PrimaryOnly);      my $loadDiagram = $self->_TableLoader('Diagram');
686      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn', $self->PrimaryOnly);      my $loadRoleOccursIn = $self->_TableLoader('RoleOccursIn');
687      my $loadSubsystem = $self->_TableLoader('Subsystem');      my $loadSubsystem = $self->_TableLoader('Subsystem');
688      my $loadRole = $self->_TableLoader('Role', $self->PrimaryOnly);      my $loadRole = $self->_TableLoader('Role');
689      my $loadRoleEC = $self->_TableLoader('RoleEC', $self->PrimaryOnly);      my $loadRoleEC = $self->_TableLoader('RoleEC');
690      my $loadCatalyzes = $self->_TableLoader('Catalyzes', $self->PrimaryOnly);      my $loadIsIdentifiedByEC = $self->_TableLoader('IsIdentifiedByEC');
691      my $loadSSCell = $self->_TableLoader('SSCell', $self->PrimaryOnly);      my $loadCatalyzes = $self->_TableLoader('Catalyzes');
692      my $loadContainsFeature = $self->_TableLoader('ContainsFeature', $self->PrimaryOnly);      my $loadSSCell = $self->_TableLoader('SSCell');
693      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf', $self->PrimaryOnly);      my $loadContainsFeature = $self->_TableLoader('ContainsFeature');
694      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf', $self->PrimaryOnly);      my $loadIsGenomeOf = $self->_TableLoader('IsGenomeOf');
695      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem', $self->PrimaryOnly);      my $loadIsRoleOf = $self->_TableLoader('IsRoleOf');
696      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn', $self->PrimaryOnly);      my $loadOccursInSubsystem = $self->_TableLoader('OccursInSubsystem');
697      my $loadHasSSCell = $self->_TableLoader('HasSSCell', $self->PrimaryOnly);      my $loadParticipatesIn = $self->_TableLoader('ParticipatesIn');
698      my $loadRoleSubset = $self->_TableLoader('RoleSubset', $self->PrimaryOnly);      my $loadHasSSCell = $self->_TableLoader('HasSSCell');
699      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset', $self->PrimaryOnly);      my $loadRoleSubset = $self->_TableLoader('RoleSubset');
700      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles', $self->PrimaryOnly);      my $loadGenomeSubset = $self->_TableLoader('GenomeSubset');
701      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfRoles = $self->_TableLoader('ConsistsOfRoles');
702      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes');
703      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset');
704      my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset');
705        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass');
706      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
707          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
708      } else {      } else {
709          Trace("Generating subsystem data.") if T(2);          Trace("Generating subsystem data.") if T(2);
710          # This hash will contain the role for each EC. When we're done, this          # This hash will contain the roles for each EC. When we're done, this
711          # information will be used to generate the Catalyzes table.          # information will be used to generate the Catalyzes table.
712          my %ecToRoles = ();          my %ecToRoles = ();
713          # Loop through the subsystems. Our first task will be to create the          # Loop through the subsystems. Our first task will be to create the
# Line 776  Line 721 
721              # Get the subsystem object.              # Get the subsystem object.
722              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
723              # Only proceed if the subsystem has a spreadsheet.              # Only proceed if the subsystem has a spreadsheet.
724              if (! $sub->{empty_ss}) {              if (defined($sub) && ! $sub->{empty_ss}) {
725                  Trace("Creating subsystem $subsysID.") if T(3);                  Trace("Creating subsystem $subsysID.") if T(3);
726                  $loadSubsystem->Add("subsystemIn");                  $loadSubsystem->Add("subsystemIn");
727                  # Create the subsystem record.                  # Create the subsystem record.
# Line 786  Line 731 
731                  # Now for the classification string. This comes back as a list                  # Now for the classification string. This comes back as a list
732                  # reference and we convert it to a space-delimited string.                  # reference and we convert it to a space-delimited string.
733                  my $classList = $fig->subsystem_classification($subsysID);                  my $classList = $fig->subsystem_classification($subsysID);
734                  my $classString = join(" : ", grep { $_ } @$classList);                  my $classString = join($FIG_Config::splitter, grep { $_ } @$classList);
735                  $loadSubsystemClass->Put($subsysID, $classString);                  $loadSubsystemClass->Put($subsysID, $classString);
736                  # 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.
737                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
738                        # Get the role's abbreviation.
739                        my $abbr = $sub->get_role_abbr($col);
740                      # Connect to this role.                      # Connect to this role.
741                      $loadOccursInSubsystem->Add("roleIn");                      $loadOccursInSubsystem->Add("roleIn");
742                      $loadOccursInSubsystem->Put($roleID, $subsysID, $col);                      $loadOccursInSubsystem->Put($roleID, $subsysID, $abbr, $col);
743                      # If it's a new role, add it to the role table.                      # If it's a new role, add it to the role table.
744                      if (! exists $roleData{$roleID}) {                      if (! exists $roleData{$roleID}) {
745                          # Get the role's abbreviation.                          # Get the role's abbreviation.
                         my $abbr = $sub->get_role_abbr($col);  
746                          # Add the role.                          # Add the role.
747                          $loadRole->Put($roleID, $abbr);                          $loadRole->Put($roleID);
748                          $roleData{$roleID} = 1;                          $roleData{$roleID} = 1;
749                          # Check for an EC number.                          # Check for an EC number.
750                          if ($roleID =~ /\(EC ([^.]+\.[^.]+\.[^.]+\.[^)]+)\)\s*$/) {                          if ($roleID =~ /\(EC (\d+\.\d+\.\d+\.\d+)\s*\)\s*$/) {
751                              my $ec = $1;                              my $ec = $1;
752                              $loadRoleEC->Put($roleID, $ec);                              $loadIsIdentifiedByEC->Put($roleID, $ec);
753                              $ecToRoles{$ec} = $roleID;                              # Check to see if this is our first encounter with this EC.
754                                if (exists $ecToRoles{$ec}) {
755                                    # No, so just add this role to the EC list.
756                                    push @{$ecToRoles{$ec}}, $roleID;
757                                } else {
758                                    # Output this EC.
759                                    $loadRoleEC->Put($ec);
760                                    # Create its role list.
761                                    $ecToRoles{$ec} = [$roleID];
762                                }
763                          }                          }
764                      }                      }
765                  }                  }
# Line 917  Line 872 
872              # Now we need to link all the map's roles to it.              # Now we need to link all the map's roles to it.
873              # A hash is used to prevent duplicates.              # A hash is used to prevent duplicates.
874              my %roleHash = ();              my %roleHash = ();
875              for my $role ($fig->map_to_ecs($map)) {              for my $ec ($fig->map_to_ecs($map)) {
876                  if (exists $ecToRoles{$role} && ! $roleHash{$role}) {                  if (exists $ecToRoles{$ec}) {
877                      $loadRoleOccursIn->Put($ecToRoles{$role}, $map);                      for my $role (@{$ecToRoles{$ec}}) {
878                            if (! $roleHash{$role}) {
879                                $loadRoleOccursIn->Put($role, $map);
880                      $roleHash{$role} = 1;                      $roleHash{$role} = 1;
881                  }                  }
882              }              }
883          }          }
884                }
885            }
886          # Before we leave, we must create the Catalyzes table. We start with the reactions,          # Before we leave, we must create the Catalyzes table. We start with the reactions,
887          # then use the "ecToRoles" table to convert EC numbers to role IDs.          # then use the "ecToRoles" table to convert EC numbers to role IDs.
888          my @reactions = $fig->all_reactions();          my @reactions = $fig->all_reactions();
889          for my $reactionID (@reactions) {          for my $reactionID (@reactions) {
890              # Get this reaction's list of roles. The results will be EC numbers.              # Get this reaction's list of roles. The results will be EC numbers.
891              my @roles = $fig->catalyzed_by($reactionID);              my @ecs = $fig->catalyzed_by($reactionID);
892              # Loop through the roles, creating catalyzation records.              # Loop through the roles, creating catalyzation records.
893              for my $thisRole (@roles) {              for my $thisEC (@ecs) {
894                  if (exists $ecToRoles{$thisRole}) {                  if (exists $ecToRoles{$thisEC}) {
895                      $loadCatalyzes->Put($ecToRoles{$thisRole}, $reactionID);                      for my $thisRole (@{$ecToRoles{$thisEC}}) {
896                            $loadCatalyzes->Put($thisRole, $reactionID);
897                        }
898                  }                  }
899              }              }
900          }          }
# Line 981  Line 942 
942      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
943      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
944      my $loadProperty = $self->_TableLoader('Property');      my $loadProperty = $self->_TableLoader('Property');
945      my $loadHasProperty = $self->_TableLoader('HasProperty', $self->PrimaryOnly);      my $loadHasProperty = $self->_TableLoader('HasProperty');
946      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
947          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
948      } else {      } else {
# Line 989  Line 950 
950          # Create a hash for storing property IDs.          # Create a hash for storing property IDs.
951          my %propertyKeys = ();          my %propertyKeys = ();
952          my $nextID = 1;          my $nextID = 1;
953            # Get the attributes we intend to store in the property table.
954            my $propKeys = $self->{propKeys};
955          # Loop through the genomes.          # Loop through the genomes.
956          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
957              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
958              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
959              # Get the genome's features. The feature ID is the first field in the              # Initialize a counter.
             # tuples returned by "all_features_detailed". We use "all_features_detailed"  
             # rather than "all_features" because we want all features regardless of type.  
             my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};  
             my $featureCount = 0;  
960              my $propertyCount = 0;              my $propertyCount = 0;
961              # Loop through the features, creating HasProperty records.              # Get the properties for this genome's features.
962              for my $fid (@features) {              my @attributes = $fig->get_attributes("fig|$genomeID%", $propKeys);
963                  # Get all attributes for this feature. We do this one feature at a time              Trace("Property list built for $genomeID.") if T(3);
964                  # to insure we do not get any genome attributes.              # Loop through the results, creating HasProperty records.
965                  my @attributeList = $fig->get_attributes($fid, '', '', '');              for my $attributeData (@attributes) {
966                  # Add essentiality and virulence attributes.                  # Pull apart the attribute tuple.
967                  if ($fig->essential($fid)) {                  my ($fid, $key, $value, $url) = @{$attributeData};
                     push @attributeList, [$fid, 'essential', 1, ''];  
                 }  
                 if ($fig->virulent($fid)) {  
                     push @attributeList, [$fid, 'virulent', 1, ''];  
                 }  
                 if (scalar @attributeList) {  
                     $featureCount++;  
                 }  
                 # Loop through the attributes.  
                 for my $tuple (@attributeList) {  
                     $propertyCount++;  
                     # Get this attribute value's data. Note that we throw away the FID,  
                     # since it will always be the same as the value if "$fid".  
                     my (undef, $key, $value, $url) = @{$tuple};  
968                      # Concatenate the key and value and check the "propertyKeys" hash to                      # Concatenate the key and value and check the "propertyKeys" hash to
969                      # see if we already have an ID for it. We use a tab for the separator                      # see if we already have an ID for it. We use a tab for the separator
970                      # character.                      # character.
# Line 1037  Line 982 
982                      # Create the HasProperty entry for this feature/property association.                      # Create the HasProperty entry for this feature/property association.
983                      $loadHasProperty->Put($fid, $propertyID, $url);                      $loadHasProperty->Put($fid, $propertyID, $url);
984                  }                  }
             }  
985              # Update the statistics.              # Update the statistics.
986              Trace("$propertyCount attributes processed for $featureCount features.") if T(3);              Trace("$propertyCount attributes processed.") if T(3);
             $loadHasProperty->Add("featuresIn", $featureCount);  
987              $loadHasProperty->Add("propertiesIn", $propertyCount);              $loadHasProperty->Add("propertiesIn", $propertyCount);
988          }          }
989      }      }
# Line 1085  Line 1028 
1028      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1029      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1030      my $loadAnnotation = $self->_TableLoader('Annotation');      my $loadAnnotation = $self->_TableLoader('Annotation');
1031      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation', $self->PrimaryOnly);      my $loadIsTargetOfAnnotation = $self->_TableLoader('IsTargetOfAnnotation');
1032      my $loadSproutUser = $self->_TableLoader('SproutUser', $self->PrimaryOnly);      my $loadSproutUser = $self->_TableLoader('SproutUser');
1033      my $loadUserAccess = $self->_TableLoader('UserAccess', $self->PrimaryOnly);      my $loadUserAccess = $self->_TableLoader('UserAccess');
1034      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation', $self->PrimaryOnly);      my $loadMadeAnnotation = $self->_TableLoader('MadeAnnotation');
1035      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1036          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1037      } else {      } else {
# Line 1192  Line 1135 
1135      # Get the genome hash.      # Get the genome hash.
1136      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1137      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1138      my $loadComesFrom = $self->_TableLoader('ComesFrom', $self->PrimaryOnly);      my $loadComesFrom = $self->_TableLoader('ComesFrom');
1139      my $loadSource = $self->_TableLoader('Source');      my $loadSource = $self->_TableLoader('Source');
1140      my $loadSourceURL = $self->_TableLoader('SourceURL');      my $loadSourceURL = $self->_TableLoader('SourceURL');
1141      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
# Line 1329  Line 1272 
1272      Compound      Compound
1273      CompoundName      CompoundName
1274      CompoundCAS      CompoundCAS
1275        IsIdentifiedByCAS
1276        HasCompoundName
1277      IsAComponentOf      IsAComponentOf
1278    
1279  This method proceeds reaction by reaction rather than genome by genome.  This method proceeds reaction by reaction rather than genome by genome.
# Line 1350  Line 1295 
1295      my $fig = $self->{fig};      my $fig = $self->{fig};
1296      # Create load objects for each of the tables we're loading.      # Create load objects for each of the tables we're loading.
1297      my $loadReaction = $self->_TableLoader('Reaction');      my $loadReaction = $self->_TableLoader('Reaction');
1298      my $loadReactionURL = $self->_TableLoader('ReactionURL', $self->PrimaryOnly);      my $loadReactionURL = $self->_TableLoader('ReactionURL');
1299      my $loadCompound = $self->_TableLoader('Compound', $self->PrimaryOnly);      my $loadCompound = $self->_TableLoader('Compound');
1300      my $loadCompoundName = $self->_TableLoader('CompoundName', $self->PrimaryOnly);      my $loadCompoundName = $self->_TableLoader('CompoundName');
1301      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS', $self->PrimaryOnly);      my $loadCompoundCAS = $self->_TableLoader('CompoundCAS');
1302      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf', $self->PrimaryOnly);      my $loadIsAComponentOf = $self->_TableLoader('IsAComponentOf');
1303        my $loadIsIdentifiedByCAS = $self->_TableLoader('IsIdentifiedByCAS');
1304        my $loadHasCompoundName = $self->_TableLoader('HasCompoundName');
1305      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1306          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1307      } else {      } else {
1308          Trace("Generating annotation data.") if T(2);          Trace("Generating reaction data.") if T(2);
1309            # We need some hashes to prevent duplicates.
1310            my %compoundNames = ();
1311            my %compoundCASes = ();
1312          # First we create the compounds.          # First we create the compounds.
1313          my @compounds = $fig->all_compounds();          my @compounds = $fig->all_compounds();
1314          for my $cid (@compounds) {          for my $cid (@compounds) {
# Line 1367  Line 1317 
1317              # Each name will be given a priority number, starting with 1.              # Each name will be given a priority number, starting with 1.
1318              my $prio = 1;              my $prio = 1;
1319              for my $name (@names) {              for my $name (@names) {
1320                  $loadCompoundName->Put($cid, $name, $prio++);                  if (! exists $compoundNames{$name}) {
1321                        $loadCompoundName->Put($name);
1322                        $compoundNames{$name} = 1;
1323                    }
1324                    $loadHasCompoundName->Put($cid, $name, $prio++);
1325              }              }
1326              # Create the main compound record. Note that the first name              # Create the main compound record. Note that the first name
1327              # becomes the label.              # becomes the label.
# Line 1376  Line 1330 
1330              # Check for a CAS ID.              # Check for a CAS ID.
1331              my $cas = $fig->cas($cid);              my $cas = $fig->cas($cid);
1332              if ($cas) {              if ($cas) {
1333                  $loadCompoundCAS->Put($cid, $cas);                  $loadIsIdentifiedByCAS->Put($cid, $cas);
1334                    if (! exists $compoundCASes{$cas}) {
1335                        $loadCompoundCAS->Put($cas);
1336                        $compoundCASes{$cas} = 1;
1337                    }
1338              }              }
1339          }          }
1340          # All the compounds are set up, so we need to loop through the reactions next. First,          # All the compounds are set up, so we need to loop through the reactions next. First,
# Line 1413  Line 1371 
1371      return $retVal;      return $retVal;
1372  }  }
1373    
 =head3 LoadGroupData  
   
 C<< my $stats = $spl->LoadGroupData(); >>  
   
 Load the genome Groups into Sprout.  
   
 The following relations are loaded by this method.  
   
     GenomeGroups  
   
 Currently, we do not use groups. We used to use them for NMPDR groups,  
 butThere is no direct support for genome groups in FIG, so we access the SEED  
 files directly.  
   
 =over 4  
   
 =item RETURNS  
   
 Returns a statistics object for the loads.  
   
 =back  
   
 =cut  
 #: Return Type $%;  
 sub LoadGroupData {  
     # Get this object instance.  
     my ($self) = @_;  
     # Get the FIG object.  
     my $fig = $self->{fig};  
     # Get the genome hash.  
     my $genomeHash = $self->{genomes};  
     # Create a load object for the table we're loading.  
     my $loadGenomeGroups = $self->_TableLoader('GenomeGroups');  
     if ($self->{options}->{loadOnly}) {  
         Trace("Loading from existing files.") if T(2);  
     } else {  
         Trace("Generating group data.") if T(2);  
         # Currently there are no groups.  
     }  
     # Finish the load.  
     my $retVal = $self->_FinishAll();  
     return $retVal;  
 }  
   
1374  =head3 LoadSynonymData  =head3 LoadSynonymData
1375    
1376  C<< my $stats = $spl->LoadSynonymData(); >>  C<< my $stats = $spl->LoadSynonymData(); >>
# Line 1498  Line 1412 
1412          Trace("Generating synonym group data.") if T(2);          Trace("Generating synonym group data.") if T(2);
1413          # Get the database handle.          # Get the database handle.
1414          my $dbh = $fig->db_handle();          my $dbh = $fig->db_handle();
1415          # Ask for the synonyms.          # Ask for the synonyms. Note that "maps_to" is a group name, and "syn_id" is a PEG ID or alias.
1416          my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");          my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1417          my $result = $sth->execute();          my $result = $sth->execute();
1418          if (! defined($result)) {          if (! defined($result)) {
# Line 1510  Line 1424 
1424              my $featureCount = 0;              my $featureCount = 0;
1425              # Loop through the synonym/peg pairs.              # Loop through the synonym/peg pairs.
1426              while (my @row = $sth->fetchrow()) {              while (my @row = $sth->fetchrow()) {
1427                  # Get the synonym ID and feature ID.                  # Get the synonym group ID and feature ID.
1428                  my ($syn_id, $peg) = @row;                  my ($syn_id, $peg) = @row;
1429                  # Insure it's for one of our genomes.                  # Insure it's for one of our genomes.
1430                  my $genomeID = FIG::genome_of($peg);                  my $genomeID = FIG::genome_of($peg);
# Line 1613  Line 1527 
1527    
1528  The following relations are loaded by this method.  The following relations are loaded by this method.
1529    
     DrugProject  
     ContainsTopic  
     DrugTopic  
     ContainsAnalysisOf  
1530      PDB      PDB
1531      IncludesBound      DocksWith
1532      IsBoundIn      IsProteinForFeature
     BindsWith  
1533      Ligand      Ligand
     DescribesProteinForFeature  
     FeatureConservation  
1534    
1535  The source information for these relations is taken from flat files in the  The source information for these relations is taken from attributes. The
1536  C<$FIG_Config::drug_directory>. The file C<master_tables.list> contains  C<PDB> attribute links a PDB to a feature, and is used to build B<IsProteinForFeature>.
1537  a list of drug project names paired with file names. The named file (in the  The C<zinc_name> attribute describes the ligands. The C<docking_results>
1538  same directory) contains all the data for the project.  attribute contains the information for the B<DocksWith> relationship. It is
1539    expected that additional attributes and tables will be added in the future.
1540    
1541  =over 4  =over 4
1542    
# Line 1648  Line 1556 
1556      # Get the genome hash.      # Get the genome hash.
1557      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1558      # Create load objects for the tables we're loading.      # Create load objects for the tables we're loading.
     my $loadDrugProject = $self->_TableLoader('DrugProject');  
     my $loadContainsTopic = $self->_TableLoader('ContainsTopic');  
     my $loadDrugTopic = $self->_TableLoader('DrugTopic');  
     my $loadContainsAnalysisOf = $self->_TableLoader('ContainsAnalysisOf');  
1559      my $loadPDB = $self->_TableLoader('PDB');      my $loadPDB = $self->_TableLoader('PDB');
     my $loadIncludesBound = $self->_TableLoader('IncludesBound');  
     my $loadIsBoundIn = $self->_TableLoader('IsBoundIn');  
     my $loadBindsWith = $self->_TableLoader('BindsWith');  
1560      my $loadLigand = $self->_TableLoader('Ligand');      my $loadLigand = $self->_TableLoader('Ligand');
1561      my $loadDescribesProteinForFeature = $self->_TableLoader('DescribesProteinForFeature');      my $loadIsProteinForFeature = $self->_TableLoader('IsProteinForFeature');
1562      my $loadFeatureConservation = $self->_TableLoader('FeatureConservation');      my $loadDocksWith = $self->_TableLoader('DocksWith');
1563      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1564          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1565      } else {      } else {
1566          Trace("Generating drug target data.") if T(2);          Trace("Generating drug target data.") if T(2);
1567          # Load the project list. The file comes in as a list of chomped lines,          # First comes the "DocksWith" relationship. This will give us a list of PDBs.
1568          # and we split them on the TAB character to make the project name the          # We can also encounter PDBs when we process "IsProteinForFeature". To manage
1569          # key and the file name the value of the resulting hash.          # this process, PDB information is collected in a hash table and then
1570          my %projects = map { split /\t/, $_ } Tracer::GetFile("$FIG_Config::drug_directory/master_tables.list");          # unspooled after both relationships are created.
1571          # Create hashes for the derived objects: PDBs, Features, and Ligands. These objects          my %pdbHash = ();
1572          # may occur multiple times in a single project file or even in multiple project          Trace("Generating docking data.") if T(2);
1573          # files.          # Get all the docking data. This may cause problems if there are too many PDBs,
1574          my %ligands = ();          # at which point we'll need another algorithm. The indicator that this is
1575          my %pdbs = ();          # happening will be a timeout error in the next statement.
1576          my %features = ();          my @dockData = $fig->query_attributes('$key = ? AND $value < ?',
1577          my %bindings = ();                                                ['docking_results', $FIG_Config::dockLimit]);
1578          # Set up a counter for drug topics. This will be used as the key.          Trace(scalar(@dockData) . " rows of docking data found.") if T(3);
1579          my $topicCounter = 0;          for my $dockData (@dockData) {
1580          # Loop through the projects. We sort the keys not because we need them sorted, but              # Get the docking data components.
1581          # because it makes it easier to infer our progress from trace messages.              my ($pdbID, $docking_key, @valueData) = @{$dockData};
1582          for my $project (sort keys %projects) {              # Fix the PDB ID. It's supposed to be lower-case, but this does not always happen.
1583              Trace("Processing project $project.") if T(3);              $pdbID = lc $pdbID;
1584              # Only proceed if the download file exists.              # Strip off the object type.
1585              my $projectFile = "$FIG_Config::drug_directory/$projects{$project}";              $pdbID =~ s/pdb://;
1586              if (! -f $projectFile) {              # Extract the ZINC ID from the docking key. Note that there are two possible
1587                  Trace("Project file $projectFile not found.") if T(0);              # formats.
1588              } else {              my (undef, $zinc_id) = $docking_key =~ /^docking_results::(ZINC)?(\d+)$/;
1589                  # Create the project record.              if (! $zinc_id) {
1590                  $loadDrugProject->Put($project);                  Trace("Invalid docking result key $docking_key for $pdbID.") if T(0);
1591                  # Create a hash for the topics. Each project has one or more topics. The                  $loadDocksWith->Add("errors");
1592                  # topic is identified by a URL, a category, and an identifier.              } else {
1593                  my %topics = ();                  # Get the pieces of the value and parse the energy.
1594                  # Now we can open the project file.                  # Note that we don't care about the rank, since
1595                  Trace("Reading project file $projectFile.") if T(3);                  # we can sort on the energy level itself in our database.
1596                  Open(\*PROJECT, "<$projectFile");                  my ($energy, $tool, $type) = @valueData;
1597                  # Get the first record, which is a list of column headers. We don't use this                  my ($rank, $total, $vanderwaals, $electrostatic) = split /\s*;\s*/, $energy;
1598                  # for anything, but it may be useful for debugging.                  # Ignore predicted results.
1599                  my $headerLine = <PROJECT>;                  if ($type ne "Predicted") {
1600                  # Loop through the rest of the records.                      # Count this docking result.
1601                  while (! eof PROJECT) {                      if (! exists $pdbHash{$pdbID}) {
1602                      # Get the current line of data. Note that not all lines will have all                          $pdbHash{$pdbID} = 1;
1603                      # the fields. In particular, the CLIBE data is fairly rare.                      } else {
1604                      my ($authorOrganism, $category, $tag, $refURL, $peg, $conservation,                          $pdbHash{$pdbID}++;
1605                          $pdbBound, $pdbBoundEval, $pdbFree, $pdbFreeEval, $pdbFreeTitle,                      }
1606                          $protDistInfo, $passAspInfo, $passAspFile, $passWeightInfo,                      # Write the result to the output.
1607                          $passWeightFile, $clibeInfo, $clibeURL, $clibeTotalEnergy,                      $loadDocksWith->Put($pdbID, $zinc_id, $electrostatic, $type, $tool,
1608                          $clibeVanderwaals, $clibeHBonds, $clibeEI, $clibeSolvationE)                                          $total, $vanderwaals);
                        = Tracer::GetLine(\*PROJECT);  
                     # The tag contains an identifier for the current line of data followed  
                     # by a text statement that generally matches a property name in the  
                     # main database. We split it up, since the identifier goes with  
                     # the PDB data and the text statement is part of the topic.  
                     my ($lineID, $topicTag) = split /\s*,\s*/, $tag;  
                     $loadDrugProject->Add("data line");  
                     # Check for a new topic.  
                     my $topicData = "$category\t$topicTag\t$refURL";  
                     if (! exists $topics{$topicData}) {  
                         # Here we have a new topic. Compute its ID.  
                         $topicCounter++;  
                         $topics{$topicData} = $topicCounter;  
                         # Create its database record.  
                         $loadDrugTopic->Put($topicCounter, $refURL, $category, $authorOrganism,  
                                             $topicTag);  
                         # Connect it to the project.  
                         $loadContainsTopic->Put($project, $topicCounter);  
                         $loadDrugTopic->Add("topic");  
                     }  
                     # Now we know the topic ID exists in the hash and the topic will  
                     # appear in the database, so we get this topic's ID.  
                     my $topicID = $topics{$topicData};  
                     # If the feature in this line is new, we need to save its conservation  
                     # number.  
                     if (! exists $features{$peg}) {  
                         $loadFeatureConservation->Put($peg, $conservation);  
                         $features{$peg} = 1;  
                     }  
                     # Now we have two PDBs to deal with-- a bound PDB and a free PDB.  
                     # The free PDB will have data about docking points; the bound PDB  
                     # will have data about docking. We store both types as PDBs, and  
                     # the special data comes from relationships. First we process the  
                     # bound PDB.  
                     if ($pdbBound) {  
                         $loadPDB->Add("bound line");  
                         # Insure this PDB is in the database.  
                         $self->CreatePDB($pdbBound, lc "$pdbFreeTitle (bound)", "bound", \%pdbs, $loadPDB);  
                         # Connect it to this topic.  
                         $loadIncludesBound->Put($topicID, $pdbBound);  
                         # Check for CLIBE data.  
                         if ($clibeInfo) {  
                             $loadLigand->Add("clibes");  
                             # We have CLIBE data, so we create a ligand and relate it to the PDB.  
                             if (! exists $ligands{$clibeInfo}) {  
                                 # This is a new ligand, so create its record.  
                                 $loadLigand->Put($clibeInfo);  
                                 $loadLigand->Add("ligand");  
                                 # Make sure we know this ligand already exists.  
                                 $ligands{$clibeInfo} = 1;  
                             }  
                             # Now connect the PDB to the ligand using the CLIBE data.  
                             $loadBindsWith->Put($pdbBound, $clibeInfo, $clibeURL, $clibeHBonds, $clibeEI,  
                                                 $clibeSolvationE, $clibeVanderwaals);  
                         }  
                         # Connect this PDB to the feature.  
                         $loadDescribesProteinForFeature->Put($pdbBound, $peg, $protDistInfo, $pdbBoundEval);  
                     }  
                     # Next is the free PDB.  
                     if ($pdbFree) {  
                         $loadPDB->Add("free line");  
                         # Insure this PDB is in the database.  
                         $self->CreatePDB($pdbFree, lc $pdbFreeTitle, "free", \%pdbs, $loadPDB);  
                         # Connect it to this topic.  
                         $loadContainsAnalysisOf->Put($topicID, $pdbFree, $passAspInfo,  
                                                      $passWeightFile, $passWeightInfo, $passAspFile);  
                         # Connect this PDB to the feature.  
                         $loadDescribesProteinForFeature->Put($pdbFree, $peg, $protDistInfo, $pdbFreeEval);  
                     }  
                     # If we have both PDBs, we may need to link them.  
                     if ($pdbFree && $pdbBound) {  
                         $loadIsBoundIn->Add("connection");  
                         # Insure we only link them once.  
                         my $bindingKey =  "$pdbFree\t$pdbBound";  
                         if (! exists $bindings{$bindingKey}) {  
                             $loadIsBoundIn->Add("newConnection");  
                             $loadIsBoundIn->Put($pdbFree, $pdbBound);  
                             $bindings{$bindingKey} = 1;  
1609                          }                          }
1610                      }                      }
1611                  }                  }
1612                  # Close off this project.          Trace("Connecting features.") if T(2);
1613                  close PROJECT;          # Loop through the genomes.
1614            for my $genome (sort keys %{$genomeHash}) {
1615                Trace("Generating PDBs for $genome.") if T(3);
1616                # Get all of the PDBs that BLAST against this genome's features.
1617                my @attributeData = $fig->get_attributes("fig|$genome%", 'PDB::%');
1618                for my $pdbData (@attributeData) {
1619                    # The PDB ID is coded as a subkey.
1620                    if ($pdbData->[1] !~ /PDB::(.+)/i) {
1621                        Trace("Invalid PDB ID \"$pdbData->[1]\" in attribute table.") if T(0);
1622                        $loadPDB->Add("errors");
1623                    } else {
1624                        my $pdbID = $1;
1625                        # Insure the PDB is in the hash.
1626                        if (! exists $pdbHash{$pdbID}) {
1627                            $pdbHash{$pdbID} = 0;
1628                        }
1629                        # The score and locations are coded in the attribute value.
1630                        if ($pdbData->[2] !~ /^([^;]+)(.*)$/) {
1631                            Trace("Invalid PDB data for $pdbID and feature $pdbData->[0].") if T(0);
1632                            $loadIsProteinForFeature->Add("errors");
1633                        } else {
1634                            my ($score, $locData) = ($1,$2);
1635                            # The location data may not be present, so we have to start with some
1636                            # defaults and then check.
1637                            my ($start, $end) = (1, 0);
1638                            if ($locData) {
1639                                $locData =~ /(\d+)-(\d+)/;
1640                                $start = $1;
1641                                $end = $2;
1642                            }
1643                            # If we still don't have the end location, compute it from
1644                            # the feature length.
1645                            if (! $end) {
1646                                # Most features have one location, but we do a list iteration
1647                                # just in case.
1648                                my @locations = $fig->feature_location($pdbData->[0]);
1649                                $end = 0;
1650                                for my $loc (@locations) {
1651                                    my $locObject = BasicLocation->new($loc);
1652                                    $end += $locObject->Length;
1653                                }
1654                            }
1655                            # Decode the score.
1656                            my $realScore = FIGRules::DecodeScore($score);
1657                            # Connect the PDB to the feature.
1658                            $loadIsProteinForFeature->Put($pdbData->[0], $pdbID, $start, $realScore, $end);
1659                        }
1660                    }
1661                }
1662            }
1663            # We've got all our PDBs now, so we unspool them from the hash.
1664            Trace("Generating PDBs. " . scalar(keys %pdbHash) . " found.") if T(2);
1665            my $count = 0;
1666            for my $pdbID (sort keys %pdbHash) {
1667                $loadPDB->Put($pdbID, $pdbHash{$pdbID});
1668                $count++;
1669                Trace("$count PDBs processed.") if T(3) && ($count % 500 == 0);
1670            }
1671            # Finally we create the ligand table. This information can be found in the
1672            # zinc_name attribute.
1673            Trace("Loading ligands.") if T(2);
1674            # The ligand list is huge, so we have to get it in pieces. We also have to check for duplicates.
1675            my $last_zinc_id = "";
1676            my $zinc_id = "";
1677            my $done = 0;
1678            while (! $done) {
1679                # Get the next 10000 ligands. We insist that the object ID is greater than
1680                # the last ID we processed.
1681                Trace("Loading batch starting with ZINC:$zinc_id.") if T(3);
1682                my @attributeData = $fig->query_attributes('$object > ? AND $key = ? ORDER BY $object LIMIT 10000',
1683                                                           ["ZINC:$zinc_id", "zinc_name"]);
1684                Trace(scalar(@attributeData) . " attribute rows returned.") if T(3);
1685                if (! @attributeData) {
1686                    # Here there are no attributes left, so we quit the loop.
1687                    $done = 1;
1688                } else {
1689                    # Process the attribute data we've received.
1690                    for my $zinc_data (@attributeData) {
1691                        # The ZINC ID is found in the first return column, prefixed with the word ZINC.
1692                        if ($zinc_data->[0] =~ /^ZINC:(\d+)$/) {
1693                            $zinc_id = $1;
1694                            # Check for a duplicate.
1695                            if ($zinc_id eq $last_zinc_id) {
1696                                $loadLigand->Add("duplicate");
1697                            } else {
1698                                # Here it's safe to output the ligand. The ligand name is the attribute value
1699                                # (third column in the row).
1700                                $loadLigand->Put($zinc_id, $zinc_data->[2]);
1701                                # Insure we don't try to add this ID again.
1702                                $last_zinc_id = $zinc_id;
1703                            }
1704                        } else {
1705                            Trace("Invalid zinc ID \"$zinc_data->[0]\" in attribute table.") if T(0);
1706                            $loadLigand->Add("errors");
1707                        }
1708              }              }
1709          }          }
1710      }      }
1711            Trace("Ligands loaded.") if T(2);
1712        }
1713      # Finish the load.      # Finish the load.
1714      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1715      return $retVal;      return $retVal;
# Line 1801  Line 1720 
1720    
1721  =head3 SpecialAttribute  =head3 SpecialAttribute
1722    
1723  C<< my $count = SproutLoad::SpecialAttribute($id, \@attributes, $idxMatch, $idxValue, $pattern, $loader); >>  C<< my $count = SproutLoad::SpecialAttribute($id, \@attributes, $idxMatch, \@idxValues, $pattern, $loader); >>
1724    
1725  Look for special attributes of a given type. A special attribute is found by comparing one of  Look for special attributes of a given type. A special attribute is found by comparing one of
1726  the columns of the incoming attribute list to a search pattern. If a match is found, then  the columns of the incoming attribute list to a search pattern. If a match is found, then
1727  another column is put into an output table connected to the specified ID.  a set of columns is put into an output table connected to the specified ID.
1728    
1729  For example, when processing features, the attribute list we look at has three columns: attribute  For example, when processing features, the attribute list we look at has three columns: attribute
1730  name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name  name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name
1731  begins with C<iedb_>. The call signature is therefore  begins with C<iedb_>. The call signature is therefore
1732    
1733      my $found = SpecialAttribute($fid, \@attributeList, 0, 2, '^iedb_', $loadFeatureIEDB);      my $found = SpecialAttribute($fid, \@attributeList, 0, [0,2], '^iedb_', $loadFeatureIEDB);
1734    
1735  The pattern is matched against column 0, and if we have a match, then column 2's value is put  The pattern is matched against column 0, and if we have a match, then column 2's value is put
1736  to the output along with the specified feature ID.  to the output along with the specified feature ID.
# Line 1832  Line 1751 
1751  Index in each tuple of the column to be matched against the pattern. If the match is  Index in each tuple of the column to be matched against the pattern. If the match is
1752  successful, an output record will be generated.  successful, an output record will be generated.
1753    
1754  =item idxValue  =item idxValues
1755    
1756  Index in each tuple of the column to be put as the second column of the output.  Reference to a list containing the indexes in each tuple of the columns to be put as
1757    the second column of the output.
1758    
1759  =item pattern  =item pattern
1760    
# Line 1857  Line 1777 
1777    
1778  sub SpecialAttribute {  sub SpecialAttribute {
1779      # Get the parameters.      # Get the parameters.
1780      my ($id, $attributes, $idxMatch, $idxValue, $pattern, $loader) = @_;      my ($id, $attributes, $idxMatch, $idxValues, $pattern, $loader) = @_;
1781      # Declare the return variable.      # Declare the return variable.
1782      my $retVal = 0;      my $retVal = 0;
1783      # Loop through the attribute rows.      # Loop through the attribute rows.
1784      for my $row (@{$attributes}) {      for my $row (@{$attributes}) {
1785          # Check for a match.          # Check for a match.
1786          if ($row->[$idxMatch] =~ m/$pattern/i) {          if ($row->[$idxMatch] =~ m/$pattern/i) {
1787              # We have a match, so output a row.              # We have a match, so output a row. This is a bit tricky, since we may
1788              $loader->Put($id, $row->[$idxValue]);              # be putting out multiple columns of data from the input.
1789                my $value = join(" ", map { $row->[$_] } @{$idxValues});
1790                $loader->Put($id, $value);
1791              $retVal++;              $retVal++;
1792          }          }
1793      }      }
# Line 1874  Line 1796 
1796      return $retVal;      return $retVal;
1797  }  }
1798    
 =head3 CreatePDB  
   
 C<< $loader->CreatePDB($pdbID, $title, $type, \%pdbHash); >>  
   
 Insure that a PDB record exists for the identified PDB. If one does not exist, it will be  
 created.  
   
 =over 4  
   
 =item pdbID  
   
 ID string (usually an unqualified file name) for the desired PDB.  
   
 =item title  
   
 Title to use if the PDB must be created.  
   
 =item type  
   
 Type of PDB: C<free> or C<bound>  
   
 =item pdbHash  
   
 Hash containing the IDs of PDBs that have already been created.  
   
 =item pdbLoader  
   
 Load object for the PDB table.  
   
 =back  
   
 =cut  
   
 sub CreatePDB {  
     # Get the parameters.  
     my ($self, $pdbID, $title, $type, $pdbHash, $pdbLoader) = @_;  
     $pdbLoader->Add("PDB check");  
     # Check to see if this is a new PDB.  
     if (! exists $pdbHash->{$pdbID}) {  
         # It is, so we create it.  
         $pdbLoader->Put($pdbID, $title, $type);  
         $pdbHash->{$pdbID} = 1;  
         # Count it.  
         $pdbLoader->Add("PDB-$type");  
     }  
 }  
   
1799  =head3 TableLoader  =head3 TableLoader
1800    
1801  Create an ERDBLoad object for the specified table. The object is also added to  Create an ERDBLoad object for the specified table. The object is also added to
# Line 1935  Line 1810 
1810    
1811  Name of the table (relation) being loaded.  Name of the table (relation) being loaded.
1812    
 =item ignore  
   
 TRUE if the table should be ignored entirely, else FALSE.  
   
1813  =item RETURN  =item RETURN
1814    
1815  Returns an ERDBLoad object for loading the specified table.  Returns an ERDBLoad object for loading the specified table.
# Line 1949  Line 1820 
1820    
1821  sub _TableLoader {  sub _TableLoader {
1822      # Get the parameters.      # Get the parameters.
1823      my ($self, $tableName, $ignore) = @_;      my ($self, $tableName) = @_;
1824      # Create the load object.      # Create the load object.
1825      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly,      my $retVal = ERDBLoad->new($self->{erdb}, $tableName, $self->{loadDirectory}, $self->LoadOnly);
                                $ignore);  
1826      # Cache it in the loader list.      # Cache it in the loader list.
1827      push @{$self->{loaders}}, $retVal;      push @{$self->{loaders}}, $retVal;
1828      # Return it to the caller.      # Return it to the caller.
# Line 2024  Line 1894 
1894      return $retVal;      return $retVal;
1895  }  }
1896    
1897    =head3 GetGenomeAttributes
1898    
1899    C<< my $aHashRef = GetGenomeAttributes($fig, $genomeID, \@fids, \@propKeys); >>
1900    
1901    Return a hash of attributes keyed on feature ID. This method gets all the NMPDR-related
1902    attributes for all the features of a genome in a single call, then organizes them into
1903    a hash.
1904    
1905    =over 4
1906    
1907    =item fig
1908    
1909    FIG-like object for accessing attributes.
1910    
1911    =item genomeID
1912    
1913    ID of the genome who's attributes are desired.
1914    
1915    =item fids
1916    
1917    Reference to a list of the feature IDs whose attributes are to be kept.
1918    
1919    =item propKeys
1920    
1921    A list of the keys to retrieve.
1922    
1923    =item RETURN
1924    
1925    Returns a reference to a hash. The key of the hash is the feature ID. The value is the
1926    reference to a list of the feature's attribute tuples. Each tuple contains the feature ID,
1927    the attribute key, and one or more attribute values.
1928    
1929    =back
1930    
1931    =cut
1932    
1933    sub GetGenomeAttributes {
1934        # Get the parameters.
1935        my ($fig, $genomeID, $fids, $propKeys) = @_;
1936        # Declare the return variable.
1937        my $retVal = {};
1938        # Initialize the hash. This not only enables us to easily determine which FIDs to
1939        # keep, it insures that the caller sees a list reference for every known fid,
1940        # simplifying the logic.
1941        for my $fid (@{$fids}) {
1942            $retVal->{$fid} = [];
1943        }
1944        # Get the attributes. If ev_code_cron is running, we may get a timeout error, so
1945        # an eval is used.
1946        my @aList = ();
1947        eval {
1948            @aList = $fig->get_attributes("fig|$genomeID%", $propKeys);
1949            Trace(scalar(@aList) . " attributes returned for genome $genomeID.") if T(3);
1950        };
1951        # Check for a problem.
1952        if ($@) {
1953            Trace("Retrying attributes for $genomeID due to error: $@") if T(1);
1954            # Our fallback plan is to process the attributes in blocks of 100. This is much slower,
1955            # but allows us to continue processing.
1956            my $nFids = scalar @{$fids};
1957            for (my $i = 0; $i < $nFids; $i += 100) {
1958                # Determine the index of the last feature ID we'll be specifying on this pass.
1959                # Normally it's $i + 99, but if we're close to the end it may be less.
1960                my $end = ($i + 100 > $nFids ? $nFids - 1 : $i + 99);
1961                # Get a slice of the fid list.
1962                my @slice = @{$fids}[$i .. $end];
1963                # Get the relevant attributes.
1964                Trace("Retrieving attributes for fids $i to $end.") if T(3);
1965                my @aShort = $fig->get_attributes(\@slice, $propKeys);
1966                Trace(scalar(@aShort) . " attributes returned for fids $i to $end.") if T(3);
1967                push @aList, @aShort;
1968            }
1969        }
1970        # Now we should have all the interesting attributes in @aList. Populate the hash with
1971        # them.
1972        for my $aListEntry (@aList) {
1973            my $fid = $aListEntry->[0];
1974            if (exists $retVal->{$fid}) {
1975                push @{$retVal->{$fid}}, $aListEntry;
1976            }
1977        }
1978        # Return the result.
1979        return $retVal;
1980    }
1981    
1982    
1983  1;  1;

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