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revision 1.81, Wed Dec 20 20:03:25 2006 UTC revision 1.94, Thu Dec 6 14:58:03 2007 UTC
# Line 6  Line 6 
6      use Data::Dumper;      use Data::Dumper;
7      use XML::Simple;      use XML::Simple;
8      use DBQuery;      use DBQuery;
9      use DBObject;      use ERDBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
     use FIG;  
13      use CGI;      use CGI;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
# Line 228  Line 227 
227    
228  =head3 Indexes  =head3 Indexes
229    
230  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
231  all be from the same relation. The alternate indexes assist in ordering results  index must all be from the same relation. The alternate indexes assist in searching
232  from a query. A relationship can have up to two indexes-- a I<to-index> and a  on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
233  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
234  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
235  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
236  the genomes of a contig. A relationship's index must specify only fields in  the genomes of a contig. In addition, it can have zero or more alternate
237    indexes. A relationship's index must specify only fields in
238  the relationship.  the relationship.
239    
240  The indexes for an entity must be listed inside the B<Indexes> tag. The from-index  The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
241  of a relationship is specified using the B<FromIndex> tag; the to-index is specified  The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
242  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
243    
244  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 303  Line 303 
303    
304  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
305  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306  fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing  fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
307  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
308    
309  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
310    
# Line 372  Line 372 
372                   'medium-string' =>                   'medium-string' =>
373                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                 indexMod =>   0, notes => "character string, 0 to 160 characters"},                                 indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                     'long-string' =>
376                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
377                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
378                  );                  );
379    
380  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 410  Line 413 
413    
414  =head3 new  =head3 new
415    
416  C<< my $database = ERDB->new($dbh, $metaFileName); >>      my $database = ERDB->new($dbh, $metaFileName);
417    
418  Create a new ERDB object.  Create a new ERDB object.
419    
# Line 444  Line 447 
447    
448  =head3 ShowMetaData  =head3 ShowMetaData
449    
450  C<< $erdb->ShowMetaData($fileName); >>      $erdb->ShowMetaData($fileName);
451    
452  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
453  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 485  Line 488 
488    
489  =head3 DisplayMetaData  =head3 DisplayMetaData
490    
491  C<< my $html = $erdb->DisplayMetaData(); >>      my $html = $erdb->DisplayMetaData();
492    
493  Return an HTML description of the database. This description can be used to help users create  Return an HTML description of the database. This description can be used to help users create
494  the data to be loaded into the relations and form queries. The output is raw includable HTML  the data to be loaded into the relations and form queries. The output is raw includable HTML
# Line 548  Line 551 
551          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
552              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
553          }          }
554          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
555            my $relCount = keys %{$relationshipList};
556            if ($relCount > 0) {
557                # First, we set up the relationship subsection.
558          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
559          # Loop through the relationships.          # Loop through the relationships.
560          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
# Line 564  Line 570 
570          }          }
571          # Close off the relationship list.          # Close off the relationship list.
572          $retVal .= "</ul>\n";          $retVal .= "</ul>\n";
573            }
574          # Get the entity's relations.          # Get the entity's relations.
575          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
576          # Create a header for the relation subsection.          # Create a header for the relation subsection.
# Line 637  Line 644 
644    
645  =head3 DumpMetaData  =head3 DumpMetaData
646    
647  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
648    
649  Return a dump of the metadata structure.  Return a dump of the metadata structure.
650    
# Line 650  Line 657 
657      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
658  }  }
659    
660    =head3 CreatePPO
661    
662        ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
663    
664    Create a PPO XML file from an ERDB data definition XML file. At the
665    current time, the PPO XML file can be used to create a database with
666    similar functionality. Eventually, the PPO will be able to use the
667    created XML to access the live ERDB database.
668    
669    =over 4
670    
671    =item erdbXMLFile
672    
673    Name of the XML data definition file for the ERDB database. This
674    file must exist.
675    
676    =item ppoXMLFile
677    
678    Output file for the PPO XML definition. If this file exists, it
679    will be overwritten.
680    
681    =back
682    
683    =cut
684    
685    sub CreatePPO {
686        # Get the parameters.
687        my ($erdbXMLFile, $ppoXMLFile) = @_;
688        # First, we want to slurp in the ERDB XML file in its raw form.
689        my $xml = ReadMetaXML($erdbXMLFile);
690        # Create a variable to hold all of the objects in the PPO project.
691        my @objects = ();
692        # Get the relationship hash.
693        my $relationships = $xml->{Relationships};
694        # Loop through the entities.
695        my $entities = $xml->{Entities};
696        for my $entityName (keys %{$entities}) {
697            # Get the entity's data structures.
698            my $entityObject = $entities->{$entityName};
699            # We put the object's fields in here, according to their type.
700            my (@object_refs, @scalars, @indexes, @arrays);
701            # Create the ID field for the entity. We get the key type from the
702            # entity object and compute the corresponding SQL type.
703            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
704            push @scalars, { label => 'id', type => $type };
705            # Loop through the entity fields.
706            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
707                # Get the field object.
708                my $fieldObject = $entityObject->{Fields}->{$fieldName};
709                # Convert it to a scalar tag.
710                my $scalar = _CreatePPOField($fieldName, $fieldObject);
711                # If we have a relation, this field is stored in an array.
712                # otherwise, it is a scalar. The array tag has scalars
713                # stored as an XML array. In ERDB, there is only ever one,
714                # but PPO can have more.
715                my $relation = $fieldObject->{relation};
716                if ($relation) {
717                    push @arrays, { scalar => [$scalar] };
718                } else {
719                    push @scalars, $scalar;
720                }
721            }
722            # Loop through the relationships. If this entity is the to-entity
723            # on a relationship of 1M arity, then it is implemented as a PPO
724            # object reference.
725            for my $relationshipName (keys %{$relationships}) {
726                # Get the relationship data.
727                my $relationshipData = $relationships->{$relationshipName};
728                # If we have a from for this entity and an arity of 1M, we
729                # have an object reference.
730                if ($relationshipData->{to} eq $entityName &&
731                    $relationshipData->{arity} eq '1M') {
732                    # Build the object reference tag.
733                    push @object_refs, { label => $relationshipName,
734                                         type => $relationshipData->{from} };
735                }
736            }
737            # Create the indexes.
738            my $indexList = $entityObject->{Indexes};
739            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
740            # Build the object XML tree.
741            my $object = { label => $entityName,
742                           object_ref => \@object_refs,
743                           scalar => \@scalars,
744                           index => \@indexes,
745                           array => \@arrays
746                          };
747            # Push the object onto the objects list.
748            push @objects, $object;
749        }
750        # Loop through the relationships, searching for MMs. The 1Ms were
751        # already handled by the entity search above.
752        for my $relationshipName (keys %{$relationships}) {
753            # Get this relationship's object.
754            my $relationshipObject = $relationships->{$relationshipName};
755            # Only proceed if it's many-to-many.
756            if ($relationshipObject->{arity} eq 'MM') {
757                # Create the tag lists for the relationship object.
758                my (@object_refs, @scalars, @indexes);
759                # The relationship will be created as an object with object
760                # references for its links to the participating entities.
761                my %links = ( from_link => $relationshipObject->{from},
762                              to_link => $relationshipObject->{to} );
763                for my $link (keys %links) {
764                    # Create an object_ref tag for this piece of the
765                    # relationship (from or to).
766                    my $object_ref = { label => $link,
767                                       type => $links{$link} };
768                    push @object_refs, $object_ref;
769                }
770                # Loop through the intersection data fields, creating scalar tags.
771                # There are no fancy array tags in a relationship.
772                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
773                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
774                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
775                }
776                # Finally, the indexes: currently we cannot support the to-index and
777                # from-index in PPO, so we just process the alternate indexes.
778                my $indexList = $relationshipObject->{Indexes};
779                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
780                # Wrap up all the stuff about this relationship.
781                my $object = { label => $relationshipName,
782                               scalar => \@scalars,
783                               object_ref => \@object_refs,
784                               index => \@indexes
785                             };
786                # Push it into the object list.
787                push @objects, $object;
788            }
789        }
790        # Compute a title.
791        my $title;
792        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
793            # Here we have a standard file name we can use for a title.
794            $title = $2;
795        } else {
796            # Here the file name is non-standard, so we carve up the
797            # database title.
798            $title = $xml->{Title}->{content};
799            $title =~ s/\s\.,//g;
800        }
801        # Wrap up the XML as a project.
802        my $ppoXML = { project => { label => $title,
803                                    object => \@objects }};
804        # Write out the results.
805        my $ppoString = XML::Simple::XMLout($ppoXML,
806                                            AttrIndent => 1,
807                                            KeepRoot => 1);
808        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
809    }
810    
811  =head3 FindIndexForEntity  =head3 FindIndexForEntity
812    
813  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>      my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
814    
815  This method locates the entry in an entity's index list that begins with the  This method locates the entry in an entity's index list that begins with the
816  specified attribute name. If the entity has no index list, one will be  specified attribute name. If the entity has no index list, one will be
# Line 722  Line 880 
880    
881  =head3 CreateTables  =head3 CreateTables
882    
883  C<< $erdb->CreateTables(); >>      $erdb->CreateTables();
884    
885  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
886  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 739  Line 897 
897      # Loop through the relations.      # Loop through the relations.
898      for my $relationName (@relNames) {      for my $relationName (@relNames) {
899          # Create a table for this relation.          # Create a table for this relation.
900          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
901          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
902      }      }
903  }  }
904    
905  =head3 CreateTable  =head3 CreateTable
906    
907  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>      $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
908    
909  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
910    
# Line 802  Line 960 
960      my $estimation = undef;      my $estimation = undef;
961      if ($estimatedRows) {      if ($estimatedRows) {
962          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
963            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
964      }      }
965      # Create the table.      # Create the table.
966      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
# Line 816  Line 975 
975    
976  =head3 VerifyFields  =head3 VerifyFields
977    
978  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
979    
980  Run through the list of proposed field values, insuring that all the character fields are  Run through the list of proposed field values, insuring that all the character fields are
981  below the maximum length. If any fields are too long, they will be truncated in place.  below the maximum length. If any fields are too long, they will be truncated in place.
# Line 859  Line 1018 
1018              my $oldString = $fieldList->[$i];              my $oldString = $fieldList->[$i];
1019              if (length($oldString) > $maxLen) {              if (length($oldString) > $maxLen) {
1020                  # Here it's too big, so we truncate it.                  # Here it's too big, so we truncate it.
1021                  Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);                  Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1022                  $fieldList->[$i] = substr $oldString, 0, $maxLen;                  $fieldList->[$i] = substr $oldString, 0, $maxLen;
1023                  $retVal++;                  $retVal++;
1024              }              }
# Line 871  Line 1030 
1030    
1031  =head3 DigestFields  =head3 DigestFields
1032    
1033  C<< $erdb->DigestFields($relName, $fieldList); >>      $erdb->DigestFields($relName, $fieldList);
1034    
1035  Digest the strings in the field list that correspond to data type C<hash-string> in the  Digest the strings in the field list that correspond to data type C<hash-string> in the
1036  specified relation.  specified relation.
# Line 911  Line 1070 
1070    
1071  =head3 DigestKey  =head3 DigestKey
1072    
1073  C<< my $digested = $erdb->DigestKey($keyValue); >>      my $digested = $erdb->DigestKey($keyValue);
1074    
1075  Return the digested value of a symbolic key. The digested value can then be plugged into a  Return the digested value of a symbolic key. The digested value can then be plugged into a
1076  key-based search into a table with key-type hash-string.  key-based search into a table with key-type hash-string.
# Line 944  Line 1103 
1103    
1104  =head3 CreateIndex  =head3 CreateIndex
1105    
1106  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1107    
1108  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
1109  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
# Line 1000  Line 1159 
1159    
1160  =head3 GetSecondaryFields  =head3 GetSecondaryFields
1161    
1162  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>      my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1163    
1164  This method will return a list of the name and type of each of the secondary  This method will return a list of the name and type of each of the secondary
1165  fields for a specified entity. Secondary fields are stored in two-column tables  fields for a specified entity. Secondary fields are stored in two-column tables
# Line 1041  Line 1200 
1200    
1201  =head3 GetFieldRelationName  =head3 GetFieldRelationName
1202    
1203  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>      my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1204    
1205  Return the name of the relation containing a specified field.  Return the name of the relation containing a specified field.
1206    
# Line 1082  Line 1241 
1241    
1242  =head3 DeleteValue  =head3 DeleteValue
1243    
1244  C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>      my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1245    
1246  Delete secondary field values from the database. This method can be used to delete all  Delete secondary field values from the database. This method can be used to delete all
1247  values of a specified field for a particular entity instance, or only a single value.  values of a specified field for a particular entity instance, or only a single value.
# Line 1165  Line 1324 
1324    
1325  =head3 LoadTables  =head3 LoadTables
1326    
1327  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>      my $stats = $erdb->LoadTables($directoryName, $rebuild);
1328    
1329  This method will load the database tables from a directory. The tables must already have been created  This method will load the database tables from a directory. The tables must already have been created
1330  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
# Line 1225  Line 1384 
1384    
1385  =head3 GetTableNames  =head3 GetTableNames
1386    
1387  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1388    
1389  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1390    
# Line 1242  Line 1401 
1401    
1402  =head3 GetEntityTypes  =head3 GetEntityTypes
1403    
1404  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1405    
1406  Return a list of the entity type names.  Return a list of the entity type names.
1407    
# Line 1259  Line 1418 
1418    
1419  =head3 GetDataTypes  =head3 GetDataTypes
1420    
1421  C<< my %types = ERDB::GetDataTypes(); >>      my %types = ERDB::GetDataTypes();
1422    
1423  Return a table of ERDB data types. The table returned is a hash of hashes.  Return a table of ERDB data types. The table returned is a hash of hashes.
1424  The keys of the big hash are the datatypes. Each smaller hash has several  The keys of the big hash are the datatypes. Each smaller hash has several
# Line 1278  Line 1437 
1437    
1438  =head3 IsEntity  =head3 IsEntity
1439    
1440  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1441    
1442  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1443    
# Line 1305  Line 1464 
1464    
1465  =head3 Get  =head3 Get
1466    
1467  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1468    
1469  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
1470  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 1313  Line 1472 
1472  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
1473  $genus.  $genus.
1474    
1475  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1476    
1477  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
1478  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1479    
1480  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1481    
1482  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1483  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 1330  Line 1489 
1489  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
1490  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
1491    
1492  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1493    
1494  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
1495  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
# Line 1366  Line 1525 
1525  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
1526  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1527    
1528  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1529    
1530  Note that the case is important. Only an uppercase "ORDER BY" with a single space will  Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1531  be processed. The idea is to make it less likely to find the verb by accident.  be processed. The idea is to make it less likely to find the verb by accident.
# Line 1379  Line 1538 
1538  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1539  a positive number. So, for example  a positive number. So, for example
1540    
1541  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>      "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1542    
1543  will only return the first ten genomes for the specified genus. The ORDER BY clause is not  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1544  required. For example, to just get the first 10 genomes in the B<Genome> table, you could  required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1545  use  use
1546    
1547  C<< "LIMIT 10" >>      "LIMIT 10"
1548    
1549  =item params  =item params
1550    
# Line 1406  Line 1565 
1565      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1566          $self->_SetupSQL($objectNames, $filterClause);          $self->_SetupSQL($objectNames, $filterClause);
1567      # Create the query.      # Create the query.
1568      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1569          ".* $suffix";          ".* $suffix";
1570      my $sth = $self->_GetStatementHandle($command, $params);      my $sth = $self->_GetStatementHandle($command, $params);
1571      # Now we create the relation map, which enables DBQuery to determine the order, name      # Now we create the relation map, which enables DBQuery to determine the order, name
# Line 1424  Line 1583 
1583    
1584  =head3 Search  =head3 Search
1585    
1586  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>      my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1587    
1588  Perform a full text search with filtering. The search will be against a specified object  Perform a full text search with filtering. The search will be against a specified object
1589  in the object name list. That object will get an extra field containing the search  in the object name list. That object will get an extra field containing the search
# Line 1507  Line 1666 
1666              $self->_SetupSQL($objectNames, $filterClause, $matchClause);              $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1667          # Create the query. Note that the match clause is inserted at the front of          # Create the query. Note that the match clause is inserted at the front of
1668          # the select fields.          # the select fields.
1669          my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .          my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1670              ".* $suffix";              ".* $suffix";
1671          my $sth = $self->_GetStatementHandle($command, \@myParams);          my $sth = $self->_GetStatementHandle($command, \@myParams);
1672          # Now we create the relation map, which enables DBQuery to determine the order, name          # Now we create the relation map, which enables DBQuery to determine the order, name
# Line 1521  Line 1680 
1680    
1681  =head3 GetFlat  =head3 GetFlat
1682    
1683  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>      my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1684    
1685  This is a variation of L</GetAll> that asks for only a single field per record and  This is a variation of L</GetAll> that asks for only a single field per record and
1686  returns a single flattened list.  returns a single flattened list.
# Line 1574  Line 1733 
1733    
1734  =head3 SpecialFields  =head3 SpecialFields
1735    
1736  C<< my %specials = $erdb->SpecialFields($entityName); >>      my %specials = $erdb->SpecialFields($entityName);
1737    
1738  Return a hash mapping special fields in the specified entity to the value of their  Return a hash mapping special fields in the specified entity to the value of their
1739  C<special> attribute. This enables the subclass to get access to the special field  C<special> attribute. This enables the subclass to get access to the special field
# Line 1616  Line 1775 
1775    
1776  =head3 Delete  =head3 Delete
1777    
1778  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1779    
1780  Delete an entity instance from the database. The instance is deleted along with all entity and  Delete an entity instance from the database. The instance is deleted along with all entity and
1781  relationship instances dependent on it. The definition of I<dependence> is recursive.  relationship instances dependent on it. The definition of I<dependence> is recursive.
# Line 1801  Line 1960 
1960    
1961  =head3 Disconnect  =head3 Disconnect
1962    
1963  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>      $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
1964    
1965  Disconnect an entity instance from all the objects to which it is related. This  Disconnect an entity instance from all the objects to which it is related. This
1966  will delete each relationship instance that connects to the specified entity.  will delete each relationship instance that connects to the specified entity.
# Line 1841  Line 2000 
2000          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
2001              if ($structure->{$dir} eq $originEntityName) {              if ($structure->{$dir} eq $originEntityName) {
2002                  # Delete all relationship instances on this side of the entity instance.                  # Delete all relationship instances on this side of the entity instance.
2003                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2004                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2005                  $found = 1;                  $found = 1;
2006              }              }
# Line 1854  Line 2014 
2014    
2015  =head3 DeleteRow  =head3 DeleteRow
2016    
2017  C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>      $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2018    
2019  Delete a row from a relationship. In most cases, only the from-link and to-link are  Delete a row from a relationship. In most cases, only the from-link and to-link are
2020  needed; however, for relationships with intersection data values can be specified  needed; however, for relationships with intersection data values can be specified
# Line 1907  Line 2067 
2067      $dbh->SQL($command, undef, @parms);      $dbh->SQL($command, undef, @parms);
2068  }  }
2069    
2070    =head3 DeleteLike
2071    
2072        my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2073    
2074    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2075    filter, only fields from the relationship itself can be used.
2076    
2077    =over 4
2078    
2079    =item relName
2080    
2081    Name of the relationship whose records are to be deleted.
2082    
2083    =item filter
2084    
2085    A filter clause (L</Get>-style) for the delete query.
2086    
2087    =item parms
2088    
2089    Reference to a list of parameters for the filter clause.
2090    
2091    =item RETURN
2092    
2093    Returns a count of the number of rows deleted.
2094    
2095    =back
2096    
2097    =cut
2098    
2099    sub DeleteLike {
2100        # Get the parameters.
2101        my ($self, $objectName, $filter, $parms) = @_;
2102        # Declare the return variable.
2103        my $retVal;
2104        # Insure the parms argument is an array reference if the caller left it off.
2105        if (! defined($parms)) {
2106            $parms = [];
2107        }
2108        # Insure we have a relationship. The main reason for this is if we delete an entity
2109        # instance we have to yank out a bunch of other stuff with it.
2110        if ($self->IsEntity($objectName)) {
2111            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2112        } else {
2113            # Create the SQL command suffix to get the desierd records.
2114            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2115            # Convert it to a DELETE command.
2116            my $command = "DELETE $suffix";
2117            # Execute the command.
2118            my $dbh = $self->{_dbh};
2119            my $result = $dbh->SQL($command, 0, @{$parms});
2120            # Check the results. Note we convert the "0D0" result to a real zero.
2121            # A failure causes an abnormal termination, so the caller isn't going to
2122            # worry about it.
2123            if (! defined $result) {
2124                Confess("Error deleting from $objectName: " . $dbh->errstr());
2125            } elsif ($result == 0) {
2126                $retVal = 0;
2127            } else {
2128                $retVal = $result;
2129            }
2130        }
2131        # Return the result count.
2132        return $retVal;
2133    }
2134    
2135  =head3 SortNeeded  =head3 SortNeeded
2136    
2137  C<< my $parms = $erdb->SortNeeded($relationName); >>      my $parms = $erdb->SortNeeded($relationName);
2138    
2139  Return the pipe command for the sort that should be applied to the specified  Return the pipe command for the sort that should be applied to the specified
2140  relation when creating the load file.  relation when creating the load file.
# Line 2007  Line 2232 
2232    
2233  =head3 GetList  =head3 GetList
2234    
2235  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>      my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2236    
2237  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
2238  specified filter clause.  specified filter clause.
# Line 2035  Line 2260 
2260  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
2261  particular genus and sorts them by species name.  particular genus and sorts them by species name.
2262    
2263  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
2264    
2265  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
2266  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
# Line 2047  Line 2272 
2272    
2273  =item RETURN  =item RETURN
2274    
2275  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2276    
2277  =back  =back
2278    
# Line 2070  Line 2295 
2295    
2296  =head3 GetCount  =head3 GetCount
2297    
2298  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2299    
2300  Return the number of rows found by a specified query. This method would  Return the number of rows found by a specified query. This method would
2301  normally be used to count the records in a single table. For example, in a  normally be used to count the records in a single table. For example, in a
# Line 2163  Line 2388 
2388    
2389  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
2390    
2391  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $sentence = $erdb->ComputeObjectSentence($objectName);
2392    
2393  Check an object name, and if it is a relationship convert it to a relationship sentence.  Check an object name, and if it is a relationship convert it to a relationship sentence.
2394    
# Line 2198  Line 2423 
2423    
2424  =head3 DumpRelations  =head3 DumpRelations
2425    
2426  C<< $erdb->DumpRelations($outputDirectory); >>      $erdb->DumpRelations($outputDirectory);
2427    
2428  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
2429  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 2240  Line 2465 
2465    
2466  =head3 InsertValue  =head3 InsertValue
2467    
2468  C<< $erdb->InsertValue($entityID, $fieldName, $value); >>      $erdb->InsertValue($entityID, $fieldName, $value);
2469    
2470  This method will insert a new value into the database. The value must be one  This method will insert a new value into the database. The value must be one
2471  associated with a secondary relation, since primary values cannot be inserted:  associated with a secondary relation, since primary values cannot be inserted:
# Line 2303  Line 2528 
2528    
2529  =head3 InsertObject  =head3 InsertObject
2530    
2531  C<< $erdb->InsertObject($objectType, \%fieldHash); >>      $erdb->InsertObject($objectType, \%fieldHash);
2532    
2533  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2534  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 2312  Line 2537 
2537  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2538  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2539    
2540  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>      $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2541    
2542  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2543  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2544    
2545  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>      $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2546    
2547  =over 4  =over 4
2548    
# Line 2428  Line 2653 
2653                  if (!$retVal) {                  if (!$retVal) {
2654                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2655                      Confess("Error inserting into $relationName: $errorString");                      Confess("Error inserting into $relationName: $errorString");
2656                    } else {
2657                        Trace("Insert successful using $parameterList[0].") if T(3);
2658                  }                  }
2659              }              }
2660          }          }
# Line 2438  Line 2665 
2665    
2666  =head3 UpdateEntity  =head3 UpdateEntity
2667    
2668  C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>      $erdb->UpdateEntity($entityName, $id, \%fields);
2669    
2670  Update the values of an entity. This is an unprotected update, so it should only be  Update the values of an entity. This is an unprotected update, so it should only be
2671  done if the database resides on a database server.  done if the database resides on a database server.
# Line 2496  Line 2723 
2723    
2724  =head3 LoadTable  =head3 LoadTable
2725    
2726  C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag);
2727    
2728  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2729  first.  first.
# Line 2539  Line 2766 
2766      if ($truncateFlag) {      if ($truncateFlag) {
2767          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2768          # Compute the row count estimate. We take the size of the load file,          # Compute the row count estimate. We take the size of the load file,
2769          # divide it by the estimated row size, and then multiply by 1.5 to          # divide it by the estimated row size, and then multiply by 2 to
2770          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2771          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2772          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2773          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 8 / $rowSize;
2774            if ($estimate < 1000) {
2775                $estimate = 1000;
2776            }
2777          # Re-create the table without its index.          # Re-create the table without its index.
2778          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2779          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 2587  Line 2817 
2817              # primary relations are allowed that privilege.              # primary relations are allowed that privilege.
2818              Trace("Checking for full-text index on $relationName.") if T(2);              Trace("Checking for full-text index on $relationName.") if T(2);
2819              if ($self->_IsPrimary($relationName)) {              if ($self->_IsPrimary($relationName)) {
2820                  # Get the relation's entity/relationship structure.                  $self->CreateSearchIndex($relationName);
                 my $structure = $self->_GetStructure($relationName);  
                 Trace("Checking for search fields in $relationName.") if T(3);  
                 # Check for a searchable fields list.  
                 if (exists $structure->{searchFields}) {  
                     # Here we know that we need to create a full-text search index.  
                     # Get an SQL-formatted field name list.  
                     my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));  
                     # Create the index.  
                     $dbh->create_index(tbl => $relationName, idx => "search_idx",  
                                        flds => $fields, kind => 'fulltext');  
                     Trace("Index created for $fields in $relationName.") if T(2);  
                 }  
2821              }              }
2822          }          }
2823      }      }
# Line 2611  Line 2829 
2829      return $retVal;      return $retVal;
2830  }  }
2831    
2832    =head3 CreateSearchIndex
2833    
2834        $erdb->CreateSearchIndex($objectName);
2835    
2836    Check for a full-text search index on the specified entity or relationship object, and
2837    if one is required, rebuild it.
2838    
2839    =over 4
2840    
2841    =item objectName
2842    
2843    Name of the entity or relationship to be indexed.
2844    
2845    =back
2846    
2847    =cut
2848    
2849    sub CreateSearchIndex {
2850        # Get the parameters.
2851        my ($self, $objectName) = @_;
2852        # Get the relation's entity/relationship structure.
2853        my $structure = $self->_GetStructure($objectName);
2854        # Get the database handle.
2855        my $dbh = $self->{_dbh};
2856        Trace("Checking for search fields in $objectName.") if T(3);
2857        # Check for a searchable fields list.
2858        if (exists $structure->{searchFields}) {
2859            # Here we know that we need to create a full-text search index.
2860            # Get an SQL-formatted field name list.
2861            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2862            # Create the index. If it already exists, it will be dropped.
2863            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2864                               flds => $fields, kind => 'fulltext');
2865            Trace("Index created for $fields in $objectName.") if T(2);
2866        }
2867    }
2868    
2869  =head3 DropRelation  =head3 DropRelation
2870    
2871  C<< $erdb->DropRelation($relationName); >>      $erdb->DropRelation($relationName);
2872    
2873  Physically drop a relation from the database.  Physically drop a relation from the database.
2874    
# Line 2641  Line 2896 
2896    
2897  =head3 MatchSqlPattern  =head3 MatchSqlPattern
2898    
2899  C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>      my $matched = ERDB::MatchSqlPattern($value, $pattern);
2900    
2901  Determine whether or not a specified value matches an SQL pattern. An SQL  Determine whether or not a specified value matches an SQL pattern. An SQL
2902  pattern has two wild card characters: C<%> that matches multiple characters,  pattern has two wild card characters: C<%> that matches multiple characters,
# Line 2724  Line 2979 
2979    
2980  =head3 GetEntity  =head3 GetEntity
2981    
2982  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $entityObject = $erdb->GetEntity($entityType, $ID);
2983    
2984  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
2985    
# Line 2740  Line 2995 
2995    
2996  =item RETURN  =item RETURN
2997    
2998  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2999  instance is found with the specified key.  instance is found with the specified key.
3000    
3001  =back  =back
# Line 2760  Line 3015 
3015    
3016  =head3 GetChoices  =head3 GetChoices
3017    
3018  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>      my @values = $erdb->GetChoices($entityName, $fieldName);
3019    
3020  Return a list of all the values for the specified field that are represented in the  Return a list of all the values for the specified field that are represented in the
3021  specified entity.  specified entity.
# Line 2815  Line 3070 
3070    
3071  =head3 GetEntityValues  =head3 GetEntityValues
3072    
3073  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3074    
3075  Return a list of values from a specified entity instance. If the entity instance  Return a list of values from a specified entity instance. If the entity instance
3076  does not exist, an empty list is returned.  does not exist, an empty list is returned.
# Line 2859  Line 3114 
3114    
3115  =head3 GetAll  =head3 GetAll
3116    
3117  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3118    
3119  Return a list of values taken from the objects returned by a query. The first three  Return a list of values taken from the objects returned by a query. The first three
3120  parameters correspond to the parameters of the L</Get> method. The final parameter is  parameters correspond to the parameters of the L</Get> method. The final parameter is
# Line 2873  Line 3128 
3128  fields specified returns multiple values, they are flattened in with the rest. For  fields specified returns multiple values, they are flattened in with the rest. For
3129  example, the following call will return a list of the features in a particular  example, the following call will return a list of the features in a particular
3130  spreadsheet cell, and each feature will be represented by a list containing the  spreadsheet cell, and each feature will be represented by a list containing the
3131  feature ID followed by all of its aliases.  feature ID followed by all of its essentiality determinations.
3132    
3133  C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>      @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']);
3134    
3135  =over 4  =over 4
3136    
# Line 2953  Line 3208 
3208    
3209  =head3 Exists  =head3 Exists
3210    
3211  C<< my $found = $sprout->Exists($entityName, $entityID); >>      my $found = $sprout->Exists($entityName, $entityID);
3212    
3213  Return TRUE if an entity exists, else FALSE.  Return TRUE if an entity exists, else FALSE.
3214    
# Line 2988  Line 3243 
3243    
3244  =head3 EstimateRowSize  =head3 EstimateRowSize
3245    
3246  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>      my $rowSize = $erdb->EstimateRowSize($relName);
3247    
3248  Estimate the row size of the specified relation. The estimated row size is computed by adding  Estimate the row size of the specified relation. The estimated row size is computed by adding
3249  up the average length for each data type.  up the average length for each data type.
# Line 3026  Line 3281 
3281    
3282  =head3 GetFieldTable  =head3 GetFieldTable
3283    
3284  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>      my $fieldHash = $self->GetFieldTable($objectnName);
3285    
3286  Get the field structure for a specified entity or relationship.  Get the field structure for a specified entity or relationship.
3287    
# Line 3055  Line 3310 
3310    
3311  =head3 SplitKeywords  =head3 SplitKeywords
3312    
3313  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>      my @keywords = ERDB::SplitKeywords($keywordString);
3314    
3315  This method returns a list of the positive keywords in the specified  This method returns a list of the positive keywords in the specified
3316  keyword string. All of the operators will have been stripped off,  keyword string. All of the operators will have been stripped off,
# Line 3104  Line 3359 
3359    
3360  =head3 ValidateFieldName  =head3 ValidateFieldName
3361    
3362  C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>      my $okFlag = ERDB::ValidateFieldName($fieldName);
3363    
3364  Return TRUE if the specified field name is valid, else FALSE. Valid field names must  Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3365  be hyphenated words subject to certain restrictions.  be hyphenated words subject to certain restrictions.
# Line 3159  Line 3414 
3414    
3415  =head3 ReadMetaXML  =head3 ReadMetaXML
3416    
3417  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>      my $rawMetaData = ERDB::ReadDBD($fileName);
3418    
3419  This method reads a raw database definition XML file and returns it.  This method reads a raw database definition XML file and returns it.
3420  Normally, the metadata used by the ERDB system has been processed and  Normally, the metadata used by the ERDB system has been processed and
# Line 3192  Line 3447 
3447    
3448  =head3 GetEntityFieldHash  =head3 GetEntityFieldHash
3449    
3450  C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>      my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3451    
3452  Get the field hash of the named entity in the specified raw XML structure.  Get the field hash of the named entity in the specified raw XML structure.
3453  The field hash may not exist, in which case we need to create it.  The field hash may not exist, in which case we need to create it.
# Line 3234  Line 3489 
3489    
3490  =head3 WriteMetaXML  =head3 WriteMetaXML
3491    
3492  C<< ERDB::WriteMetaXML($structure, $fileName); >>      ERDB::WriteMetaXML($structure, $fileName);
3493    
3494  Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is  Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3495  used to update the database definition. It must be used with care, however, since it  used to update the database definition. It must be used with care, however, since it
# Line 3273  Line 3528 
3528  Except for C<[p]>, all the codes are closed by slash-codes. So, for  Except for C<[p]>, all the codes are closed by slash-codes. So, for
3529  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3530    
3531  C<< my $realHtml = ERDB::HTMLNote($dataString); >>      my $realHtml = ERDB::HTMLNote($dataString);
3532    
3533  =over 4  =over 4
3534    
# Line 3297  Line 3552 
3552      # Substitute the bulletin board codes.      # Substitute the bulletin board codes.
3553      $retVal =~ s!\[(/?[bi])\]!<$1>!g;      $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3554      $retVal =~ s!\[p\]!</p><p>!g;      $retVal =~ s!\[p\]!</p><p>!g;
3555        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3556        $retVal =~ s!\[/link\]!</a>!g;
3557        # Return the result.
3558        return $retVal;
3559    }
3560    
3561    =head3 BeginTran
3562    
3563        $erdb->BeginTran();
3564    
3565    Start a database transaction.
3566    
3567    =cut
3568    
3569    sub BeginTran {
3570        my ($self) = @_;
3571        $self->{_dbh}->begin_tran();
3572    
3573    }
3574    
3575    =head3 CommitTran
3576    
3577        $erdb->CommitTran();
3578    
3579    Commit an active database transaction.
3580    
3581    =cut
3582    
3583    sub CommitTran {
3584        my ($self) = @_;
3585        $self->{_dbh}->commit_tran();
3586    }
3587    
3588    =head3 RollbackTran
3589    
3590        $erdb->RollbackTran();
3591    
3592    Roll back an active database transaction.
3593    
3594    =cut
3595    
3596    sub RollbackTran {
3597        my ($self) = @_;
3598        $self->{_dbh}->roll_tran();
3599    }
3600    
3601    =head3 UpdateField
3602    
3603        my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3604    
3605    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3606    returned.
3607    
3608    =over 4
3609    
3610    =item fieldName
3611    
3612    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3613    
3614    =item oldValue
3615    
3616    Value to be modified. All occurrences of this value in the named field will be replaced by the
3617    new value.
3618    
3619    =item newValue
3620    
3621    New value to be substituted for the old value when it's found.
3622    
3623    =item filter
3624    
3625    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3626    
3627    =item parms
3628    
3629    Reference to a list of parameter values in the filter.
3630    
3631    =item RETURN
3632    
3633    Returns the number of rows modified.
3634    
3635    =back
3636    
3637    =cut
3638    
3639    sub UpdateField {
3640        # Get the parameters.
3641        my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3642        # Get the object and field names from the field name parameter.
3643        $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3644        my $objectName = $1;
3645        my $realFieldName = _FixName($2);
3646        # Add the old value to the filter. Note we allow the possibility that no
3647        # filter was specified.
3648        my $realFilter = "$fieldName = ?";
3649        if ($filter) {
3650            $realFilter .= " AND $filter";
3651        }
3652        # Format the query filter.
3653        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3654            $self->_SetupSQL([$objectName], $realFilter);
3655        # Create the query. Since there is only one object name, the mapped-name data is not
3656        # necessary. Neither is the FROM clause.
3657        $suffix =~ s/^FROM.+WHERE\s+//;
3658        # Create the update statement.
3659        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3660        # Get the database handle.
3661        my $dbh = $self->{_dbh};
3662        # Add the old and new values to the parameter list. Note we allow the possibility that
3663        # there are no user-supplied parameters.
3664        my @params = ($newValue, $oldValue);
3665        if (defined $parms) {
3666            push @params, @{$parms};
3667        }
3668        # Execute the update.
3669        my $retVal = $dbh->SQL($command, 0, @params);
3670        # Make the funky zero a real zero.
3671        if ($retVal == 0) {
3672            $retVal = 0;
3673        }
3674      # Return the result.      # Return the result.
3675      return $retVal;      return $retVal;
3676  }  }
# Line 3306  Line 3680 
3680    
3681  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3682    
3683  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3684    
3685  Return a list of the useful attributes that would be returned by a B<Cross> call  Return a list of the useful attributes that would be returned by a B<Cross> call
3686  from an entity of the source entity type through the specified relationship. This  from an entity of the source entity type through the specified relationship. This
# Line 3367  Line 3741 
3741    
3742  =head3 FindColumn  =head3 FindColumn
3743    
3744  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
3745    
3746  Return the location a desired column in a data mining header line. The data  Return the location a desired column in a data mining header line. The data
3747  mining header line is a tab-separated list of column names. The column  mining header line is a tab-separated list of column names. The column
# Line 3425  Line 3799 
3799    
3800  =head3 ParseColumns  =head3 ParseColumns
3801    
3802  C<< my @columns = ERDB::ParseColumns($line); >>      my @columns = ERDB::ParseColumns($line);
3803    
3804  Convert the specified data line to a list of columns.  Convert the specified data line to a list of columns.
3805    
# Line 3457  Line 3831 
3831    
3832  =head2 Virtual Methods  =head2 Virtual Methods
3833    
3834    =head3 _CreatePPOIndex
3835    
3836        my $index = ERDB::_CreatePPOIndex($indexObject);
3837    
3838    Convert the XML for an ERDB index to the XML structure for a PPO
3839    index.
3840    
3841    =over 4
3842    
3843    ERDB XML structure for an index.
3844    
3845    =item RETURN
3846    
3847    PPO XML structure for the same index.
3848    
3849    =back
3850    
3851    =cut
3852    
3853    sub _CreatePPOIndex {
3854        # Get the parameters.
3855        my ($indexObject) = @_;
3856        # The incoming index contains a list of the index fields in the IndexFields
3857        # member. We loop through it to create the index tags.
3858        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3859        # Wrap the fields in attribute tags.
3860        my $retVal = { attribute => \@fields };
3861        # Return the result.
3862        return $retVal;
3863    }
3864    
3865    =head3 _CreatePPOField
3866    
3867        my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
3868    
3869    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3870    
3871    =over 4
3872    
3873    =item fieldName
3874    
3875    Name of the scalar field.
3876    
3877    =item fieldObject
3878    
3879    ERDB XML structure describing the field.
3880    
3881    =item RETURN
3882    
3883    Returns a PPO XML structure for the same field.
3884    
3885    =back
3886    
3887    =cut
3888    
3889    sub _CreatePPOField {
3890        # Get the parameters.
3891        my ($fieldName, $fieldObject) = @_;
3892        # Get the field type.
3893        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3894        # Fix up the field name.
3895        $fieldName = _FixName($fieldName);
3896        # Build the scalar tag.
3897        my $retVal = { label => $fieldName, type => $type };
3898        # Return the result.
3899        return $retVal;
3900    }
3901    
3902  =head3 CleanKeywords  =head3 CleanKeywords
3903    
3904  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>      my $cleanedString = $erdb->CleanKeywords($searchExpression);
3905    
3906  Clean up a search expression or keyword list. This is a virtual method that may  Clean up a search expression or keyword list. This is a virtual method that may
3907  be overridden by the subclass. The base-class method removes extra spaces  be overridden by the subclass. The base-class method removes extra spaces
# Line 3496  Line 3938 
3938    
3939  =head3 GetSourceObject  =head3 GetSourceObject
3940    
3941  C<< my $source = $erdb->GetSourceObject($entityName); >>      my $source = $erdb->GetSourceObject($entityName);
3942    
3943  Return the object to be used in loading special attributes of the specified entity. The  Return the object to be used in loading special attributes of the specified entity. The
3944  algorithm for loading special attributes is stored in the C<DataGen> elements of the  algorithm for loading special attributes is stored in the C<DataGen> elements of the
# Line 3506  Line 3948 
3948    
3949  =head3 _RelationMap  =head3 _RelationMap
3950    
3951  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>      my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
3952    
3953  Create the relation map for an SQL query. The relation map is used by B<DBObject>  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3954  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
3955    
3956  =over 4  =over 4
# Line 3525  Line 3967 
3967  =item RETURN  =item RETURN
3968    
3969  Returns a list of 2-tuples. Each tuple consists of an object name as used in the  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3970  query followed by the actual name of that object. This enables the B<DBObject> to  query followed by the actual name of that object. This enables the B<ERDBObject> to
3971  determine the order of the tables in the query and which object name belongs to each  determine the order of the tables in the query and which object name belongs to each
3972  mapped object name. Most of the time these two values are the same; however, if a  mapped object name. Most of the time these two values are the same; however, if a
3973  relation occurs twice in the query, the relation name in the field list and WHERE  relation occurs twice in the query, the relation name in the field list and WHERE
# Line 3819  Line 4261 
4261  sub _GetStatementHandle {  sub _GetStatementHandle {
4262      # Get the parameters.      # Get the parameters.
4263      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4264        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4265      # Trace the query.      # Trace the query.
4266      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4267      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 4068  Line 4511 
4511    
4512  =head3 _LoadMetaData  =head3 _LoadMetaData
4513    
4514        my $metadata = ERDB::_LoadMetaData($filename);
4515    
4516  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4517  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
4518  load or use the database. The schema for the XML file is F<ERDatabase.xml>.  load or use the database. The schema for the XML file is F<ERDatabase.xml>.
# Line 4217  Line 4662 
4662              if ($found == 0) {              if ($found == 0) {
4663                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4664              }              }
4665              # Now we need to convert the relation's index list to an index table. We begin by creating              # Attach all the indexes to the relation.
4666              # an empty table in the relation structure.              _ProcessIndexes($indexList, $relation);
             $relation->{Indexes} = { };  
             # Loop through the indexes.  
             my $count = 0;  
             for my $index (@{$indexList}) {  
                 # Add this index to the index table.  
                 _AddIndex("idx$count", $relation, $index);  
                 # Increment the counter so that the next index has a different name.  
                 $count++;  
             }  
4667          }          }
4668          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4669          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 4241  Line 4677 
4677          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4678          # Format a description for the FROM field.          # Format a description for the FROM field.
4679          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4680          my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";          my $fromComment = "[b]id[/b] of the source [b][link #$fromEntity]$fromEntity\[/link][/b].";
4681          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4682          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4683          # Add the FROM field.          # Add the FROM field.
# Line 4251  Line 4687 
4687                                                      PrettySort => 1});                                                      PrettySort => 1});
4688          # Format a description for the TO field.          # Format a description for the TO field.
4689          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4690          my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";          my $toComment = "[b]id[/b] of the target [b][link #$toEntity]$toEntity\[/link][/b].";
4691          # Get the TO entity's key type.          # Get the TO entity's key type.
4692          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4693          # Add the TO field.          # Add the TO field.
# Line 4263  Line 4699 
4699          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
4700                               Indexes => { } };                               Indexes => { } };
4701          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
4702    
4703            # Add the alternate indexes (if any). This MUST be done before the FROM and
4704            # TO indexes, because it erases the relation's index list.
4705            if (exists $relationshipStructure->{Indexes}) {
4706                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
4707            }
4708            # Add the relation to the master table.
4709          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
4710          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
4711          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
4712          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
4713      }      }
4714      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 4425  Line 4867 
4867      _AddIndex("idx$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4868  }  }
4869    
4870    =head3 _ProcessIndexes
4871    
4872        ERDB::_ProcessIndexes($indexList, $relation);
4873    
4874    Build the data structures for the specified indexes in the specified relation.
4875    
4876    =over 4
4877    
4878    =item indexList
4879    
4880    Reference to a list of indexes. Each index is a hash reference containing an optional
4881    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
4882    to a list of index field structures. An index field structure, in turn, is a reference
4883    to a hash that contains a C<name> attribute for the field name and an C<order>
4884    attribute that specifies either C<ascending> or C<descending>. In this sense the
4885    index list encapsulates the XML C<Indexes> structure in the database definition.
4886    
4887    =item relation
4888    
4889    The structure that describes the current relation. The new index descriptors will
4890    be stored in the structure's C<Indexes> member. Any previous data in the structure
4891    will be lost.
4892    
4893    =back
4894    
4895    =cut
4896    
4897    sub _ProcessIndexes {
4898        # Get the parameters.
4899        my ($indexList, $relation) = @_;
4900        # Now we need to convert the relation's index list to an index table. We begin by creating
4901        # an empty table in the relation structure.
4902        $relation->{Indexes} = { };
4903        # Loop through the indexes.
4904        my $count = 0;
4905        for my $index (@{$indexList}) {
4906            # Add this index to the index table.
4907            _AddIndex("idx$count", $relation, $index);
4908            # Increment the counter so that the next index has a different name.
4909            $count++;
4910        }
4911    }
4912    
4913  =head3 _AddIndex  =head3 _AddIndex
4914    
4915  Add an index to a relation structure.  Add an index to a relation structure.
# Line 4954  Line 5439 
5439      # Compute the number of columns.      # Compute the number of columns.
5440      my $colCount = @colNames;      my $colCount = @colNames;
5441      # Generate the title row.      # Generate the title row.
5442      my $htmlString = "<p><table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";      my $htmlString = "<table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";
5443      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
5444      $htmlString .= "<tr>";      $htmlString .= "<tr>";
5445      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 4973  Line 5458 
5458  =cut  =cut
5459    
5460  sub _CloseTable {  sub _CloseTable {
5461      return "</table></p>\n";      return "</table>\n";
5462  }  }
5463    
5464  =head3 _ShowField  =head3 _ShowField
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