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revision 1.36, Fri May 19 07:26:17 2006 UTC revision 1.64, Sat Aug 12 08:43:37 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 138  Line 136 
136      # We only need it if load-only is NOT specified.      # We only need it if load-only is NOT specified.
137      if (! $options->{loadOnly}) {      if (! $options->{loadOnly}) {
138          if (! defined $subsysFile || $subsysFile eq '') {          if (! defined $subsysFile || $subsysFile eq '') {
139              # Here we want all the NMPDR subsystems. First we get the whole list.              # Here we want all the usable subsystems. First we get the whole list.
140              my @subs = $fig->all_subsystems();              my @subs = $fig->all_subsystems();
141              # Loop through, checking for the NMPDR file.              # Loop through, checking for usability.
142              for my $sub (@subs) {              for my $sub (@subs) {
143                  if (-e "$FIG_Config::data/Subsystems/$sub/NMPDR") {                  if ($fig->usable_subsystem($sub)) {
144                      $subsystems{$sub} = 1;                      $subsystems{$sub} = 1;
145                  }                  }
146              }              }
# Line 175  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 342  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 377  Line 375 
375                  for my $coupleData (@couplings) {                  for my $coupleData (@couplings) {
376                      my ($peg2, $score) = @{$coupleData};                      my ($peg2, $score) = @{$coupleData};
377                      # Compute the coupling ID.                      # Compute the coupling ID.
378                      my $coupleID = Sprout::CouplingID($peg1, $peg2);                      my $coupleID = $self->{erdb}->CouplingID($peg1, $peg2);
379                      if (! exists $dupHash{$coupleID}) {                      if (! exists $dupHash{$coupleID}) {
380                          $loadCoupling->Add("couplingIn");                          $loadCoupling->Add("couplingIn");
381                          # Here we have a new coupling to store in the load files.                          # Here we have a new coupling to store in the load files.
# Line 413  Line 411 
411                              }                              }
412                          }                          }
413                          for my $evidenceID (keys %evidenceMap) {                          for my $evidenceID (keys %evidenceMap) {
414                                # Get the ID for this evidence.
415                                $pchID++;
416                              # Create the evidence record.                              # Create the evidence record.
417                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};                              my ($peg3, $peg4, $usage) = @{$evidenceMap{$evidenceID}};
418                              $loadPCH->Put($evidenceID, $usage);                              $loadPCH->Put($pchID, $usage);
419                              # Connect it to the coupling.                              # Connect it to the coupling.
420                              $loadIsEvidencedBy->Put($coupleID, $evidenceID);                              $loadIsEvidencedBy->Put($coupleID, $pchID);
421                              # Connect it to the features.                              # Connect it to the features.
422                              $loadUsesAsEvidence->Put($evidenceID, $peg3, 1);                              $loadUsesAsEvidence->Put($pchID, $peg3, 1);
423                              $loadUsesAsEvidence->Put($evidenceID, $peg4, 2);                              $loadUsesAsEvidence->Put($pchID, $peg4, 2);
424                          }                          }
425                      }                      }
426                  }                  }
# Line 488  Line 488 
488              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
489              # Get the feature list for this genome.              # Get the feature list for this genome.
490              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed($genomeID);
491                # Sort and count the list.
492                my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
493                my $count = scalar @featureTuples;
494                Trace("$count features found for genome $genomeID.") if T(3);
495                # Set up for our duplicate-feature check.
496                my $oldFeatureID = "";
497              # Loop through the features.              # Loop through the features.
498              for my $featureData (@{$features}) {              for my $featureTuple (@featureTuples) {
                 $loadFeature->Add("featureIn");  
499                  # Split the tuple.                  # Split the tuple.
500                  my ($featureID, $locations, undef, $type) = @{$featureData};                  my ($featureID, $locations, undef, $type) = @{$featureTuple};
501                    # Check for duplicates.
502                    if ($featureID eq $oldFeatureID) {
503                        Trace("Duplicate feature $featureID found.") if T(1);
504                    } else {
505                        $oldFeatureID = $featureID;
506                        # Count this feature.
507                        $loadFeature->Add("featureIn");
508                  # Create the feature record.                  # Create the feature record.
509                  $loadFeature->Put($featureID, 1, $type);                  $loadFeature->Put($featureID, 1, $type);
510                  # Link it to the parent genome.                  # Link it to the parent genome.
# Line 548  Line 560 
560              }              }
561          }          }
562      }      }
563        }
564      # Finish the loads.      # Finish the loads.
565      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
566      return $retVal;      return $retVal;
# Line 636  Line 649 
649  The following relations are loaded by this method.  The following relations are loaded by this method.
650    
651      Subsystem      Subsystem
652        SubsystemClass
653      Role      Role
654      RoleEC      RoleEC
655      SSCell      SSCell
# Line 698  Line 712 
712      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);      my $loadConsistsOfGenomes = $self->_TableLoader('ConsistsOfGenomes', $self->PrimaryOnly);
713      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);      my $loadHasRoleSubset = $self->_TableLoader('HasRoleSubset', $self->PrimaryOnly);
714      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);      my $loadHasGenomeSubset = $self->_TableLoader('HasGenomeSubset', $self->PrimaryOnly);
715        my $loadSubsystemClass = $self->_TableLoader('SubsystemClass', $self->PrimaryOnly);
716      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
717          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
718      } else {      } else {
# Line 723  Line 738 
738                  my $curator = $sub->get_curator();                  my $curator = $sub->get_curator();
739                  my $notes = $sub->get_notes();                  my $notes = $sub->get_notes();
740                  $loadSubsystem->Put($subsysID, $curator, $notes);                  $loadSubsystem->Put($subsysID, $curator, $notes);
741                    my $classList = $fig->subsystem_classification($subsysID);
742                    my @classes = @$classList;
743                    if (@classes) {
744                        for my $class (@classes) {
745                            $loadSubsystemClass->Put($subsysID, $class);
746                        }
747                    }
748                  # 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.
749                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                  for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
750                      # Connect to this role.                      # Connect to this role.
# Line 766  Line 788 
788                          # part of the spreadsheet cell ID.                          # part of the spreadsheet cell ID.
789                          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {                          for (my $col = 0; defined($roleID = $sub->get_role($col)); $col++) {
790                              # Get the features in the spreadsheet cell for this genome and role.                              # Get the features in the spreadsheet cell for this genome and role.
791                              my @pegs = $sub->get_pegs_from_cell($row, $col);                              my @pegs = grep { !$fig->is_deleted_fid($_) } $sub->get_pegs_from_cell($row, $col);
792                              # Only proceed if features exist.                              # Only proceed if features exist.
793                              if (@pegs > 0) {                              if (@pegs > 0) {
794                                  # Create the spreadsheet cell.                                  # Create the spreadsheet cell.
# Line 787  Line 809 
809                          if ($pegCount > 0) {                          if ($pegCount > 0) {
810                              Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);                              Trace("$pegCount PEGs in $cellCount cells for $genomeID.") if T(3);
811                              $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);                              $loadParticipatesIn->Put($genomeID, $subsysID, $variantCode);
                             # Partition the PEGs found into clusters.  
                             my @clusters = $fig->compute_clusters(\@pegsFound, $sub);  
812                              # Create a hash mapping PEG IDs to cluster numbers.                              # Create a hash mapping PEG IDs to cluster numbers.
813                              # We default to -1 for all of them.                              # We default to -1 for all of them.
814                              my %clusterOf = map { $_ => -1 } @pegsFound;                              my %clusterOf = map { $_ => -1 } @pegsFound;
815                                # Partition the PEGs found into clusters.
816                                my @clusters = $fig->compute_clusters([keys %clusterOf], $sub);
817                              for (my $i = 0; $i <= $#clusters; $i++) {                              for (my $i = 0; $i <= $#clusters; $i++) {
818                                  my $subList = $clusters[$i];                                  my $subList = $clusters[$i];
819                                  for my $peg (@{$subList}) {                                  for my $peg (@{$subList}) {
# Line 839  Line 861 
861                      }                      }
862                  }                  }
863              }              }
864            }
865              # Now we loop through the diagrams. We need to create the diagram records              # Now we loop through the diagrams. We need to create the diagram records
866              # and link each diagram to its roles. Note that only roles which occur              # and link each diagram to its roles. Note that only roles which occur
867              # in subsystems (and therefore appear in the %ecToRoles hash) are              # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 872  Line 895 
895                  }                  }
896              }              }
897          }          }
     }  
898      # Finish the load.      # Finish the load.
899      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
900      return $retVal;      return $retVal;
# Line 1034  Line 1056 
1056          # Loop through the genomes.          # Loop through the genomes.
1057          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1058              Trace("Processing $genomeID.") if T(3);              Trace("Processing $genomeID.") if T(3);
1059                # Create a hash of timestamps. We use this to prevent duplicate time stamps
1060                # from showing up for a single PEG's annotations.
1061                my %seenTimestamps = ();
1062              # Get the genome's annotations.              # Get the genome's annotations.
1063              my @annotations = $fig->read_all_annotations($genomeID);              my @annotations = $fig->read_all_annotations($genomeID);
1064              Trace("Processing annotations.") if T(2);              Trace("Processing annotations.") if T(2);
1065              for my $tuple (@annotations) {              for my $tuple (@annotations) {
                 # Create a hash of timestamps. We use this to prevent duplicate time stamps  
                 # from showing up for a single PEG's annotations.  
                 my %seenTimestamps = ();  
1066                  # Get the annotation tuple.                  # Get the annotation tuple.
1067                  my ($peg, $timestamp, $user, $text) = @{$tuple};                  my ($peg, $timestamp, $user, $text) = @{$tuple};
1068                  # Here we fix up the annotation text. "\r" is removed,                  # Here we fix up the annotation text. "\r" is removed,
1069                  # and "\t" and "\n" are escaped. Note we use the "s"                  # and "\t" and "\n" are escaped. Note we use the "gs"
1070                  # modifier so that new-lines inside the text do not                  # modifier so that new-lines inside the text do not
1071                  # stop the substitution search.                  # stop the substitution search.
1072                  $text =~ s/\r//gs;                  $text =~ s/\r//gs;
# Line 1207  Line 1229 
1229      } else {      } else {
1230          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1231          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1232          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1233          my $orgLine;          my $orgLine;
1234          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1235              # Clean the input line.              # Clean the input line.
# Line 1219  Line 1241 
1241          close ORGS;          close ORGS;
1242          # Now the function file.          # Now the function file.
1243          my $funcLine;          my $funcLine;
1244          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1245          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1246              # Clean the line ending.              # Clean the line ending.
1247              chomp $funcLine;              chomp $funcLine;
# Line 1398  Line 1420 
1420      return $retVal;      return $retVal;
1421  }  }
1422    
1423    =head3 LoadSynonymData
1424    
1425    C<< my $stats = $spl->LoadSynonymData(); >>
1426    
1427    Load the synonym groups into Sprout.
1428    
1429    The following relations are loaded by this method.
1430    
1431        SynonymGroup
1432        IsSynonymGroupFor
1433    
1434    The source information for these relations is taken from the C<maps_to_id> method
1435    of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1436    SQL against the FIG database.
1437    
1438    =over 4
1439    
1440    =item RETURNS
1441    
1442    Returns a statistics object for the loads.
1443    
1444    =back
1445    
1446    =cut
1447    #: Return Type $%;
1448    sub LoadSynonymData {
1449        # Get this object instance.
1450        my ($self) = @_;
1451        # Get the FIG object.
1452        my $fig = $self->{fig};
1453        # Get the genome hash.
1454        my $genomeHash = $self->{genomes};
1455        # Create a load object for the table we're loading.
1456        my $loadSynonymGroup = $self->_TableLoader('SynonymGroup');
1457        my $loadIsSynonymGroupFor = $self->_TableLoader('IsSynonymGroupFor');
1458        if ($self->{options}->{loadOnly}) {
1459            Trace("Loading from existing files.") if T(2);
1460        } else {
1461            Trace("Generating synonym group data.") if T(2);
1462            # Get the database handle.
1463            my $dbh = $fig->db_handle();
1464            # Ask for the synonyms.
1465            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1466            my $result = $sth->execute();
1467            if (! defined($result)) {
1468                Confess("Database error in Synonym load: " . $sth->errstr());
1469            } else {
1470                # Remember the current synonym.
1471                my $current_syn = "";
1472                # Count the features.
1473                my $featureCount = 0;
1474                # Loop through the synonym/peg pairs.
1475                while (my @row = $sth->fetchrow()) {
1476                    # Get the synonym ID and feature ID.
1477                    my ($syn_id, $peg) = @row;
1478                    # Insure it's for one of our genomes.
1479                    my $genomeID = FIG::genome_of($peg);
1480                    if (exists $genomeHash->{$genomeID}) {
1481                        # Verify the synonym.
1482                        if ($syn_id ne $current_syn) {
1483                            # It's new, so put it in the group table.
1484                            $loadSynonymGroup->Put($syn_id);
1485                            $current_syn = $syn_id;
1486                        }
1487                        # Connect the synonym to the peg.
1488                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1489                        # Count this feature.
1490                        $featureCount++;
1491                        if ($featureCount % 1000 == 0) {
1492                            Trace("$featureCount features processed.") if T(3);
1493                        }
1494                    }
1495                }
1496            }
1497        }
1498        # Finish the load.
1499        my $retVal = $self->_FinishAll();
1500        return $retVal;
1501    }
1502    
1503    =head3 LoadFamilyData
1504    
1505    C<< my $stats = $spl->LoadFamilyData(); >>
1506    
1507    Load the protein families into Sprout.
1508    
1509    The following relations are loaded by this method.
1510    
1511        Family
1512        IsFamilyForFeature
1513    
1514    The source information for these relations is taken from the C<families_for_protein>,
1515    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1516    
1517    =over 4
1518    
1519    =item RETURNS
1520    
1521    Returns a statistics object for the loads.
1522    
1523    =back
1524    
1525    =cut
1526    #: Return Type $%;
1527    sub LoadFamilyData {
1528        # Get this object instance.
1529        my ($self) = @_;
1530        # Get the FIG object.
1531        my $fig = $self->{fig};
1532        # Get the genome hash.
1533        my $genomeHash = $self->{genomes};
1534        # Create load objects for the tables we're loading.
1535        my $loadFamily = $self->_TableLoader('Family');
1536        my $loadIsFamilyForFeature = $self->_TableLoader('IsFamilyForFeature');
1537        if ($self->{options}->{loadOnly}) {
1538            Trace("Loading from existing files.") if T(2);
1539        } else {
1540            Trace("Generating family data.") if T(2);
1541            # Create a hash for the family IDs.
1542            my %familyHash = ();
1543            # Loop through the genomes.
1544            for my $genomeID (sort keys %{$genomeHash}) {
1545                Trace("Processing features for $genomeID.") if T(2);
1546                # Loop through this genome's PEGs.
1547                for my $fid ($fig->all_features($genomeID, "peg")) {
1548                    $loadIsFamilyForFeature->Add("features", 1);
1549                    # Get this feature's families.
1550                    my @families = $fig->families_for_protein($fid);
1551                    # Loop through the families, connecting them to the feature.
1552                    for my $family (@families) {
1553                        $loadIsFamilyForFeature->Put($family, $fid);
1554                        # If this is a new family, create a record for it.
1555                        if (! exists $familyHash{$family}) {
1556                            $familyHash{$family} = 1;
1557                            $loadFamily->Add("families", 1);
1558                            my $size = $fig->sz_family($family);
1559                            my $func = $fig->family_function($family);
1560                            $loadFamily->Put($family, $size, $func);
1561                        }
1562                    }
1563                }
1564            }
1565        }
1566        # Finish the load.
1567        my $retVal = $self->_FinishAll();
1568        return $retVal;
1569    }
1570    
1571  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1572    
1573  =head3 TableLoader  =head3 TableLoader
# Line 1465  Line 1635 
1635      my $retVal = Stats->new();      my $retVal = Stats->new();
1636      # Get the loader list.      # Get the loader list.
1637      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1638        # Create a hash to hold the statistics objects, keyed on relation name.
1639        my %loaderHash = ();
1640      # 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
1641      # 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.
1642      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1643          # Get the relation name.          # Get the relation name.
1644          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1477  Line 1649 
1649              # Here we really need to finish.              # Here we really need to finish.
1650              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1651              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1652                $loaderHash{$relName} = $stats;
1653            }
1654        }
1655        # Now we loop through again, actually loading the tables. We want to finish before
1656        # loading so that if something goes wrong at this point, all the load files are usable
1657        # and we don't have to redo all that work.
1658        for my $relName (sort keys %loaderHash) {
1659            # Get the statistics for this relation.
1660            my $stats = $loaderHash{$relName};
1661            # Check for a database load.
1662              if ($self->{options}->{dbLoad}) {              if ($self->{options}->{dbLoad}) {
1663                  # 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.
1664                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
# Line 1487  Line 1669 
1669              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1670              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1671          }          }
     }  
1672      # Return the load statistics.      # Return the load statistics.
1673      return $retVal;      return $retVal;
1674  }  }

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