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revision 1.46, Mon Jun 26 19:13:16 2006 UTC revision 1.62, Sun Jul 30 05:44:57 2006 UTC
# Line 136  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 340  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 375  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 411  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 486  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 546  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 843  Line 858 
858                      }                      }
859                  }                  }
860              }              }
861            }
862              # 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
863              # 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
864              # in subsystems (and therefore appear in the %ecToRoles hash) are              # in subsystems (and therefore appear in the %ecToRoles hash) are
# Line 876  Line 892 
892                  }                  }
893              }              }
894          }          }
     }  
895      # Finish the load.      # Finish the load.
896      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
897      return $retVal;      return $retVal;
# Line 1211  Line 1226 
1226      } else {      } else {
1227          Trace("Generating external data.") if T(2);          Trace("Generating external data.") if T(2);
1228          # We loop through the files one at a time. First, the organism file.          # We loop through the files one at a time. First, the organism file.
1229          Open(\*ORGS, "<$FIG_Config::global/ext_org.table");          Open(\*ORGS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_org.table |");
1230          my $orgLine;          my $orgLine;
1231          while (defined($orgLine = <ORGS>)) {          while (defined($orgLine = <ORGS>)) {
1232              # Clean the input line.              # Clean the input line.
# Line 1223  Line 1238 
1238          close ORGS;          close ORGS;
1239          # Now the function file.          # Now the function file.
1240          my $funcLine;          my $funcLine;
1241          Open(\*FUNCS, "<$FIG_Config::global/ext_func.table");          Open(\*FUNCS, "sort +0 -1 -u -t\"\t\" $FIG_Config::global/ext_func.table |");
1242          while (defined($funcLine = <FUNCS>)) {          while (defined($funcLine = <FUNCS>)) {
1243              # Clean the line ending.              # Clean the line ending.
1244              chomp $funcLine;              chomp $funcLine;
# Line 1414  Line 1429 
1429      IsSynonymGroupFor      IsSynonymGroupFor
1430    
1431  The source information for these relations is taken from the C<maps_to_id> method  The source information for these relations is taken from the C<maps_to_id> method
1432  of the B<FIG> object. The process starts from the features, so it is possible  of the B<FIG> object. Unfortunately, to make this work, we need to use direct
1433  that there will be duplicates in the SynonymGroup load file, since the relationship  SQL against the FIG database.
 is one-to-many toward the features. The automatic sort on primary entity relations  
 will fix this for us.  
1434    
1435  =over 4  =over 4
1436    
# Line 1443  Line 1456 
1456          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1457      } else {      } else {
1458          Trace("Generating synonym group data.") if T(2);          Trace("Generating synonym group data.") if T(2);
1459            # Get the database handle.
1460            my $dbh = $fig->db_handle();
1461            # Ask for the synonyms.
1462            my $sth = $dbh->prepare_command("SELECT maps_to, syn_id FROM peg_synonyms ORDER BY maps_to");
1463            my $result = $sth->execute();
1464            if (! defined($result)) {
1465                Confess("Database error in Synonym load: " . $sth->errstr());
1466            } else {
1467                # Remember the current synonym.
1468                my $current_syn = "";
1469                # Count the features.
1470                my $featureCount = 0;
1471                # Loop through the synonym/peg pairs.
1472                while (my @row = $sth->fetchrow()) {
1473                    # Get the synonym ID and feature ID.
1474                    my ($syn_id, $peg) = @row;
1475                    # Insure it's for one of our genomes.
1476                    my $genomeID = FIG::genome_of($peg);
1477                    if (exists $genomeHash->{$genomeID}) {
1478                        # Verify the synonym.
1479                        if ($syn_id ne $current_syn) {
1480                            # It's new, so put it in the group table.
1481                            $loadSynonymGroup->Put($syn_id);
1482                            $current_syn = $syn_id;
1483                        }
1484                        # Connect the synonym to the peg.
1485                        $loadIsSynonymGroupFor->Put($syn_id, $peg);
1486                        # Count this feature.
1487                        $featureCount++;
1488                        if ($featureCount % 1000 == 0) {
1489                            Trace("$featureCount features processed.") if T(3);
1490                        }
1491                    }
1492                }
1493            }
1494        }
1495        # Finish the load.
1496        my $retVal = $self->_FinishAll();
1497        return $retVal;
1498    }
1499    
1500    =head3 LoadFamilyData
1501    
1502    C<< my $stats = $spl->LoadFamilyData(); >>
1503    
1504    Load the protein families into Sprout.
1505    
1506    The following relations are loaded by this method.
1507    
1508        Family
1509        ContainsFeature
1510    
1511    The source information for these relations is taken from the C<families_for_protein>,
1512    C<family_function>, and C<sz_family> methods of the B<FIG> object.
1513    
1514    =over 4
1515    
1516    =item RETURNS
1517    
1518    Returns a statistics object for the loads.
1519    
1520    =back
1521    
1522    =cut
1523    #: Return Type $%;
1524    sub LoadFamilyData {
1525        # Get this object instance.
1526        my ($self) = @_;
1527        # Get the FIG object.
1528        my $fig = $self->{fig};
1529        # Get the genome hash.
1530        my $genomeHash = $self->{genomes};
1531        # Create load objects for the tables we're loading.
1532        my $loadFamily = $self->_TableLoader('Family');
1533        my $loadContainsFeature = $self->_TableLoader('ContainsFeature');
1534        if ($self->{options}->{loadOnly}) {
1535            Trace("Loading from existing files.") if T(2);
1536        } else {
1537            Trace("Generating family data.") if T(2);
1538            # Create a hash for the family IDs.
1539            my %familyHash = ();
1540          # Loop through the genomes.          # Loop through the genomes.
1541          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1542              Trace("Processing $genomeID.") if T(3);              Trace("Processing features for $genomeID.") if T(2);
1543              # Get all of the features for this genome. The only method that does this is              # Loop through this genome's PEGs.
1544              # all_features_detailed, which returns extra baggage that we discard.              for my $fid ($fig->all_features($genomeID, "peg")) {
1545              my $featureData = $fig->all_features_detailed($genomeID);                  $loadContainsFeature->Add("features", 1);
1546              my @fids = map { $_->[0] } @{$featureData};                  # Get this feature's families.
1547              Trace(scalar(@fids) . " features found for genome $genomeID.") if T(3);                  my @families = $fig->families_for_protein($fid);
1548              # Loop through the feature IDs.                  # Loop through the families, connecting them to the feature.
1549              for my $fid (@fids) {                  for my $family (@families) {
1550                  # Get the group for this feature.                      $loadContainsFeature->Put($family, $fid);
1551                  my $synonym = $fig->maps_to_id($fid);                      # If this is a new family, create a record for it.
1552                  # Only proceed if the synonym is a real group.                      if (! exists $familyHash{$family}) {
1553                  if ($synonym ne $fid) {                          $familyHash{$family} = 1;
1554                      $loadSynonymGroup->Put($synonym);                          $loadFamily->Add("families", 1);
1555                      $loadIsSynonymGroupFor->Put($synonym, $fid);                          my $size = $fig->sz_family($family);
1556                            my $func = $fig->family_function($family);
1557                            $loadFamily->Put($family, $size, $func);
1558                        }
1559                  }                  }
1560              }              }
1561          }          }
# Line 1468  Line 1565 
1565      return $retVal;      return $retVal;
1566  }  }
1567    
   
1568  =head2 Internal Utility Methods  =head2 Internal Utility Methods
1569    
1570  =head3 TableLoader  =head3 TableLoader
# Line 1536  Line 1632 
1632      my $retVal = Stats->new();      my $retVal = Stats->new();
1633      # Get the loader list.      # Get the loader list.
1634      my $loadList = $self->{loaders};      my $loadList = $self->{loaders};
1635        # Create a hash to hold the statistics objects, keyed on relation name.
1636        my %loaderHash = ();
1637      # 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
1638      # 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.
1639      while (my $loader = pop @{$loadList}) {      while (my $loader = pop @{$loadList}) {
1640          # Get the relation name.          # Get the relation name.
1641          my $relName = $loader->RelName;          my $relName = $loader->RelName;
# Line 1548  Line 1646 
1646              # Here we really need to finish.              # Here we really need to finish.
1647              Trace("Finishing $relName.") if T(2);              Trace("Finishing $relName.") if T(2);
1648              my $stats = $loader->Finish();              my $stats = $loader->Finish();
1649                $loaderHash{$relName} = $stats;
1650            }
1651        }
1652        # Now we loop through again, actually loading the tables. We want to finish before
1653        # loading so that if something goes wrong at this point, all the load files are usable
1654        # and we don't have to redo all that work.
1655        for my $relName (sort keys %loaderHash) {
1656            # Get the statistics for this relation.
1657            my $stats = $loaderHash{$relName};
1658            # Check for a database load.
1659              if ($self->{options}->{dbLoad}) {              if ($self->{options}->{dbLoad}) {
1660                  # 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.
1661                  Trace("Loading relation $relName.") if T(2);                  Trace("Loading relation $relName.") if T(2);
# Line 1558  Line 1666 
1666              $retVal->Accumulate($stats);              $retVal->Accumulate($stats);
1667              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);              Trace("Statistics for $relName:\n" . $stats->Show()) if T(2);
1668          }          }
     }  
1669      # Return the load statistics.      # Return the load statistics.
1670      return $retVal;      return $retVal;
1671  }  }
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