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revision 1.26, Mon Jan 30 21:57:02 2006 UTC revision 1.52, Mon Jul 10 21:34:11 2006 UTC
# Line 30  Line 30 
30      $stats->Accumulate($spl->LoadFeatureData());      $stats->Accumulate($spl->LoadFeatureData());
31      print $stats->Show();      print $stats->Show();
32    
 This module makes use of the internal Sprout property C<_erdb>.  
   
33  It is worth noting that the FIG object does not need to be a real one. Any object  It is worth noting that the FIG object does not need to be a real one. Any object
34  that implements the FIG methods for data retrieval could be used. So, for example,  that implements the FIG methods for data retrieval could be used. So, for example,
35  this object could be used to copy data from one Sprout database to another, or  this object could be used to copy data from one Sprout database to another, or
# Line 80  Line 78 
78  =item subsysFile  =item subsysFile
79    
80  Either the name of the file containing the list of trusted subsystems or a reference  Either the name of the file containing the list of trusted subsystems or a reference
81  to a list of subsystem names. If nothing is specified, all known subsystems will be  to a list of subsystem names. If nothing is specified, all NMPDR subsystems will be
82  considered trusted. Only subsystem data related to the trusted subsystems is loaded.  considered trusted. (A subsystem is considered NMPDR if it has a file named C<NMPDR>
83    in its data directory.) Only subsystem data related to the trusted subsystems is loaded.
84    
85  =item options  =item options
86    
# Line 94  Line 93 
93  sub new {  sub new {
94      # Get the parameters.      # Get the parameters.
95      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;      my ($class, $sprout, $fig, $genomeFile, $subsysFile, $options) = @_;
96      # Load the list of genomes into a hash.      # Create the genome hash.
97      my %genomes;      my %genomes = ();
98        # We only need it if load-only is NOT specified.
99        if (! $options->{loadOnly}) {
100      if (! defined($genomeFile) || $genomeFile eq '') {      if (! defined($genomeFile) || $genomeFile eq '') {
101          # Here we want all the complete genomes and an access code of 1.          # Here we want all the complete genomes and an access code of 1.
102          my @genomeList = $fig->genomes(1);          my @genomeList = $fig->genomes(1);
# Line 129  Line 130 
130              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");              Confess("Invalid genome parameter ($type) in SproutLoad constructor.");
131          }          }
132      }      }
133        }
134      # Load the list of trusted subsystems.      # Load the list of trusted subsystems.
135      my %subsystems = ();      my %subsystems = ();
136        # We only need it if load-only is NOT specified.
137        if (! $options->{loadOnly}) {
138      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
139          # Here we want all the subsystems.              # Here we want all the NMPDR subsystems. First we get the whole list.
140          %subsystems = map { $_ => 1 } $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141                # Loop through, checking for the NMPDR file.
142                for my $sub (@subs) {
143                    if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {
144                        $subsystems{$sub} = 1;
145                    }
146                }
147      } else {      } else {
148          my $type = ref $subsysFile;          my $type = ref $subsysFile;
149          if ($type eq 'ARRAY') {          if ($type eq 'ARRAY') {
# Line 153  Line 163 
163              Confess("Invalid subsystem parameter in SproutLoad constructor.");              Confess("Invalid subsystem parameter in SproutLoad constructor.");
164          }          }
165      }      }
166        }
167      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
168      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
169      # Create the Sprout load object.      # Create the Sprout load object.
# Line 162  Line 173 
173                    subsystems => \%subsystems,                    subsystems => \%subsystems,
174                    sprout => $sprout,                    sprout => $sprout,
175                    loadDirectory => $directory,                    loadDirectory => $directory,
176                    erdb => $sprout->{_erdb},                    erdb => $sprout,
177                    loaders => [],                    loaders => [],
178                    options => $options                    options => $options
179                   };                   };
# Line 250  Line 261 
261              $loadGenome->Add("genomeIn");              $loadGenome->Add("genomeIn");
262              # The access code comes in via the genome hash.              # The access code comes in via the genome hash.
263              my $accessCode = $genomeHash->{$genomeID};              my $accessCode = $genomeHash->{$genomeID};
264              # Get the genus, species, and strain from the scientific name. Note that we append              # Get the genus, species, and strain from the scientific name.
             # the genome ID to the strain. In some cases this is the totality of the strain name.  
265              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);              my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
266              my $extra = join " ", @extraData, "[$genomeID]";              my $extra = join " ", @extraData;
267              # Get the full taxonomy.              # Get the full taxonomy.
268              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
269              # Output the genome record.              # Output the genome record.
# Line 330  Line 340 
340      my $fig = $self->{fig};      my $fig = $self->{fig};
341      # Get the genome hash.      # Get the genome hash.
342      my $genomeFilter = $self->{genomes};      my $genomeFilter = $self->{genomes};
343      my $genomeCount = (keys %{$genomeFilter});      # Set up an ID counter for the PCHs.
344      my $featureCount = $genomeCount * 4000;      my $pchID = 0;
345      # Start the loads.      # Start the loads.
346      my $loadCoupling = $self->_TableLoader('Coupling');      my $loadCoupling = $self->_TableLoader('Coupling');
347      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);      my $loadIsEvidencedBy = $self->_TableLoader('IsEvidencedBy', $self->PrimaryOnly);
# Line 360  Line 370 
370                  Trace("Processing PEG $peg1 for $genome.") if T(4);                  Trace("Processing PEG $peg1 for $genome.") if T(4);
371                  # Get a list of the coupled PEGs.                  # Get a list of the coupled PEGs.
372                  my @couplings = $fig->coupled_to($peg1);                  my @couplings = $fig->coupled_to($peg1);
373                    Trace(scalar(@couplings) . " couplings found for $peg1.") if T(4);
374                  # For each coupled PEG, we need to verify that a coupling already                  # For each coupled PEG, we need to verify that a coupling already
375                  # exists. If not, we have to create one.                  # exists. If not, we have to create one.
376                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
377                        Trace("Coupling string is $coupleData (should be an array).") if T(4);
378                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
379                      # Compute the coupling ID.                      # Compute the coupling ID.
380                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
381                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
382                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
383                          # 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 401  Line 413 
413                              }                              }
414                          }                          }
415                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
416                                # Get the ID for this evidence.
417                                $pchID++;
418                              # Create the evidence record.                              # Create the evidence record.
419                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
420                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
421                              # Connect it to the coupling.                              # Connect it to the coupling.
422                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
423                              # Connect it to the features.                              # Connect it to the features.
424                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
425                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
426                          }                          }
427                      }                      }
428                  }                  }
# Line 436  Line 450 
450      FeatureTranslation      FeatureTranslation
451      FeatureUpstream      FeatureUpstream
452      IsLocatedIn      IsLocatedIn
453        HasFeature
454    
455  =over 4  =over 4
456    
# Line 461  Line 476 
476      my $loadFeatureLink = $self->_TableLoader('FeatureLink');      my $loadFeatureLink = $self->_TableLoader('FeatureLink');
477      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');      my $loadFeatureTranslation = $self->_TableLoader('FeatureTranslation');
478      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');      my $loadFeatureUpstream = $self->_TableLoader('FeatureUpstream');
479        my $loadHasFeature = $self->_TableLoader('HasFeature');
480      # 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
481      # locations.      # locations.
482      my $chunkSize = $self->{sprout}->MaxSegment();      my $chunkSize = $self->{sprout}->MaxSegment();
# Line 481  Line 497 
497                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureData};
498                  # Create the feature record.                  # Create the feature record.
499                  $loadFeature->Put($featureID, 1, $type);                  $loadFeature->Put($featureID, 1, $type);
500                    # Link it to the parent genome.
501                    $loadHasFeature->Put($genomeID, $featureID, $type);
502                  # Create the aliases.                  # Create the aliases.
503                  for my $alias ($fig->feature_aliases($featureID)) {                  for my $alias ($fig->feature_aliases($featureID)) {
504                      $loadFeatureAlias->Put($featureID, $alias);                      $loadFeatureAlias->Put($featureID, $alias);
# Line 620  Line 638 
638  The following relations are loaded by this method.  The following relations are loaded by this method.
639    
640      Subsystem      Subsystem
641        SubsystemClass
642      Role      Role
643      RoleEC      RoleEC
644      SSCell      SSCell
# Line 682  Line 701 
701      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
702      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
703      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
704        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
705      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
706          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
707      } else {      } else {
# Line 697  Line 717 
717          my ($genomeID, $roleID);          my ($genomeID, $roleID);
718          my %roleData = ();          my %roleData = ();
719          for my $subsysID (@subsysIDs) {          for my $subsysID (@subsysIDs) {
             Trace("Creating subsystem $subsysID.") if T(3);  
             $loadSubsystem->Add("subsystemIn");  
720              # Get the subsystem object.              # Get the subsystem object.
721              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
722                # Only proceed if the subsystem has a spreadsheet.
723                if (! $sub->{empty_ss}) {
724                    Trace("Creating subsystem $subsysID.") if T(3);
725                    $loadSubsystem->Add("subsystemIn");
726              # Create the subsystem record.              # Create the subsystem record.
727              my $curator = $sub->get_curator();              my $curator = $sub->get_curator();
728              my $notes = $sub->get_notes();              my $notes = $sub->get_notes();
729              $loadSubsystem->Put($subsysID, $curator, $notes);              $loadSubsystem->Put($subsysID, $curator, $notes);
730                    my $class = $fig->subsystem_classification($subsysID);
731                    if ($class) {
732                        $loadSubsystemClass->Put($subsysID, $class);
733                    }
734              # 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.
735              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {              for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
736                  # Connect to this role.                  # Connect to this role.
# Line 748  Line 774 
774                      # part of the spreadsheet cell ID.                      # part of the spreadsheet cell ID.
775                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                      for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
776                          # Get the features in the spreadsheet cell for this genome and role.                          # Get the features in the spreadsheet cell for this genome and role.
777                          my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
778                          # Only proceed if features exist.                          # Only proceed if features exist.
779                          if (@pegs > 0) {                          if (@pegs > 0) {
780                              # Create the spreadsheet cell.                              # Create the spreadsheet cell.
# Line 769  Line 795 
795                      if ($pegCount > 0) {                      if ($pegCount > 0) {
796                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                          Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
797                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                          $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                         # Partition the PEGs found into clusters.  
                         my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
798                          # Create a hash mapping PEG IDs to cluster numbers.                          # Create a hash mapping PEG IDs to cluster numbers.
799                          # We default to -1 for all of them.                          # We default to -1 for all of them.
800                          my %clusterOf = map { $_ => -1 } @pegsFound;                          my %clusterOf = map { $_ => -1 } @pegsFound;
801                                # Partition the PEGs found into clusters.
802                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
803                          for (my $i = 0; $i <= $#clusters; $i++) {                          for (my $i = 0; $i <= $#clusters; $i++) {
804                              my $subList = $clusters[$i];                              my $subList = $clusters[$i];
805                              for my $peg (@{$subList}) {                              for my $peg (@{$subList}) {
# Line 801  Line 827 
827                  # Connect the subset to the subsystem.                  # Connect the subset to the subsystem.
828                  $loadHasRoleSubset->Put($subsysID, $actualID);                  $loadHasRoleSubset->Put($subsysID, $actualID);
829                  # Connect the subset to its roles.                  # Connect the subset to its roles.
830                  my @roles = $sub->get_subset($subsetID);                      my @roles = $sub->get_subsetC_roles($subsetID);
831                  for my $roleID (@roles) {                  for my $roleID (@roles) {
832                      $loadConsistsOfRoles->Put($actualID, $roleID);                      $loadConsistsOfRoles->Put($actualID, $roleID);
833                  }                  }
# Line 854  Line 880 
880              }              }
881          }          }
882      }      }
883        }
884      # Finish the load.      # Finish the load.
885      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
886      return $retVal;      return $retVal;
# Line 1015  Line 1042 
1042          # Loop through the genomes.          # Loop through the genomes.
1043          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1044              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);  
1045                  # 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
1046                  # from showing up for a single PEG's annotations.                  # from showing up for a single PEG's annotations.
1047                  my %seenTimestamps = ();                  my %seenTimestamps = ();
1048                  # Loop through the annotations.              # Get the genome's annotations.
1049                  for my $tuple ($fig->feature_annotations($peg, "raw")) {              my @annotations = $fig->read_all_annotations($genomeID);
1050                      my ($fid, $timestamp, $user, $text) = @{$tuple};              Trace("Processing annotations.") if T(2);
1051                for my $tuple (@annotations) {
1052                    # Get the annotation tuple.
1053                    my ($peg, $timestamp, $user, $text) = @{$tuple};
1054                      # Here we fix up the annotation text. "\r" is removed,                      # Here we fix up the annotation text. "\r" is removed,
1055                      # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1056                      # modifier so that new-lines inside the text do not                      # modifier so that new-lines inside the text do not
1057                      # stop the substitution search.                      # stop the substitution search.
1058                      $text =~ s/\r//gs;                      $text =~ s/\r//gs;
# Line 1039  Line 1065 
1065                          # 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
1066                          # the key is unique.                          # the key is unique.
1067                          my $keyStamp = $timestamp;                          my $keyStamp = $timestamp;
1068                          while ($seenTimestamps{$keyStamp}) {                      while ($seenTimestamps{"$peg:$keyStamp"}) {
1069                              $keyStamp++;                              $keyStamp++;
1070                          }                          }
                         $seenTimestamps{$keyStamp} = 1;  
1071                          my $annotationID = "$peg:$keyStamp";                          my $annotationID = "$peg:$keyStamp";
1072                        $seenTimestamps{$annotationID} = 1;
1073                          # Insure the user exists.                          # Insure the user exists.
1074                          if (! $users{$user}) {                          if (! $users{$user}) {
1075                              $loadSproutUser->Put($user, "SEED user");                              $loadSproutUser->Put($user, "SEED user");
# Line 1061  Line 1087 
1087                  }                  }
1088              }              }
1089          }          }
     }  
1090      # Finish the load.      # Finish the load.
1091      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1092      return $retVal;      return $retVal;
# Line 1381  Line 1406 
1406      return $retVal;      return $retVal;
1407  }  }
1408    
1409    =head3 LoadSynonymData
1410    
1411    C<< my $stats = $spl->LoadSynonymData(); >>
1412    
1413    Load the synonym groups into Sprout.
1414    
1415    The following relations are loaded by this method.
1416    
1417        SynonymGroup
1418        IsSynonymGroupFor
1419    
1420    The source information for these relations is taken from the C<maps_to_id> method
1421    of the B<FIG> object. The process starts from the features, so it is possible
1422    that there will be duplicates in the SynonymGroup load file, since the relationship
1423    is one-to-many toward the features. The automatic sort on primary entity relations
1424    will fix this for us.
1425    
1426    =over 4
1427    
1428    =item RETURNS
1429    
1430    Returns a statistics object for the loads.
1431    
1432    =back
1433    
1434    =cut
1435    #: Return Type $%;
1436    sub LoadSynonymData {
1437        # Get this object instance.
1438        my ($self) = @_;
1439        # Get the FIG object.
1440        my $fig = $self->{fig};
1441        # Get the genome hash.
1442        my $genomeHash = $self->{genomes};
1443        # Create a load object for the table we're loading.
1444        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1445        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1446        if ($self->{options}->{loadOnly}) {
1447            Trace("Loading from existing files.") if T(2);
1448        } else {
1449            Trace("Generating synonym group data.") if T(2);
1450            # Loop through the genomes.
1451            for my $genomeID (sort keys %{$genomeHash}) {
1452                Trace("Processing $genomeID.") if T(3);
1453                # Get all of the features for this genome. The only method that does this is
1454                # all_features_detailed, which returns extra baggage that we discard.
1455                my $featureData = $fig->all_features_detailed($genomeID);
1456                my @fids = map { $_->[0] } @{$featureData};
1457                Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);
1458                # Loop through the feature IDs.
1459                for my $fid (@fids) {
1460                    # Get the group for this feature.
1461                    my $synonym = $fig->maps_to_id($fid);
1462                    # Only proceed if the synonym is a real group.
1463                    if ($synonym ne $fid) {
1464                        $loadSynonymGroup->Put($synonym);
1465                        $loadIsSynonymGroupFor->Put($synonym, $fid);
1466                    }
1467                }
1468            }
1469        }
1470        # Finish the load.
1471        my $retVal = $self->_FinishAll();
1472        return $retVal;
1473    }
1474    
1475    
1476  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1477    
1478  =head3 TableLoader  =head3 TableLoader
# Line 1448  Line 1540 
1540      my $retVal = Stats->new();      my $retVal = Stats->new();
1541      # Get the loader list.      # Get the loader list.
1542      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1543        # Create a hash to hold the statistics objects, keyed on relation name.
1544        my %loaderHash = ();
1545      # 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
1546      # 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.
1547      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1548          # Get the relation name.          # Get the relation name.
1549          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1460  Line 1554 
1554              # Here we really need to finish.              # Here we really need to finish.
1555              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1556              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1557              if ($self->{options}->{dbLoad} && ! $loader->Ignore) {              $loaderHash{$relName} = $stats;
1558            }
1559        }
1560        # Now we loop through again, actually loading the tables. We want to finish before
1561        # loading so that if something goes wrong at this point, all the load files are usable
1562        # and we don't have to redo all that work.
1563        for my $relName (sort keys %loaderHash) {
1564            # Get the statistics for this relation.
1565            my $stats = $loaderHash{$relName};
1566            # Check for a database load.
1567            if ($self->{options}->{dbLoad}) {
1568                  # Here we want to use the load file just created to load the database.                  # Here we want to use the load file just created to load the database.
1569                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
1570                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);                  my $newStats = $self->{sprout}->LoadUpdate(1, [$relName]);
# Line 1470  Line 1574 
1574              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1575              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1576          }          }
     }  
1577      # Return the load statistics.      # Return the load statistics.
1578      return $retVal;      return $retVal;
1579  }  }

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