Diff of /Sprout/ERDB.pm

-revision 1.48, Wed Jun 21 03:12:20 2006 UTC
+revision 1.95, Wed Jan 23 00:56:31 2008 UTC
 Line 6
      use Data::Dumper;
      use XML::Simple;
      use DBQuery;
-     use DBObject;
+     use ERDBObject;
      use Stats;
      use Time::HiRes qw(gettimeofday);
      use Digest::MD5 qw(md5_base64);
-     use FIG;
+     use CGI;
+ #    use WikiTools;  ## HACK
  =head1 Entity-Relationship Database Package
-Line 59
+Line 60
  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
- The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to
+ The database itself is described by an XML file. In addition to all the data required to define
- all the data required to define the entities, relationships, and attributes, the schema provides
+ the entities, relationships, and attributes, the schema provides space for notes describing
- space for notes describing the data and what it means. These notes are used by L</ShowMetaData>
+ the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
- to generate documentation for the database.
+ for the database.
+ Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
+ in which case it will be used to generate a text search index in which the user searches for words
+ in the field instead of a particular field value.
  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
  was inserted by the L</InsertObject> method.
- To facilitate testing, the ERDB module supports automatic generation of test data. This process
- is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet
- fully implemented.
  =head2 XML Database Description
  =head3 Data Types
-Line 91
+Line 92
 -bit signed integer
+ =item counter
+-bit unsigned integer
  =item date
 -bit unsigned integer, representing a PERL date/time value
-Line 186
+Line 191
  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
  and the first character should be a letter. Most underlying databases are case-insensitive
- with the respect to field names, so a best practice is to use lower-case letters only.
+ with the respect to field names, so a best practice is to use lower-case letters only. Finally,
+ the name C<search-relevance> has special meaning for full-text searches and should not be
+ used as a field name.
  =item type
-Line 205
+Line 212
  entity, the fields without a relation attribute are said to belong to the
  I<primary relation>. This relation has the same name as the entity itself.
+ =item searchable
+ If specified, then the field is a candidate for full-text searching. A single full-text
+ index will be created for each relation with at least one searchable field in it.
+ For best results, this option should only be used for string or text fields.
+ =item special
+ This attribute allows the subclass to assign special meaning for certain fields.
+ The interpretation is up to the subclass itself. Currently, only entity fields
+ can have this attribute.
  =back
  =head3 Indexes
- An entity can have multiple alternate indexes associated with it. The fields must
+ An entity can have multiple alternate indexes associated with it. The fields in an
- be from the primary relation. The alternate indexes assist in ordering results
+ index must all be from the same relation. The alternate indexes assist in searching
- from a query. A relationship can have up to two indexes-- a I<to-index> and a
+ on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
- I<from-index>. These order the results when crossing the relationship. For
+ I<from-index> that order the results when crossing the relationship. For
  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
  from-index would order the contigs of a ganome, and the to-index would order
- the genomes of a contig. A relationship's index must specify only fields in
+ the genomes of a contig. In addition, it can have zero or more alternate
+ indexes. A relationship's index must specify only fields in
  the relationship.
- The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
+ The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
- of a relationship is specified using the B<FromIndex> tag; the to-index is specified
+ The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
- using the B<ToIndex> tag.
+ specified using the B<ToIndex> tag.
  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
  tag containing the B<IndexField> tags. These specify, in order, the fields used in
-Line 238
+Line 258
  =back
- The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
+ The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
+ have a B<Unique> attribute. If specified, the index will be generated as a unique
+ index.
  =head3 Object and Field Names
-Line 282
+Line 304
  A relationship is described by the C<Relationship> tag. Within a relationship,
  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
- fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
+ fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
- the to-index.
+ the to-index, and an C<Indexes> tag containing the alternate indexes.
  The C<Relationship> tag has the following attributes.
-Line 316
+Line 338
  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
- # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation
+ # of the specified type. "avgLen" is the average byte length for estimating
- # string is specified in the field definition. "avgLen" is the average byte length for estimating
+ # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
- # record sizes.
+ # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
- my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },
+ # index
-                   int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },
+ my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
-                   string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },
+                                indexMod =>   0, notes => "single ASCII character"},
-                   text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },
+                   int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
-                   date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
+                                indexMod =>   0, notes => "signed 32-bit integer"},
-                   float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },
+                   counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
-                   boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },
+                                indexMod =>   0, notes => "unsigned 32-bit integer"},
+                   string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 255 characters"},
+                   text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
+                                indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
+                   date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
+                                indexMod =>   0, notes => "signed, 64-bit integer"},
+                   float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
+                                indexMod =>   0, notes => "64-bit double precision floating-point number"},
+                   boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
+                                indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
                   'hash-string' =>
-                              { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },
+                              { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
+                                indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
                   'id-string' =>
-                              { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, dataGen => "SringGen(22)" },
+                              { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 25 characters"},
                   'key-string' =>
-                              { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },
+                              { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 40 characters"},
                   'name-string' =>
-                              { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },
+                              { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 80 characters"},
                   'medium-string' =>
-                              { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },
+                              { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 160 characters"},
+                  'long-string' =>
+                              { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
+                                indexMod =>   0, notes => "character string, 0 to 500 characters"},
                  );
  # Table translating arities into natural language.
-Line 344
+Line 384
                     'MM' => 'many-to-many'
                   );
- # Table for interpreting string patterns.
+ # Options for XML input and output.
+ my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
+                                   Entities => 'Entity',
+                                   Fields => 'Field',
+                                   Indexes => 'Index',
+                                   IndexFields => 'IndexField'
+                                 },
+                   KeyAttr =>    { Relationship => 'name',
+                                   Entity => 'name',
+                                   Field => 'name'
+                                 },
+                   SuppressEmpty => 1,
+                  );
- my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",
+ my %XmlInOpts  = (
-                      '9' => "0123456789",
+                   ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
-                      'X' => "abcdefghijklmnopqrstuvwxyz0123456789",
+                   ForceContent => 1,
-                      'V' => "aeiou",
+                   NormalizeSpace => 2,
-                      'K' => "bcdfghjklmnoprstvwxyz"
+                  );
+ my %XmlOutOpts = (
+                   RootName => 'Database',
+                   XMLDecl => 1,
                     );
  =head2 Public Methods
  =head3 new
- C<< my $database = ERDB->new($dbh, $metaFileName); >>
+     my $database = ERDB->new($dbh, $metaFileName);
  Create a new ERDB object.
-Line 377
+Line 434
  sub new {
      # Get the parameters.
-     my ($class, $dbh, $metaFileName, $options) = @_;
+     my ($class, $dbh, $metaFileName, %options) = @_;
      # Load the meta-data.
      my $metaData = _LoadMetaData($metaFileName);
      # Create the object.
-Line 391
+Line 448
  =head3 ShowMetaData
- C<< $erdb->ShowMetaData($fileName); >>
+     $erdb->ShowMetaData($fileName);
  This method outputs a description of the database. This description can be used to help users create
  the data to be loaded into the relations.
-Line 432
+Line 489
  =head3 DisplayMetaData
- C<< my $html = $erdb->DisplayMetaData(); >>
+     my $html = $erdb->DisplayMetaData();
  Return an HTML description of the database. This description can be used to help users create
  the data to be loaded into the relations and form queries. The output is raw includable HTML
-Line 493
+Line 550
          my $entityData = $entityList->{$key};
          # If there's descriptive text, display it.
          if (my $notes = $entityData->{Notes}) {
-             $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
+             $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
          }
-         # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
+         # See if we need a list of the entity's relationships.
+         my $relCount = keys %{$relationshipList};
+         if ($relCount > 0) {
+             # First, we set up the relationship subsection.
          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
          # Loop through the relationships.
          for my $relationship (sort keys %{$relationshipList}) {
-Line 511
+Line 571
          }
          # Close off the relationship list.
          $retVal .= "</ul>\n";
+         }
          # Get the entity's relations.
          my $relationList = $entityData->{Relations};
          # Create a header for the relation subsection.
-Line 550
+Line 611
          $retVal .= "</p>\n";
          # If there are notes on this relationship, display them.
          if (my $notes = $relationshipStructure->{Notes}) {
-             $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
+             $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
          }
          # Generate the relationship's relation table.
          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
-Line 584
+Line 645
  =head3 DumpMetaData
- C<< $erdb->DumpMetaData(); >>
+     $erdb->DumpMetaData();
  Return a dump of the metadata structure.
-Line 597
+Line 658
      return Data::Dumper::Dumper($self->{_metaData});
  }
+ =head3 GenerateWikiData
+     my @wikiLines = $erdb->GenerateWikiData();
+ Build a description of the database for the wiki. The database will be
+ organized into a single page, with sections for each entity and relationship.
+ The return value is a list of text lines.
+ =cut
+ sub GenerateWikiData {
+     # Get the parameters.
+     my ($self) = @_;
+     # We'll build the wiki text in here.
+     my @retVal = ();
+     # Get the metadata object.
+     my $metadata = $self->{_metaData};
+     # Get the title string. This will become the page name.
+     my $title = $metadata->{Title}->{content};
+     # Get the entity and relationship lists.
+     my $entityList = $metadata->{Entities};
+     my $relationshipList = $metadata->{Relationships};
+     # Start with the introductory text.
+     push @retVal, WikiTools::Heading(2, "Introduction");
+     if (my $notes = $metadata->{Notes}) {
+         push @retVal, WikiNote($notes->{content});
+     }
+     # Start the entity section.
+     push @retVal, WikiTools::Heading(2, "Entities");
+     # Loop through the entities. Note that unlike the situation with HTML, we
+     # don't need to generate the table of contents manually, just the data
+     # itself.
+     for my $key (sort keys %$entityList) {
+         # Create a header for this entity.
+         push @retVal, "", WikiTools::Heading(3, $key);
+         # Get the entity data.
+         my $entityData = $entityList->{$key};
+         # Plant the notes here, if there are any.
+         if (my $notes = $entityData->{Notes}) {
+             push @retVal, "", WikiNote($notes->{content});
+         }
+         # Get the entity's relations.
+         my $relationList = $entityData->{Relations};
+         # Loop through the relations, displaying them.
+         for my $relation (sort keys %{$relationList}) {
+             my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
+             push @retVal, $wikiString;
+         }
+         # Now we list the entity's relationships (if any). First, we build a list
+         # of the relationships relevant to this entity.
+         my @rels = ();
+         for my $rel (sort keys %$relationshipList) {
+             my $relStructure = $relationshipList->{$rel};
+             if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
+                 # Get the relationship sentence.
+                 my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
+                 # Linkify it.
+                 my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
+                 $relSentence =~ s/$rel/$linkedRel/;
+                 push @rels, $relSentence;
+             }
+         }
+         # Add the relationships as a Wiki list.
+         push @retVal, WikiTools::List(@rels);
+     }
+     # Now the entities are documented. Next we do the relationships.
+     push @retVal, WikiTools::Heading(2, "Relationships");
+     for my $key (sort keys %$relationshipList) {
+         my $relationshipData = $relationshipList->{$key};
+         # Create the relationship heading.
+         push @retVal, WikiTools::Heading(3, $key);
+         # Describe the relationship arity. Note there's a bit of trickiness involving recursive
+         # many-to-many relationships. In a normal many-to-many we use two sentences to describe
+         # the arity (one for each direction). This is a bad idea for a recursive relationship,
+         # since both sentences will say the same thing.
+         my $arity = $relationshipData->{arity};
+         my $fromEntity = $relationshipData->{from};
+         my $toEntity = $relationshipData->{to};
+         my @listElements = ();
+         my $boldCode = WikiTools::BoldCode();
+         if ($arity eq "11") {
+             push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
+         } else {
+             push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.\n";
+             if ($arity eq "MM" && $fromEntity ne $toEntity) {
+                 push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.\n";
+             }
+         }
+         push @retVal, WikiTools::List(@listElements);
+         # Plant the notes here, if there are any.
+         if (my $notes = $relationshipData->{Notes}) {
+             push @retVal, "", WikiNote($notes->{content});
+         }
+         # Finally, the relationship table.
+         my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
+         push @retVal, $wikiString;
+     }
+     # All done. Return the lines.
+     return @retVal;
+ }
+ =head3 CreatePPO
+     ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
+ Create a PPO XML file from an ERDB data definition XML file. At the
+ current time, the PPO XML file can be used to create a database with
+ similar functionality. Eventually, the PPO will be able to use the
+ created XML to access the live ERDB database.
+ =over 4
+ =item erdbXMLFile
+ Name of the XML data definition file for the ERDB database. This
+ file must exist.
+ =item ppoXMLFile
+ Output file for the PPO XML definition. If this file exists, it
+ will be overwritten.
+ =back
+ =cut
+ sub CreatePPO {
+     # Get the parameters.
+     my ($erdbXMLFile, $ppoXMLFile) = @_;
+     # First, we want to slurp in the ERDB XML file in its raw form.
+     my $xml = ReadMetaXML($erdbXMLFile);
+     # Create a variable to hold all of the objects in the PPO project.
+     my @objects = ();
+     # Get the relationship hash.
+     my $relationships = $xml->{Relationships};
+     # Loop through the entities.
+     my $entities = $xml->{Entities};
+     for my $entityName (keys %{$entities}) {
+         # Get the entity's data structures.
+         my $entityObject = $entities->{$entityName};
+         # We put the object's fields in here, according to their type.
+         my (@object_refs, @scalars, @indexes, @arrays);
+         # Create the ID field for the entity. We get the key type from the
+         # entity object and compute the corresponding SQL type.
+         my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
+         push @scalars, { label => 'id', type => $type };
+         # Loop through the entity fields.
+         for my $fieldName ( keys %{$entityObject->{Fields}} ) {
+             # Get the field object.
+             my $fieldObject = $entityObject->{Fields}->{$fieldName};
+             # Convert it to a scalar tag.
+             my $scalar = _CreatePPOField($fieldName, $fieldObject);
+             # If we have a relation, this field is stored in an array.
+             # otherwise, it is a scalar. The array tag has scalars
+             # stored as an XML array. In ERDB, there is only ever one,
+             # but PPO can have more.
+             my $relation = $fieldObject->{relation};
+             if ($relation) {
+                 push @arrays, { scalar => [$scalar] };
+             } else {
+                 push @scalars, $scalar;
+             }
+         }
+         # Loop through the relationships. If this entity is the to-entity
+         # on a relationship of 1M arity, then it is implemented as a PPO
+         # object reference.
+         for my $relationshipName (keys %{$relationships}) {
+             # Get the relationship data.
+             my $relationshipData = $relationships->{$relationshipName};
+             # If we have a from for this entity and an arity of 1M, we
+             # have an object reference.
+             if ($relationshipData->{to} eq $entityName &&
+                 $relationshipData->{arity} eq '1M') {
+                 # Build the object reference tag.
+                 push @object_refs, { label => $relationshipName,
+                                      type => $relationshipData->{from} };
+             }
+         }
+         # Create the indexes.
+         my $indexList = $entityObject->{Indexes};
+         push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
+         # Build the object XML tree.
+         my $object = { label => $entityName,
+                        object_ref => \@object_refs,
+                        scalar => \@scalars,
+                        index => \@indexes,
+                        array => \@arrays
+                       };
+         # Push the object onto the objects list.
+         push @objects, $object;
+     }
+     # Loop through the relationships, searching for MMs. The 1Ms were
+     # already handled by the entity search above.
+     for my $relationshipName (keys %{$relationships}) {
+         # Get this relationship's object.
+         my $relationshipObject = $relationships->{$relationshipName};
+         # Only proceed if it's many-to-many.
+         if ($relationshipObject->{arity} eq 'MM') {
+             # Create the tag lists for the relationship object.
+             my (@object_refs, @scalars, @indexes);
+             # The relationship will be created as an object with object
+             # references for its links to the participating entities.
+             my %links = ( from_link => $relationshipObject->{from},
+                           to_link => $relationshipObject->{to} );
+             for my $link (keys %links) {
+                 # Create an object_ref tag for this piece of the
+                 # relationship (from or to).
+                 my $object_ref = { label => $link,
+                                    type => $links{$link} };
+                 push @object_refs, $object_ref;
+             }
+             # Loop through the intersection data fields, creating scalar tags.
+             # There are no fancy array tags in a relationship.
+             for my $fieldName (keys %{$relationshipObject->{Fields}}) {
+                 my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
+                 push @scalars, _CreatePPOField($fieldName, $fieldObject);
+             }
+             # Finally, the indexes: currently we cannot support the to-index and
+             # from-index in PPO, so we just process the alternate indexes.
+             my $indexList = $relationshipObject->{Indexes};
+             push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
+             # Wrap up all the stuff about this relationship.
+             my $object = { label => $relationshipName,
+                            scalar => \@scalars,
+                            object_ref => \@object_refs,
+                            index => \@indexes
+                          };
+             # Push it into the object list.
+             push @objects, $object;
+         }
+     }
+     # Compute a title.
+     my $title;
+     if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
+         # Here we have a standard file name we can use for a title.
+         $title = $2;
+     } else {
+         # Here the file name is non-standard, so we carve up the
+         # database title.
+         $title = $xml->{Title}->{content};
+         $title =~ s/\s\.,//g;
+     }
+     # Wrap up the XML as a project.
+     my $ppoXML = { project => { label => $title,
+                                 object => \@objects }};
+     # Write out the results.
+     my $ppoString = XML::Simple::XMLout($ppoXML,
+                                         AttrIndent => 1,
+                                         KeepRoot => 1);
+     Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
+ }
+ =head3 FindIndexForEntity
+     my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
+ This method locates the entry in an entity's index list that begins with the
+ specified attribute name. If the entity has no index list, one will be
+ created. This method works on raw XML, not a live ERDB object.
+ =over 4
+ =item xml
+ The raw XML structure defining the database.
+ =item entityName
+ The name of the relevant entity.
+ =item attributeName
+ The name of the attribute relevant to the search.
+ =item RETURN
+ The numerical index in the index list of the index entry for the specified entity and
+ attribute, or C<undef> if no such index exists.
+ =back
+ =cut
+ sub FindIndexForEntity {
+     # Get the parameters.
+     my ($xml, $entityName, $attributeName) = @_;
+     # Declare the return variable.
+     my $retVal;
+     # Get the named entity.
+     my $entityData = $xml->{Entities}->{$entityName};
+     if (! $entityData) {
+         Confess("Entity $entityName not found in DBD structure.");
+     } else {
+         # Insure it has an index list.
+         if (! exists $entityData->{Indexes}) {
+             $entityData->{Indexes} = [];
+         } else {
+             # Search for the desired index.
+             my $indexList = $entityData->{Indexes};
+             my $n = scalar @{$indexList};
+             Trace("Searching $n indexes in index list for $entityName.") if T(2);
+             # We use an indexed FOR here because we're returning an
+             # index number instead of an object. We do THAT so we can
+             # delete the index from the list if needed.
+             for (my $i = 0; $i < $n && !defined($retVal); $i++) {
+                 my $index = $indexList->[$i];
+                 my $fields = $index->{IndexFields};
+                 # Technically this IF should be safe (that is, we are guaranteed
+                 # the existence of a "$fields->[0]"), because when we load the XML
+                 # we have SuppressEmpty specified.
+                 if ($fields->[0]->{name} eq $attributeName) {
+                     $retVal = $i;
+                 }
+             }
+         }
+     }
+     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
+     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
+     # Return the result.
+     return $retVal;
+ }
  =head3 CreateTables
- C<< $erdb->CreateTables(); >>
+     $erdb->CreateTables();
  This method creates the tables for the database from the metadata structure loaded by the
  constructor. It is expected this function will only be used on rare occasions, when the
-Line 616
+Line 1000
      # Loop through the relations.
      for my $relationName (@relNames) {
          # Create a table for this relation.
-         $self->CreateTable($relationName);
+         $self->CreateTable($relationName, 1);
          Trace("Relation $relationName created.") if T(2);
      }
  }
  =head3 CreateTable
- C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
+     $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
  Create the table for a relation and optionally create its indexes.
-Line 679
+Line 1063
      my $estimation = undef;
      if ($estimatedRows) {
          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
+         Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
      }
      # Create the table.
      Trace("Creating table $relationName: $fieldThing") if T(2);
      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
      Trace("Relation $relationName created in database.") if T(2);
-     # If we want to build the indexes, we do it here.
+     # If we want to build the indexes, we do it here. Note that the full-text search
+     # index will not be built until the table has been loaded.
      if ($indexFlag) {
          $self->CreateIndex($relationName);
      }
-Line 692
+Line 1078
  =head3 VerifyFields
- C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
+     my $count = $erdb->VerifyFields($relName, \@fieldList);
  Run through the list of proposed field values, insuring that all the character fields are
  below the maximum length. If any fields are too long, they will be truncated in place.
-Line 735
+Line 1121
              my $oldString = $fieldList->[$i];
              if (length($oldString) > $maxLen) {
                  # Here it's too big, so we truncate it.
-                 Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
+                 Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
                  $fieldList->[$i] = substr $oldString, 0, $maxLen;
                  $retVal++;
              }
-Line 747
+Line 1133
  =head3 DigestFields
- C<< $erdb->DigestFields($relName, $fieldList); >>
+     $erdb->DigestFields($relName, $fieldList);
  Digest the strings in the field list that correspond to data type C<hash-string> in the
  specified relation.
-Line 787
+Line 1173
  =head3 DigestKey
- C<< my $digested = $erdb->DigestKey($keyValue); >>
+     my $digested = $erdb->DigestKey($keyValue);
  Return the digested value of a symbolic key. The digested value can then be plugged into a
  key-based search into a table with key-type hash-string.
-Line 820
+Line 1206
  =head3 CreateIndex
- C<< $erdb->CreateIndex($relationName); >>
+     $erdb->CreateIndex($relationName);
  Create the indexes for a relation. If a table is being loaded from a large source file (as
  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
-Line 841
+Line 1227
      for my $indexName (keys %{$indexHash}) {
          my $indexData = $indexHash->{$indexName};
          # Get the index's field list.
-         my @fieldList = _FixNames(@{$indexData->{IndexFields}});
+         my @rawFields = @{$indexData->{IndexFields}};
+         # Get a hash of the relation's field types.
+         my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
+         # We need to check for text fields so we can append a length limitation for them. To do
+         # that, we need the relation's field list.
+         my $relFields = $relationData->{Fields};
+         for (my $i = 0; $i <= $#rawFields; $i++) {
+             # Get the field type.
+             my $field = $rawFields[$i];
+             my $type = $types{$field};
+             # Ask if it requires using prefix notation for the index.
+             my $mod = $TypeTable{$type}->{indexMod};
+             Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
+             if ($mod) {
+                 # Append the prefix length to the field name,
+                 $rawFields[$i] .= "($mod)";
+             }
+         }
+         my @fieldList = _FixNames(@rawFields);
          my $flds = join(', ', @fieldList);
          # Get the index's uniqueness flag.
-         my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
+         my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
          # Create the index.
          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
-                                     flds => $flds, unique => $unique);
+                                     flds => $flds, kind => $unique);
          if ($rv) {
              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
          } else {
-Line 856
+Line 1260
      }
  }
+ =head3 GetSecondaryFields
+     my %fieldTuples = $erdb->GetSecondaryFields($entityName);
+ This method will return a list of the name and type of each of the secondary
+ fields for a specified entity. Secondary fields are stored in two-column tables
+ in addition to the primary entity table. This enables the field to have no value
+ or to have multiple values.
+ =over 4
+ =item entityName
+ Name of the entity whose secondary fields are desired.
+ =item RETURN
+ Returns a hash mapping the field names to their field types.
+ =back
+ =cut
+ sub GetSecondaryFields {
+     # Get the parameters.
+     my ($self, $entityName) = @_;
+     # Declare the return variable.
+     my %retVal = ();
+     # Look for the entity.
+     my $table = $self->GetFieldTable($entityName);
+     # Loop through the fields, pulling out the secondaries.
+     for my $field (sort keys %{$table}) {
+         if ($table->{$field}->{relation} ne $entityName) {
+             # Here we have a secondary field.
+             $retVal{$field} = $table->{$field}->{type};
+         }
+     }
+     # Return the result.
+     return %retVal;
+ }
+ =head3 GetFieldRelationName
+     my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
+ Return the name of the relation containing a specified field.
+ =over 4
+ =item objectName
+ Name of the entity or relationship containing the field.
+ =item fieldName
+ Name of the relevant field in that entity or relationship.
+ =item RETURN
+ Returns the name of the database relation containing the field, or C<undef> if
+ the field does not exist.
+ =back
+ =cut
+ sub GetFieldRelationName {
+     # Get the parameters.
+     my ($self, $objectName, $fieldName) = @_;
+     # Declare the return variable.
+     my $retVal;
+     # Get the object field table.
+     my $table = $self->GetFieldTable($objectName);
+     # Only proceed if the field exists.
+     if (exists $table->{$fieldName}) {
+         # Determine the name of the relation that contains this field.
+         $retVal = $table->{$fieldName}->{relation};
+     }
+     # Return the result.
+     return $retVal;
+ }
+ =head3 DeleteValue
+     my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
+ Delete secondary field values from the database. This method can be used to delete all
+ values of a specified field for a particular entity instance, or only a single value.
+ Secondary fields are stored in two-column relations separate from an entity's primary
+ table, and as a result a secondary field can legitimately have no value or multiple
+ values. Therefore, it makes sense to talk about deleting secondary fields where it
+ would not make sense for primary fields.
+ =over 4
+ =item entityName
+ Name of the entity from which the fields are to be deleted.
+ =item id
+ ID of the entity instance to be processed. If the instance is not found, this
+ method will have no effect. If C<undef> is specified, all values for all of
+ the entity instances will be deleted.
+ =item fieldName
+ Name of the field whose values are to be deleted.
+ =item fieldValue (optional)
+ Value to be deleted. If not specified, then all values of the specified field
+ will be deleted for the entity instance. If specified, then only the values which
+ match this parameter will be deleted.
+ =item RETURN
+ Returns the number of rows deleted.
+ =back
+ =cut
+ sub DeleteValue {
+     # Get the parameters.
+     my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
+     # Declare the return value.
+     my $retVal = 0;
+     # We need to set up an SQL command to do the deletion. First, we
+     # find the name of the field's relation.
+     my $table = $self->GetFieldTable($entityName);
+     my $field = $table->{$fieldName};
+     my $relation = $field->{relation};
+     # Make sure this is a secondary field.
+     if ($relation eq $entityName) {
+         Confess("Cannot delete values of $fieldName for $entityName.");
+     } else {
+         # Set up the SQL command to delete all values.
+         my $sql = "DELETE FROM $relation";
+         # Build the filter.
+         my @filters = ();
+         my @parms = ();
+         # Check for a filter by ID.
+         if (defined $id) {
+             push @filters, "id = ?";
+             push @parms, $id;
+         }
+         # Check for a filter by value.
+         if (defined $fieldValue) {
+             push @filters, "$fieldName = ?";
+             push @parms, $fieldValue;
+         }
+         # Append the filters to the command.
+         if (@filters) {
+             $sql .= " WHERE " . join(" AND ", @filters);
+         }
+         # Execute the command.
+         my $dbh = $self->{_dbh};
+         $retVal = $dbh->SQL($sql, 0, @parms);
+     }
+     # Return the result.
+     return $retVal;
+ }
  =head3 LoadTables
- C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
+     my $stats = $erdb->LoadTables($directoryName, $rebuild);
  This method will load the database tables from a directory. The tables must already have been created
  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
-Line 918
+Line 1487
  =head3 GetTableNames
- C<< my @names = $erdb->GetTableNames; >>
+     my @names = $erdb->GetTableNames;
  Return a list of the relations required to implement this database.
-Line 935
+Line 1504
  =head3 GetEntityTypes
- C<< my @names = $erdb->GetEntityTypes; >>
+     my @names = $erdb->GetEntityTypes;
  Return a list of the entity type names.
-Line 950
+Line 1519
      return sort keys %{$entityList};
  }
+ =head3 GetDataTypes
+     my %types = ERDB::GetDataTypes();
+ Return a table of ERDB data types. The table returned is a hash of hashes.
+ The keys of the big hash are the datatypes. Each smaller hash has several
+ values used to manage the data. The most interesting is the SQL type (key
+ C<sqlType>) and the descriptive node (key C<notes>).
+ Note that changing the values in the smaller hashes will seriously break
+ things, so this data should be treated as read-only.
+ =cut
+ sub GetDataTypes {
+     return %TypeTable;
+ }
  =head3 IsEntity
- C<< my $flag = $erdb->IsEntity($entityName); >>
+     my $flag = $erdb->IsEntity($entityName);
  Return TRUE if the parameter is an entity name, else FALSE.
-Line 979
+Line 1567
  =head3 Get
- C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
+     my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
  This method returns a query object for entities of a specified type using a specified filter.
  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
-Line 987
+Line 1575
  following call requests all B<Genome> objects for the genus specified in the variable
  $genus.
- C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
+     $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
  The WHERE clause contains a single question mark, so there is a single additional
  parameter representing the parameter value. It would also be possible to code
- C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
+     $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
  however, this version of the call would generate a syntax error if there were any quote
  characters inside the variable C<$genus>.
-Line 1004
+Line 1592
  It is possible to specify multiple entity and relationship names in order to retrieve more than
  one object's data at the same time, which allows highly complex joined queries. For example,
- C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
+     $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
  If multiple names are specified, then the query processor will automatically determine a
  join path between the entities and relationships. The algorithm used is very simplistic.
-Line 1040
+Line 1628
  with an ORDER BY clause. For example, the following filter string gets all genomes for a
  particular genus and sorts them by species name.
- C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
+     "Genome(genus) = ? ORDER BY Genome(species)"
  Note that the case is important. Only an uppercase "ORDER BY" with a single space will
  be processed. The idea is to make it less likely to find the verb by accident.
-Line 1053
+Line 1641
  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
  a positive number. So, for example
- C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
+     "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
  required. For example, to just get the first 10 genomes in the B<Genome> table, you could
  use
- C<< "LIMIT 10" >>
+     "LIMIT 10"
  =item params
-Line 1080
+Line 1668
      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
          $self->_SetupSQL($objectNames, $filterClause);
      # Create the query.
-     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
+     my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
          ".* $suffix";
      my $sth = $self->_GetStatementHandle($command, $params);
      # Now we create the relation map, which enables DBQuery to determine the order, name
-Line 1094
+Line 1682
      return $retVal;
  }
- =head3 GetFlat
- C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
- This is a variation of L</GetAll> that asks for only a single field per record and
+ =head3 Search
- returns a single flattened list.
+     my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
+ Perform a full text search with filtering. The search will be against a specified object
+ in the object name list. That object will get an extra field containing the search
+ relevance. Note that except for the search expression, the parameters of this method are
+ the same as those for L</Get> and follow the same rules.
  =over 4
+ =item searchExpression
+ Boolean search expression for the text fields of the target object. The default mode for
+ a Boolean search expression is OR, but we want the default to be AND, so we will
+ add a C<+> operator to each word with no other operator before it.
+ =item idx
+ Index in the I<$objectNames> list of the table to be searched in full-text mode.
  =item objectNames
  List containing the names of the entity and relationship objects to be retrieved.
  =item filterClause
- WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
+ WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
- be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
+ be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
- B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
+ specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
- parameter list as additional parameters. The fields in a filter clause can come from primary
+ in the filter clause should be added to the parameter list as additional parameters. The
- entity relations, relationship relations, or secondary entity relations; however, all of the
+ fields in a filter clause can come from primary entity relations, relationship relations,
- entities and relationships involved must be included in the list of object names.
+ or secondary entity relations; however, all of the entities and relationships involved must
+ be included in the list of object names.
- =item parameterList
- List of the parameters to be substituted in for the parameters marks in the filter clause.
- =item field
+ =item params
- Name of the field to be used to get the elements of the list returned.
+ Reference to a list of parameter values to be substituted into the filter clause.
  =item RETURN
- Returns a list of values.
+ Returns a query object for the specified search.
  =back
  =cut
- #: Return Type @;
- sub GetFlat {
+ sub Search {
      # Get the parameters.
-     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
+     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
-     # Construct the query.
+     # Declare the return variable.
-     my $query = $self->Get($objectNames, $filterClause, $parameterList);
+     my $retVal;
-     # Create the result list.
+     # Create a safety copy of the parameter list. Note we have to be careful to insure
-     my @retVal = ();
+     # a parameter list exists before we copy it.
-     # Loop through the records, adding the field values found to the result list.
+     my @myParams = ();
-     while (my $row = $query->Fetch()) {
+     if (defined $params) {
+         @myParams = @{$params};
+     }
+     # Get the first object's structure so we have access to the searchable fields.
+     my $object1Name = $objectNames->[$idx];
+     my $object1Structure = $self->_GetStructure($object1Name);
+     # Get the field list.
+     if (! exists $object1Structure->{searchFields}) {
+         Confess("No searchable index for $object1Name.");
+     } else {
+         # Get the field list.
+         my @fields = @{$object1Structure->{searchFields}};
+         # Clean the search expression.
+         my $actualKeywords = $self->CleanKeywords($searchExpression);
+         # Prefix a "+" to each uncontrolled word. This converts the default
+         # search mode from OR to AND.
+         $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
+         Trace("Actual keywords for search are\n$actualKeywords") if T(3);
+         # We need two match expressions, one for the filter clause and one in the
+         # query itself. Both will use a parameter mark, so we need to push the
+         # search expression onto the front of the parameter list twice.
+         unshift @myParams, $actualKeywords, $actualKeywords;
+         # Build the match expression.
+         my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
+         my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
+         # Process the SQL stuff.
+         my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
+             $self->_SetupSQL($objectNames, $filterClause, $matchClause);
+         # Create the query. Note that the match clause is inserted at the front of
+         # the select fields.
+         my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
+             ".* $suffix";
+         my $sth = $self->_GetStatementHandle($command, \@myParams);
+         # Now we create the relation map, which enables DBQuery to determine the order, name
+         # and mapped name for each object in the query.
+         my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
+         # Return the statement object.
+         $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
+     }
+     return $retVal;
+ }
+ =head3 GetFlat
+     my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
+ This is a variation of L</GetAll> that asks for only a single field per record and
+ returns a single flattened list.
+ =over 4
+ =item objectNames
+ List containing the names of the entity and relationship objects to be retrieved.
+ =item filterClause
+ WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
+ be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
+ B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
+ parameter list as additional parameters. The fields in a filter clause can come from primary
+ entity relations, relationship relations, or secondary entity relations; however, all of the
+ entities and relationships involved must be included in the list of object names.
+ =item parameterList
+ List of the parameters to be substituted in for the parameters marks in the filter clause.
+ =item field
+ Name of the field to be used to get the elements of the list returned.
+ =item RETURN
+ Returns a list of values.
+ =back
+ =cut
+ #: Return Type @;
+ sub GetFlat {
+     # Get the parameters.
+     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
+     # Construct the query.
+     my $query = $self->Get($objectNames, $filterClause, $parameterList);
+     # Create the result list.
+     my @retVal = ();
+     # Loop through the records, adding the field values found to the result list.
+     while (my $row = $query->Fetch()) {
          push @retVal, $row->Value($field);
      }
      # Return the list created.
      return @retVal;
  }
+ =head3 SpecialFields
+     my %specials = $erdb->SpecialFields($entityName);
+ Return a hash mapping special fields in the specified entity to the value of their
+ C<special> attribute. This enables the subclass to get access to the special field
+ attributes without needed to plumb the internal ERDB data structures.
+ =over 4
+ =item entityName
+ Name of the entity whose special fields are desired.
+ =item RETURN
+ Returns a hash. The keys of the hash are the special field names, and the values
+ are the values from each special field's C<special> attribute.
+ =back
+ =cut
+ sub SpecialFields {
+     # Get the parameters.
+     my ($self, $entityName) = @_;
+     # Declare the return variable.
+     my %retVal = ();
+     # Find the entity's data structure.
+     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
+     # Loop through its fields, adding each special field to the return hash.
+     my $fieldHash = $entityData->{Fields};
+     for my $fieldName (keys %{$fieldHash}) {
+         my $fieldData = $fieldHash->{$fieldName};
+         if (exists $fieldData->{special}) {
+             $retVal{$fieldName} = $fieldData->{special};
+         }
+     }
+     # Return the result.
+     return %retVal;
+ }
  =head3 Delete
- C<< my $stats = $erdb->Delete($entityName, $objectID); >>
+     my $stats = $erdb->Delete($entityName, $objectID, %options);
  Delete an entity instance from the database. The instance is deleted along with all entity and
- relationship instances dependent on it. The idea of dependence here is recursive. An object is
+ relationship instances dependent on it. The definition of I<dependence> is recursive.
- always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
- relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
+ An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
+ relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
  dependent relationship.
  =over 4
-Line 1168
+Line 1898
  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
  then it is presumed to by a LIKE pattern.
- =item testFlag
+ =item options
- If TRUE, the delete statements will be traced without being executed.
+ A hash detailing the options for this delete operation.
  =item RETURN
-Line 1179
+Line 1909
  =back
+ The permissible options for this method are as follows.
+ =over 4
+ =item testMode
+ If TRUE, then the delete statements will be traced, but no changes will be made to the database.
+ =item keepRoot
+ If TRUE, then the entity instances will not be deleted, only the dependent records.
+ =back
  =cut
  #: Return Type $%;
  sub Delete {
      # Get the parameters.
-     my ($self, $entityName, $objectID, $testFlag) = @_;
+     my ($self, $entityName, $objectID, %options) = @_;
      # Declare the return variable.
      my $retVal = Stats->new();
      # Get the DBKernel object.
-Line 1200
+Line 1944
      # FROM-relationships and entities.
      my @fromPathList = ();
      my @toPathList = ();
-     # This final hash is used to remember what work still needs to be done. We push paths
+     # This final list is used to remember what work still needs to be done. We push paths
      # onto the list, then pop them off to extend the paths. We prime it with the starting
      # point. Note that we will work hard to insure that the last item on a path in the
-     # TODO list is always an entity.
+     # to-do list is always an entity.
      my @todoList = ([$entityName]);
      while (@todoList) {
          # Get the current path.
-Line 1211
+Line 1955
          # Copy it into a list.
          my @stackedPath = @{$current};
          # Pull off the last item on the path. It will always be an entity.
-         my $entityName = pop @stackedPath;
+         my $myEntityName = pop @stackedPath;
          # Add it to the alreadyFound list.
-         $alreadyFound{$entityName} = 1;
+         $alreadyFound{$myEntityName} = 1;
+         # Figure out if we need to delete this entity.
+         if ($myEntityName ne $entityName || ! $options{keepRoot}) {
          # Get the entity data.
-         my $entityData = $self->_GetStructure($entityName);
+             my $entityData = $self->_GetStructure($myEntityName);
-         # The first task is to loop through the entity's relation. A DELETE command will
+             # Loop through the entity's relations. A DELETE command will be needed for each of them.
-         # be needed for each of them.
          my $relations = $entityData->{Relations};
          for my $relation (keys %{$relations}) {
              my @augmentedList = (@stackedPath, $relation);
              push @fromPathList, \@augmentedList;
          }
+         }
          # Now we need to look for relationships connected to this entity.
          my $relationshipList = $self->{_metaData}->{Relationships};
          for my $relationshipName (keys %{$relationshipList}) {
              my $relationship = $relationshipList->{$relationshipName};
              # Check the FROM field. We're only interested if it's us.
-             if ($relationship->{from} eq $entityName) {
+             if ($relationship->{from} eq $myEntityName) {
                  # Add the path to this relationship.
-                 my @augmentedList = (@stackedPath, $entityName, $relationshipName);
+                 my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
                  push @fromPathList, \@augmentedList;
                  # Check the arity. If it's MM we're done. If it's 1M
                  # and the target hasn't been seen yet, we want to
-Line 1249
+Line 1995
              }
              # Now check the TO field. In this case only the relationship needs
              # deletion.
-             if ($relationship->{to} eq $entityName) {
+             if ($relationship->{to} eq $myEntityName) {
-                 my @augmentedList = (@stackedPath, $entityName, $relationshipName);
+                 my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
                  push @toPathList, \@augmentedList;
              }
          }
      }
      # Create the first qualifier for the WHERE clause. This selects the
      # keys of the primary entity records to be deleted. When we're deleting
-     # from a dependent table, we construct a join page from the first qualifier
+     # from a dependent table, we construct a join path from the first qualifier
      # to the table containing the dependent records to delete.
      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
      # We need to make two passes. The first is through the to-list, and
-Line 1296
+Line 2042
                  }
              }
              # Now we have our desired DELETE statement.
-             if ($testFlag) {
+             if ($options{testMode}) {
                  # Here the user wants to trace without executing.
                  Trace($stmt) if T(0);
              } else {
-                 # Here we can delete. Note that the SQL method dies with a confessing
+                 # Here we can delete. Note that the SQL method dies with a confession
                  # if an error occurs, so we just go ahead and do it.
                  Trace("Executing delete from $target using '$objectID'.") if T(3);
                  my $rv = $db->SQL($stmt, 0, $objectID);
-Line 1315
+Line 2061
      return $retVal;
  }
+ =head3 Disconnect
+     $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
+ Disconnect an entity instance from all the objects to which it is related. This
+ will delete each relationship instance that connects to the specified entity.
+ =over 4
+ =item relationshipName
+ Name of the relationship whose instances are to be deleted.
+ =item originEntityName
+ Name of the entity that is to be disconnected.
+ =item originEntityID
+ ID of the entity that is to be disconnected.
+ =back
+ =cut
+ sub Disconnect {
+     # Get the parameters.
+     my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
+     # Get the relationship descriptor.
+     my $structure = $self->_GetStructure($relationshipName);
+     # Insure we have a relationship.
+     if (! exists $structure->{from}) {
+         Confess("$relationshipName is not a relationship in the database.");
+     } else {
+         # Get the database handle.
+         my $dbh = $self->{_dbh};
+         # We'll set this value to 1 if we find our entity.
+         my $found = 0;
+         # Loop through the ends of the relationship.
+         for my $dir ('from', 'to') {
+             if ($structure->{$dir} eq $originEntityName) {
+                 $found = 1;
+                 # Here we want to delete all relationship instances on this side of the
+                 # entity instance.
+                 Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
+                 # We do this delete in batches to keep it from dragging down the
+                 # server.
+                 my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
+                 my $done = 0;
+                 while (! $done) {
+                     # Do the delete.
+                     my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
+                     # See if we're done. We're done if no rows were found or the delete is unlimited.
+                     $done = ($rows == 0 || ! $limitClause);
+                 }
+             }
+         }
+         # Insure we found the entity on at least one end.
+         if (! $found) {
+             Confess("Entity \"$originEntityName\" does not use $relationshipName.");
+         }
+     }
+ }
+ =head3 DeleteRow
+     $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
+ Delete a row from a relationship. In most cases, only the from-link and to-link are
+ needed; however, for relationships with intersection data values can be specified
+ for the other fields using a hash.
+ =over 4
+ =item relationshipName
+ Name of the relationship from which the row is to be deleted.
+ =item fromLink
+ ID of the entity instance in the From direction.
+ =item toLink
+ ID of the entity instance in the To direction.
+ =item values
+ Reference to a hash of other values to be used for filtering the delete.
+ =back
+ =cut
+ sub DeleteRow {
+     # Get the parameters.
+     my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
+     # Create a hash of all the filter information.
+     my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
+     if (defined $values) {
+         for my $key (keys %{$values}) {
+             $filter{$key} = $values->{$key};
+         }
+     }
+     # Build an SQL statement out of the hash.
+     my @filters = ();
+     my @parms = ();
+     for my $key (keys %filter) {
+         push @filters, _FixName($key) . " = ?";
+         push @parms, $filter{$key};
+     }
+     Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
+     my $command = "DELETE FROM $relationshipName WHERE " .
+                   join(" AND ", @filters);
+     # Execute it.
+     my $dbh = $self->{_dbh};
+     $dbh->SQL($command, undef, @parms);
+ }
+ =head3 DeleteLike
+     my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
+ Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
+ filter, only fields from the relationship itself can be used.
+ =over 4
+ =item relName
+ Name of the relationship whose records are to be deleted.
+ =item filter
+ A filter clause (L</Get>-style) for the delete query.
+ =item parms
+ Reference to a list of parameters for the filter clause.
+ =item RETURN
+ Returns a count of the number of rows deleted.
+ =back
+ =cut
+ sub DeleteLike {
+     # Get the parameters.
+     my ($self, $objectName, $filter, $parms) = @_;
+     # Declare the return variable.
+     my $retVal;
+     # Insure the parms argument is an array reference if the caller left it off.
+     if (! defined($parms)) {
+         $parms = [];
+     }
+     # Insure we have a relationship. The main reason for this is if we delete an entity
+     # instance we have to yank out a bunch of other stuff with it.
+     if ($self->IsEntity($objectName)) {
+         Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
+     } else {
+         # Create the SQL command suffix to get the desierd records.
+         my ($suffix) = $self->_SetupSQL([$objectName], $filter);
+         # Convert it to a DELETE command.
+         my $command = "DELETE $suffix";
+         # Execute the command.
+         my $dbh = $self->{_dbh};
+         my $result = $dbh->SQL($command, 0, @{$parms});
+         # Check the results. Note we convert the "0D0" result to a real zero.
+         # A failure causes an abnormal termination, so the caller isn't going to
+         # worry about it.
+         if (! defined $result) {
+             Confess("Error deleting from $objectName: " . $dbh->errstr());
+         } elsif ($result == 0) {
+             $retVal = 0;
+         } else {
+             $retVal = $result;
+         }
+     }
+     # Return the result count.
+     return $retVal;
+ }
+ =head3 SortNeeded
+     my $parms = $erdb->SortNeeded($relationName);
+ Return the pipe command for the sort that should be applied to the specified
+ relation when creating the load file.
+ For example, if the load file should be sorted ascending by the first
+ field, this method would return
+     sort -k1 -t"\t"
+ If the first field is numeric, the method would return
+     sort -k1n -t"\t"
+ Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
+ keys using a sort.
+ =over 4
+ =item relationName
+ Name of the relation to be examined.
+ =item
+ Returns the sort command to use for sorting the relation, suitable for piping.
+ =back
+ =cut
+ #: Return Type $;
+ sub SortNeeded {
+     # Get the parameters.
+     my ($self, $relationName) = @_;
+     # Declare a descriptor to hold the names of the key fields.
+     my @keyNames = ();
+     # Get the relation structure.
+     my $relationData = $self->_FindRelation($relationName);
+     # Find out if the relation is a primary entity relation,
+     # a relationship relation, or a secondary entity relation.
+     my $entityTable = $self->{_metaData}->{Entities};
+     my $relationshipTable = $self->{_metaData}->{Relationships};
+     if (exists $entityTable->{$relationName}) {
+         # Here we have a primary entity relation.
+         push @keyNames, "id";
+     } elsif (exists $relationshipTable->{$relationName}) {
+         # Here we have a relationship. We sort using the FROM index.
+         my $relationshipData = $relationshipTable->{$relationName};
+         my $index = $relationData->{Indexes}->{idxFrom};
+         push @keyNames, @{$index->{IndexFields}};
+     } else {
+         # Here we have a secondary entity relation, so we have a sort on the ID field.
+         push @keyNames, "id";
+     }
+     # Now we parse the key names into sort parameters. First, we prime the return
+     # string.
+     my $retVal = "sort -t\"\t\" ";
+     # Get the relation's field list.
+     my @fields = @{$relationData->{Fields}};
+     # Loop through the keys.
+     for my $keyData (@keyNames) {
+         # Get the key and the ordering.
+         my ($keyName, $ordering);
+         if ($keyData =~ /^([^ ]+) DESC/) {
+             ($keyName, $ordering) = ($1, "descending");
+         } else {
+             ($keyName, $ordering) = ($keyData, "ascending");
+         }
+         # Find the key's position and type.
+         my $fieldSpec;
+         for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
+             my $thisField = $fields[$i];
+             if ($thisField->{name} eq $keyName) {
+                 # Get the sort modifier for this field type. The modifier
+                 # decides whether we're using a character, numeric, or
+                 # floating-point sort.
+                 my $modifier = $TypeTable{$thisField->{type}}->{sort};
+                 # If the index is descending for this field, denote we want
+                 # to reverse the sort order on this field.
+                 if ($ordering eq 'descending') {
+                     $modifier .= "r";
+                 }
+                 # Store the position and modifier into the field spec, which
+                 # will stop the inner loop. Note that the field number is
+                 # 1-based in the sort command, so we have to increment the
+                 # index.
+                 $fieldSpec = ($i + 1) . $modifier;
+             }
+         }
+         # Add this field to the sort command.
+         $retVal .= " -k$fieldSpec";
+     }
+     # Return the result.
+     return $retVal;
+ }
  =head3 GetList
- C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
+     my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
  Return a list of object descriptors for the specified objects as determined by the
  specified filter clause.
-Line 1345
+Line 2373
  with an ORDER BY clause. For example, the following filter string gets all genomes for a
  particular genus and sorts them by species name.
- C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
+     "Genome(genus) = ? ORDER BY Genome(species)"
  The rules for field references in a sort order are the same as those for field references in the
  filter clause in general; however, odd things may happen if a sort field is from a secondary
-Line 1357
+Line 2385
  =item RETURN
- Returns a list of B<DBObject>s that satisfy the query conditions.
+ Returns a list of B<ERDBObject>s that satisfy the query conditions.
  =back
-Line 1380
+Line 2408
  =head3 GetCount
- C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
+     my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
  Return the number of rows found by a specified query. This method would
  normally be used to count the records in a single table. For example, in a
-Line 1431
+Line 2459
  sub GetCount {
      # Get the parameters.
      my ($self, $objectNames, $filter, $params) = @_;
+     # Insure the params argument is an array reference if the caller left it off.
+     if (! defined($params)) {
+         $params = [];
+     }
      # Declare the return variable.
      my $retVal;
      # Find out if we're counting an entity or a relationship.
-Line 1469
+Line 2501
  =head3 ComputeObjectSentence
- C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
+     my $sentence = $erdb->ComputeObjectSentence($objectName);
  Check an object name, and if it is a relationship convert it to a relationship sentence.
-Line 1504
+Line 2536
  =head3 DumpRelations
- C<< $erdb->DumpRelations($outputDirectory); >>
+     $erdb->DumpRelations($outputDirectory);
  Write the contents of all the relations to tab-delimited files in the specified directory.
  Each file will have the same name as the relation dumped, with an extension of DTX.
-Line 1544
+Line 2576
      }
  }
+ =head3 InsertValue
+     $erdb->InsertValue($entityID, $fieldName, $value);
+ This method will insert a new value into the database. The value must be one
+ associated with a secondary relation, since primary values cannot be inserted:
+ they occur exactly once. Secondary values, on the other hand, can be missing
+ or multiply-occurring.
+ =over 4
+ =item entityID
+ ID of the object that is to receive the new value.
+ =item fieldName
+ Field name for the new value-- this includes the entity name, since
+ field names are of the format I<objectName>C<(>I<fieldName>C<)>.
+ =item value
+ New value to be put in the field.
+ =back
+ =cut
+ sub InsertValue {
+     # Get the parameters.
+     my ($self, $entityID, $fieldName, $value) = @_;
+     # Parse the entity name and the real field name.
+     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
+         my $entityName = $1;
+         my $fieldTitle = $2;
+         # Get its descriptor.
+         if (!$self->IsEntity($entityName)) {
+             Confess("$entityName is not a valid entity.");
+         } else {
+             my $entityData = $self->{_metaData}->{Entities}->{$entityName};
+             # Find the relation containing this field.
+             my $fieldHash = $entityData->{Fields};
+             if (! exists $fieldHash->{$fieldTitle}) {
+                 Confess("$fieldTitle not found in $entityName.");
+             } else {
+                 my $relation = $fieldHash->{$fieldTitle}->{relation};
+                 if ($relation eq $entityName) {
+                     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
+                 } else {
+                     # Now we can create an INSERT statement.
+                     my $dbh = $self->{_dbh};
+                     my $fixedName = _FixName($fieldTitle);
+                     my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
+                     # Execute the command.
+                     $dbh->SQL($statement, 0, $entityID, $value);
+                 }
+             }
+         }
+     } else {
+         Confess("$fieldName is not a valid field name.");
+     }
+ }
  =head3 InsertObject
- C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
+     $erdb->InsertObject($objectType, \%fieldHash);
  Insert an object into the database. The object is defined by a type name and then a hash
  of field names to values. Field values in the primary relation are represented by scalars.
-Line 1555
+Line 2650
  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
  C<ZP_00210270.1> and C<gi|46206278>.
- 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']});
  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
- 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'});
  =over 4
-Line 1572
+Line 2667
  Hash of field names to values.
- =item RETURN
- Returns 1 if successful, 0 if an error occurred.
  =back
  =cut
-Line 1674
+Line 2765
                  $retVal = $sth->execute(@parameterList);
                  if (!$retVal) {
                      my $errorString = $sth->errstr();
-                     Trace("Insert error: $errorString.") if T(0);
+                     Confess("Error inserting into $relationName: $errorString");
+                 } else {
+                     Trace("Insert successful using $parameterList[0].") if T(3);
                  }
              }
          }
      }
-     # Return the success indicator.
+     # Return a 1 for backward compatability.
-     return $retVal;
+     return 1;
+ }
+ =head3 UpdateEntity
+     $erdb->UpdateEntity($entityName, $id, \%fields);
+ Update the values of an entity. This is an unprotected update, so it should only be
+ done if the database resides on a database server.
+ =over 4
+ =item entityName
+ Name of the entity to update. (This is the entity type.)
+ =item id
+ ID of the entity to update. If no entity exists with this ID, an error will be thrown.
+ =item fields
+ Reference to a hash mapping field names to their new values. All of the fields named
+ must be in the entity's primary relation, and they cannot any of them be the ID field.
+ =back
+ =cut
+ sub UpdateEntity {
+     # Get the parameters.
+     my ($self, $entityName, $id, $fields) = @_;
+     # Get a list of the field names being updated.
+     my @fieldList = keys %{$fields};
+     # Verify that the fields exist.
+     my $checker = $self->GetFieldTable($entityName);
+     for my $field (@fieldList) {
+         if ($field eq 'id') {
+             Confess("Cannot update the ID field for entity $entityName.");
+         } elsif ($checker->{$field}->{relation} ne $entityName) {
+             Confess("Cannot find $field in primary relation of $entityName.");
+         }
+     }
+     # Build the SQL statement.
+     my @sets = ();
+     my @valueList = ();
+     for my $field (@fieldList) {
+         push @sets, _FixName($field) . " = ?";
+         push @valueList, $fields->{$field};
+     }
+     my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
+     # Add the ID to the list of binding values.
+     push @valueList, $id;
+     # Call SQL to do the work.
+     my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
+     # Check for errors.
+     if ($rows == 0) {
+         Confess("Entity $id of type $entityName not found.");
+     }
  }
  =head3 LoadTable
- C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
+     my $results = $erdb->LoadTable($fileName, $relationName, %options);
  Load data from a tab-delimited file into a specified table, optionally re-creating the table
  first.
-Line 1700
+Line 2851
  Name of the relation to be loaded. This is the same as the table name.
- =item truncateFlag
+ =item options
- TRUE if the table should be dropped and re-created, else FALSE
+ A hash of load options.
  =item RETURN
-Line 1710
+Line 2861
  =back
+ The permissible options are as follows.
+ =over 4
+ =item truncate
+ If TRUE, then the table will be erased before loading.
+ =item mode
+ Mode in which the load should operate, either C<low_priority> or C<concurrent>.
+ This option is only applicable to a MySQL database.
+ =item partial
+ If TRUE, then it is assumed that this is a partial load, and the table will not
+ be analyzed and compacted at the end.
+ =back
  =cut
  sub LoadTable {
      # Get the parameters.
-     my ($self, $fileName, $relationName, $truncateFlag) = @_;
+     my ($self, $fileName, $relationName, %options) = @_;
      # Create the statistical return object.
      my $retVal = _GetLoadStats();
      # Trace the fact of the load.
-Line 1725
+Line 2896
      # Get the relation data.
      my $relation = $self->_FindRelation($relationName);
      # Check the truncation flag.
-     if ($truncateFlag) {
+     if ($options{truncate}) {
          Trace("Creating table $relationName") if T(2);
          # Compute the row count estimate. We take the size of the load file,
-         # 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
          # leave extra room. We postulate a minimum row count of 1000 to
          # prevent problems with incoming empty load files.
          my $rowSize = $self->EstimateRowSize($relationName);
-         my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
+         my $estimate = $fileSize * 8 / $rowSize;
+         if ($estimate < 1000) {
+             $estimate = 1000;
+         }
          # Re-create the table without its index.
          $self->CreateTable($relationName, 0, $estimate);
          # If this is a pre-index DBMS, create the index here.
-Line 1748
+Line 2922
      # Load the table.
      my $rv;
      eval {
-         $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
+         $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
      };
      if (!defined $rv) {
          $retVal->AddMessage($@) if ($@);
-         $retVal->AddMessage("Table load failed for $relationName using $fileName.");
+         $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
          Trace("Table load failed for $relationName.") if T(1);
      } else {
          # Here we successfully loaded the table.
-Line 1760
+Line 2934
          my $size = -s $fileName;
          Trace("$size bytes loaded into $relationName.") if T(2);
          # If we're rebuilding, we need to create the table indexes.
-         if ($truncateFlag && ! $dbh->{_preIndex}) {
+         if ($options{truncate}) {
+             # Indexes are created here for PostGres. For PostGres, indexes are
+             # best built at the end. For MySQL, the reverse is true.
+             if (! $dbh->{_preIndex}) {
              eval {
                  $self->CreateIndex($relationName);
              };
-Line 1768
+Line 2945
                  $retVal->AddMessage($@);
              }
          }
+             # The full-text index (if any) is always built last, even for MySQL.
+             # First we need to see if this table has a full-text index. Only
+             # primary relations are allowed that privilege.
+             Trace("Checking for full-text index on $relationName.") if T(2);
+             if ($self->_IsPrimary($relationName)) {
+                 $self->CreateSearchIndex($relationName);
+             }
+         }
      }
      # Analyze the table to improve performance.
+     if (! $options{partial}) {
+         Trace("Analyzing and compacting $relationName.") if T(3);
      $dbh->vacuum_it($relationName);
+     }
+     Trace("$relationName load completed.") if T(3);
      # Return the statistics.
      return $retVal;
  }
- =head3 GenerateEntity
+ =head3 CreateSearchIndex
- C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
+     $erdb->CreateSearchIndex($objectName);
- Generate the data for a new entity instance. This method creates a field hash suitable for
+ Check for a full-text search index on the specified entity or relationship object, and
- passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest
+ if one is required, rebuild it.
- of the fields are generated using information in the database schema.
- Each data type has a default algorithm for generating random test data. This can be overridden
- by including a B<DataGen> element in the field. If this happens, the content of the element is
- executed as a PERL program in the context of this module. The element may make use of a C<$this>
- variable which contains the field hash as it has been built up to the current point. If any
- fields are dependent on other fields, the C<pass> attribute can be used to control the order
- in which the fields are generated. A field with a high data pass number will be generated after
- a field with a lower one. If any external values are needed, they should be passed in via the
- optional third parameter, which will be available to the data generation script under the name
- C<$value>. Several useful utility methods are provided for generating random values, including
- L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated
- in the form of a timestamp number rather than a string.
  =over 4
- =item id
+ =item objectName
- ID to assign to the new entity.
+ Name of the entity or relationship to be indexed.
- =item type
+ =back
- Type name for the new entity.
+ =cut
- =item values
+ sub CreateSearchIndex {
+     # Get the parameters.
+     my ($self, $objectName) = @_;
+     # Get the relation's entity/relationship structure.
+     my $structure = $self->_GetStructure($objectName);
+     # Get the database handle.
+     my $dbh = $self->{_dbh};
+     Trace("Checking for search fields in $objectName.") if T(3);
+     # Check for a searchable fields list.
+     if (exists $structure->{searchFields}) {
+         # Here we know that we need to create a full-text search index.
+         # Get an SQL-formatted field name list.
+         my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
+         # Create the index. If it already exists, it will be dropped.
+         $dbh->create_index(tbl => $objectName, idx => "search_idx",
+                            flds => $fields, kind => 'fulltext');
+         Trace("Index created for $fields in $objectName.") if T(2);
+     }
+ }
- Hash containing additional values that might be needed by the data generation methods (optional).
+ =head3 DropRelation
+     $erdb->DropRelation($relationName);
+ Physically drop a relation from the database.
+ =over 4
+ =item relationName
+ Name of the relation to drop. If it does not exist, this method will have
+ no effect.
  =back
  =cut
- sub GenerateEntity {
+ sub DropRelation {
      # Get the parameters.
-     my ($self, $id, $type, $values) = @_;
+     my ($self, $relationName) = @_;
-     # Create the return hash.
+     # Get the database handle.
-     my $this = { id => $id };
+     my $dbh = $self->{_dbh};
-     # Get the metadata structure.
+     # Drop the relation. The method used here has no effect if the relation
-     my $metadata = $self->{_metaData};
+     # does not exist.
-     # Get this entity's list of fields.
+     Trace("Invoking DB Kernel to drop $relationName.") if T(3);
-     if (!exists $metadata->{Entities}->{$type}) {
+     $dbh->drop_table(tbl => $relationName);
-         Confess("Unrecognized entity type $type in GenerateEntity.");
+ }
-     } else {
-         my $entity = $metadata->{Entities}->{$type};
+ =head3 MatchSqlPattern
-         my $fields = $entity->{Fields};
-         # Generate data from the fields.
+     my $matched = ERDB::MatchSqlPattern($value, $pattern);
-         _GenerateFields($this, $fields, $type, $values);
+ Determine whether or not a specified value matches an SQL pattern. An SQL
+ pattern has two wild card characters: C<%> that matches multiple characters,
+ and C<_> that matches a single character. These can be escaped using a
+ backslash (C<\>). We pull this off by converting the SQL pattern to a
+ PERL regular expression. As per SQL rules, the match is case-insensitive.
+ =over 4
+ =item value
+ Value to be matched against the pattern. Note that an undefined or empty
+ value will not match anything.
+ =item pattern
+ SQL pattern against which to match the value. An undefined or empty pattern will
+ match everything.
+ =item RETURN
+ Returns TRUE if the value and pattern match, else FALSE.
+ =back
+ =cut
+ sub MatchSqlPattern {
+     # Get the parameters.
+     my ($value, $pattern) = @_;
+     # Declare the return variable.
+     my $retVal;
+     # Insure we have a pattern.
+     if (! defined($pattern) || $pattern eq "") {
+         $retVal = 1;
+     } else {
+         # Break the pattern into pieces around the wildcard characters. Because we
+         # use parentheses in the split function's delimiter expression, we'll get
+         # list elements for the delimiters as well as the rest of the string.
+         my @pieces = split /([_%]|\\[_%])/, $pattern;
+         # Check some fast special cases.
+         if ($pattern eq '%') {
+             # A null pattern matches everything.
+             $retVal = 1;
+         } elsif (@pieces == 1) {
+             # No wildcards, so we have a literal comparison. Note we're case-insensitive.
+             $retVal = (lc($value) eq lc($pattern));
+         } elsif (@pieces == 2 && $pieces[1] eq '%') {
+             # A wildcard at the end, so we have a substring match. This is also case-insensitive.
+             $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
+         } else {
+             # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
+             my $realPattern = "";
+             for my $piece (@pieces) {
+                 # Determine the type of piece.
+                 if ($piece eq "") {
+                     # Empty pieces are ignored.
+                 } elsif ($piece eq "%") {
+                     # Here we have a multi-character wildcard. Note that it can match
+                     # zero or more characters.
+                     $realPattern .= ".*"
+                 } elsif ($piece eq "_") {
+                     # Here we have a single-character wildcard.
+                     $realPattern .= ".";
+                 } elsif ($piece eq "\\%" || $piece eq "\\_") {
+                     # This is an escape sequence (which is a rare thing, actually).
+                     $realPattern .= substr($piece, 1, 1);
+                 } else {
+                     # Here we have raw text.
+                     $realPattern .= quotemeta($piece);
      }
-     # Return the hash created.
+             }
-     return $this;
+             # Do the match.
+             $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
+         }
+     }
+     # Return the result.
+     return $retVal;
  }
  =head3 GetEntity
- C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
+     my $entityObject = $erdb->GetEntity($entityType, $ID);
  Return an object describing the entity instance with a specified ID.
-Line 1851
+Line 3130
  =item RETURN
- Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
+ Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
  instance is found with the specified key.
  =back
-Line 1869
+Line 3148
      return $retVal;
  }
+ =head3 GetChoices
+     my @values = $erdb->GetChoices($entityName, $fieldName);
+ Return a list of all the values for the specified field that are represented in the
+ specified entity.
+ Note that if the field is not indexed, then this will be a very slow operation.
+ =over 4
+ =item entityName
+ Name of an entity in the database.
+ =item fieldName
+ Name of a field belonging to the entity. This is a raw field name without
+ the standard parenthesized notation used in most calls.
+ =item RETURN
+ Returns a list of the distinct values for the specified field in the database.
+ =back
+ =cut
+ sub GetChoices {
+     # Get the parameters.
+     my ($self, $entityName, $fieldName) = @_;
+     # Declare the return variable.
+     my @retVal;
+     # Get the entity data structure.
+     my $entityData = $self->_GetStructure($entityName);
+     # Get the field.
+     my $fieldHash = $entityData->{Fields};
+     if (! exists $fieldHash->{$fieldName}) {
+         Confess("$fieldName not found in $entityName.");
+     } else {
+         # Get the name of the relation containing the field.
+         my $relation = $fieldHash->{$fieldName}->{relation};
+         # Fix up the field name.
+         my $realName = _FixName($fieldName);
+         # Get the database handle.
+         my $dbh = $self->{_dbh};
+         # Query the database.
+         my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
+         # Clean the results. They are stored as a list of lists, and we just want the one list.
+         @retVal = sort map { $_->[0] } @{$results};
+     }
+     # Return the result.
+     return @retVal;
+ }
  =head3 GetEntityValues
- C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
+     my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
- Return a list of values from a specified entity instance.
+ Return a list of values from a specified entity instance. If the entity instance
+ does not exist, an empty list is returned.
  =over 4
-Line 1914
+Line 3249
  =head3 GetAll
- C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
+     my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
  Return a list of values taken from the objects returned by a query. The first three
  parameters correspond to the parameters of the L</Get> method. The final parameter is
-Line 1928
+Line 3263
  fields specified returns multiple values, they are flattened in with the rest. For
  example, the following call will return a list of the features in a particular
  spreadsheet cell, and each feature will be represented by a list containing the
- feature ID followed by all of its aliases.
+ feature ID followed by all of its essentiality determinations.
- C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
+     @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']);
  =over 4
-Line 2001
+Line 3336
          push @retVal, \@rowData;
          $fetched++;
      }
+     Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
      # Return the resulting list.
      return @retVal;
  }
+ =head3 Exists
+     my $found = $sprout->Exists($entityName, $entityID);
+ Return TRUE if an entity exists, else FALSE.
+ =over 4
+ =item entityName
+ Name of the entity type (e.g. C<Feature>) relevant to the existence check.
+ =item entityID
+ ID of the entity instance whose existence is to be checked.
+ =item RETURN
+ Returns TRUE if the entity instance exists, else FALSE.
+ =back
+ =cut
+ #: Return Type $;
+ sub Exists {
+     # Get the parameters.
+     my ($self, $entityName, $entityID) = @_;
+     # Check for the entity instance.
+     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
+     my $testInstance = $self->GetEntity($entityName, $entityID);
+     # Return an existence indicator.
+     my $retVal = ($testInstance ? 1 : 0);
+     return $retVal;
+ }
  =head3 EstimateRowSize
- C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
+     my $rowSize = $erdb->EstimateRowSize($relName);
  Estimate the row size of the specified relation. The estimated row size is computed by adding
  up the average length for each data type.
-Line 2039
+Line 3410
          my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
          $retVal += $fieldLen;
      }
      # Return the result.
      return $retVal;
+ }
+ =head3 GetFieldTable
+     my $fieldHash = $self->GetFieldTable($objectnName);
+ Get the field structure for a specified entity or relationship.
+ =over 4
+ =item objectName
+ Name of the desired entity or relationship.
+ =item RETURN
+ The table containing the field descriptors for the specified object.
+ =back
+ =cut
+ sub GetFieldTable {
+     # Get the parameters.
+     my ($self, $objectName) = @_;
+     # Get the descriptor from the metadata.
+     my $objectData = $self->_GetStructure($objectName);
+     # Return the object's field table.
+     return $objectData->{Fields};
+ }
+ =head3 SplitKeywords
+     my @keywords = ERDB::SplitKeywords($keywordString);
+ This method returns a list of the positive keywords in the specified
+ keyword string. All of the operators will have been stripped off,
+ and if the keyword is preceded by a minus operator (C<->), it will
+ not be in the list returned. The idea here is to get a list of the
+ keywords the user wants to see. The list will be processed to remove
+ duplicates.
+ It is possible to create a string that confuses this method. For example
+     frog toad -frog
+ would return both C<frog> and C<toad>. If this is a problem we can deal
+ with it later.
+ =over 4
+ =item keywordString
+ The keyword string to be parsed.
+ =item RETURN
+ Returns a list of the words in the keyword string the user wants to
+ see.
+ =back
+ =cut
+ sub SplitKeywords {
+     # Get the parameters.
+     my ($keywordString) = @_;
+     # Make a safety copy of the string. (This helps during debugging.)
+     my $workString = $keywordString;
+     # Convert operators we don't care about to spaces.
+     $workString =~ tr/+"()<>/ /;
+     # Split the rest of the string along space boundaries. Note that we
+     # eliminate any words that are zero length or begin with a minus sign.
+     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
+     # Use a hash to remove duplicates.
+     my %words = map { $_ => 1 } @wordList;
+     # Return the result.
+     return sort keys %words;
+ }
+ =head3 ValidateFieldName
+     my $okFlag = ERDB::ValidateFieldName($fieldName);
+ Return TRUE if the specified field name is valid, else FALSE. Valid field names must
+ be hyphenated words subject to certain restrictions.
+ =over 4
+ =item fieldName
+ Field name to be validated.
+ =item RETURN
+ Returns TRUE if the field name is valid, else FALSE.
+ =back
+ =cut
+ sub ValidateFieldName {
+     # Get the parameters.
+     my ($fieldName) = @_;
+     # Declare the return variable. The field name is valid until we hear
+     # differently.
+     my $retVal = 1;
+     # Compute the maximum name length.
+     my $maxLen = $TypeTable{'name-string'}->{maxLen};
+     # Look for bad stuff in the name.
+     if ($fieldName =~ /--/) {
+         # Here we have a doubled minus sign.
+         Trace("Field name $fieldName has a doubled hyphen.") if T(1);
+         $retVal = 0;
+     } elsif ($fieldName !~ /^[A-Za-z]/) {
+         # Here the field name is missing the initial letter.
+         Trace("Field name $fieldName does not begin with a letter.") if T(1);
+         $retVal = 0;
+     } elsif (length($fieldName) > $maxLen) {
+         # Here the field name is too long.
+         Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
+     } else {
+         # Strip out the minus signs. Everything remaining must be a letter,
+         # underscore, or digit.
+         my $strippedName = $fieldName;
+         $strippedName =~ s/-//g;
+         if ($strippedName !~ /^(\w|\d)+$/) {
+             Trace("Field name $fieldName contains illegal characters.") if T(1);
+             $retVal = 0;
+         }
+     }
+     # Return the result.
+     return $retVal;
+ }
+ =head3 ReadMetaXML
+     my $rawMetaData = ERDB::ReadDBD($fileName);
+ This method reads a raw database definition XML file and returns it.
+ Normally, the metadata used by the ERDB system has been processed and
+ modified to make it easier to load and retrieve the data; however,
+ this method can be used to get the data in its raw form.
+ =over 4
+ =item fileName
+ Name of the XML file to read.
+ =item RETURN
+ Returns a hash reference containing the raw XML data from the specified file.
+ =back
+ =cut
+ sub ReadMetaXML {
+     # Get the parameters.
+     my ($fileName) = @_;
+     # Read the XML.
+     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
+     Trace("XML metadata loaded from file $fileName.") if T(1);
+     # Return the result.
+     return $retVal;
+ }
+ =head3 GetEntityFieldHash
+     my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
+ Get the field hash of the named entity in the specified raw XML structure.
+ The field hash may not exist, in which case we need to create it.
+ =over 4
+ =item structure
+ Raw XML structure defininng the database. This is not the run-time XML used by
+ an ERDB object, since that has all sorts of optimizations built-in.
+ =item entityName
+ Name of the entity whose field structure is desired.
+ =item RETURN
+ Returns the field hash used to define the entity's fields.
+ =back
+ =cut
+ sub GetEntityFieldHash {
+     # Get the parameters.
+     my ($structure, $entityName) = @_;
+     # Get the entity structure.
+     my $entityData = $structure->{Entities}->{$entityName};
+     # Look for a field structure.
+     my $retVal = $entityData->{Fields};
+     # If it doesn't exist, create it.
+     if (! defined($retVal)) {
+         $entityData->{Fields} = {};
+         $retVal = $entityData->{Fields};
+     }
+     # Return the result.
+     return $retVal;
+ }
+ =head3 WriteMetaXML
+     ERDB::WriteMetaXML($structure, $fileName);
+ Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
+ used to update the database definition. It must be used with care, however, since it
+ will only work on a raw structure, not on the processed structure created by an ERDB
+ constructor.
+ =over 4
+ =item structure
+ XML structure to be written to the file.
+ =item fileName
+ Name of the output file to which the updated XML should be stored.
+ =back
+ =cut
+ sub WriteMetaXML {
+     # Get the parameters.
+     my ($structure, $fileName) = @_;
+     # Compute the output.
+     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
+     # Write it to the file.
+     my $xmlOut = Open(undef, ">$fileName");
+     print $xmlOut $fileString;
+ }
+ =head3 HTMLNote
+ Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
+ supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
+ Except for C<[p]>, all the codes are closed by slash-codes. So, for
+ example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
+     my $realHtml = ERDB::HTMLNote($dataString);
+ =over 4
+ =item dataString
+ String to convert to HTML.
+ =item RETURN
+ An HTML string derived from the input string.
+ =back
+ =cut
+ sub HTMLNote {
+     # Get the parameter.
+     my ($dataString) = @_;
+     # HTML-escape the text.
+     my $retVal = CGI::escapeHTML($dataString);
+     # Substitute the bulletin board codes.
+     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
+     $retVal =~ s!\[p\]!</p><p>!g;
+     $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
+     $retVal =~ s!\[/link\]!</a>!g;
+     # Return the result.
+     return $retVal;
+ }
+ =head3 WikiNote
+ Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
+ supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
+ Except for C<[p]>, all the codes are closed by slash-codes. So, for
+ example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
+     my $wikiText = ERDB::WikiNote($dataString);
+ =over 4
+ =item dataString
+ String to convert to Wiki text.
+ =item RETURN
+ An Wiki text string derived from the input string.
+ =back
+ =cut
+ sub WikiNote {
+     # Get the parameter.
+     my ($dataString) = @_;
+     # HTML-escape the text.
+     my $retVal = CGI::escapeHTML($dataString);
+     # Substitute the bulletin board codes.
+     my $italic = WikiTools::ItalicCode();
+     $retVal =~ s/\[\/?i\]/$italic/g;
+     my $bold = WikiTools::BoldCode();
+     $retVal =~ s/\[\/?b\]/$bold/g;
+     # Paragraph breaks are the same no matter which Wiki you're using.
+     $retVal =~ s!\[p\]!\n\n!g;
+     # Now we do the links, which are complicated by the need to know two
+     # things: the target URL and the text.
+     while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
+         # Replace the matched string with the Wiki markup for links. Note that
+         # $-[0] is the starting position of the match for the entire expression,
+         # and $+[0] is past the ending position.
+         substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
+     }
+     # Return the result.
+     return $retVal;
+ }
+ =head3 BeginTran
+     $erdb->BeginTran();
+ Start a database transaction.
+ =cut
+ sub BeginTran {
+     my ($self) = @_;
+     $self->{_dbh}->begin_tran();
+ }
+ =head3 CommitTran
+     $erdb->CommitTran();
+ Commit an active database transaction.
+ =cut
+ sub CommitTran {
+     my ($self) = @_;
+     $self->{_dbh}->commit_tran();
+ }
+ =head3 RollbackTran
+     $erdb->RollbackTran();
+ Roll back an active database transaction.
+ =cut
+ sub RollbackTran {
+     my ($self) = @_;
+     $self->{_dbh}->roll_tran();
  }
- =head3 GetFieldTable
+ =head3 UpdateField
- C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
+     my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
- Get the field structure for a specified entity or relationship.
+ Update all occurrences of a specific field value to a new value. The number of rows changed will be
+ returned.
  =over 4
- =item objectName
+ =item fieldName
- Name of the desired entity or relationship.
+ Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
+ =item oldValue
+ Value to be modified. All occurrences of this value in the named field will be replaced by the
+ new value.
+ =item newValue
+ New value to be substituted for the old value when it's found.
+ =item filter
+ A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
+ =item parms
+ Reference to a list of parameter values in the filter.
  =item RETURN
- The table containing the field descriptors for the specified object.
+ Returns the number of rows modified.
  =back
  =cut
- sub GetFieldTable {
+ sub UpdateField {
      # Get the parameters.
-     my ($self, $objectName) = @_;
+     my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
-     # Get the descriptor from the metadata.
+     # Get the object and field names from the field name parameter.
-     my $objectData = $self->_GetStructure($objectName);
+     $fieldName =~ /^([^(]+)\(([^)]+)\)/;
-     # Return the object's field table.
+     my $objectName = $1;
-     return $objectData->{Fields};
+     my $realFieldName = _FixName($2);
+     # Add the old value to the filter. Note we allow the possibility that no
+     # filter was specified.
+     my $realFilter = "$fieldName = ?";
+     if ($filter) {
+         $realFilter .= " AND $filter";
  }
+     # Format the query filter.
+     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
+         $self->_SetupSQL([$objectName], $realFilter);
+     # Create the query. Since there is only one object name, the mapped-name data is not
+     # necessary. Neither is the FROM clause.
+     $suffix =~ s/^FROM.+WHERE\s+//;
+     # Create the update statement.
+     my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
+     # Get the database handle.
+     my $dbh = $self->{_dbh};
+     # Add the old and new values to the parameter list. Note we allow the possibility that
+     # there are no user-supplied parameters.
+     my @params = ($newValue, $oldValue);
+     if (defined $parms) {
+         push @params, @{$parms};
+     }
+     # Execute the update.
+     my $retVal = $dbh->SQL($command, 0, @params);
+     # Make the funky zero a real zero.
+     if ($retVal == 0) {
+         $retVal = 0;
+     }
+     # Return the result.
+     return $retVal;
+ }
  =head2 Data Mining Methods
  =head3 GetUsefulCrossValues
- C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
+     my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
  Return a list of the useful attributes that would be returned by a B<Cross> call
  from an entity of the source entity type through the specified relationship. This
-Line 2137
+Line 3923
  =head3 FindColumn
- C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
+     my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
  Return the location a desired column in a data mining header line. The data
  mining header line is a tab-separated list of column names. The column
-Line 2195
+Line 3981
  =head3 ParseColumns
- C<< my @columns = ERDB->ParseColumns($line); >>
+     my @columns = ERDB::ParseColumns($line);
  Convert the specified data line to a list of columns.
-Line 2216
+Line 4002
  sub ParseColumns {
      # Get the parameters.
-     my ($self, $line) = @_;
+     my ($line) = @_;
      # Chop off the line-end.
      chomp $line;
      # Split it into a list.
-Line 2225
+Line 4011
      return @retVal;
  }
+ =head2 Virtual Methods
+ =head3 _CreatePPOIndex
+     my $index = ERDB::_CreatePPOIndex($indexObject);
+ Convert the XML for an ERDB index to the XML structure for a PPO
+ index.
+ =over 4
+ =item indexObject
+ ERDB XML structure for an index.
+ =item RETURN
+ PPO XML structure for the same index.
+ =back
+ =cut
+ sub _CreatePPOIndex {
+     # Get the parameters.
+     my ($indexObject) = @_;
+     # The incoming index contains a list of the index fields in the IndexFields
+     # member. We loop through it to create the index tags.
+     my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
+     # Wrap the fields in attribute tags.
+     my $retVal = { attribute => \@fields };
+     # Return the result.
+     return $retVal;
+ }
+ =head3 _CreatePPOField
+     my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
+ Convert the ERDB XML structure for a field to a PPO scalar XML structure.
+ =over 4
+ =item fieldName
+ Name of the scalar field.
+ =item fieldObject
+ ERDB XML structure describing the field.
+ =item RETURN
+ Returns a PPO XML structure for the same field.
+ =back
+ =cut
+ sub _CreatePPOField {
+     # Get the parameters.
+     my ($fieldName, $fieldObject) = @_;
+     # Get the field type.
+     my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
+     # Fix up the field name.
+     $fieldName = _FixName($fieldName);
+     # Build the scalar tag.
+     my $retVal = { label => $fieldName, type => $type };
+     # Return the result.
+     return $retVal;
+ }
+ =head3 CleanKeywords
+     my $cleanedString = $erdb->CleanKeywords($searchExpression);
+ Clean up a search expression or keyword list. This is a virtual method that may
+ be overridden by the subclass. The base-class method removes extra spaces
+ and converts everything to lower case.
+ =over 4
+ =item searchExpression
+ Search expression or keyword list to clean. Note that a search expression may
+ contain boolean operators which need to be preserved. This includes leading
+ minus signs.
+ =item RETURN
+ Cleaned expression or keyword list.
+ =back
+ =cut
+ sub CleanKeywords {
+     # Get the parameters.
+     my ($self, $searchExpression) = @_;
+     # Lower-case the expression and copy it into the return variable. Note that we insure we
+     # don't accidentally end up with an undefined value.
+     my $retVal = lc($searchExpression || "");
+     # Remove extra spaces.
+     $retVal =~ s/\s+/ /g;
+     $retVal =~ s/(^\s+)|(\s+$)//g;
+     # Return the result.
+     return $retVal;
+ }
+ =head3 GetSourceObject
+     my $source = $erdb->GetSourceObject($entityName);
+ Return the object to be used in loading special attributes of the specified entity. The
+ algorithm for loading special attributes is stored in the C<DataGen> elements of the
+ XML
  =head2 Internal Utility Methods
- =head3 SetupSQL
+ =head3 _RelationMap
+     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
+ Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
+ to determine how to interpret the results of the query.
+ =over 4
+ =item mappedNameHashRef
+ Reference to a hash that maps modified object names to real object names.
+ =item mappedNameListRef
+ Reference to a list of modified object names in the order they appear in the
+ SELECT list.
+ =item RETURN
+ Returns a list of 2-tuples. Each tuple consists of an object name as used in the
+ query followed by the actual name of that object. This enables the B<ERDBObject> to
+ determine the order of the tables in the query and which object name belongs to each
+ mapped object name. Most of the time these two values are the same; however, if a
+ relation occurs twice in the query, the relation name in the field list and WHERE
+ clause will use a mapped name (generally the actual relation name with a numeric
+ suffix) that does not match the actual relation name.
+ =back
+ =cut
+ sub _RelationMap {
+     # Get the parameters.
+     my ($mappedNameHashRef, $mappedNameListRef) = @_;
+     # Declare the return variable.
+     my @retVal = ();
+     # Build the map.
+     for my $mappedName (@{$mappedNameListRef}) {
+         push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
+     }
+     # Return it.
+     return @retVal;
+ }
+ =head3 _SetupSQL
  Process a list of object names and a filter clause so that they can be used to
  build an SQL statement. This method takes in a reference to a list of object names
-Line 2247
+Line 4196
  A string containing the WHERE clause for the query (without the C<WHERE>) and also
  optionally the C<ORDER BY> and C<LIMIT> clauses.
+ =item matchClause
+ An optional full-text search clause. If specified, it will be inserted at the
+ front of the WHERE clause. It should already be SQL-formatted; that is, the
+ field names should be in the form I<table>C<.>I<fieldName>.
  =item RETURN
  Returns a three-element list. The first element is the SQL statement suffix, beginning
-Line 2259
+Line 4214
  =cut
  sub _SetupSQL {
-     my ($self, $objectNames, $filterClause) = @_;
+     my ($self, $objectNames, $filterClause, $matchClause) = @_;
      # Adjust the list of object names to account for multiple occurrences of the
      # same object. We start with a hash table keyed on object name that will
      # return the object suffix. The first time an object is encountered it will
-Line 2308
+Line 4263
      # FROM name1, name2, ... nameN
      #
      my $suffix = "FROM " . join(', ', @fromList);
+     # Now for the WHERE. First, we need a place for the filter string.
+     my $filterString = "";
+     # We will also keep a list of conditions to add to the WHERE clause in order to link
+     # entities and relationships as well as primary relations to secondary ones.
+     my @joinWhere = ();
      # Check for a filter clause.
      if ($filterClause) {
          # Here we have one, so we convert its field names and add it to the query. First,
          # We create a copy of the filter string we can work with.
-         my $filterString = $filterClause;
+         $filterString = $filterClause;
          # Next, we sort the object names by length. This helps protect us from finding
          # object names inside other object names when we're doing our search and replace.
          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
-         # We will also keep a list of conditions to add to the WHERE clause in order to link
-         # entities and relationships as well as primary relations to secondary ones.
-         my @joinWhere = ();
          # The final preparatory step is to create a hash table of relation names. The
          # table begins with the relation names already in the SELECT command. We may
          # need to add relations later if there is filtering on a field in a secondary
-Line 2386
+Line 4343
                  }
              }
          }
+     }
          # The next step is to join the objects together. We only need to do this if there
          # is more than one object in the object list. We start with the first object and
          # run through the objects after it. Note also that we make a safety copy of the
-         # list before running through it.
+     # list before running through it, because we shift off the first object before
+     # processing the rest.
          my @mappedObjectList = @mappedNameList;
          my $lastMappedObject = shift @mappedObjectList;
          # Get the join table.
-Line 2418
+Line 4377
          # here is we want the filter clause to be empty if there's no WHERE filter.
          # We'll put the ORDER BY / LIMIT clauses in the following variable.
          my $orderClause = "";
+     # This is only necessary if we have a filter string in which the ORDER BY
+     # and LIMIT clauses can live.
+     if ($filterString) {
          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
          # operator so that we find the first occurrence of either verb.
          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
-Line 2426
+Line 4388
              $orderClause = $2 . substr($filterString, $pos);
              $filterString = $1;
          }
-         # Add the filter and the join clauses (if any) to the SELECT command.
+     }
+     # All the things that are supposed to be in the WHERE clause of the
+     # SELECT command need to be put into @joinWhere so we can string them
+     # together. We begin with the match clause. This is important,
+     # because the match clause's parameter mark must precede any parameter
+     # marks in the filter string.
+     if ($matchClause) {
+         push @joinWhere, $matchClause;
+     }
+     # Add the filter string. We put it in parentheses to avoid operator
+     # precedence problems with the match clause or the joins.
          if ($filterString) {
              Trace("Filter string is \"$filterString\".") if T(4);
              push @joinWhere, "($filterString)";
          }
+     # String it all together into a big filter clause.
          if (@joinWhere) {
              $suffix .= " WHERE " . join(' AND ', @joinWhere);
          }
-         # Add the sort or limit clause (if any) to the SELECT command.
+     # Add the sort or limit clause (if any).
          if ($orderClause) {
              $suffix .= " $orderClause";
          }
-     }
      # Return the suffix, the mapped name list, and the mapped name hash.
      return ($suffix, \@mappedNameList, \%mappedNameHash);
  }
- =head3 GetStatementHandle
+ =head3 _GetStatementHandle
  This method will prepare and execute an SQL query, returning the statement handle.
  The main reason for doing this here is so that everybody who does SQL queries gets
-Line 2473
+Line 4445
  sub _GetStatementHandle {
      # Get the parameters.
      my ($self, $command, $params) = @_;
+     Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
      # Trace the query.
      Trace("SQL query: $command") if T(SQL => 3);
      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
-Line 2481
+Line 4454
      # Prepare the command.
      my $sth = $dbh->prepare_command($command);
      # Execute it with the parameters bound in.
-     $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
+     $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
      # Return the statement handle.
      return $sth;
  }
- =head3 GetLoadStats
+ =head3 _GetLoadStats
  Return a blank statistics object for use by the load methods.
-Line 2498
+Line 4471
      return Stats->new();
  }
- =head3 GenerateFields
+ =head3 _DumpRelation
- Generate field values from a field structure and store in a specified table. The field names
- are first sorted by pass count, certain pre-defined fields are removed from the list, and
- then we rip through them evaluation the data generation string. Fields in the primary relation
- are stored as scalars; fields in secondary relations are stored as value lists.
- This is a static method.
- =over 4
- =item this
- Hash table into which the field values should be placed.
- =item fields
- Field structure from which the field descriptors should be taken.
- =item type
- Type name of the object whose fields are being generated.
- =item values (optional)
- Reference to a value structure from which additional values can be taken.
- =item from (optiona)
- Reference to the source entity instance if relationship data is being generated.
- =item to (optional)
- Reference to the target entity instance if relationship data is being generated.
- =back
- =cut
- sub _GenerateFields {
-     # Get the parameters.
-     my ($this, $fields, $type, $values, $from, $to) = @_;
-     # Sort the field names by pass number.
-     my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};
-     # Loop through the field names, generating data.
-     for my $name (@fieldNames) {
-         # Only proceed if this field needs to be generated.
-         if (!exists $this->{$name}) {
-             # Get this field's data generation descriptor.
-             my $fieldDescriptor = $fields->{$name};
-             my $data = $fieldDescriptor->{DataGen};
-             # Get the code to generate the field value.
-             my $codeString = $data->{content};
-             # Determine whether or not this field is in the primary relation.
-             if ($fieldDescriptor->{relation} eq $type) {
-                 # Here we have a primary relation field. Store the field value as
-                 # a scalar.
-                 $this->{$name} = eval($codeString);
-             } else {
-                 # Here we have a secondary relation field. Create a null list
-                 # and push the desired number of field values onto it.
-                 my @fieldValues = ();
-                 my $count = IntGen(0,$data->{testCount});
-                 for (my $i = 0; $i < $count; $i++) {
-                     my $newValue = eval($codeString);
-                     push @fieldValues, $newValue;
-                 }
-                 # Store the value list in the main hash.
-                 $this->{$name} = \@fieldValues;
-             }
-         }
-     }
- }
- =head3 DumpRelation
- Dump the specified relation's to the specified output file in tab-delimited format.
+ Dump the specified relation to the specified output file in tab-delimited format.
  This is an instance method.
-Line 2622
+Line 4521
      close DTXOUT;
  }
- =head3 GetStructure
+ =head3 _GetStructure
  Get the data structure for a specified entity or relationship.
-Line 2661
+Line 4560
      return $retVal;
  }
- =head3 GetRelationTable
+ =head3 _GetRelationTable
  Get the list of relations for a specified entity or relationship.
-Line 2690
+Line 4591
      return $objectData->{Relations};
  }
- =head3 ValidateFieldNames
+ =head3 _ValidateFieldNames
  Determine whether or not the field names are valid. A description of the problems with the names
  will be written to the standard error output. If there is an error, this method will abort. This is
-Line 2717
+Line 4618
          for my $object (values %{$metadata->{$section}}) {
              # Loop through the object's fields.
              for my $fieldName (keys %{$object->{Fields}}) {
-                 # Now we make some initial validations.
+                 # If this field name is invalid, set the return value to zero
-                 if ($fieldName =~ /--/) {
+                 # so we know we encountered an error.
-                     # Here we have a doubled minus sign.
+                 if (! ValidateFieldName($fieldName)) {
-                     print STDERR "Field name $fieldName has a doubled hyphen.\n";
-                     $retVal = 0;
-                 } elsif ($fieldName !~ /^[A-Za-z]/) {
-                     # Here the field name is missing the initial letter.
-                     print STDERR "Field name $fieldName does not begin with a letter.\n";
-                     $retVal = 0;
-                 } else {
-                     # Strip out the minus signs. Everything remaining must be a letter
-                     # or digit.
-                     my $strippedName = $fieldName;
-                     $strippedName =~ s/-//g;
-                     if ($strippedName !~ /^[A-Za-z0-9]+$/) {
-                         print STDERR "Field name $fieldName contains illegal characters.\n";
                          $retVal = 0;
                      }
                  }
              }
          }
-     }
      # If an error was found, fail.
      if ($retVal  == 0) {
          Confess("Errors found in field names.");
      }
  }
- =head3 LoadRelation
+ =head3 _LoadRelation
  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
  file with the same name as the relation exists in the specified directory.
-Line 2796
+Line 4683
      # be a null string.
      if ($fileName ne "") {
          # Load the relation from the file.
-         $retVal = $self->LoadTable($fileName, $relationName, $rebuild);
+         $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
      } elsif ($rebuild) {
          # Here we are rebuilding, but no file exists, so we just re-create the table.
          $self->CreateTable($relationName, 1);
-Line 2805
+Line 4692
      return $retVal;
  }
- =head3 LoadMetaData
+ =head3 _LoadMetaData
+     my $metadata = ERDB::_LoadMetaData($filename);
  This method loads the data describing this database from an XML file into a metadata structure.
  The resulting structure is a set of nested hash tables containing all the information needed to
-Line 2830
+Line 4720
  sub _LoadMetaData {
      # Get the parameters.
      my ($filename) = @_;
-     Trace("Reading Sprout DBD from $filename.") if T(2);
+     Trace("Reading DBD from $filename.") if T(2);
      # Slurp the XML file into a variable. Extensive use of options is used to insure we
      # get the exact structure we want.
-     my $metadata = XML::Simple::XMLin($filename,
+     my $metadata = ReadMetaXML($filename);
-                                       GroupTags => { Relationships => 'Relationship',
-                                                      Entities => 'Entity',
-                                                      Fields => 'Field',
-                                                      Indexes => 'Index',
-                                                      IndexFields => 'IndexField'},
-                                       KeyAttr => { Relationship => 'name',
-                                                    Entity => 'name',
-                                                    Field => 'name'},
-                                       ForceArray => ['Field', 'Index', 'IndexField'],
-                                       ForceContent => 1,
-                                       NormalizeSpace => 2
-                                       );
-     Trace("XML metadata loaded from file $filename.") if T(1);
      # Before we go any farther, we need to validate the field and object names. If an error is found,
      # the method below will fail.
      _ValidateFieldNames($metadata);
-Line 2969
+Line 4846
              if ($found == 0) {
                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
              }
-             # Now we need to convert the relation's index list to an index table. We begin by creating
+             # Attach all the indexes to the relation.
-             # an empty table in the relation structure.
+             _ProcessIndexes($indexList, $relation);
-             $relation->{Indexes} = { };
-             # Loop through the indexes.
-             my $count = 0;
-             for my $index (@{$indexList}) {
-                 # Add this index to the index table.
-                 _AddIndex("idx$relationName$count", $relation, $index);
-                 # Increment the counter so that the next index has a different name.
-                 $count++;
-             }
          }
          # Finally, we add the relation structure to the entity.
          $entityStructure->{Relations} = $relationTable;
-Line 2993
+Line 4861
          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
          # Format a description for the FROM field.
          my $fromEntity = $relationshipStructure->{from};
-         my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
+         my $fromComment = "[b]id[/b] of the source [b][link #$fromEntity]$fromEntity\[/link][/b].";
          # Get the FROM entity's key type.
          my $fromType = $entityList->{$fromEntity}->{keyType};
          # Add the FROM field.
-Line 3003
+Line 4871
                                                      PrettySort => 1});
          # Format a description for the TO field.
          my $toEntity = $relationshipStructure->{to};
-         my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
+         my $toComment = "[b]id[/b] of the target [b][link #$toEntity]$toEntity\[/link][/b].";
          # Get the TO entity's key type.
          my $toType = $entityList->{$toEntity}->{keyType};
          # Add the TO field.
-Line 3015
+Line 4883
          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
                               Indexes => { } };
          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
+         # Add the alternate indexes (if any). This MUST be done before the FROM and
+         # TO indexes, because it erases the relation's index list.
+         if (exists $relationshipStructure->{Indexes}) {
+             _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
+         }
+         # Add the relation to the master table.
          # Create the FROM and TO indexes.
          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
-         # Add the relation to the master table.
          $masterRelationTable{$relationshipName} = $thisRelation;
      }
      # Now store the master relation table in the metadata structure.
-Line 3132
+Line 5006
      return $metadata;
  }
- =head3 SortNeeded
+ =head3 _CreateRelationshipIndex
- C<< my $flag = $erdb->SortNeeded($relationName); >>
- Return TRUE if the specified relation should be sorted during loading to remove duplicate keys,
- else FALSE.
- =over 4
- =item relationName
- Name of the relation to be examined.
- =item RETURN
- Returns TRUE if the relation needs a sort, else FALSE.
- =back
- =cut
- #: Return Type $;
- sub SortNeeded {
-     # Get the parameters.
-     my ($self, $relationName) = @_;
-     # Declare the return variable.
-     my $retVal = 0;
-     # Find out if the relation is a primary entity relation.
-     my $entityTable = $self->{_metaData}->{Entities};
-     if (exists $entityTable->{$relationName}) {
-         my $keyType = $entityTable->{$relationName}->{keyType};
-         Trace("Relation $relationName found in entity table with key type $keyType.") if T(3);
-         # If the key is not a hash string, we must do the sort.
-         if ($keyType ne 'hash-string') {
-             $retVal = 1;
-         }
-     }
-     # Return the result.
-     return $retVal;
- }
- =head3 CreateRelationshipIndex
  Create an index for a relationship's relation.
-Line 3213
+Line 5047
      if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
          $newIndex->{Unique} = 'true';
      }
      # Add the index to the relation.
-     _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
+     _AddIndex("idx$indexKey", $relationStructure, $newIndex);
+ }
+ =head3 _ProcessIndexes
+     ERDB::_ProcessIndexes($indexList, $relation);
+ Build the data structures for the specified indexes in the specified relation.
+ =over 4
+ =item indexList
+ Reference to a list of indexes. Each index is a hash reference containing an optional
+ C<Notes> value that describes the index and an C<IndexFields> value that is a reference
+ to a list of index field structures. An index field structure, in turn, is a reference
+ to a hash that contains a C<name> attribute for the field name and an C<order>
+ attribute that specifies either C<ascending> or C<descending>. In this sense the
+ index list encapsulates the XML C<Indexes> structure in the database definition.
+ =item relation
+ The structure that describes the current relation. The new index descriptors will
+ be stored in the structure's C<Indexes> member. Any previous data in the structure
+ will be lost.
+ =back
+ =cut
+ sub _ProcessIndexes {
+     # Get the parameters.
+     my ($indexList, $relation) = @_;
+     # Now we need to convert the relation's index list to an index table. We begin by creating
+     # an empty table in the relation structure.
+     $relation->{Indexes} = { };
+     # Loop through the indexes.
+     my $count = 0;
+     for my $index (@{$indexList}) {
+         # Add this index to the index table.
+         _AddIndex("idx$count", $relation, $index);
+         # Increment the counter so that the next index has a different name.
+         $count++;
+     }
  }
- =head3 AddIndex
+ =head3 _AddIndex
  Add an index to a relation structure.
-Line 3263
+Line 5140
      $relationStructure->{Indexes}->{$indexName} = $newIndex;
  }
- =head3 FixupFields
+ =head3 _FixupFields
  This method fixes the field list for an entity or relationship. It will add the caller-specified
  relation name to fields that do not have a name and set the C<PrettySort> value as specified.
-Line 3301
+Line 5178
          # Here it doesn't, so we create a new one.
          $structure->{Fields} = { };
      } else {
-         # Here we have a field list. Loop through its fields.
+         # Here we have a field list. We need to track the searchable fields, so we
+         # create a list for stashing them.
+         my @textFields = ();
+         # Loop through the fields.
          my $fieldStructures = $structure->{Fields};
          for my $fieldName (keys %{$fieldStructures}) {
              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
-Line 3310
+Line 5190
              my $type = $fieldData->{type};
              # Plug in a relation name if it is needed.
              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
-             # Plug in a data generator if we need one.
+             # Check for searchability.
-             if (!exists $fieldData->{DataGen}) {
+             if ($fieldData->{searchable}) {
-                 # The data generator will use the default for the field's type.
+                 # Only allow this for a primary relation.
-                 $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };
+                 if ($fieldData->{relation} ne $defaultRelationName) {
+                     Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
+                 } else {
+                     push @textFields, $fieldName;
+                 }
              }
-             # Plug in the defaults for the optional data generation parameters.
-             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });
              # Add the PrettySortValue.
              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
          }
+         # If there are searchable fields, remember the fact.
+         if (@textFields) {
+             $structure->{searchFields} = \@textFields;
+         }
      }
  }
- =head3 FixName
+ =head3 _FixName
  Fix the incoming field name so that it is a legal SQL column name.
-Line 3352
+Line 5238
      return $fieldName;
  }
- =head3 FixNames
+ =head3 _FixNames
  Fix all the field names in a list.
-Line 3383
+Line 5269
      return @result;
  }
- =head3 AddField
+ =head3 _AddField
  Add a field to a field list.
-Line 3418
+Line 5304
      $fieldList->{$fieldName} = $fieldStructure;
  }
- =head3 ReOrderRelationTable
+ =head3 _ReOrderRelationTable
  This method will take a relation table and re-sort it according to the implicit ordering of the
  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
-Line 3479
+Line 5365
  }
- =head3 IsPrimary
+ =head3 _IsPrimary
  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
  if it has the same name as an entity or relationship.
-Line 3515
+Line 5401
      return $retVal;
  }
- =head3 FindRelation
+ =head3 _FindRelation
  Return the descriptor for the specified relation.
-Line 3546
+Line 5432
  =head2 HTML Documentation Utility Methods
- =head3 ComputeRelationshipSentence
+ =head3 _ComputeRelationshipSentence
  The relationship sentence consists of the relationship name between the names of the
  two related entities and an arity indicator.
-Line 3576
+Line 5462
      # Get the parameters.
      my ($relationshipName, $relationshipStructure) = @_;
      # Format the relationship sentence.
-     my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";
+     my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
      # Compute the arity.
      my $arityCode = $relationshipStructure->{arity};
      my $arity = $ArityTable{$arityCode};
-Line 3584
+Line 5470
      return $result;
  }
- =head3 ComputeRelationshipHeading
+ =head3 _ComputeRelationshipHeading
  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
  names hyperlinked to the appropriate entity sections of the document.
-Line 3621
+Line 5507
      return $result;
  }
- =head3 ShowRelationTable
+ =head3 _WikiRelationTable
+ Generate the Wiki text for a particular relation. The relation's data will be formatted as a
+ table with three columns-- the field name, the field type, and the field description.
+ This is a static method.
+ =over 4
+ =item relationName
+ Name of the relation being formatted.
+ =item relationData
+ Hash containing the relation's fields and indexes.
+ =item RETURN
+ Returns a Wiki string that can be used to display the relation name and all of its fields.
+ =back
+ =cut
+ sub _WikiRelationTable {
+     # Get the parameters.
+     my ($relationName, $relationData) = @_;
+     # We'll create a list of lists in here, then call WikiTools::Table to
+     # convert it into a table.
+     my @rows = ();
+     # Push in the header row.
+     push @rows, [qw(Field Type Description)];
+     # Loop through the fields.
+     for my $field (@{$relationData->{Fields}}) {
+         # Create this field's row. We always have a name and type.
+         my @row = ($field->{name}, $field->{type});
+         # If we have a description, add it as the third column.
+         if (exists $field->{Notes}) {
+             push @row, WikiNote($field->{Notes}->{content});
+         }
+         # Push this row onto the table list.
+         push @rows, \@row;
+     }
+     # Store the rows as a Wiki table.
+     my $retVal = WikiTools::Table(@rows);
+     # Now we show the relation's indexes. These are formatted as another
+     # table.
+     @rows = ();
+     # Push in the header row.
+     push @rows, [qw(Index Unique Fields Notes)];
+     # Get the index hash.
+     my $indexTable = $relationData->{Indexes};
+     # Loop through the indexes. For an entity, there is always at least one index.
+     # For a relationship, there are at least two. The upshot is we don't need to
+     # worry about accidentally generating a frivolous table here.
+     for my $indexName (sort keys %$indexTable) {
+         my $indexData = $indexTable->{$indexName};
+         # Determine whether or not the index is unique.
+         my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
+                       "yes" : "");
+         # Get the field list.
+         my $fields = join(', ', @{$indexData->{IndexFields}});
+         # Get the note text.
+         my $description = "";
+         if (my $note = $indexData->{Notes}) {
+             $description = WikiNote($note->{content});
+         }
+         # Format this row.
+         my @row = ($indexName, $unique, $fields, $description);
+         push @rows, \@row;
+     }
+     # Add the index list to the result.
+     $retVal .= "\n\n" . WikiTools::Table(@rows);
+ }
+ =head3 _ShowRelationTable
  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
  table with three columns-- the field name, the field type, and the field description.
-Line 3671
+Line 5634
          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
          # Add any note text.
          if (my $note = $indexData->{Notes}) {
-             $htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";
+             $htmlString .= "<li>" . HTMLNote($note->{content}) . "</li>\n";
          }
          # Add the fiield list.
          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
-Line 3682
+Line 5645
      $htmlString .= "</ul>\n";
  }
- =head3 OpenFieldTable
+ =head3 _OpenFieldTable
  This method creates the header string for the field table generated by L</ShowMetaData>.
-Line 3707
+Line 5670
      return _OpenTable($tablename, 'Field', 'Type', 'Description');
  }
- =head3 OpenTable
+ =head3 _OpenTable
  This method creates the header string for an HTML table.
-Line 3737
+Line 5700
      # Compute the number of columns.
      my $colCount = @colNames;
      # Generate the title row.
-     my $htmlString = "<p><table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";
+     my $htmlString = "<table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";
      # Loop through the columns, adding the column header rows.
      $htmlString .= "<tr>";
      for my $colName (@colNames) {
-Line 3747
+Line 5710
      return $htmlString;
  }
- =head3 CloseTable
+ =head3 _CloseTable
  This method returns the HTML for closing a table.
-Line 3756
+Line 5719
  =cut
  sub _CloseTable {
-     return "</table></p>\n";
+     return "</table>\n";
  }
- =head3 ShowField
+ =head3 _ShowField
  This method returns the HTML for displaying a row of field information in a field table.
-Line 3786
+Line 5749
      my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";
      # If we have content, add it as a third column.
      if (exists $fieldData->{Notes}) {
-         $htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";
+         $htmlString .= "<td>" . HTMLNote($fieldData->{Notes}->{content}) . "</td>";
      }
      # Close off the row.
      $htmlString .= "</tr>\n";
-Line 3794
+Line 5757
      return $htmlString;
  }
- =head3 HTMLNote
- Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
- supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
- Except for C<[p]>, all the codes are closed by slash-codes. So, for
- example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
- This is a static method.
- =over 4
- =item dataString
- String to convert to HTML.
- =item RETURN
- An HTML string derived from the input string.
- =back
- =cut
- sub _HTMLNote {
-     # Get the parameter.
-     my ($dataString) = @_;
-     # Substitute the codes.
-     $dataString =~ s!\[(/?[bi])\]!<$1>!g;
-     $dataString =~ s!\[p\]!</p><p>!g;
-     # Return the result.
-     return $dataString;
- }
- =head2 Data Generation Utilities
- =head3 IntGen
- C<< my $integer = IntGen($min, $max); >>
- Returns a random number between the specified minimum and maximum (inclusive).
- =over 4
- =item min
- Minimum permissible return value.
- =item max
- Maximum permissible return value.
- =item RETURN
- Returns a value no lower than the minimum and no greater than the maximum.
- =back
- =cut
- sub IntGen {
-     # Get the parameters.
-     my ($min, $max) = @_;
-     # Determine the range of possible values. Note we put some space well above the
-     # maximum value to give it a fighting chance of apppearing in the list.
-     my $span = $max + 0.99 - $min;
-     # Create an integer in the range.
-     my $retVal = $min + int(rand($span));
-     # Return the result.
-     return $retVal;
- }
- =head3 RandChar
- C<< my $char = RandChar($sourceString); >>
- Select a random character from a string.
- =over 4
- =item sourceString
- String from which the random character should be selected.
- =item RETURN
- Returns a single character from the incoming string.
- =back
- =cut
- sub RandChar {
-     # Get the parameter.
-     my ($sourceString) = @_;
-     # Select a random character.
-     my $retVal = IntGen(0, (length $sourceString) - 1);
-     # Return it.
-     return substr($sourceString, $retVal, 1);
- }
- =head3 RandChars
- C<< my $string = RandChars($sourceString, $length); >>
- Create a string from characters taken from a source string.
- =over 4
- =item sourceString
- String from which the random characters should be selected.
- =item length
- Number of characters to put in the output string.
- =item RETURN
- Returns a string of the specified length consisting of characters taken from the
- source string.
- =back
- =cut
- sub RandChars {
-     # Get the parameters.
-     my ($sourceString, $length) = @_;
-     # Call RandChar repeatedly to generate the string.
-     my $retVal = "";
-     for (my $i = 0; $i < $length; $i++) {
-         $retVal .= RandChar($sourceString);
-     }
-     # Return the result.
-     return $retVal;
- }
- =head3 RandParam
- C<< my $value = RandParam($parm1, $parm2, ... $parmN); >>
- Return a randomly-selected value from the parameter list.
- =over 4
- =item parm1, parm2, ... parmN
- List of values of which one will be selected.
- =item RETURN
- Returns a randomly-chosen value from the specified list.
- =back
- =cut
- sub RandParam {
-     # Get the parameter.
-     my @parms = @_;
-     # Choose a random parameter from the list.
-     my $chosenIndex = IntGen(0, $#parms);
-     return $parms[$chosenIndex];
- }
- =head3 StringGen
- C<< my $string = StringGen($pattern1, $pattern2, ... $patternN); >>
- Returns a random string derived from a randomly-chosen format pattern. The pattern
- can either be a number (indicating the number of characters desired, or the letter
- C<P> followed by a picture. The picture should contain C<A> when a letter is desired,
- C<9> when a digit is desired, C<V> when a vowel is desired, C<K> when a consonant is
- desired, and C<X> when a letter or a digit is desired. Any other character will be
- translated as a literal.
- =over 4
- =item pattern1, pattern2, ... patternN
- List of patterns to be used to generate string values.
- =item RETURN
- A single string generated from a pattern.
- =back
- =cut
- sub StringGen {
-     # Get the parameters.
-     my @patterns = @_;
-     # Choose the appropriate pattern.
-     my $chosenPattern = RandParam(@patterns);
-     # Declare the return variable.
-     my $retVal = "";
-     # Determine whether this is a count or a picture pattern.
-     if ($chosenPattern =~ m/^\d+/) {
-         # Here we have a count. Get the string of source characters.
-         my $letterString = $PictureTable{'X'};
-         my $stringLen = length $letterString;
-         # Save the number of characters we have to generate.
-         my $charsLeft = $chosenPattern;
-         # Loop until the return variable is full.
-         while ($charsLeft > 0) {
-             # Generate a random position in the soruce string.
-             my $stringIndex = IntGen(0, $stringLen - 1);
-             # Compute the number of characters to pull out of the source string.
-             my $chunkSize = $stringLen - $stringIndex;
-             if ($chunkSize > $charsLeft) { $chunkSize = $charsLeft; }
-             # Stuff this chunk into the return value.
-             $retVal .= substr($letterString, $stringIndex, $chunkSize);
-             # Record the data moved.
-             $charsLeft -= $chunkSize;
-         }
-     } elsif ($chosenPattern =~ m/^P/) {
-         # Here we have a picture string. We will move through the picture one
-         # character at a time generating data.
-         for (my $i = 1; $i < length $chosenPattern; $i++) {
-             # Get this picture character.
-             my $chr = substr($chosenPattern, $i, 1);
-             # Check to see if the picture char is one we recognize.
-             if (exists $PictureTable{$chr}) {
-                 # Choose a random character from the available values for this
-                 # picture character.
-                 $retVal .= RandChar($PictureTable{$chr});
-             } else {
-                 # Copy in the picture character as a literal.
-                 $retVal .= $chr;
-             }
-         }
-     } else {
-         # Here we have neither a picture string or a letter count, so we treat
-         # the string as a literal.
-         $retVal = $chosenPattern;
-     }
-     # Return the string formed.
-     return $retVal;
- }
- =head3 DateGen
- C<< my $date = DateGen($startDayOffset, $endDayOffset, $minutes); >>
- Return a numeric timestamp within the specified range of days with the specified minute
- value. The range of days is specified relevant to the current day. Thus, the call
- C<< my $date = DateGen(-1, 5, 720); >>
- will return a timestamp at noon (72 minutes past midnight) sometime during the week that
- began on the preceding day. If you want a random minute of the day, simply combine with
- a call to L</IntGen>, as follows.
- C<< my $date = DateGen(-1, 5, IntGen(0, 1439)); >>
- =over 4
- =item startDayOffset
- The earliest day that can be returned, relative to the current day.
- =item endDayOffset
- The latest day that can be returned, related to the current day.
- =item minutes
- Number of minutes into the selected day that should be used.
- =back
- =cut
- sub DateGen {
-     # Get the parameters.
-     my ($startDayOffset, $endDayOffset, $minutes) = @_;
-     # Get midnight of the current day.
-     my $now = time();
-     my ($sec, $min, $hour) = localtime($now);
-     my $today = $now - (($hour * 60 + $min) * 60 + $sec);
-     # Compute the day we want.
-     my $newDay = IntGen($startDayOffset, $endDayOffset) * 86400 + $today;
-     # Add the minutes.
-     my $retVal = $newDay + $minutes * 60;
-     # Return the result.
-     return $retVal;
- }
- =head3 FloatGen
- C<< my $number = FloatGen($min, $max); >>
- Return a random floating-point number greater than or equal to the specified minimum and
- less than the specified maximum.
- =over 4
- =item min
- Minimum permissible value for the number returned.
- =item max
- Maximum permissible value for the number returned.
- =item RETURN
- Returns a floating-point number anywhere in the specified range.
- =back
- =cut
- sub FloatGen {
-     # Get the parameters.
-     my ($min, $max) = @_;
-     # Generate the result.
-     my $retVal = rand($max - $min) + $min;
-     return $retVal;
- }
- =head3 ListGen
- C<< my @list = ListGen($pattern, $count); >>
- Return a list containing a fixed number of randomly-generated strings.
- =over 4
- =item pattern
- A pattern (in the form expected by L</StringGen>) that should be used to generate the
- strings in the list.
- =item count
- The number of list entries to generate.
- =item RETURN
- Returns a list consisting of the specified number of strings.
- =back
- =cut
- sub ListGen {
-     # Get the parameters.
-     my ($pattern, $count) = @_;
-     # Generate the list.
-     my @retVal = ();
-     for (my $i = 0; $i < $count; $i++) {
-         push @retVal, StringGen($pattern);
-     }
-     # Return it.
-     return @retVal;
- }
 ;

 Legend:



Removed from v.1.48
 


changed lines


 
Added in v.1.95
 Legend:



Removed from v.1.48
 


changed lines


 
Added in v.1.95
-Removed from v.1.48
+Added in v.1.95

MCS Webmaster	ViewVC Help
Powered by ViewVC 1.0.3