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revision 1.92, Mon Jun 11 18:51:23 2007 UTC revision 1.100, Tue Aug 12 06:07:06 2008 UTC
# Line 11  Line 11 
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
13      use CGI;      use CGI;
14        use WikiTools;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 389  Line 390 
390                                    Entities => 'Entity',                                    Entities => 'Entity',
391                                    Fields => 'Field',                                    Fields => 'Field',
392                                    Indexes => 'Index',                                    Indexes => 'Index',
393                                    IndexFields => 'IndexField'                                    IndexFields => 'IndexField',
394                                      Issues => 'Issue',
395                                      Shapes => 'Shape'
396                                  },                                  },
397                    KeyAttr =>    { Relationship => 'name',                    KeyAttr =>    { Relationship => 'name',
398                                    Entity => 'name',                                    Entity => 'name',
399                                    Field => 'name'                                    Field => 'name',
400                                      Shape => 'name'
401                                  },                                  },
402                    SuppressEmpty => 1,                    SuppressEmpty => 1,
403                   );                   );
404    
405  my %XmlInOpts  = (  my %XmlInOpts  = (
406                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],                    ForceArray => [qw(Field Index IndexField Relationship Entity Shape)],
407                    ForceContent => 1,                    ForceContent => 1,
408                    NormalizeSpace => 2,                    NormalizeSpace => 2,
409                   );                   );
# Line 408  Line 412 
412                    XMLDecl => 1,                    XMLDecl => 1,
413                   );                   );
414    
   
415  =head2 Public Methods  =head2 Public Methods
416    
417  =head3 new  =head3 new
418    
419  C<< my $database = ERDB->new($dbh, $metaFileName); >>      my $database = ERDB->new($dbh, $metaFileName);
420    
421  Create a new ERDB object.  Create a new ERDB object.
422    
# Line 433  Line 436 
436    
437  sub new {  sub new {
438      # Get the parameters.      # Get the parameters.
439      my ($class, $dbh, $metaFileName, $options) = @_;      my ($class, $dbh, $metaFileName, %options) = @_;
440      # Load the meta-data.      # Load the meta-data.
441      my $metaData = _LoadMetaData($metaFileName);      my $metaData = _LoadMetaData($metaFileName);
442      # Create the object.      # Create the object.
# Line 447  Line 450 
450    
451  =head3 ShowMetaData  =head3 ShowMetaData
452    
453  C<< $erdb->ShowMetaData($fileName); >>      $erdb->ShowMetaData($fileName);
454    
455  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
456  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 488  Line 491 
491    
492  =head3 DisplayMetaData  =head3 DisplayMetaData
493    
494  C<< my $html = $erdb->DisplayMetaData(); >>      my $html = $erdb->DisplayMetaData();
495    
496  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
497  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 644  Line 647 
647    
648  =head3 DumpMetaData  =head3 DumpMetaData
649    
650  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
651    
652  Return a dump of the metadata structure.  Return a dump of the metadata structure.
653    
# Line 657  Line 660 
660      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
661  }  }
662    
663    =head3 GenerateWikiData
664    
665        my @wikiLines = $erdb->GenerateWikiData();
666    
667    Build a description of the database for the wiki. The database will be
668    organized into a single page, with sections for each entity and relationship.
669    The return value is a list of text lines.
670    
671    =cut
672    
673    sub GenerateWikiData {
674        # Get the parameters.
675        my ($self) = @_;
676        # We'll build the wiki text in here.
677        my @retVal = ();
678        # Get the metadata object.
679        my $metadata = $self->{_metaData};
680        # Get the title string. This will become the page name.
681        my $title = $metadata->{Title}->{content};
682        # Get the entity and relationship lists.
683        my $entityList = $metadata->{Entities};
684        my $relationshipList = $metadata->{Relationships};
685        my $shapeList = $metadata->{Shapes};
686        # Start with the introductory text.
687        push @retVal, WikiTools::Heading(2, "Introduction");
688        if (my $notes = $metadata->{Notes}) {
689            push @retVal, WikiNote($notes->{content});
690        }
691        # Generate issue list.
692        if (my $issues = $metadata->{Issues}) {
693            push @retVal, WikiTools::Heading(3, 'Issues');
694            push @retVal, WikiTools::List(map { $_->{content} } @{$issues});
695        }
696        # Start the entity section.
697        push @retVal, WikiTools::Heading(2, "Entities");
698        # Loop through the entities. Note that unlike the situation with HTML, we
699        # don't need to generate the table of contents manually, just the data
700        # itself.
701        for my $key (sort keys %$entityList) {
702            # Create a header for this entity.
703            push @retVal, "", WikiTools::Heading(3, $key);
704            # Get the entity data.
705            my $entityData = $entityList->{$key};
706            # Plant the notes here, if there are any.
707            push @retVal, _ObjectNotes($entityData);
708            # Now we list the entity's relationships (if any). First, we build a list
709            # of the relationships relevant to this entity.
710            my @rels = ();
711            for my $rel (sort keys %$relationshipList) {
712                my $relStructure = $relationshipList->{$rel};
713                if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
714                    # Get the relationship sentence.
715                    my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
716                    # Linkify it.
717                    my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
718                    $relSentence =~ s/$rel/$linkedRel/;
719                    push @rels, $relSentence;
720                }
721            }
722            # Add the relationships as a Wiki list.
723            push @retVal, WikiTools::List(@rels);
724            # Get the entity's relations.
725            my $relationList = $entityData->{Relations};
726            # Loop through the relations, displaying them.
727            for my $relation (sort keys %{$relationList}) {
728                my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
729                push @retVal, $wikiString;
730            }
731        }
732        # Now the entities are documented. Next we do the relationships.
733        push @retVal, WikiTools::Heading(2, "Relationships");
734        for my $key (sort keys %$relationshipList) {
735            my $relationshipData = $relationshipList->{$key};
736            # Create the relationship heading.
737            push @retVal, WikiTools::Heading(3, $key);
738            # Describe the relationship arity. Note there's a bit of trickiness involving recursive
739            # many-to-many relationships. In a normal many-to-many we use two sentences to describe
740            # the arity (one for each direction). This is a bad idea for a recursive relationship,
741            # since both sentences will say the same thing.
742            my $arity = $relationshipData->{arity};
743            my $fromEntity = $relationshipData->{from};
744            my $toEntity = $relationshipData->{to};
745            my @listElements = ();
746            my $boldCode = WikiTools::BoldCode();
747            if ($arity eq "11") {
748                push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
749            } else {
750                push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.";
751                if ($arity eq "MM" && $fromEntity ne $toEntity) {
752                    push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.";
753                }
754            }
755            push @retVal, WikiTools::List(@listElements);
756            # Plant the notes here, if there are any.
757            push @retVal, _ObjectNotes($relationshipData);
758            # Finally, the relationship table.
759            my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
760            push @retVal, $wikiString;
761        }
762        # Now loop through the miscellaneous shapes.
763        if ($shapeList) {
764            push @retVal, WikiTools::Heading(2, "Miscellaneous");
765            for my $shape (sort keys %$shapeList) {
766                push @retVal, WikiTools::Heading(3, $shape);
767                my $shapeData = $shapeList->{$shape};
768                push @retVal, _ObjectNotes($shapeData);
769            }
770        }
771        # All done. Return the lines.
772        return @retVal;
773    }
774    
775    
776  =head3 CreatePPO  =head3 CreatePPO
777    
778  C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>      ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
779    
780  Create a PPO XML file from an ERDB data definition XML file. At the  Create a PPO XML file from an ERDB data definition XML file. At the
781  current time, the PPO XML file can be used to create a database with  current time, the PPO XML file can be used to create a database with
# Line 810  Line 926 
926    
927  =head3 FindIndexForEntity  =head3 FindIndexForEntity
928    
929  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>      my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
930    
931  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
932  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 880  Line 996 
996    
997  =head3 CreateTables  =head3 CreateTables
998    
999  C<< $erdb->CreateTables(); >>      $erdb->CreateTables();
1000    
1001  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
1002  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 904  Line 1020 
1020    
1021  =head3 CreateTable  =head3 CreateTable
1022    
1023  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>      $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
1024    
1025  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
1026    
# Line 946  Line 1062 
1062          # Push the result into the field list.          # Push the result into the field list.
1063          push @fieldList, $fieldString;          push @fieldList, $fieldString;
1064      }      }
     # If this is a root table, add the "new_record" flag. It defaults to 0, so  
     if ($rootFlag) {  
         push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";  
     }  
1065      # Convert the field list into a comma-delimited string.      # Convert the field list into a comma-delimited string.
1066      my $fieldThing = join(', ', @fieldList);      my $fieldThing = join(', ', @fieldList);
1067      # Insure the table is not already there.      # Insure the table is not already there.
# Line 960  Line 1072 
1072      my $estimation = undef;      my $estimation = undef;
1073      if ($estimatedRows) {      if ($estimatedRows) {
1074          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1075            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1076      }      }
1077      # Create the table.      # Create the table.
1078      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
# Line 974  Line 1087 
1087    
1088  =head3 VerifyFields  =head3 VerifyFields
1089    
1090  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
1091    
1092  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
1093  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 1029  Line 1142 
1142    
1143  =head3 DigestFields  =head3 DigestFields
1144    
1145  C<< $erdb->DigestFields($relName, $fieldList); >>      $erdb->DigestFields($relName, $fieldList);
1146    
1147  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
1148  specified relation.  specified relation.
# Line 1069  Line 1182 
1182    
1183  =head3 DigestKey  =head3 DigestKey
1184    
1185  C<< my $digested = $erdb->DigestKey($keyValue); >>      my $digested = $erdb->DigestKey($keyValue);
1186    
1187  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
1188  key-based search into a table with key-type hash-string.  key-based search into a table with key-type hash-string.
# Line 1102  Line 1215 
1215    
1216  =head3 CreateIndex  =head3 CreateIndex
1217    
1218  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1219    
1220  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
1221  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 1158  Line 1271 
1271    
1272  =head3 GetSecondaryFields  =head3 GetSecondaryFields
1273    
1274  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>      my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1275    
1276  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
1277  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 1199  Line 1312 
1312    
1313  =head3 GetFieldRelationName  =head3 GetFieldRelationName
1314    
1315  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>      my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1316    
1317  Return the name of the relation containing a specified field.  Return the name of the relation containing a specified field.
1318    
# Line 1240  Line 1353 
1353    
1354  =head3 DeleteValue  =head3 DeleteValue
1355    
1356  C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>      my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1357    
1358  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
1359  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 1323  Line 1436 
1436    
1437  =head3 LoadTables  =head3 LoadTables
1438    
1439  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>      my $stats = $erdb->LoadTables($directoryName, $rebuild);
1440    
1441  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
1442  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 1383  Line 1496 
1496    
1497  =head3 GetTableNames  =head3 GetTableNames
1498    
1499  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1500    
1501  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1502    
# Line 1400  Line 1513 
1513    
1514  =head3 GetEntityTypes  =head3 GetEntityTypes
1515    
1516  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1517    
1518  Return a list of the entity type names.  Return a list of the entity type names.
1519    
# Line 1415  Line 1528 
1528      return sort keys %{$entityList};      return sort keys %{$entityList};
1529  }  }
1530    
1531    =head3 GetConnectingRelationships
1532    
1533        my @list = $erdb->GetConnectingRelationships($entityName);
1534    
1535    Return a list of the relationships connected to the specified entity.
1536    
1537    =over 4
1538    
1539    =item entityName
1540    
1541    Entity whose connected relationships are desired.
1542    
1543    =item RETURN
1544    
1545    Returns a list of the relationships that originate from the entity.
1546    If the entity is on the from end, it will return the relationship
1547    name. If the entity is on the to end it will return the converse of
1548    the relationship name.
1549    
1550    =back
1551    
1552    =cut
1553    
1554    sub GetConnectingRelationships {
1555        # Get the parameters.
1556        my ($self, $entityName) = @_;
1557        # Declare the return variable.
1558        my @retVal;
1559        # Get the relationship list.
1560        my $relationships = $self->{_metaData}->{Relationships};
1561        # Find the entity.
1562        my $entity = $self->{_metaData}->{Entities}->{$entityName};
1563        # Only proceed if the entity exists.
1564        if (! defined $entity) {
1565            Trace("Entity $entityName not found.") if T(3);
1566        } else {
1567            # Loop through the relationships.
1568            my @rels = keys %$relationships;
1569            Trace(scalar(@rels) . " relationships found in connection search.") if T(3);
1570            for my $relationshipName (@rels) {
1571                my $relationship = $relationships->{$relationshipName};
1572                if ($relationship->{from} eq $entityName) {
1573                    # Here we have a forward relationship.
1574                    push @retVal, $relationshipName;
1575                } elsif ($relationship->{to} eq $entityName) {
1576                    # Here we have a backward relationship. In this case, the
1577                    # converse relationship name is preferred if it exists.
1578                    my $converse = $relationship->{converse} || $relationshipName;
1579                    push @retVal, $converse;
1580                }
1581            }
1582        }
1583        # Return the result.
1584        return @retVal;
1585    }
1586    
1587    
1588    
1589    
1590  =head3 GetDataTypes  =head3 GetDataTypes
1591    
1592  C<< my %types = ERDB::GetDataTypes(); >>      my %types = ERDB::GetDataTypes();
1593    
1594  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.
1595  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 1436  Line 1608 
1608    
1609  =head3 IsEntity  =head3 IsEntity
1610    
1611  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1612    
1613  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1614    
# Line 1463  Line 1635 
1635    
1636  =head3 Get  =head3 Get
1637    
1638  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1639    
1640  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.
1641  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 1471  Line 1643 
1643  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
1644  $genus.  $genus.
1645    
1646  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1647    
1648  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
1649  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1650    
1651  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1652    
1653  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
1654  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 1488  Line 1660 
1660  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
1661  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,
1662    
1663  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1664    
1665  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
1666  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 1524  Line 1696 
1696  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
1697  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1698    
1699  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1700    
1701  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
1702  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 1537  Line 1709 
1709  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
1710  a positive number. So, for example  a positive number. So, for example
1711    
1712  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>      "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1713    
1714  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
1715  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
1716  use  use
1717    
1718  C<< "LIMIT 10" >>      "LIMIT 10"
1719    
1720  =item params  =item params
1721    
# Line 1564  Line 1736 
1736      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1737          $self->_SetupSQL($objectNames, $filterClause);          $self->_SetupSQL($objectNames, $filterClause);
1738      # Create the query.      # Create the query.
1739      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1740          ".* $suffix";          ".* $suffix";
1741      my $sth = $self->_GetStatementHandle($command, $params);      my $sth = $self->_GetStatementHandle($command, $params);
1742      # 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 1582  Line 1754 
1754    
1755  =head3 Search  =head3 Search
1756    
1757  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>      my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1758    
1759  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
1760  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 1665  Line 1837 
1837              $self->_SetupSQL($objectNames, $filterClause, $matchClause);              $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1838          # 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
1839          # the select fields.          # the select fields.
1840          my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .          my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1841              ".* $suffix";              ".* $suffix";
1842          my $sth = $self->_GetStatementHandle($command, \@myParams);          my $sth = $self->_GetStatementHandle($command, \@myParams);
1843          # 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 1679  Line 1851 
1851    
1852  =head3 GetFlat  =head3 GetFlat
1853    
1854  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>      my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1855    
1856  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
1857  returns a single flattened list.  returns a single flattened list.
# Line 1732  Line 1904 
1904    
1905  =head3 SpecialFields  =head3 SpecialFields
1906    
1907  C<< my %specials = $erdb->SpecialFields($entityName); >>      my %specials = $erdb->SpecialFields($entityName);
1908    
1909  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
1910  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 1774  Line 1946 
1946    
1947  =head3 Delete  =head3 Delete
1948    
1949  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1950    
1951  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
1952  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 1959  Line 2131 
2131    
2132  =head3 Disconnect  =head3 Disconnect
2133    
2134  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>      $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2135    
2136  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
2137  will delete each relationship instance that connects to the specified entity.  will delete each relationship instance that connects to the specified entity.
# Line 1998  Line 2170 
2170          # Loop through the ends of the relationship.          # Loop through the ends of the relationship.
2171          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
2172              if ($structure->{$dir} eq $originEntityName) {              if ($structure->{$dir} eq $originEntityName) {
                 # Delete all relationship instances on this side of the entity instance.  
                 Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");  
                 $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);  
2173                  $found = 1;                  $found = 1;
2174                    # Here we want to delete all relationship instances on this side of the
2175                    # entity instance.
2176                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2177                    # We do this delete in batches to keep it from dragging down the
2178                    # server.
2179                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2180                    my $done = 0;
2181                    while (! $done) {
2182                        # Do the delete.
2183                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2184                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2185                        $done = ($rows == 0 || ! $limitClause);
2186                    }
2187              }              }
2188          }          }
2189          # Insure we found the entity on at least one end.          # Insure we found the entity on at least one end.
# Line 2013  Line 2195 
2195    
2196  =head3 DeleteRow  =head3 DeleteRow
2197    
2198  C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>      $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2199    
2200  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
2201  needed; however, for relationships with intersection data values can be specified  needed; however, for relationships with intersection data values can be specified
# Line 2068  Line 2250 
2250    
2251  =head3 DeleteLike  =head3 DeleteLike
2252    
2253  C<< my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms); >>      my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2254    
2255  Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal  Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2256  filter, only fields from the relationship itself can be used.  filter, only fields from the relationship itself can be used.
# Line 2133  Line 2315 
2315    
2316  =head3 SortNeeded  =head3 SortNeeded
2317    
2318  C<< my $parms = $erdb->SortNeeded($relationName); >>      my $parms = $erdb->SortNeeded($relationName);
2319    
2320  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
2321  relation when creating the load file.  relation when creating the load file.
# Line 2189  Line 2371 
2371      }      }
2372      # Now we parse the key names into sort parameters. First, we prime the return      # Now we parse the key names into sort parameters. First, we prime the return
2373      # string.      # string.
2374      my $retVal = "sort -t\"\t\" ";      my $retVal = "sort -T\"$FIG_Config::temp\" -t\"\t\" ";
2375      # Get the relation's field list.      # Get the relation's field list.
2376      my @fields = @{$relationData->{Fields}};      my @fields = @{$relationData->{Fields}};
2377      # Loop through the keys.      # Loop through the keys.
# Line 2219  Line 2401 
2401                  # will stop the inner loop. Note that the field number is                  # will stop the inner loop. Note that the field number is
2402                  # 1-based in the sort command, so we have to increment the                  # 1-based in the sort command, so we have to increment the
2403                  # index.                  # index.
2404                  $fieldSpec = ($i + 1) . $modifier;                  my $realI = $i + 1;
2405                    $fieldSpec = "$realI,$realI$modifier";
2406              }              }
2407          }          }
2408          # Add this field to the sort command.          # Add this field to the sort command.
# Line 2231  Line 2414 
2414    
2415  =head3 GetList  =head3 GetList
2416    
2417  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>      my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2418    
2419  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
2420  specified filter clause.  specified filter clause.
# Line 2259  Line 2442 
2442  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
2443  particular genus and sorts them by species name.  particular genus and sorts them by species name.
2444    
2445  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
2446    
2447  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
2448  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 2294  Line 2477 
2477    
2478  =head3 GetCount  =head3 GetCount
2479    
2480  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2481    
2482  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
2483  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 2387  Line 2570 
2570    
2571  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
2572    
2573  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $sentence = $erdb->ComputeObjectSentence($objectName);
2574    
2575  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.
2576    
# Line 2422  Line 2605 
2605    
2606  =head3 DumpRelations  =head3 DumpRelations
2607    
2608  C<< $erdb->DumpRelations($outputDirectory); >>      $erdb->DumpRelations($outputDirectory);
2609    
2610  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.
2611  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 2464  Line 2647 
2647    
2648  =head3 InsertValue  =head3 InsertValue
2649    
2650  C<< $erdb->InsertValue($entityID, $fieldName, $value); >>      $erdb->InsertValue($entityID, $fieldName, $value);
2651    
2652  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
2653  associated with a secondary relation, since primary values cannot be inserted:  associated with a secondary relation, since primary values cannot be inserted:
# Line 2527  Line 2710 
2710    
2711  =head3 InsertObject  =head3 InsertObject
2712    
2713  C<< $erdb->InsertObject($objectType, \%fieldHash); >>      $erdb->InsertObject($objectType, \%fieldHash);
2714    
2715  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
2716  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 2536  Line 2719 
2719  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
2720  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2721    
2722  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']});
2723    
2724  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
2725  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>.
2726    
2727  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'});
2728    
2729  =over 4  =over 4
2730    
# Line 2610  Line 2793 
2793                  push @missing, $fieldName;                  push @missing, $fieldName;
2794              }              }
2795          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
         }  
2796          # Only proceed if there are no missing fields.          # Only proceed if there are no missing fields.
2797          if (@missing > 0) {          if (@missing > 0) {
2798              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
# Line 2664  Line 2842 
2842    
2843  =head3 UpdateEntity  =head3 UpdateEntity
2844    
2845  C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>      $erdb->UpdateEntity($entityName, $id, \%fields);
2846    
2847  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
2848  done if the database resides on a database server.  done if the database resides on a database server.
# Line 2722  Line 2900 
2900    
2901  =head3 LoadTable  =head3 LoadTable
2902    
2903  C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      my $results = $erdb->LoadTable($fileName, $relationName, %options);
2904    
2905  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2906  first.  first.
# Line 2737  Line 2915 
2915    
2916  Name of the relation to be loaded. This is the same as the table name.  Name of the relation to be loaded. This is the same as the table name.
2917    
2918  =item truncateFlag  =item options
2919    
2920  TRUE if the table should be dropped and re-created, else FALSE  A hash of load options.
2921    
2922  =item RETURN  =item RETURN
2923    
# Line 2747  Line 2925 
2925    
2926  =back  =back
2927    
2928    The permissible options are as follows.
2929    
2930    =over 4
2931    
2932    =item truncate
2933    
2934    If TRUE, then the table will be erased before loading.
2935    
2936    =item mode
2937    
2938    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2939    This option is only applicable to a MySQL database.
2940    
2941    =item partial
2942    
2943    If TRUE, then it is assumed that this is a partial load, and the table will not
2944    be analyzed and compacted at the end.
2945    
2946    =back
2947    
2948  =cut  =cut
2949  sub LoadTable {  sub LoadTable {
2950      # Get the parameters.      # Get the parameters.
2951      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $fileName, $relationName, %options) = @_;
2952      # Create the statistical return object.      # Create the statistical return object.
2953      my $retVal = _GetLoadStats();      my $retVal = _GetLoadStats();
2954      # Trace the fact of the load.      # Trace the fact of the load.
# Line 2762  Line 2960 
2960      # Get the relation data.      # Get the relation data.
2961      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
2962      # Check the truncation flag.      # Check the truncation flag.
2963      if ($truncateFlag) {      if ($options{truncate}) {
2964          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2965          # 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,
2966          # 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
2967          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2968          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2969          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2970          my $estimate = $fileSize * 1.5 / $rowSize;          my $estimate = $fileSize * 8 / $rowSize;
2971          if ($estimate < 1000) {          if ($estimate < 1000) {
2972              $estimate = 1000;              $estimate = 1000;
2973          }          }
# Line 2788  Line 2986 
2986      # Load the table.      # Load the table.
2987      my $rv;      my $rv;
2988      eval {      eval {
2989          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
2990      };      };
2991      if (!defined $rv) {      if (!defined $rv) {
2992          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
# Line 2799  Line 2997 
2997          $retVal->Add("tables");          $retVal->Add("tables");
2998          my $size = -s $fileName;          my $size = -s $fileName;
2999          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
3000            $retVal->Add("bytes", $size);
3001          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
3002          if ($truncateFlag) {          if ($options{truncate}) {
3003              # Indexes are created here for PostGres. For PostGres, indexes are              # Indexes are created here for PostGres. For PostGres, indexes are
3004              # best built at the end. For MySQL, the reverse is true.              # best built at the end. For MySQL, the reverse is true.
3005              if (! $dbh->{_preIndex}) {              if (! $dbh->{_preIndex}) {
# Line 2821  Line 3020 
3020          }          }
3021      }      }
3022      # Analyze the table to improve performance.      # Analyze the table to improve performance.
3023        if (! $options{partial}) {
3024      Trace("Analyzing and compacting $relationName.") if T(3);      Trace("Analyzing and compacting $relationName.") if T(3);
3025      $dbh->vacuum_it($relationName);          $self->Analyze($relationName);
3026        }
3027      Trace("$relationName load completed.") if T(3);      Trace("$relationName load completed.") if T(3);
3028      # Return the statistics.      # Return the statistics.
3029      return $retVal;      return $retVal;
3030  }  }
3031    
3032    =head3 Analyze
3033    
3034        $erdb->Analyze($tableName);
3035    
3036    Analyze and compact a table in the database. This is useful after a load
3037    to improve the performance of the indexes.
3038    
3039    =over 4
3040    
3041    =item tableName
3042    
3043    Name of the table to be analyzed and compacted.
3044    
3045    =back
3046    
3047    =cut
3048    
3049    sub Analyze {
3050        # Get the parameters.
3051        my ($self, $tableName) = @_;
3052        # Analyze the table.
3053        $self->{_dbh}->vacuum_it($tableName);
3054    }
3055    
3056    =head3 TruncateTable
3057    
3058        $erdb->TruncateTable($table);
3059    
3060    Delete all rows from a table quickly. This uses the built-in SQL
3061    C<TRUNCATE> statement, which effectively drops and re-creates a table
3062    with all its settings intact.
3063    
3064    =over 4
3065    
3066    =item table
3067    
3068    Name of the table to be cleared.
3069    
3070    =back
3071    
3072    =cut
3073    
3074    sub TruncateTable {
3075        # Get the parameters.
3076        my ($self, $table) = @_;
3077        # Get the database handle.
3078        my $dbh = $self->{_dbh};
3079        # Execute a truncation comment.
3080        $dbh->SQL("TRUNCATE TABLE $table");
3081    }
3082    
3083    
3084  =head3 CreateSearchIndex  =head3 CreateSearchIndex
3085    
3086  C<< $erdb->CreateSearchIndex($objectName); >>      $erdb->CreateSearchIndex($objectName);
3087    
3088  Check for a full-text search index on the specified entity or relationship object, and  Check for a full-text search index on the specified entity or relationship object, and
3089  if one is required, rebuild it.  if one is required, rebuild it.
# Line 2867  Line 3120 
3120    
3121  =head3 DropRelation  =head3 DropRelation
3122    
3123  C<< $erdb->DropRelation($relationName); >>      $erdb->DropRelation($relationName);
3124    
3125  Physically drop a relation from the database.  Physically drop a relation from the database.
3126    
# Line 2895  Line 3148 
3148    
3149  =head3 MatchSqlPattern  =head3 MatchSqlPattern
3150    
3151  C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>      my $matched = ERDB::MatchSqlPattern($value, $pattern);
3152    
3153  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
3154  pattern has two wild card characters: C<%> that matches multiple characters,  pattern has two wild card characters: C<%> that matches multiple characters,
# Line 2978  Line 3231 
3231    
3232  =head3 GetEntity  =head3 GetEntity
3233    
3234  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $entityObject = $erdb->GetEntity($entityType, $ID);
3235    
3236  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
3237    
# Line 3014  Line 3267 
3267    
3268  =head3 GetChoices  =head3 GetChoices
3269    
3270  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>      my @values = $erdb->GetChoices($entityName, $fieldName);
3271    
3272  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
3273  specified entity.  specified entity.
# Line 3069  Line 3322 
3322    
3323  =head3 GetEntityValues  =head3 GetEntityValues
3324    
3325  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3326    
3327  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
3328  does not exist, an empty list is returned.  does not exist, an empty list is returned.
# Line 3113  Line 3366 
3366    
3367  =head3 GetAll  =head3 GetAll
3368    
3369  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3370    
3371  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
3372  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 3129  Line 3382 
3382  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
3383  feature ID followed by all of its essentiality determinations.  feature ID followed by all of its essentiality determinations.
3384    
3385  C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']); >>      @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']);
3386    
3387  =over 4  =over 4
3388    
# Line 3207  Line 3460 
3460    
3461  =head3 Exists  =head3 Exists
3462    
3463  C<< my $found = $sprout->Exists($entityName, $entityID); >>      my $found = $sprout->Exists($entityName, $entityID);
3464    
3465  Return TRUE if an entity exists, else FALSE.  Return TRUE if an entity exists, else FALSE.
3466    
# Line 3242  Line 3495 
3495    
3496  =head3 EstimateRowSize  =head3 EstimateRowSize
3497    
3498  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>      my $rowSize = $erdb->EstimateRowSize($relName);
3499    
3500  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
3501  up the average length for each data type.  up the average length for each data type.
# Line 3280  Line 3533 
3533    
3534  =head3 GetFieldTable  =head3 GetFieldTable
3535    
3536  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>      my $fieldHash = $self->GetFieldTable($objectnName);
3537    
3538  Get the field structure for a specified entity or relationship.  Get the field structure for a specified entity or relationship.
3539    
# Line 3309  Line 3562 
3562    
3563  =head3 SplitKeywords  =head3 SplitKeywords
3564    
3565  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>      my @keywords = ERDB::SplitKeywords($keywordString);
3566    
3567  This method returns a list of the positive keywords in the specified  This method returns a list of the positive keywords in the specified
3568  keyword string. All of the operators will have been stripped off,  keyword string. All of the operators will have been stripped off,
# Line 3358  Line 3611 
3611    
3612  =head3 ValidateFieldName  =head3 ValidateFieldName
3613    
3614  C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>      my $okFlag = ERDB::ValidateFieldName($fieldName);
3615    
3616  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
3617  be hyphenated words subject to certain restrictions.  be hyphenated words subject to certain restrictions.
# Line 3413  Line 3666 
3666    
3667  =head3 ReadMetaXML  =head3 ReadMetaXML
3668    
3669  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>      my $rawMetaData = ERDB::ReadDBD($fileName);
3670    
3671  This method reads a raw database definition XML file and returns it.  This method reads a raw database definition XML file and returns it.
3672  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 3446  Line 3699 
3699    
3700  =head3 GetEntityFieldHash  =head3 GetEntityFieldHash
3701    
3702  C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>      my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3703    
3704  Get the field hash of the named entity in the specified raw XML structure.  Get the field hash of the named entity in the specified raw XML structure.
3705  The field hash may not exist, in which case we need to create it.  The field hash may not exist, in which case we need to create it.
# Line 3488  Line 3741 
3741    
3742  =head3 WriteMetaXML  =head3 WriteMetaXML
3743    
3744  C<< ERDB::WriteMetaXML($structure, $fileName); >>      ERDB::WriteMetaXML($structure, $fileName);
3745    
3746  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
3747  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 3527  Line 3780 
3780  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
3781  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3782    
3783  C<< my $realHtml = ERDB::HTMLNote($dataString); >>      my $realHtml = ERDB::HTMLNote($dataString);
3784    
3785  =over 4  =over 4
3786    
# Line 3557  Line 3810 
3810      return $retVal;      return $retVal;
3811  }  }
3812    
3813    =head3 WikiNote
3814    
3815    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3816    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3817    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3818    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3819    
3820        my $wikiText = ERDB::WikiNote($dataString);
3821    
3822    =over 4
3823    
3824    =item dataString
3825    
3826    String to convert to Wiki text.
3827    
3828    =item RETURN
3829    
3830    An Wiki text string derived from the input string.
3831    
3832    =back
3833    
3834    =cut
3835    
3836    sub WikiNote {
3837        # Get the parameter.
3838        my ($dataString) = @_;
3839        # HTML-escape the text.
3840        my $retVal = CGI::escapeHTML($dataString);
3841        # Substitute the bulletin board codes.
3842        my $italic = WikiTools::ItalicCode();
3843        $retVal =~ s/\[\/?i\]/$italic/g;
3844        my $bold = WikiTools::BoldCode();
3845        $retVal =~ s/\[\/?b\]/$bold/g;
3846        # Paragraph breaks are the same no matter which Wiki you're using.
3847        $retVal =~ s!\[p\]!\n\n!g;
3848        # Now we do the links, which are complicated by the need to know two
3849        # things: the target URL and the text.
3850        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3851            # Replace the matched string with the Wiki markup for links. Note that
3852            # $-[0] is the starting position of the match for the entire expression,
3853            # and $+[0] is past the ending position.
3854            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3855        }
3856        # Return the result.
3857        return $retVal;
3858    }
3859    
3860  =head3 BeginTran  =head3 BeginTran
3861    
3862  C<< $erdb->BeginTran(); >>      $erdb->BeginTran();
3863    
3864  Start a database transaction.  Start a database transaction.
3865    
# Line 3573  Line 3873 
3873    
3874  =head3 CommitTran  =head3 CommitTran
3875    
3876  C<< $erdb->CommitTran(); >>      $erdb->CommitTran();
3877    
3878  Commit an active database transaction.  Commit an active database transaction.
3879    
# Line 3586  Line 3886 
3886    
3887  =head3 RollbackTran  =head3 RollbackTran
3888    
3889  C<< $erdb->RollbackTran(); >>      $erdb->RollbackTran();
3890    
3891  Roll back an active database transaction.  Roll back an active database transaction.
3892    
# Line 3599  Line 3899 
3899    
3900  =head3 UpdateField  =head3 UpdateField
3901    
3902  C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>      my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3903    
3904  Update all occurrences of a specific field value to a new value. The number of rows changed will be  Update all occurrences of a specific field value to a new value. The number of rows changed will be
3905  returned.  returned.
# Line 3679  Line 3979 
3979    
3980  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3981    
3982  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3983    
3984  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
3985  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 3740  Line 4040 
4040    
4041  =head3 FindColumn  =head3 FindColumn
4042    
4043  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
4044    
4045  Return the location a desired column in a data mining header line. The data  Return the location a desired column in a data mining header line. The data
4046  mining header line is a tab-separated list of column names. The column  mining header line is a tab-separated list of column names. The column
# Line 3798  Line 4098 
4098    
4099  =head3 ParseColumns  =head3 ParseColumns
4100    
4101  C<< my @columns = ERDB::ParseColumns($line); >>      my @columns = ERDB::ParseColumns($line);
4102    
4103  Convert the specified data line to a list of columns.  Convert the specified data line to a list of columns.
4104    
# Line 3832  Line 4132 
4132    
4133  =head3 _CreatePPOIndex  =head3 _CreatePPOIndex
4134    
4135  C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>      my $index = ERDB::_CreatePPOIndex($indexObject);
4136    
4137  Convert the XML for an ERDB index to the XML structure for a PPO  Convert the XML for an ERDB index to the XML structure for a PPO
4138  index.  index.
4139    
4140  =over 4  =over 4
4141    
4142    =item indexObject
4143    
4144  ERDB XML structure for an index.  ERDB XML structure for an index.
4145    
4146  =item RETURN  =item RETURN
# Line 3863  Line 4165 
4165    
4166  =head3 _CreatePPOField  =head3 _CreatePPOField
4167    
4168  C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>      my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
4169    
4170  Convert the ERDB XML structure for a field to a PPO scalar XML structure.  Convert the ERDB XML structure for a field to a PPO scalar XML structure.
4171    
# Line 3900  Line 4202 
4202    
4203  =head3 CleanKeywords  =head3 CleanKeywords
4204    
4205  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>      my $cleanedString = $erdb->CleanKeywords($searchExpression);
4206    
4207  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
4208  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 3937  Line 4239 
4239    
4240  =head3 GetSourceObject  =head3 GetSourceObject
4241    
4242  C<< my $source = $erdb->GetSourceObject($entityName); >>      my $source = $erdb->GetSourceObject($entityName);
4243    
4244  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
4245  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 3947  Line 4249 
4249    
4250  =head3 _RelationMap  =head3 _RelationMap
4251    
4252  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>      my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
4253    
4254  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
4255  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
# Line 4260  Line 4562 
4562  sub _GetStatementHandle {  sub _GetStatementHandle {
4563      # Get the parameters.      # Get the parameters.
4564      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4565        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4566      # Trace the query.      # Trace the query.
4567      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4568      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 4497  Line 4800 
4800      # be a null string.      # be a null string.
4801      if ($fileName ne "") {      if ($fileName ne "") {
4802          # Load the relation from the file.          # Load the relation from the file.
4803          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4804      } elsif ($rebuild) {      } elsif ($rebuild) {
4805          # Here we are rebuilding, but no file exists, so we just re-create the table.          # Here we are rebuilding, but no file exists, so we just re-create the table.
4806          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 4509  Line 4812 
4812    
4813  =head3 _LoadMetaData  =head3 _LoadMetaData
4814    
4815  C<< my $metadata = ERDB::_LoadMetaData($filename); >>      my $metadata = ERDB::_LoadMetaData($filename);
4816    
4817  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.
4818  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
# Line 4867  Line 5170 
5170    
5171  =head3 _ProcessIndexes  =head3 _ProcessIndexes
5172    
5173  C<< ERDB::_ProcessIndexes($indexList, $relation); >>      ERDB::_ProcessIndexes($indexList, $relation);
5174    
5175  Build the data structures for the specified indexes in the specified relation.  Build the data structures for the specified indexes in the specified relation.
5176    
# Line 5244  Line 5547 
5547      return $retVal;      return $retVal;
5548  }  }
5549    
5550  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5551    
5552  =head3 _ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5553    
# Line 5276  Line 5579 
5579      # Get the parameters.      # Get the parameters.
5580      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5581      # Format the relationship sentence.      # Format the relationship sentence.
5582      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5583      # Compute the arity.      # Compute the arity.
5584      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5585      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 5321  Line 5624 
5624      return $result;      return $result;
5625  }  }
5626    
5627    =head3 _WikiRelationTable
5628    
5629    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5630    table with three columns-- the field name, the field type, and the field description.
5631    
5632    This is a static method.
5633    
5634    =over 4
5635    
5636    =item relationName
5637    
5638    Name of the relation being formatted.
5639    
5640    =item relationData
5641    
5642    Hash containing the relation's fields and indexes.
5643    
5644    =item RETURN
5645    
5646    Returns a Wiki string that can be used to display the relation name and all of its fields.
5647    
5648    =back
5649    
5650    =cut
5651    
5652    sub _WikiRelationTable {
5653        # Get the parameters.
5654        my ($relationName, $relationData) = @_;
5655        # We'll create a list of lists in here, then call WikiTools::Table to
5656        # convert it into a table.
5657        my @rows = ();
5658        # Push in the header row.
5659        push @rows, [qw(Field Type Description)];
5660        # Loop through the fields.
5661        for my $field (@{$relationData->{Fields}}) {
5662            # Create this field's row. We always have a name and type.
5663            my @row = ($field->{name}, $field->{type});
5664            # If we have a description, add it as the third column.
5665            if (exists $field->{Notes}) {
5666                push @row, WikiNote($field->{Notes}->{content});
5667            }
5668            # Push this row onto the table list.
5669            push @rows, \@row;
5670        }
5671        # Store the rows as a Wiki table with a level-4 heading.
5672        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5673                          WikiTools::Table(@rows));
5674        # Now we show the relation's indexes. These are formatted as another
5675        # table.
5676        @rows = ();
5677        # Push in the header row.
5678        push @rows, [qw(Index Unique Fields Notes)];
5679        # Get the index hash.
5680        my $indexTable = $relationData->{Indexes};
5681        # Loop through the indexes. For an entity, there is always at least one index.
5682        # For a relationship, there are at least two. The upshot is we don't need to
5683        # worry about accidentally generating a frivolous table here.
5684        for my $indexName (sort keys %$indexTable) {
5685            my $indexData = $indexTable->{$indexName};
5686            # Determine whether or not the index is unique.
5687            my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
5688                          "yes" : "");
5689            # Get the field list.
5690            my $fields = join(', ', @{$indexData->{IndexFields}});
5691            # Get the note text.
5692            my $description = "";
5693            if (my $note = $indexData->{Notes}) {
5694                $description = WikiNote($note->{content});
5695            }
5696            # Format this row.
5697            my @row = ($indexName, $unique, $fields, $description);
5698            push @rows, \@row;
5699        }
5700        # Add the index list to the result.
5701        $retVal .= "\n\n" . WikiTools::Table(@rows);
5702    }
5703    
5704  =head3 _ShowRelationTable  =head3 _ShowRelationTable
5705    
5706  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
# Line 5494  Line 5874 
5874      return $htmlString;      return $htmlString;
5875  }  }
5876    
5877    =head3 _ObjectNotes
5878    
5879        my @noteParagraphs = _ObjectNotes($objectData);
5880    
5881    Return a list of the notes and asides for an entity or relationship in
5882    Wiki format.
5883    
5884    =over 4
5885    
5886    =item objectData
5887    
5888    The metadata for the desired entity or relationship.
5889    
5890    =item RETURN
5891    
5892    Returns a list of text paragraphs in Wiki markup form.
5893    
5894    =back
5895    
5896    =cut
5897    
5898    sub _ObjectNotes {
5899        # Get the parameters.
5900        my ($objectData) = @_;
5901        # Declare the return variable.
5902        my @retVal;
5903        # Loop through the types of notes.
5904        for my $noteType (qw(Notes Asides)) {
5905            my $text = $objectData->{$noteType};
5906            if ($text) {
5907                push @retVal, "", WikiNote($text->{content});
5908            }
5909        }
5910        # Return the result.
5911        return @retVal;
5912    }
5913    
5914  1;  1;

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