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revision 1.92, Mon Jun 11 18:51:23 2007 UTC revision 1.99, Fri Jul 11 01:04:08 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 960  Line 1076 
1076      my $estimation = undef;      my $estimation = undef;
1077      if ($estimatedRows) {      if ($estimatedRows) {
1078          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1079            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1080      }      }
1081      # Create the table.      # Create the table.
1082      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
# Line 974  Line 1091 
1091    
1092  =head3 VerifyFields  =head3 VerifyFields
1093    
1094  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
1095    
1096  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
1097  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 1146 
1146    
1147  =head3 DigestFields  =head3 DigestFields
1148    
1149  C<< $erdb->DigestFields($relName, $fieldList); >>      $erdb->DigestFields($relName, $fieldList);
1150    
1151  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
1152  specified relation.  specified relation.
# Line 1069  Line 1186 
1186    
1187  =head3 DigestKey  =head3 DigestKey
1188    
1189  C<< my $digested = $erdb->DigestKey($keyValue); >>      my $digested = $erdb->DigestKey($keyValue);
1190    
1191  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
1192  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 1219 
1219    
1220  =head3 CreateIndex  =head3 CreateIndex
1221    
1222  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1223    
1224  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
1225  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 1275 
1275    
1276  =head3 GetSecondaryFields  =head3 GetSecondaryFields
1277    
1278  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>      my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1279    
1280  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
1281  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 1316 
1316    
1317  =head3 GetFieldRelationName  =head3 GetFieldRelationName
1318    
1319  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>      my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1320    
1321  Return the name of the relation containing a specified field.  Return the name of the relation containing a specified field.
1322    
# Line 1240  Line 1357 
1357    
1358  =head3 DeleteValue  =head3 DeleteValue
1359    
1360  C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>      my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1361    
1362  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
1363  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 1440 
1440    
1441  =head3 LoadTables  =head3 LoadTables
1442    
1443  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>      my $stats = $erdb->LoadTables($directoryName, $rebuild);
1444    
1445  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
1446  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 1500 
1500    
1501  =head3 GetTableNames  =head3 GetTableNames
1502    
1503  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1504    
1505  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1506    
# Line 1400  Line 1517 
1517    
1518  =head3 GetEntityTypes  =head3 GetEntityTypes
1519    
1520  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1521    
1522  Return a list of the entity type names.  Return a list of the entity type names.
1523    
# Line 1417  Line 1534 
1534    
1535  =head3 GetDataTypes  =head3 GetDataTypes
1536    
1537  C<< my %types = ERDB::GetDataTypes(); >>      my %types = ERDB::GetDataTypes();
1538    
1539  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.
1540  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 1553 
1553    
1554  =head3 IsEntity  =head3 IsEntity
1555    
1556  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1557    
1558  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1559    
# Line 1463  Line 1580 
1580    
1581  =head3 Get  =head3 Get
1582    
1583  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1584    
1585  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.
1586  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 1588 
1588  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
1589  $genus.  $genus.
1590    
1591  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1592    
1593  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
1594  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1595    
1596  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1597    
1598  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
1599  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 1488  Line 1605 
1605  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
1606  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,
1607    
1608  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1609    
1610  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
1611  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 1641 
1641  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
1642  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1643    
1644  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1645    
1646  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
1647  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 1654 
1654  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
1655  a positive number. So, for example  a positive number. So, for example
1656    
1657  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>      "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1658    
1659  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
1660  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
1661  use  use
1662    
1663  C<< "LIMIT 10" >>      "LIMIT 10"
1664    
1665  =item params  =item params
1666    
# Line 1564  Line 1681 
1681      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1682          $self->_SetupSQL($objectNames, $filterClause);          $self->_SetupSQL($objectNames, $filterClause);
1683      # Create the query.      # Create the query.
1684      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1685          ".* $suffix";          ".* $suffix";
1686      my $sth = $self->_GetStatementHandle($command, $params);      my $sth = $self->_GetStatementHandle($command, $params);
1687      # 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 1699 
1699    
1700  =head3 Search  =head3 Search
1701    
1702  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>      my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1703    
1704  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
1705  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 1782 
1782              $self->_SetupSQL($objectNames, $filterClause, $matchClause);              $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1783          # 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
1784          # the select fields.          # the select fields.
1785          my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .          my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1786              ".* $suffix";              ".* $suffix";
1787          my $sth = $self->_GetStatementHandle($command, \@myParams);          my $sth = $self->_GetStatementHandle($command, \@myParams);
1788          # 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 1796 
1796    
1797  =head3 GetFlat  =head3 GetFlat
1798    
1799  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>      my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1800    
1801  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
1802  returns a single flattened list.  returns a single flattened list.
# Line 1732  Line 1849 
1849    
1850  =head3 SpecialFields  =head3 SpecialFields
1851    
1852  C<< my %specials = $erdb->SpecialFields($entityName); >>      my %specials = $erdb->SpecialFields($entityName);
1853    
1854  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
1855  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 1891 
1891    
1892  =head3 Delete  =head3 Delete
1893    
1894  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1895    
1896  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
1897  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 2076 
2076    
2077  =head3 Disconnect  =head3 Disconnect
2078    
2079  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>      $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2080    
2081  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
2082  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 2115 
2115          # Loop through the ends of the relationship.          # Loop through the ends of the relationship.
2116          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
2117              if ($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);  
2118                  $found = 1;                  $found = 1;
2119                    # Here we want to delete all relationship instances on this side of the
2120                    # entity instance.
2121                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2122                    # We do this delete in batches to keep it from dragging down the
2123                    # server.
2124                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2125                    my $done = 0;
2126                    while (! $done) {
2127                        # Do the delete.
2128                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2129                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2130                        $done = ($rows == 0 || ! $limitClause);
2131                    }
2132              }              }
2133          }          }
2134          # Insure we found the entity on at least one end.          # Insure we found the entity on at least one end.
# Line 2013  Line 2140 
2140    
2141  =head3 DeleteRow  =head3 DeleteRow
2142    
2143  C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>      $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2144    
2145  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
2146  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 2195 
2195    
2196  =head3 DeleteLike  =head3 DeleteLike
2197    
2198  C<< my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms); >>      my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2199    
2200  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
2201  filter, only fields from the relationship itself can be used.  filter, only fields from the relationship itself can be used.
# Line 2133  Line 2260 
2260    
2261  =head3 SortNeeded  =head3 SortNeeded
2262    
2263  C<< my $parms = $erdb->SortNeeded($relationName); >>      my $parms = $erdb->SortNeeded($relationName);
2264    
2265  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
2266  relation when creating the load file.  relation when creating the load file.
# Line 2231  Line 2358 
2358    
2359  =head3 GetList  =head3 GetList
2360    
2361  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>      my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2362    
2363  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
2364  specified filter clause.  specified filter clause.
# Line 2259  Line 2386 
2386  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
2387  particular genus and sorts them by species name.  particular genus and sorts them by species name.
2388    
2389  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
2390    
2391  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
2392  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 2421 
2421    
2422  =head3 GetCount  =head3 GetCount
2423    
2424  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2425    
2426  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
2427  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 2514 
2514    
2515  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
2516    
2517  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $sentence = $erdb->ComputeObjectSentence($objectName);
2518    
2519  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.
2520    
# Line 2422  Line 2549 
2549    
2550  =head3 DumpRelations  =head3 DumpRelations
2551    
2552  C<< $erdb->DumpRelations($outputDirectory); >>      $erdb->DumpRelations($outputDirectory);
2553    
2554  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.
2555  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 2591 
2591    
2592  =head3 InsertValue  =head3 InsertValue
2593    
2594  C<< $erdb->InsertValue($entityID, $fieldName, $value); >>      $erdb->InsertValue($entityID, $fieldName, $value);
2595    
2596  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
2597  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 2654 
2654    
2655  =head3 InsertObject  =head3 InsertObject
2656    
2657  C<< $erdb->InsertObject($objectType, \%fieldHash); >>      $erdb->InsertObject($objectType, \%fieldHash);
2658    
2659  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
2660  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 2663 
2663  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
2664  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2665    
2666  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']});
2667    
2668  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
2669  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>.
2670    
2671  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'});
2672    
2673  =over 4  =over 4
2674    
# Line 2664  Line 2791 
2791    
2792  =head3 UpdateEntity  =head3 UpdateEntity
2793    
2794  C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>      $erdb->UpdateEntity($entityName, $id, \%fields);
2795    
2796  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
2797  done if the database resides on a database server.  done if the database resides on a database server.
# Line 2722  Line 2849 
2849    
2850  =head3 LoadTable  =head3 LoadTable
2851    
2852  C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      my $results = $erdb->LoadTable($fileName, $relationName, %options);
2853    
2854  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2855  first.  first.
# Line 2737  Line 2864 
2864    
2865  Name of the relation to be loaded. This is the same as the table name.  Name of the relation to be loaded. This is the same as the table name.
2866    
2867  =item truncateFlag  =item options
2868    
2869  TRUE if the table should be dropped and re-created, else FALSE  A hash of load options.
2870    
2871  =item RETURN  =item RETURN
2872    
# Line 2747  Line 2874 
2874    
2875  =back  =back
2876    
2877    The permissible options are as follows.
2878    
2879    =over 4
2880    
2881    =item truncate
2882    
2883    If TRUE, then the table will be erased before loading.
2884    
2885    =item mode
2886    
2887    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2888    This option is only applicable to a MySQL database.
2889    
2890    =item partial
2891    
2892    If TRUE, then it is assumed that this is a partial load, and the table will not
2893    be analyzed and compacted at the end.
2894    
2895    =back
2896    
2897  =cut  =cut
2898  sub LoadTable {  sub LoadTable {
2899      # Get the parameters.      # Get the parameters.
2900      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $fileName, $relationName, %options) = @_;
2901      # Create the statistical return object.      # Create the statistical return object.
2902      my $retVal = _GetLoadStats();      my $retVal = _GetLoadStats();
2903      # Trace the fact of the load.      # Trace the fact of the load.
# Line 2762  Line 2909 
2909      # Get the relation data.      # Get the relation data.
2910      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
2911      # Check the truncation flag.      # Check the truncation flag.
2912      if ($truncateFlag) {      if ($options{truncate}) {
2913          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2914          # 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,
2915          # 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
2916          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2917          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2918          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2919          my $estimate = $fileSize * 1.5 / $rowSize;          my $estimate = $fileSize * 8 / $rowSize;
2920          if ($estimate < 1000) {          if ($estimate < 1000) {
2921              $estimate = 1000;              $estimate = 1000;
2922          }          }
# Line 2788  Line 2935 
2935      # Load the table.      # Load the table.
2936      my $rv;      my $rv;
2937      eval {      eval {
2938          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
2939      };      };
2940      if (!defined $rv) {      if (!defined $rv) {
2941          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
# Line 2799  Line 2946 
2946          $retVal->Add("tables");          $retVal->Add("tables");
2947          my $size = -s $fileName;          my $size = -s $fileName;
2948          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
2949            $retVal->Add("bytes", $size);
2950          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
2951          if ($truncateFlag) {          if ($options{truncate}) {
2952              # Indexes are created here for PostGres. For PostGres, indexes are              # Indexes are created here for PostGres. For PostGres, indexes are
2953              # best built at the end. For MySQL, the reverse is true.              # best built at the end. For MySQL, the reverse is true.
2954              if (! $dbh->{_preIndex}) {              if (! $dbh->{_preIndex}) {
# Line 2821  Line 2969 
2969          }          }
2970      }      }
2971      # Analyze the table to improve performance.      # Analyze the table to improve performance.
2972        if (! $options{partial}) {
2973      Trace("Analyzing and compacting $relationName.") if T(3);      Trace("Analyzing and compacting $relationName.") if T(3);
2974      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
2975        }
2976      Trace("$relationName load completed.") if T(3);      Trace("$relationName load completed.") if T(3);
2977      # Return the statistics.      # Return the statistics.
2978      return $retVal;      return $retVal;
# Line 2830  Line 2980 
2980    
2981  =head3 CreateSearchIndex  =head3 CreateSearchIndex
2982    
2983  C<< $erdb->CreateSearchIndex($objectName); >>      $erdb->CreateSearchIndex($objectName);
2984    
2985  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
2986  if one is required, rebuild it.  if one is required, rebuild it.
# Line 2867  Line 3017 
3017    
3018  =head3 DropRelation  =head3 DropRelation
3019    
3020  C<< $erdb->DropRelation($relationName); >>      $erdb->DropRelation($relationName);
3021    
3022  Physically drop a relation from the database.  Physically drop a relation from the database.
3023    
# Line 2895  Line 3045 
3045    
3046  =head3 MatchSqlPattern  =head3 MatchSqlPattern
3047    
3048  C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>      my $matched = ERDB::MatchSqlPattern($value, $pattern);
3049    
3050  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
3051  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 3128 
3128    
3129  =head3 GetEntity  =head3 GetEntity
3130    
3131  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $entityObject = $erdb->GetEntity($entityType, $ID);
3132    
3133  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
3134    
# Line 3014  Line 3164 
3164    
3165  =head3 GetChoices  =head3 GetChoices
3166    
3167  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>      my @values = $erdb->GetChoices($entityName, $fieldName);
3168    
3169  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
3170  specified entity.  specified entity.
# Line 3069  Line 3219 
3219    
3220  =head3 GetEntityValues  =head3 GetEntityValues
3221    
3222  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3223    
3224  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
3225  does not exist, an empty list is returned.  does not exist, an empty list is returned.
# Line 3113  Line 3263 
3263    
3264  =head3 GetAll  =head3 GetAll
3265    
3266  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3267    
3268  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
3269  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 3279 
3279  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
3280  feature ID followed by all of its essentiality determinations.  feature ID followed by all of its essentiality determinations.
3281    
3282  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)']);
3283    
3284  =over 4  =over 4
3285    
# Line 3207  Line 3357 
3357    
3358  =head3 Exists  =head3 Exists
3359    
3360  C<< my $found = $sprout->Exists($entityName, $entityID); >>      my $found = $sprout->Exists($entityName, $entityID);
3361    
3362  Return TRUE if an entity exists, else FALSE.  Return TRUE if an entity exists, else FALSE.
3363    
# Line 3242  Line 3392 
3392    
3393  =head3 EstimateRowSize  =head3 EstimateRowSize
3394    
3395  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>      my $rowSize = $erdb->EstimateRowSize($relName);
3396    
3397  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
3398  up the average length for each data type.  up the average length for each data type.
# Line 3280  Line 3430 
3430    
3431  =head3 GetFieldTable  =head3 GetFieldTable
3432    
3433  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>      my $fieldHash = $self->GetFieldTable($objectnName);
3434    
3435  Get the field structure for a specified entity or relationship.  Get the field structure for a specified entity or relationship.
3436    
# Line 3309  Line 3459 
3459    
3460  =head3 SplitKeywords  =head3 SplitKeywords
3461    
3462  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>      my @keywords = ERDB::SplitKeywords($keywordString);
3463    
3464  This method returns a list of the positive keywords in the specified  This method returns a list of the positive keywords in the specified
3465  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 3508 
3508    
3509  =head3 ValidateFieldName  =head3 ValidateFieldName
3510    
3511  C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>      my $okFlag = ERDB::ValidateFieldName($fieldName);
3512    
3513  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
3514  be hyphenated words subject to certain restrictions.  be hyphenated words subject to certain restrictions.
# Line 3413  Line 3563 
3563    
3564  =head3 ReadMetaXML  =head3 ReadMetaXML
3565    
3566  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>      my $rawMetaData = ERDB::ReadDBD($fileName);
3567    
3568  This method reads a raw database definition XML file and returns it.  This method reads a raw database definition XML file and returns it.
3569  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 3596 
3596    
3597  =head3 GetEntityFieldHash  =head3 GetEntityFieldHash
3598    
3599  C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>      my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3600    
3601  Get the field hash of the named entity in the specified raw XML structure.  Get the field hash of the named entity in the specified raw XML structure.
3602  The field hash may not exist, in which case we need to create it.  The field hash may not exist, in which case we need to create it.
# Line 3488  Line 3638 
3638    
3639  =head3 WriteMetaXML  =head3 WriteMetaXML
3640    
3641  C<< ERDB::WriteMetaXML($structure, $fileName); >>      ERDB::WriteMetaXML($structure, $fileName);
3642    
3643  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
3644  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 3677 
3677  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
3678  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.  example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3679    
3680  C<< my $realHtml = ERDB::HTMLNote($dataString); >>      my $realHtml = ERDB::HTMLNote($dataString);
3681    
3682  =over 4  =over 4
3683    
# Line 3557  Line 3707 
3707      return $retVal;      return $retVal;
3708  }  }
3709    
3710    =head3 WikiNote
3711    
3712    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3713    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3714    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3715    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3716    
3717        my $wikiText = ERDB::WikiNote($dataString);
3718    
3719    =over 4
3720    
3721    =item dataString
3722    
3723    String to convert to Wiki text.
3724    
3725    =item RETURN
3726    
3727    An Wiki text string derived from the input string.
3728    
3729    =back
3730    
3731    =cut
3732    
3733    sub WikiNote {
3734        # Get the parameter.
3735        my ($dataString) = @_;
3736        # HTML-escape the text.
3737        my $retVal = CGI::escapeHTML($dataString);
3738        # Substitute the bulletin board codes.
3739        my $italic = WikiTools::ItalicCode();
3740        $retVal =~ s/\[\/?i\]/$italic/g;
3741        my $bold = WikiTools::BoldCode();
3742        $retVal =~ s/\[\/?b\]/$bold/g;
3743        # Paragraph breaks are the same no matter which Wiki you're using.
3744        $retVal =~ s!\[p\]!\n\n!g;
3745        # Now we do the links, which are complicated by the need to know two
3746        # things: the target URL and the text.
3747        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3748            # Replace the matched string with the Wiki markup for links. Note that
3749            # $-[0] is the starting position of the match for the entire expression,
3750            # and $+[0] is past the ending position.
3751            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3752        }
3753        # Return the result.
3754        return $retVal;
3755    }
3756    
3757  =head3 BeginTran  =head3 BeginTran
3758    
3759  C<< $erdb->BeginTran(); >>      $erdb->BeginTran();
3760    
3761  Start a database transaction.  Start a database transaction.
3762    
# Line 3573  Line 3770 
3770    
3771  =head3 CommitTran  =head3 CommitTran
3772    
3773  C<< $erdb->CommitTran(); >>      $erdb->CommitTran();
3774    
3775  Commit an active database transaction.  Commit an active database transaction.
3776    
# Line 3586  Line 3783 
3783    
3784  =head3 RollbackTran  =head3 RollbackTran
3785    
3786  C<< $erdb->RollbackTran(); >>      $erdb->RollbackTran();
3787    
3788  Roll back an active database transaction.  Roll back an active database transaction.
3789    
# Line 3599  Line 3796 
3796    
3797  =head3 UpdateField  =head3 UpdateField
3798    
3799  C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>      my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3800    
3801  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
3802  returned.  returned.
# Line 3679  Line 3876 
3876    
3877  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3878    
3879  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3880    
3881  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
3882  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 3937 
3937    
3938  =head3 FindColumn  =head3 FindColumn
3939    
3940  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
3941    
3942  Return the location a desired column in a data mining header line. The data  Return the location a desired column in a data mining header line. The data
3943  mining header line is a tab-separated list of column names. The column  mining header line is a tab-separated list of column names. The column
# Line 3798  Line 3995 
3995    
3996  =head3 ParseColumns  =head3 ParseColumns
3997    
3998  C<< my @columns = ERDB::ParseColumns($line); >>      my @columns = ERDB::ParseColumns($line);
3999    
4000  Convert the specified data line to a list of columns.  Convert the specified data line to a list of columns.
4001    
# Line 3832  Line 4029 
4029    
4030  =head3 _CreatePPOIndex  =head3 _CreatePPOIndex
4031    
4032  C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>      my $index = ERDB::_CreatePPOIndex($indexObject);
4033    
4034  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
4035  index.  index.
4036    
4037  =over 4  =over 4
4038    
4039    =item indexObject
4040    
4041  ERDB XML structure for an index.  ERDB XML structure for an index.
4042    
4043  =item RETURN  =item RETURN
# Line 3863  Line 4062 
4062    
4063  =head3 _CreatePPOField  =head3 _CreatePPOField
4064    
4065  C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>      my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
4066    
4067  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.
4068    
# Line 3900  Line 4099 
4099    
4100  =head3 CleanKeywords  =head3 CleanKeywords
4101    
4102  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>      my $cleanedString = $erdb->CleanKeywords($searchExpression);
4103    
4104  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
4105  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 4136 
4136    
4137  =head3 GetSourceObject  =head3 GetSourceObject
4138    
4139  C<< my $source = $erdb->GetSourceObject($entityName); >>      my $source = $erdb->GetSourceObject($entityName);
4140    
4141  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
4142  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 4146 
4146    
4147  =head3 _RelationMap  =head3 _RelationMap
4148    
4149  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>      my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
4150    
4151  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
4152  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
# Line 4260  Line 4459 
4459  sub _GetStatementHandle {  sub _GetStatementHandle {
4460      # Get the parameters.      # Get the parameters.
4461      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4462        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4463      # Trace the query.      # Trace the query.
4464      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4465      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 4497  Line 4697 
4697      # be a null string.      # be a null string.
4698      if ($fileName ne "") {      if ($fileName ne "") {
4699          # Load the relation from the file.          # Load the relation from the file.
4700          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4701      } elsif ($rebuild) {      } elsif ($rebuild) {
4702          # 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.
4703          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 4509  Line 4709 
4709    
4710  =head3 _LoadMetaData  =head3 _LoadMetaData
4711    
4712  C<< my $metadata = ERDB::_LoadMetaData($filename); >>      my $metadata = ERDB::_LoadMetaData($filename);
4713    
4714  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.
4715  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 5067 
5067    
5068  =head3 _ProcessIndexes  =head3 _ProcessIndexes
5069    
5070  C<< ERDB::_ProcessIndexes($indexList, $relation); >>      ERDB::_ProcessIndexes($indexList, $relation);
5071    
5072  Build the data structures for the specified indexes in the specified relation.  Build the data structures for the specified indexes in the specified relation.
5073    
# Line 5244  Line 5444 
5444      return $retVal;      return $retVal;
5445  }  }
5446    
5447  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5448    
5449  =head3 _ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5450    
# Line 5276  Line 5476 
5476      # Get the parameters.      # Get the parameters.
5477      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5478      # Format the relationship sentence.      # Format the relationship sentence.
5479      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5480      # Compute the arity.      # Compute the arity.
5481      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5482      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 5321  Line 5521 
5521      return $result;      return $result;
5522  }  }
5523    
5524    =head3 _WikiRelationTable
5525    
5526    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5527    table with three columns-- the field name, the field type, and the field description.
5528    
5529    This is a static method.
5530    
5531    =over 4
5532    
5533    =item relationName
5534    
5535    Name of the relation being formatted.
5536    
5537    =item relationData
5538    
5539    Hash containing the relation's fields and indexes.
5540    
5541    =item RETURN
5542    
5543    Returns a Wiki string that can be used to display the relation name and all of its fields.
5544    
5545    =back
5546    
5547    =cut
5548    
5549    sub _WikiRelationTable {
5550        # Get the parameters.
5551        my ($relationName, $relationData) = @_;
5552        # We'll create a list of lists in here, then call WikiTools::Table to
5553        # convert it into a table.
5554        my @rows = ();
5555        # Push in the header row.
5556        push @rows, [qw(Field Type Description)];
5557        # Loop through the fields.
5558        for my $field (@{$relationData->{Fields}}) {
5559            # Create this field's row. We always have a name and type.
5560            my @row = ($field->{name}, $field->{type});
5561            # If we have a description, add it as the third column.
5562            if (exists $field->{Notes}) {
5563                push @row, WikiNote($field->{Notes}->{content});
5564            }
5565            # Push this row onto the table list.
5566            push @rows, \@row;
5567        }
5568        # Store the rows as a Wiki table with a level-4 heading.
5569        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5570                          WikiTools::Table(@rows));
5571        # Now we show the relation's indexes. These are formatted as another
5572        # table.
5573        @rows = ();
5574        # Push in the header row.
5575        push @rows, [qw(Index Unique Fields Notes)];
5576        # Get the index hash.
5577        my $indexTable = $relationData->{Indexes};
5578        # Loop through the indexes. For an entity, there is always at least one index.
5579        # For a relationship, there are at least two. The upshot is we don't need to
5580        # worry about accidentally generating a frivolous table here.
5581        for my $indexName (sort keys %$indexTable) {
5582            my $indexData = $indexTable->{$indexName};
5583            # Determine whether or not the index is unique.
5584            my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
5585                          "yes" : "");
5586            # Get the field list.
5587            my $fields = join(', ', @{$indexData->{IndexFields}});
5588            # Get the note text.
5589            my $description = "";
5590            if (my $note = $indexData->{Notes}) {
5591                $description = WikiNote($note->{content});
5592            }
5593            # Format this row.
5594            my @row = ($indexName, $unique, $fields, $description);
5595            push @rows, \@row;
5596        }
5597        # Add the index list to the result.
5598        $retVal .= "\n\n" . WikiTools::Table(@rows);
5599    }
5600    
5601  =head3 _ShowRelationTable  =head3 _ShowRelationTable
5602    
5603  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 5771 
5771      return $htmlString;      return $htmlString;
5772  }  }
5773    
5774    =head3 _ObjectNotes
5775    
5776        my @noteParagraphs = _ObjectNotes($objectData);
5777    
5778    Return a list of the notes and asides for an entity or relationship in
5779    Wiki format.
5780    
5781    =over 4
5782    
5783    =item objectData
5784    
5785    The metadata for the desired entity or relationship.
5786    
5787    =item RETURN
5788    
5789    Returns a list of text paragraphs in Wiki markup form.
5790    
5791    =back
5792    
5793    =cut
5794    
5795    sub _ObjectNotes {
5796        # Get the parameters.
5797        my ($objectData) = @_;
5798        # Declare the return variable.
5799        my @retVal;
5800        # Loop through the types of notes.
5801        for my $noteType (qw(Notes Asides)) {
5802            my $text = $objectData->{$noteType};
5803            if ($text) {
5804                push @retVal, "", WikiNote($text->{content});
5805            }
5806        }
5807        # Return the result.
5808        return @retVal;
5809    }
5810    
5811  1;  1;

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