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revision 1.48, Wed Jun 21 03:12:20 2006 UTC revision 1.99, Fri Jul 11 01:04:08 2008 UTC
# Line 6  Line 6 
6      use Data::Dumper;      use Data::Dumper;
7      use XML::Simple;      use XML::Simple;
8      use DBQuery;      use DBQuery;
9      use DBObject;      use ERDBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
13      use FIG;      use CGI;
14        use WikiTools;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 59  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  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
64  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
65  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
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
 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.  
   
76  =head2 XML Database Description  =head2 XML Database Description
77    
78  =head3 Data Types  =head3 Data Types
# Line 91  Line 92 
92    
93  32-bit signed integer  32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99  =item date  =item date
100    
101  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 186  Line 191 
191    
192  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
194  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,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198  =item type  =item type
199    
# Line 205  Line 212 
212  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
213  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227  =back  =back
228    
229  =head3 Indexes  =head3 Indexes
230    
231  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
232  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
233  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
234  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
235  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
237  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
238    indexes. A relationship's index must specify only fields in
239  the relationship.  the relationship.
240    
241  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.
242  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
243  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
244    
245  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
246  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 238  Line 258 
258    
259  =back  =back
260    
261  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
262    have a B<Unique> attribute. If specified, the index will be generated as a unique
263    index.
264    
265  =head3 Object and Field Names  =head3 Object and Field Names
266    
# Line 282  Line 304 
304    
305  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
306  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
307  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
308  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
309    
310  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
311    
# Line 316  Line 338 
338    
339  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
340  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
341  # 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
342  # 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,
343  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
344  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
345                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
346                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
347                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
348                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
349                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
350                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
351                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
352                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
353                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
354                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
355                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
356                                   indexMod =>   0, notes => "signed, 64-bit integer"},
357                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
358                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
359                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
360                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
361                   'hash-string' =>                   'hash-string' =>
362                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
363                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
364                   'id-string' =>                   'id-string' =>
365                               { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, dataGen => "SringGen(22)" },                               { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
367                   'key-string' =>                   'key-string' =>
368                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
370                   'name-string' =>                   'name-string' =>
371                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
373                   'medium-string' =>                   'medium-string' =>
374                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
375                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
376                     'long-string' =>
377                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
378                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
379                  );                  );
380    
381  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 344  Line 384 
384                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
385                   );                   );
386    
387  # Table for interpreting string patterns.  # Options for XML input and output.
388    
389    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
390                                      Entities => 'Entity',
391                                      Fields => 'Field',
392                                      Indexes => 'Index',
393                                      IndexFields => 'IndexField',
394                                      Issues => 'Issue',
395                                      Shapes => 'Shape'
396                                    },
397                      KeyAttr =>    { Relationship => 'name',
398                                      Entity => 'name',
399                                      Field => 'name',
400                                      Shape => 'name'
401                                    },
402                      SuppressEmpty => 1,
403                     );
404    
405  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
406                       '9' => "0123456789",                    ForceArray => [qw(Field Index IndexField Relationship Entity Shape)],
407                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
408                       'V' => "aeiou",                    NormalizeSpace => 2,
409                       'K' => "bcdfghjklmnoprstvwxyz"                   );
410    my %XmlOutOpts = (
411                      RootName => 'Database',
412                      XMLDecl => 1,
413                     );                     );
414    
415  =head2 Public Methods  =head2 Public Methods
416    
417  =head3 new  =head3 new
418    
419  C<< my $database = ERDB->new($dbh, $metaFileName); >>      my $database = ERDB->new($dbh, $metaFileName);
420    
421  Create a new ERDB object.  Create a new ERDB object.
422    
# Line 377  Line 436 
436    
437  sub new {  sub new {
438      # Get the parameters.      # Get the parameters.
439      my ($class, $dbh, $metaFileName, $options) = @_;      my ($class, $dbh, $metaFileName, %options) = @_;
440      # Load the meta-data.      # Load the meta-data.
441      my $metaData = _LoadMetaData($metaFileName);      my $metaData = _LoadMetaData($metaFileName);
442      # Create the object.      # Create the object.
# Line 391  Line 450 
450    
451  =head3 ShowMetaData  =head3 ShowMetaData
452    
453  C<< $erdb->ShowMetaData($fileName); >>      $erdb->ShowMetaData($fileName);
454    
455  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
456  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 432  Line 491 
491    
492  =head3 DisplayMetaData  =head3 DisplayMetaData
493    
494  C<< my $html = $erdb->DisplayMetaData(); >>      my $html = $erdb->DisplayMetaData();
495    
496  Return an HTML description of the database. This description can be used to help users create  Return an HTML description of the database. This description can be used to help users create
497  the data to be loaded into the relations and form queries. The output is raw includable HTML  the data to be loaded into the relations and form queries. The output is raw includable HTML
# Line 493  Line 552 
552          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
553          # If there's descriptive text, display it.          # If there's descriptive text, display it.
554          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
555              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
556          }          }
557          # 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.
558            my $relCount = keys %{$relationshipList};
559            if ($relCount > 0) {
560                # First, we set up the relationship subsection.
561          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
562          # Loop through the relationships.          # Loop through the relationships.
563          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
# Line 511  Line 573 
573          }          }
574          # Close off the relationship list.          # Close off the relationship list.
575          $retVal .= "</ul>\n";          $retVal .= "</ul>\n";
576            }
577          # Get the entity's relations.          # Get the entity's relations.
578          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
579          # Create a header for the relation subsection.          # Create a header for the relation subsection.
# Line 550  Line 613 
613          $retVal .= "</p>\n";          $retVal .= "</p>\n";
614          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
615          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
616              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
617          }          }
618          # Generate the relationship's relation table.          # Generate the relationship's relation table.
619          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
# Line 584  Line 647 
647    
648  =head3 DumpMetaData  =head3 DumpMetaData
649    
650  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
651    
652  Return a dump of the metadata structure.  Return a dump of the metadata structure.
653    
# Line 597  Line 660 
660      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
661  }  }
662    
663    =head3 GenerateWikiData
664    
665        my @wikiLines = $erdb->GenerateWikiData();
666    
667    Build a description of the database for the wiki. The database will be
668    organized into a single page, with sections for each entity and relationship.
669    The return value is a list of text lines.
670    
671    =cut
672    
673    sub GenerateWikiData {
674        # Get the parameters.
675        my ($self) = @_;
676        # We'll build the wiki text in here.
677        my @retVal = ();
678        # Get the metadata object.
679        my $metadata = $self->{_metaData};
680        # Get the title string. This will become the page name.
681        my $title = $metadata->{Title}->{content};
682        # Get the entity and relationship lists.
683        my $entityList = $metadata->{Entities};
684        my $relationshipList = $metadata->{Relationships};
685        my $shapeList = $metadata->{Shapes};
686        # Start with the introductory text.
687        push @retVal, WikiTools::Heading(2, "Introduction");
688        if (my $notes = $metadata->{Notes}) {
689            push @retVal, WikiNote($notes->{content});
690        }
691        # Generate issue list.
692        if (my $issues = $metadata->{Issues}) {
693            push @retVal, WikiTools::Heading(3, 'Issues');
694            push @retVal, WikiTools::List(map { $_->{content} } @{$issues});
695        }
696        # Start the entity section.
697        push @retVal, WikiTools::Heading(2, "Entities");
698        # Loop through the entities. Note that unlike the situation with HTML, we
699        # don't need to generate the table of contents manually, just the data
700        # itself.
701        for my $key (sort keys %$entityList) {
702            # Create a header for this entity.
703            push @retVal, "", WikiTools::Heading(3, $key);
704            # Get the entity data.
705            my $entityData = $entityList->{$key};
706            # Plant the notes here, if there are any.
707            push @retVal, _ObjectNotes($entityData);
708            # Now we list the entity's relationships (if any). First, we build a list
709            # of the relationships relevant to this entity.
710            my @rels = ();
711            for my $rel (sort keys %$relationshipList) {
712                my $relStructure = $relationshipList->{$rel};
713                if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
714                    # Get the relationship sentence.
715                    my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
716                    # Linkify it.
717                    my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
718                    $relSentence =~ s/$rel/$linkedRel/;
719                    push @rels, $relSentence;
720                }
721            }
722            # Add the relationships as a Wiki list.
723            push @retVal, WikiTools::List(@rels);
724            # Get the entity's relations.
725            my $relationList = $entityData->{Relations};
726            # Loop through the relations, displaying them.
727            for my $relation (sort keys %{$relationList}) {
728                my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
729                push @retVal, $wikiString;
730            }
731        }
732        # Now the entities are documented. Next we do the relationships.
733        push @retVal, WikiTools::Heading(2, "Relationships");
734        for my $key (sort keys %$relationshipList) {
735            my $relationshipData = $relationshipList->{$key};
736            # Create the relationship heading.
737            push @retVal, WikiTools::Heading(3, $key);
738            # Describe the relationship arity. Note there's a bit of trickiness involving recursive
739            # many-to-many relationships. In a normal many-to-many we use two sentences to describe
740            # the arity (one for each direction). This is a bad idea for a recursive relationship,
741            # since both sentences will say the same thing.
742            my $arity = $relationshipData->{arity};
743            my $fromEntity = $relationshipData->{from};
744            my $toEntity = $relationshipData->{to};
745            my @listElements = ();
746            my $boldCode = WikiTools::BoldCode();
747            if ($arity eq "11") {
748                push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
749            } else {
750                push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.";
751                if ($arity eq "MM" && $fromEntity ne $toEntity) {
752                    push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.";
753                }
754            }
755            push @retVal, WikiTools::List(@listElements);
756            # Plant the notes here, if there are any.
757            push @retVal, _ObjectNotes($relationshipData);
758            # Finally, the relationship table.
759            my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
760            push @retVal, $wikiString;
761        }
762        # Now loop through the miscellaneous shapes.
763        if ($shapeList) {
764            push @retVal, WikiTools::Heading(2, "Miscellaneous");
765            for my $shape (sort keys %$shapeList) {
766                push @retVal, WikiTools::Heading(3, $shape);
767                my $shapeData = $shapeList->{$shape};
768                push @retVal, _ObjectNotes($shapeData);
769            }
770        }
771        # All done. Return the lines.
772        return @retVal;
773    }
774    
775    
776    =head3 CreatePPO
777    
778        ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
779    
780    Create a PPO XML file from an ERDB data definition XML file. At the
781    current time, the PPO XML file can be used to create a database with
782    similar functionality. Eventually, the PPO will be able to use the
783    created XML to access the live ERDB database.
784    
785    =over 4
786    
787    =item erdbXMLFile
788    
789    Name of the XML data definition file for the ERDB database. This
790    file must exist.
791    
792    =item ppoXMLFile
793    
794    Output file for the PPO XML definition. If this file exists, it
795    will be overwritten.
796    
797    =back
798    
799    =cut
800    
801    sub CreatePPO {
802        # Get the parameters.
803        my ($erdbXMLFile, $ppoXMLFile) = @_;
804        # First, we want to slurp in the ERDB XML file in its raw form.
805        my $xml = ReadMetaXML($erdbXMLFile);
806        # Create a variable to hold all of the objects in the PPO project.
807        my @objects = ();
808        # Get the relationship hash.
809        my $relationships = $xml->{Relationships};
810        # Loop through the entities.
811        my $entities = $xml->{Entities};
812        for my $entityName (keys %{$entities}) {
813            # Get the entity's data structures.
814            my $entityObject = $entities->{$entityName};
815            # We put the object's fields in here, according to their type.
816            my (@object_refs, @scalars, @indexes, @arrays);
817            # Create the ID field for the entity. We get the key type from the
818            # entity object and compute the corresponding SQL type.
819            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
820            push @scalars, { label => 'id', type => $type };
821            # Loop through the entity fields.
822            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
823                # Get the field object.
824                my $fieldObject = $entityObject->{Fields}->{$fieldName};
825                # Convert it to a scalar tag.
826                my $scalar = _CreatePPOField($fieldName, $fieldObject);
827                # If we have a relation, this field is stored in an array.
828                # otherwise, it is a scalar. The array tag has scalars
829                # stored as an XML array. In ERDB, there is only ever one,
830                # but PPO can have more.
831                my $relation = $fieldObject->{relation};
832                if ($relation) {
833                    push @arrays, { scalar => [$scalar] };
834                } else {
835                    push @scalars, $scalar;
836                }
837            }
838            # Loop through the relationships. If this entity is the to-entity
839            # on a relationship of 1M arity, then it is implemented as a PPO
840            # object reference.
841            for my $relationshipName (keys %{$relationships}) {
842                # Get the relationship data.
843                my $relationshipData = $relationships->{$relationshipName};
844                # If we have a from for this entity and an arity of 1M, we
845                # have an object reference.
846                if ($relationshipData->{to} eq $entityName &&
847                    $relationshipData->{arity} eq '1M') {
848                    # Build the object reference tag.
849                    push @object_refs, { label => $relationshipName,
850                                         type => $relationshipData->{from} };
851                }
852            }
853            # Create the indexes.
854            my $indexList = $entityObject->{Indexes};
855            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
856            # Build the object XML tree.
857            my $object = { label => $entityName,
858                           object_ref => \@object_refs,
859                           scalar => \@scalars,
860                           index => \@indexes,
861                           array => \@arrays
862                          };
863            # Push the object onto the objects list.
864            push @objects, $object;
865        }
866        # Loop through the relationships, searching for MMs. The 1Ms were
867        # already handled by the entity search above.
868        for my $relationshipName (keys %{$relationships}) {
869            # Get this relationship's object.
870            my $relationshipObject = $relationships->{$relationshipName};
871            # Only proceed if it's many-to-many.
872            if ($relationshipObject->{arity} eq 'MM') {
873                # Create the tag lists for the relationship object.
874                my (@object_refs, @scalars, @indexes);
875                # The relationship will be created as an object with object
876                # references for its links to the participating entities.
877                my %links = ( from_link => $relationshipObject->{from},
878                              to_link => $relationshipObject->{to} );
879                for my $link (keys %links) {
880                    # Create an object_ref tag for this piece of the
881                    # relationship (from or to).
882                    my $object_ref = { label => $link,
883                                       type => $links{$link} };
884                    push @object_refs, $object_ref;
885                }
886                # Loop through the intersection data fields, creating scalar tags.
887                # There are no fancy array tags in a relationship.
888                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
889                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
890                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
891                }
892                # Finally, the indexes: currently we cannot support the to-index and
893                # from-index in PPO, so we just process the alternate indexes.
894                my $indexList = $relationshipObject->{Indexes};
895                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
896                # Wrap up all the stuff about this relationship.
897                my $object = { label => $relationshipName,
898                               scalar => \@scalars,
899                               object_ref => \@object_refs,
900                               index => \@indexes
901                             };
902                # Push it into the object list.
903                push @objects, $object;
904            }
905        }
906        # Compute a title.
907        my $title;
908        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
909            # Here we have a standard file name we can use for a title.
910            $title = $2;
911        } else {
912            # Here the file name is non-standard, so we carve up the
913            # database title.
914            $title = $xml->{Title}->{content};
915            $title =~ s/\s\.,//g;
916        }
917        # Wrap up the XML as a project.
918        my $ppoXML = { project => { label => $title,
919                                    object => \@objects }};
920        # Write out the results.
921        my $ppoString = XML::Simple::XMLout($ppoXML,
922                                            AttrIndent => 1,
923                                            KeepRoot => 1);
924        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
925    }
926    
927    =head3 FindIndexForEntity
928    
929        my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
930    
931    This method locates the entry in an entity's index list that begins with the
932    specified attribute name. If the entity has no index list, one will be
933    created. This method works on raw XML, not a live ERDB object.
934    
935    =over 4
936    
937    =item xml
938    
939    The raw XML structure defining the database.
940    
941    =item entityName
942    
943    The name of the relevant entity.
944    
945    =item attributeName
946    
947    The name of the attribute relevant to the search.
948    
949    =item RETURN
950    
951    The numerical index in the index list of the index entry for the specified entity and
952    attribute, or C<undef> if no such index exists.
953    
954    =back
955    
956    =cut
957    
958    sub FindIndexForEntity {
959        # Get the parameters.
960        my ($xml, $entityName, $attributeName) = @_;
961        # Declare the return variable.
962        my $retVal;
963        # Get the named entity.
964        my $entityData = $xml->{Entities}->{$entityName};
965        if (! $entityData) {
966            Confess("Entity $entityName not found in DBD structure.");
967        } else {
968            # Insure it has an index list.
969            if (! exists $entityData->{Indexes}) {
970                $entityData->{Indexes} = [];
971            } else {
972                # Search for the desired index.
973                my $indexList = $entityData->{Indexes};
974                my $n = scalar @{$indexList};
975                Trace("Searching $n indexes in index list for $entityName.") if T(2);
976                # We use an indexed FOR here because we're returning an
977                # index number instead of an object. We do THAT so we can
978                # delete the index from the list if needed.
979                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
980                    my $index = $indexList->[$i];
981                    my $fields = $index->{IndexFields};
982                    # Technically this IF should be safe (that is, we are guaranteed
983                    # the existence of a "$fields->[0]"), because when we load the XML
984                    # we have SuppressEmpty specified.
985                    if ($fields->[0]->{name} eq $attributeName) {
986                        $retVal = $i;
987                    }
988                }
989            }
990        }
991        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
992        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
993        # Return the result.
994        return $retVal;
995    }
996    
997  =head3 CreateTables  =head3 CreateTables
998    
999  C<< $erdb->CreateTables(); >>      $erdb->CreateTables();
1000    
1001  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
1002  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 616  Line 1013 
1013      # Loop through the relations.      # Loop through the relations.
1014      for my $relationName (@relNames) {      for my $relationName (@relNames) {
1015          # Create a table for this relation.          # Create a table for this relation.
1016          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
1017          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
1018      }      }
1019  }  }
1020    
1021  =head3 CreateTable  =head3 CreateTable
1022    
1023  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>      $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
1024    
1025  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
1026    
# Line 679  Line 1076 
1076      my $estimation = undef;      my $estimation = undef;
1077      if ($estimatedRows) {      if ($estimatedRows) {
1078          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1079            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1080      }      }
1081      # Create the table.      # Create the table.
1082      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
1083      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
1084      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
1085      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
1086        # index will not be built until the table has been loaded.
1087      if ($indexFlag) {      if ($indexFlag) {
1088          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
1089      }      }
# Line 692  Line 1091 
1091    
1092  =head3 VerifyFields  =head3 VerifyFields
1093    
1094  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
1095    
1096  Run through the list of proposed field values, insuring that all the character fields are  Run through the list of proposed field values, insuring that all the character fields are
1097  below the maximum length. If any fields are too long, they will be truncated in place.  below the maximum length. If any fields are too long, they will be truncated in place.
# Line 735  Line 1134 
1134              my $oldString = $fieldList->[$i];              my $oldString = $fieldList->[$i];
1135              if (length($oldString) > $maxLen) {              if (length($oldString) > $maxLen) {
1136                  # Here it's too big, so we truncate it.                  # Here it's too big, so we truncate it.
1137                  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);
1138                  $fieldList->[$i] = substr $oldString, 0, $maxLen;                  $fieldList->[$i] = substr $oldString, 0, $maxLen;
1139                  $retVal++;                  $retVal++;
1140              }              }
# Line 747  Line 1146 
1146    
1147  =head3 DigestFields  =head3 DigestFields
1148    
1149  C<< $erdb->DigestFields($relName, $fieldList); >>      $erdb->DigestFields($relName, $fieldList);
1150    
1151  Digest the strings in the field list that correspond to data type C<hash-string> in the  Digest the strings in the field list that correspond to data type C<hash-string> in the
1152  specified relation.  specified relation.
# Line 787  Line 1186 
1186    
1187  =head3 DigestKey  =head3 DigestKey
1188    
1189  C<< my $digested = $erdb->DigestKey($keyValue); >>      my $digested = $erdb->DigestKey($keyValue);
1190    
1191  Return the digested value of a symbolic key. The digested value can then be plugged into a  Return the digested value of a symbolic key. The digested value can then be plugged into a
1192  key-based search into a table with key-type hash-string.  key-based search into a table with key-type hash-string.
# Line 820  Line 1219 
1219    
1220  =head3 CreateIndex  =head3 CreateIndex
1221    
1222  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1223    
1224  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
1225  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
# Line 841  Line 1240 
1240      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
1241          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
1242          # Get the index's field list.          # Get the index's field list.
1243          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
1244            # Get a hash of the relation's field types.
1245            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1246            # We need to check for text fields so we can append a length limitation for them. To do
1247            # that, we need the relation's field list.
1248            my $relFields = $relationData->{Fields};
1249            for (my $i = 0; $i <= $#rawFields; $i++) {
1250                # Get the field type.
1251                my $field = $rawFields[$i];
1252                my $type = $types{$field};
1253                # Ask if it requires using prefix notation for the index.
1254                my $mod = $TypeTable{$type}->{indexMod};
1255                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1256                if ($mod) {
1257                    # Append the prefix length to the field name,
1258                    $rawFields[$i] .= "($mod)";
1259                }
1260            }
1261            my @fieldList = _FixNames(@rawFields);
1262          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
1263          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
1264          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1265          # Create the index.          # Create the index.
1266          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1267                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
1268          if ($rv) {          if ($rv) {
1269              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1270          } else {          } else {
# Line 856  Line 1273 
1273      }      }
1274  }  }
1275    
1276    =head3 GetSecondaryFields
1277    
1278        my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1279    
1280    This method will return a list of the name and type of each of the secondary
1281    fields for a specified entity. Secondary fields are stored in two-column tables
1282    in addition to the primary entity table. This enables the field to have no value
1283    or to have multiple values.
1284    
1285    =over 4
1286    
1287    =item entityName
1288    
1289    Name of the entity whose secondary fields are desired.
1290    
1291    =item RETURN
1292    
1293    Returns a hash mapping the field names to their field types.
1294    
1295    =back
1296    
1297    =cut
1298    
1299    sub GetSecondaryFields {
1300        # Get the parameters.
1301        my ($self, $entityName) = @_;
1302        # Declare the return variable.
1303        my %retVal = ();
1304        # Look for the entity.
1305        my $table = $self->GetFieldTable($entityName);
1306        # Loop through the fields, pulling out the secondaries.
1307        for my $field (sort keys %{$table}) {
1308            if ($table->{$field}->{relation} ne $entityName) {
1309                # Here we have a secondary field.
1310                $retVal{$field} = $table->{$field}->{type};
1311            }
1312        }
1313        # Return the result.
1314        return %retVal;
1315    }
1316    
1317    =head3 GetFieldRelationName
1318    
1319        my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1320    
1321    Return the name of the relation containing a specified field.
1322    
1323    =over 4
1324    
1325    =item objectName
1326    
1327    Name of the entity or relationship containing the field.
1328    
1329    =item fieldName
1330    
1331    Name of the relevant field in that entity or relationship.
1332    
1333    =item RETURN
1334    
1335    Returns the name of the database relation containing the field, or C<undef> if
1336    the field does not exist.
1337    
1338    =back
1339    
1340    =cut
1341    
1342    sub GetFieldRelationName {
1343        # Get the parameters.
1344        my ($self, $objectName, $fieldName) = @_;
1345        # Declare the return variable.
1346        my $retVal;
1347        # Get the object field table.
1348        my $table = $self->GetFieldTable($objectName);
1349        # Only proceed if the field exists.
1350        if (exists $table->{$fieldName}) {
1351            # Determine the name of the relation that contains this field.
1352            $retVal = $table->{$fieldName}->{relation};
1353        }
1354        # Return the result.
1355        return $retVal;
1356    }
1357    
1358    =head3 DeleteValue
1359    
1360        my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1361    
1362    Delete secondary field values from the database. This method can be used to delete all
1363    values of a specified field for a particular entity instance, or only a single value.
1364    
1365    Secondary fields are stored in two-column relations separate from an entity's primary
1366    table, and as a result a secondary field can legitimately have no value or multiple
1367    values. Therefore, it makes sense to talk about deleting secondary fields where it
1368    would not make sense for primary fields.
1369    
1370    =over 4
1371    
1372    =item entityName
1373    
1374    Name of the entity from which the fields are to be deleted.
1375    
1376    =item id
1377    
1378    ID of the entity instance to be processed. If the instance is not found, this
1379    method will have no effect. If C<undef> is specified, all values for all of
1380    the entity instances will be deleted.
1381    
1382    =item fieldName
1383    
1384    Name of the field whose values are to be deleted.
1385    
1386    =item fieldValue (optional)
1387    
1388    Value to be deleted. If not specified, then all values of the specified field
1389    will be deleted for the entity instance. If specified, then only the values which
1390    match this parameter will be deleted.
1391    
1392    =item RETURN
1393    
1394    Returns the number of rows deleted.
1395    
1396    =back
1397    
1398    =cut
1399    
1400    sub DeleteValue {
1401        # Get the parameters.
1402        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1403        # Declare the return value.
1404        my $retVal = 0;
1405        # We need to set up an SQL command to do the deletion. First, we
1406        # find the name of the field's relation.
1407        my $table = $self->GetFieldTable($entityName);
1408        my $field = $table->{$fieldName};
1409        my $relation = $field->{relation};
1410        # Make sure this is a secondary field.
1411        if ($relation eq $entityName) {
1412            Confess("Cannot delete values of $fieldName for $entityName.");
1413        } else {
1414            # Set up the SQL command to delete all values.
1415            my $sql = "DELETE FROM $relation";
1416            # Build the filter.
1417            my @filters = ();
1418            my @parms = ();
1419            # Check for a filter by ID.
1420            if (defined $id) {
1421                push @filters, "id = ?";
1422                push @parms, $id;
1423            }
1424            # Check for a filter by value.
1425            if (defined $fieldValue) {
1426                push @filters, "$fieldName = ?";
1427                push @parms, $fieldValue;
1428            }
1429            # Append the filters to the command.
1430            if (@filters) {
1431                $sql .= " WHERE " . join(" AND ", @filters);
1432            }
1433            # Execute the command.
1434            my $dbh = $self->{_dbh};
1435            $retVal = $dbh->SQL($sql, 0, @parms);
1436        }
1437        # Return the result.
1438        return $retVal;
1439    }
1440    
1441  =head3 LoadTables  =head3 LoadTables
1442    
1443  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>      my $stats = $erdb->LoadTables($directoryName, $rebuild);
1444    
1445  This method will load the database tables from a directory. The tables must already have been created  This method will load the database tables from a directory. The tables must already have been created
1446  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
# Line 918  Line 1500 
1500    
1501  =head3 GetTableNames  =head3 GetTableNames
1502    
1503  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1504    
1505  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1506    
# Line 935  Line 1517 
1517    
1518  =head3 GetEntityTypes  =head3 GetEntityTypes
1519    
1520  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1521    
1522  Return a list of the entity type names.  Return a list of the entity type names.
1523    
# Line 950  Line 1532 
1532      return sort keys %{$entityList};      return sort keys %{$entityList};
1533  }  }
1534    
1535    =head3 GetDataTypes
1536    
1537        my %types = ERDB::GetDataTypes();
1538    
1539    Return a table of ERDB data types. The table returned is a hash of hashes.
1540    The keys of the big hash are the datatypes. Each smaller hash has several
1541    values used to manage the data. The most interesting is the SQL type (key
1542    C<sqlType>) and the descriptive node (key C<notes>).
1543    
1544    Note that changing the values in the smaller hashes will seriously break
1545    things, so this data should be treated as read-only.
1546    
1547    =cut
1548    
1549    sub GetDataTypes {
1550        return %TypeTable;
1551    }
1552    
1553    
1554  =head3 IsEntity  =head3 IsEntity
1555    
1556  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1557    
1558  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1559    
# Line 979  Line 1580 
1580    
1581  =head3 Get  =head3 Get
1582    
1583  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1584    
1585  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
1586  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 987  Line 1588 
1588  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
1589  $genus.  $genus.
1590    
1591  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1592    
1593  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
1594  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1595    
1596  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1597    
1598  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1599  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 1004  Line 1605 
1605  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
1606  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
1607    
1608  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1609    
1610  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
1611  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
# Line 1040  Line 1641 
1641  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
1642  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1643    
1644  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1645    
1646  Note that the case is important. Only an uppercase "ORDER BY" with a single space will  Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1647  be processed. The idea is to make it less likely to find the verb by accident.  be processed. The idea is to make it less likely to find the verb by accident.
# Line 1053  Line 1654 
1654  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1655  a positive number. So, for example  a positive number. So, for example
1656    
1657  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>      "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1658    
1659  will only return the first ten genomes for the specified genus. The ORDER BY clause is not  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1660  required. For example, to just get the first 10 genomes in the B<Genome> table, you could  required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1661  use  use
1662    
1663  C<< "LIMIT 10" >>      "LIMIT 10"
1664    
1665  =item params  =item params
1666    
# Line 1080  Line 1681 
1681      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1682          $self->_SetupSQL($objectNames, $filterClause);          $self->_SetupSQL($objectNames, $filterClause);
1683      # Create the query.      # Create the query.
1684      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1685          ".* $suffix";          ".* $suffix";
1686      my $sth = $self->_GetStatementHandle($command, $params);      my $sth = $self->_GetStatementHandle($command, $params);
1687      # Now we create the relation map, which enables DBQuery to determine the order, name      # Now we create the relation map, which enables DBQuery to determine the order, name
# Line 1094  Line 1695 
1695      return $retVal;      return $retVal;
1696  }  }
1697    
 =head3 GetFlat  
1698    
 C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>  
1699    
1700  This is a variation of L</GetAll> that asks for only a single field per record and  =head3 Search
1701  returns a single flattened list.  
1702        my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1703    
1704    Perform a full text search with filtering. The search will be against a specified object
1705    in the object name list. That object will get an extra field containing the search
1706    relevance. Note that except for the search expression, the parameters of this method are
1707    the same as those for L</Get> and follow the same rules.
1708    
1709  =over 4  =over 4
1710    
1711    =item searchExpression
1712    
1713    Boolean search expression for the text fields of the target object. The default mode for
1714    a Boolean search expression is OR, but we want the default to be AND, so we will
1715    add a C<+> operator to each word with no other operator before it.
1716    
1717    =item idx
1718    
1719    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1720    
1721  =item objectNames  =item objectNames
1722    
1723  List containing the names of the entity and relationship objects to be retrieved.  List containing the names of the entity and relationship objects to be retrieved.
1724    
1725  =item filterClause  =item filterClause
1726    
1727  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
1728  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
1729  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
1730  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
1731  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,
1732  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
1733    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.  
1734    
1735  =item field  =item params
1736    
1737  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.
1738    
1739  =item RETURN  =item RETURN
1740    
1741  Returns a list of values.  Returns a query object for the specified search.
1742    
1743  =back  =back
1744    
1745  =cut  =cut
1746  #: Return Type @;  
1747  sub GetFlat {  sub Search {
1748      # Get the parameters.      # Get the parameters.
1749      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1750      # Construct the query.      # Declare the return variable.
1751      my $query = $self->Get($objectNames, $filterClause, $parameterList);      my $retVal;
1752      # Create the result list.      # Create a safety copy of the parameter list. Note we have to be careful to insure
1753      my @retVal = ();      # a parameter list exists before we copy it.
1754      # Loop through the records, adding the field values found to the result list.      my @myParams = ();
1755      while (my $row = $query->Fetch()) {      if (defined $params) {
1756            @myParams = @{$params};
1757        }
1758        # Get the first object's structure so we have access to the searchable fields.
1759        my $object1Name = $objectNames->[$idx];
1760        my $object1Structure = $self->_GetStructure($object1Name);
1761        # Get the field list.
1762        if (! exists $object1Structure->{searchFields}) {
1763            Confess("No searchable index for $object1Name.");
1764        } else {
1765            # Get the field list.
1766            my @fields = @{$object1Structure->{searchFields}};
1767            # Clean the search expression.
1768            my $actualKeywords = $self->CleanKeywords($searchExpression);
1769            # Prefix a "+" to each uncontrolled word. This converts the default
1770            # search mode from OR to AND.
1771            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1772            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1773            # We need two match expressions, one for the filter clause and one in the
1774            # query itself. Both will use a parameter mark, so we need to push the
1775            # search expression onto the front of the parameter list twice.
1776            unshift @myParams, $actualKeywords, $actualKeywords;
1777            # Build the match expression.
1778            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1779            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1780            # Process the SQL stuff.
1781            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1782                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1783            # Create the query. Note that the match clause is inserted at the front of
1784            # the select fields.
1785            my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1786                ".* $suffix";
1787            my $sth = $self->_GetStatementHandle($command, \@myParams);
1788            # Now we create the relation map, which enables DBQuery to determine the order, name
1789            # and mapped name for each object in the query.
1790            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1791            # Return the statement object.
1792            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1793        }
1794        return $retVal;
1795    }
1796    
1797    =head3 GetFlat
1798    
1799        my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1800    
1801    This is a variation of L</GetAll> that asks for only a single field per record and
1802    returns a single flattened list.
1803    
1804    =over 4
1805    
1806    =item objectNames
1807    
1808    List containing the names of the entity and relationship objects to be retrieved.
1809    
1810    =item filterClause
1811    
1812    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1813    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1814    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1815    parameter list as additional parameters. The fields in a filter clause can come from primary
1816    entity relations, relationship relations, or secondary entity relations; however, all of the
1817    entities and relationships involved must be included in the list of object names.
1818    
1819    =item parameterList
1820    
1821    List of the parameters to be substituted in for the parameters marks in the filter clause.
1822    
1823    =item field
1824    
1825    Name of the field to be used to get the elements of the list returned.
1826    
1827    =item RETURN
1828    
1829    Returns a list of values.
1830    
1831    =back
1832    
1833    =cut
1834    #: Return Type @;
1835    sub GetFlat {
1836        # Get the parameters.
1837        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1838        # Construct the query.
1839        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1840        # Create the result list.
1841        my @retVal = ();
1842        # Loop through the records, adding the field values found to the result list.
1843        while (my $row = $query->Fetch()) {
1844          push @retVal, $row->Value($field);          push @retVal, $row->Value($field);
1845      }      }
1846      # Return the list created.      # Return the list created.
1847      return @retVal;      return @retVal;
1848  }  }
1849    
1850    =head3 SpecialFields
1851    
1852        my %specials = $erdb->SpecialFields($entityName);
1853    
1854    Return a hash mapping special fields in the specified entity to the value of their
1855    C<special> attribute. This enables the subclass to get access to the special field
1856    attributes without needed to plumb the internal ERDB data structures.
1857    
1858    =over 4
1859    
1860    =item entityName
1861    
1862    Name of the entity whose special fields are desired.
1863    
1864    =item RETURN
1865    
1866    Returns a hash. The keys of the hash are the special field names, and the values
1867    are the values from each special field's C<special> attribute.
1868    
1869    =back
1870    
1871    =cut
1872    
1873    sub SpecialFields {
1874        # Get the parameters.
1875        my ($self, $entityName) = @_;
1876        # Declare the return variable.
1877        my %retVal = ();
1878        # Find the entity's data structure.
1879        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1880        # Loop through its fields, adding each special field to the return hash.
1881        my $fieldHash = $entityData->{Fields};
1882        for my $fieldName (keys %{$fieldHash}) {
1883            my $fieldData = $fieldHash->{$fieldName};
1884            if (exists $fieldData->{special}) {
1885                $retVal{$fieldName} = $fieldData->{special};
1886            }
1887        }
1888        # Return the result.
1889        return %retVal;
1890    }
1891    
1892  =head3 Delete  =head3 Delete
1893    
1894  C<< my $stats = $erdb->Delete($entityName, $objectID); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1895    
1896  Delete an entity instance from the database. The instance is deleted along with all entity and  Delete an entity instance from the database. The instance is deleted along with all entity and
1897  relationship instances dependent on it. The idea of dependence here is recursive. An object is  relationship instances dependent on it. The definition of I<dependence> is recursive.
1898  always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  
1899  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
1900    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1901  dependent relationship.  dependent relationship.
1902    
1903  =over 4  =over 4
# Line 1168  Line 1911 
1911  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1912  then it is presumed to by a LIKE pattern.  then it is presumed to by a LIKE pattern.
1913    
1914  =item testFlag  =item options
1915    
1916  If TRUE, the delete statements will be traced without being executed.  A hash detailing the options for this delete operation.
1917    
1918  =item RETURN  =item RETURN
1919    
# Line 1179  Line 1922 
1922    
1923  =back  =back
1924    
1925    The permissible options for this method are as follows.
1926    
1927    =over 4
1928    
1929    =item testMode
1930    
1931    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1932    
1933    =item keepRoot
1934    
1935    If TRUE, then the entity instances will not be deleted, only the dependent records.
1936    
1937    =back
1938    
1939  =cut  =cut
1940  #: Return Type $%;  #: Return Type $%;
1941  sub Delete {  sub Delete {
1942      # Get the parameters.      # Get the parameters.
1943      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1944      # Declare the return variable.      # Declare the return variable.
1945      my $retVal = Stats->new();      my $retVal = Stats->new();
1946      # Get the DBKernel object.      # Get the DBKernel object.
# Line 1200  Line 1957 
1957      # FROM-relationships and entities.      # FROM-relationships and entities.
1958      my @fromPathList = ();      my @fromPathList = ();
1959      my @toPathList = ();      my @toPathList = ();
1960      # This final hash is used to remember what work still needs to be done. We push paths      # This final list is used to remember what work still needs to be done. We push paths
1961      # onto the list, then pop them off to extend the paths. We prime it with the starting      # onto the list, then pop them off to extend the paths. We prime it with the starting
1962      # point. Note that we will work hard to insure that the last item on a path in the      # point. Note that we will work hard to insure that the last item on a path in the
1963      # TODO list is always an entity.      # to-do list is always an entity.
1964      my @todoList = ([$entityName]);      my @todoList = ([$entityName]);
1965      while (@todoList) {      while (@todoList) {
1966          # Get the current path.          # Get the current path.
# Line 1211  Line 1968 
1968          # Copy it into a list.          # Copy it into a list.
1969          my @stackedPath = @{$current};          my @stackedPath = @{$current};
1970          # Pull off the last item on the path. It will always be an entity.          # Pull off the last item on the path. It will always be an entity.
1971          my $entityName = pop @stackedPath;          my $myEntityName = pop @stackedPath;
1972          # Add it to the alreadyFound list.          # Add it to the alreadyFound list.
1973          $alreadyFound{$entityName} = 1;          $alreadyFound{$myEntityName} = 1;
1974            # Figure out if we need to delete this entity.
1975            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1976          # Get the entity data.          # Get the entity data.
1977          my $entityData = $self->_GetStructure($entityName);              my $entityData = $self->_GetStructure($myEntityName);
1978          # 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.  
1979          my $relations = $entityData->{Relations};          my $relations = $entityData->{Relations};
1980          for my $relation (keys %{$relations}) {          for my $relation (keys %{$relations}) {
1981              my @augmentedList = (@stackedPath, $relation);              my @augmentedList = (@stackedPath, $relation);
1982              push @fromPathList, \@augmentedList;              push @fromPathList, \@augmentedList;
1983          }          }
1984            }
1985          # Now we need to look for relationships connected to this entity.          # Now we need to look for relationships connected to this entity.
1986          my $relationshipList = $self->{_metaData}->{Relationships};          my $relationshipList = $self->{_metaData}->{Relationships};
1987          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
1988              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
1989              # Check the FROM field. We're only interested if it's us.              # Check the FROM field. We're only interested if it's us.
1990              if ($relationship->{from} eq $entityName) {              if ($relationship->{from} eq $myEntityName) {
1991                  # Add the path to this relationship.                  # Add the path to this relationship.
1992                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1993                  push @fromPathList, \@augmentedList;                  push @fromPathList, \@augmentedList;
1994                  # Check the arity. If it's MM we're done. If it's 1M                  # Check the arity. If it's MM we're done. If it's 1M
1995                  # and the target hasn't been seen yet, we want to                  # and the target hasn't been seen yet, we want to
# Line 1249  Line 2008 
2008              }              }
2009              # Now check the TO field. In this case only the relationship needs              # Now check the TO field. In this case only the relationship needs
2010              # deletion.              # deletion.
2011              if ($relationship->{to} eq $entityName) {              if ($relationship->{to} eq $myEntityName) {
2012                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2013                  push @toPathList, \@augmentedList;                  push @toPathList, \@augmentedList;
2014              }              }
2015          }          }
2016      }      }
2017      # Create the first qualifier for the WHERE clause. This selects the      # Create the first qualifier for the WHERE clause. This selects the
2018      # keys of the primary entity records to be deleted. When we're deleting      # keys of the primary entity records to be deleted. When we're deleting
2019      # 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
2020      # to the table containing the dependent records to delete.      # to the table containing the dependent records to delete.
2021      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
2022      # We need to make two passes. The first is through the to-list, and      # We need to make two passes. The first is through the to-list, and
# Line 1296  Line 2055 
2055                  }                  }
2056              }              }
2057              # Now we have our desired DELETE statement.              # Now we have our desired DELETE statement.
2058              if ($testFlag) {              if ($options{testMode}) {
2059                  # Here the user wants to trace without executing.                  # Here the user wants to trace without executing.
2060                  Trace($stmt) if T(0);                  Trace($stmt) if T(0);
2061              } else {              } else {
2062                  # 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
2063                  # if an error occurs, so we just go ahead and do it.                  # if an error occurs, so we just go ahead and do it.
2064                  Trace("Executing delete from $target using '$objectID'.") if T(3);                  Trace("Executing delete from $target using '$objectID'.") if T(3);
2065                  my $rv = $db->SQL($stmt, 0, $objectID);                  my $rv = $db->SQL($stmt, 0, $objectID);
# Line 1315  Line 2074 
2074      return $retVal;      return $retVal;
2075  }  }
2076    
2077    =head3 Disconnect
2078    
2079        $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2080    
2081    Disconnect an entity instance from all the objects to which it is related. This
2082    will delete each relationship instance that connects to the specified entity.
2083    
2084    =over 4
2085    
2086    =item relationshipName
2087    
2088    Name of the relationship whose instances are to be deleted.
2089    
2090    =item originEntityName
2091    
2092    Name of the entity that is to be disconnected.
2093    
2094    =item originEntityID
2095    
2096    ID of the entity that is to be disconnected.
2097    
2098    =back
2099    
2100    =cut
2101    
2102    sub Disconnect {
2103        # Get the parameters.
2104        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
2105        # Get the relationship descriptor.
2106        my $structure = $self->_GetStructure($relationshipName);
2107        # Insure we have a relationship.
2108        if (! exists $structure->{from}) {
2109            Confess("$relationshipName is not a relationship in the database.");
2110        } else {
2111            # Get the database handle.
2112            my $dbh = $self->{_dbh};
2113            # We'll set this value to 1 if we find our entity.
2114            my $found = 0;
2115            # Loop through the ends of the relationship.
2116            for my $dir ('from', 'to') {
2117                if ($structure->{$dir} eq $originEntityName) {
2118                    $found = 1;
2119                    # Here we want to delete all relationship instances on this side of the
2120                    # entity instance.
2121                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2122                    # We do this delete in batches to keep it from dragging down the
2123                    # server.
2124                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2125                    my $done = 0;
2126                    while (! $done) {
2127                        # Do the delete.
2128                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2129                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2130                        $done = ($rows == 0 || ! $limitClause);
2131                    }
2132                }
2133            }
2134            # Insure we found the entity on at least one end.
2135            if (! $found) {
2136                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2137            }
2138        }
2139    }
2140    
2141    =head3 DeleteRow
2142    
2143        $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2144    
2145    Delete a row from a relationship. In most cases, only the from-link and to-link are
2146    needed; however, for relationships with intersection data values can be specified
2147    for the other fields using a hash.
2148    
2149    =over 4
2150    
2151    =item relationshipName
2152    
2153    Name of the relationship from which the row is to be deleted.
2154    
2155    =item fromLink
2156    
2157    ID of the entity instance in the From direction.
2158    
2159    =item toLink
2160    
2161    ID of the entity instance in the To direction.
2162    
2163    =item values
2164    
2165    Reference to a hash of other values to be used for filtering the delete.
2166    
2167    =back
2168    
2169    =cut
2170    
2171    sub DeleteRow {
2172        # Get the parameters.
2173        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2174        # Create a hash of all the filter information.
2175        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2176        if (defined $values) {
2177            for my $key (keys %{$values}) {
2178                $filter{$key} = $values->{$key};
2179            }
2180        }
2181        # Build an SQL statement out of the hash.
2182        my @filters = ();
2183        my @parms = ();
2184        for my $key (keys %filter) {
2185            push @filters, _FixName($key) . " = ?";
2186            push @parms, $filter{$key};
2187        }
2188        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2189        my $command = "DELETE FROM $relationshipName WHERE " .
2190                      join(" AND ", @filters);
2191        # Execute it.
2192        my $dbh = $self->{_dbh};
2193        $dbh->SQL($command, undef, @parms);
2194    }
2195    
2196    =head3 DeleteLike
2197    
2198        my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2199    
2200    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2201    filter, only fields from the relationship itself can be used.
2202    
2203    =over 4
2204    
2205    =item relName
2206    
2207    Name of the relationship whose records are to be deleted.
2208    
2209    =item filter
2210    
2211    A filter clause (L</Get>-style) for the delete query.
2212    
2213    =item parms
2214    
2215    Reference to a list of parameters for the filter clause.
2216    
2217    =item RETURN
2218    
2219    Returns a count of the number of rows deleted.
2220    
2221    =back
2222    
2223    =cut
2224    
2225    sub DeleteLike {
2226        # Get the parameters.
2227        my ($self, $objectName, $filter, $parms) = @_;
2228        # Declare the return variable.
2229        my $retVal;
2230        # Insure the parms argument is an array reference if the caller left it off.
2231        if (! defined($parms)) {
2232            $parms = [];
2233        }
2234        # Insure we have a relationship. The main reason for this is if we delete an entity
2235        # instance we have to yank out a bunch of other stuff with it.
2236        if ($self->IsEntity($objectName)) {
2237            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2238        } else {
2239            # Create the SQL command suffix to get the desierd records.
2240            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2241            # Convert it to a DELETE command.
2242            my $command = "DELETE $suffix";
2243            # Execute the command.
2244            my $dbh = $self->{_dbh};
2245            my $result = $dbh->SQL($command, 0, @{$parms});
2246            # Check the results. Note we convert the "0D0" result to a real zero.
2247            # A failure causes an abnormal termination, so the caller isn't going to
2248            # worry about it.
2249            if (! defined $result) {
2250                Confess("Error deleting from $objectName: " . $dbh->errstr());
2251            } elsif ($result == 0) {
2252                $retVal = 0;
2253            } else {
2254                $retVal = $result;
2255            }
2256        }
2257        # Return the result count.
2258        return $retVal;
2259    }
2260    
2261    =head3 SortNeeded
2262    
2263        my $parms = $erdb->SortNeeded($relationName);
2264    
2265    Return the pipe command for the sort that should be applied to the specified
2266    relation when creating the load file.
2267    
2268    For example, if the load file should be sorted ascending by the first
2269    field, this method would return
2270    
2271        sort -k1 -t"\t"
2272    
2273    If the first field is numeric, the method would return
2274    
2275        sort -k1n -t"\t"
2276    
2277    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2278    keys using a sort.
2279    
2280    =over 4
2281    
2282    =item relationName
2283    
2284    Name of the relation to be examined.
2285    
2286    =item
2287    
2288    Returns the sort command to use for sorting the relation, suitable for piping.
2289    
2290    =back
2291    
2292    =cut
2293    #: Return Type $;
2294    sub SortNeeded {
2295        # Get the parameters.
2296        my ($self, $relationName) = @_;
2297        # Declare a descriptor to hold the names of the key fields.
2298        my @keyNames = ();
2299        # Get the relation structure.
2300        my $relationData = $self->_FindRelation($relationName);
2301        # Find out if the relation is a primary entity relation,
2302        # a relationship relation, or a secondary entity relation.
2303        my $entityTable = $self->{_metaData}->{Entities};
2304        my $relationshipTable = $self->{_metaData}->{Relationships};
2305        if (exists $entityTable->{$relationName}) {
2306            # Here we have a primary entity relation.
2307            push @keyNames, "id";
2308        } elsif (exists $relationshipTable->{$relationName}) {
2309            # Here we have a relationship. We sort using the FROM index.
2310            my $relationshipData = $relationshipTable->{$relationName};
2311            my $index = $relationData->{Indexes}->{idxFrom};
2312            push @keyNames, @{$index->{IndexFields}};
2313        } else {
2314            # Here we have a secondary entity relation, so we have a sort on the ID field.
2315            push @keyNames, "id";
2316        }
2317        # Now we parse the key names into sort parameters. First, we prime the return
2318        # string.
2319        my $retVal = "sort -t\"\t\" ";
2320        # Get the relation's field list.
2321        my @fields = @{$relationData->{Fields}};
2322        # Loop through the keys.
2323        for my $keyData (@keyNames) {
2324            # Get the key and the ordering.
2325            my ($keyName, $ordering);
2326            if ($keyData =~ /^([^ ]+) DESC/) {
2327                ($keyName, $ordering) = ($1, "descending");
2328            } else {
2329                ($keyName, $ordering) = ($keyData, "ascending");
2330            }
2331            # Find the key's position and type.
2332            my $fieldSpec;
2333            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2334                my $thisField = $fields[$i];
2335                if ($thisField->{name} eq $keyName) {
2336                    # Get the sort modifier for this field type. The modifier
2337                    # decides whether we're using a character, numeric, or
2338                    # floating-point sort.
2339                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2340                    # If the index is descending for this field, denote we want
2341                    # to reverse the sort order on this field.
2342                    if ($ordering eq 'descending') {
2343                        $modifier .= "r";
2344                    }
2345                    # Store the position and modifier into the field spec, which
2346                    # will stop the inner loop. Note that the field number is
2347                    # 1-based in the sort command, so we have to increment the
2348                    # index.
2349                    $fieldSpec = ($i + 1) . $modifier;
2350                }
2351            }
2352            # Add this field to the sort command.
2353            $retVal .= " -k$fieldSpec";
2354        }
2355        # Return the result.
2356        return $retVal;
2357    }
2358    
2359  =head3 GetList  =head3 GetList
2360    
2361  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>      my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2362    
2363  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
2364  specified filter clause.  specified filter clause.
# Line 1345  Line 2386 
2386  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
2387  particular genus and sorts them by species name.  particular genus and sorts them by species name.
2388    
2389  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
2390    
2391  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
2392  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
# Line 1357  Line 2398 
2398    
2399  =item RETURN  =item RETURN
2400    
2401  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2402    
2403  =back  =back
2404    
# Line 1380  Line 2421 
2421    
2422  =head3 GetCount  =head3 GetCount
2423    
2424  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2425    
2426  Return the number of rows found by a specified query. This method would  Return the number of rows found by a specified query. This method would
2427  normally be used to count the records in a single table. For example, in a  normally be used to count the records in a single table. For example, in a
# Line 1431  Line 2472 
2472  sub GetCount {  sub GetCount {
2473      # Get the parameters.      # Get the parameters.
2474      my ($self, $objectNames, $filter, $params) = @_;      my ($self, $objectNames, $filter, $params) = @_;
2475        # Insure the params argument is an array reference if the caller left it off.
2476        if (! defined($params)) {
2477            $params = [];
2478        }
2479      # Declare the return variable.      # Declare the return variable.
2480      my $retVal;      my $retVal;
2481      # Find out if we're counting an entity or a relationship.      # Find out if we're counting an entity or a relationship.
# Line 1469  Line 2514 
2514    
2515  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
2516    
2517  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $sentence = $erdb->ComputeObjectSentence($objectName);
2518    
2519  Check an object name, and if it is a relationship convert it to a relationship sentence.  Check an object name, and if it is a relationship convert it to a relationship sentence.
2520    
# Line 1504  Line 2549 
2549    
2550  =head3 DumpRelations  =head3 DumpRelations
2551    
2552  C<< $erdb->DumpRelations($outputDirectory); >>      $erdb->DumpRelations($outputDirectory);
2553    
2554  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
2555  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 1544  Line 2589 
2589      }      }
2590  }  }
2591    
2592    =head3 InsertValue
2593    
2594        $erdb->InsertValue($entityID, $fieldName, $value);
2595    
2596    This method will insert a new value into the database. The value must be one
2597    associated with a secondary relation, since primary values cannot be inserted:
2598    they occur exactly once. Secondary values, on the other hand, can be missing
2599    or multiply-occurring.
2600    
2601    =over 4
2602    
2603    =item entityID
2604    
2605    ID of the object that is to receive the new value.
2606    
2607    =item fieldName
2608    
2609    Field name for the new value-- this includes the entity name, since
2610    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2611    
2612    =item value
2613    
2614    New value to be put in the field.
2615    
2616    =back
2617    
2618    =cut
2619    
2620    sub InsertValue {
2621        # Get the parameters.
2622        my ($self, $entityID, $fieldName, $value) = @_;
2623        # Parse the entity name and the real field name.
2624        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2625            my $entityName = $1;
2626            my $fieldTitle = $2;
2627            # Get its descriptor.
2628            if (!$self->IsEntity($entityName)) {
2629                Confess("$entityName is not a valid entity.");
2630            } else {
2631                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2632                # Find the relation containing this field.
2633                my $fieldHash = $entityData->{Fields};
2634                if (! exists $fieldHash->{$fieldTitle}) {
2635                    Confess("$fieldTitle not found in $entityName.");
2636                } else {
2637                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2638                    if ($relation eq $entityName) {
2639                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2640                    } else {
2641                        # Now we can create an INSERT statement.
2642                        my $dbh = $self->{_dbh};
2643                        my $fixedName = _FixName($fieldTitle);
2644                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2645                        # Execute the command.
2646                        $dbh->SQL($statement, 0, $entityID, $value);
2647                    }
2648                }
2649            }
2650        } else {
2651            Confess("$fieldName is not a valid field name.");
2652        }
2653    }
2654    
2655  =head3 InsertObject  =head3 InsertObject
2656    
2657  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>      $erdb->InsertObject($objectType, \%fieldHash);
2658    
2659  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2660  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 1555  Line 2663 
2663  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2664  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2665    
2666  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>      $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2667    
2668  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2669  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2670    
2671  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>      $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2672    
2673  =over 4  =over 4
2674    
# Line 1572  Line 2680 
2680    
2681  Hash of field names to values.  Hash of field names to values.
2682    
 =item RETURN  
   
 Returns 1 if successful, 0 if an error occurred.  
   
2683  =back  =back
2684    
2685  =cut  =cut
# Line 1674  Line 2778 
2778                  $retVal = $sth->execute(@parameterList);                  $retVal = $sth->execute(@parameterList);
2779                  if (!$retVal) {                  if (!$retVal) {
2780                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2781                      Trace("Insert error: $errorString.") if T(0);                      Confess("Error inserting into $relationName: $errorString");
2782                    } else {
2783                        Trace("Insert successful using $parameterList[0].") if T(3);
2784                  }                  }
2785              }              }
2786          }          }
2787      }      }
2788      # Return the success indicator.      # Return a 1 for backward compatability.
2789      return $retVal;      return 1;
2790    }
2791    
2792    =head3 UpdateEntity
2793    
2794        $erdb->UpdateEntity($entityName, $id, \%fields);
2795    
2796    Update the values of an entity. This is an unprotected update, so it should only be
2797    done if the database resides on a database server.
2798    
2799    =over 4
2800    
2801    =item entityName
2802    
2803    Name of the entity to update. (This is the entity type.)
2804    
2805    =item id
2806    
2807    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2808    
2809    =item fields
2810    
2811    Reference to a hash mapping field names to their new values. All of the fields named
2812    must be in the entity's primary relation, and they cannot any of them be the ID field.
2813    
2814    =back
2815    
2816    =cut
2817    
2818    sub UpdateEntity {
2819        # Get the parameters.
2820        my ($self, $entityName, $id, $fields) = @_;
2821        # Get a list of the field names being updated.
2822        my @fieldList = keys %{$fields};
2823        # Verify that the fields exist.
2824        my $checker = $self->GetFieldTable($entityName);
2825        for my $field (@fieldList) {
2826            if ($field eq 'id') {
2827                Confess("Cannot update the ID field for entity $entityName.");
2828            } elsif ($checker->{$field}->{relation} ne $entityName) {
2829                Confess("Cannot find $field in primary relation of $entityName.");
2830            }
2831        }
2832        # Build the SQL statement.
2833        my @sets = ();
2834        my @valueList = ();
2835        for my $field (@fieldList) {
2836            push @sets, _FixName($field) . " = ?";
2837            push @valueList, $fields->{$field};
2838        }
2839        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2840        # Add the ID to the list of binding values.
2841        push @valueList, $id;
2842        # Call SQL to do the work.
2843        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2844        # Check for errors.
2845        if ($rows == 0) {
2846            Confess("Entity $id of type $entityName not found.");
2847        }
2848  }  }
2849    
2850  =head3 LoadTable  =head3 LoadTable
2851    
2852  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      my $results = $erdb->LoadTable($fileName, $relationName, %options);
2853    
2854  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2855  first.  first.
# Line 1700  Line 2864 
2864    
2865  Name of the relation to be loaded. This is the same as the table name.  Name of the relation to be loaded. This is the same as the table name.
2866    
2867  =item truncateFlag  =item options
2868    
2869  TRUE if the table should be dropped and re-created, else FALSE  A hash of load options.
2870    
2871  =item RETURN  =item RETURN
2872    
# Line 1710  Line 2874 
2874    
2875  =back  =back
2876    
2877    The permissible options are as follows.
2878    
2879    =over 4
2880    
2881    =item truncate
2882    
2883    If TRUE, then the table will be erased before loading.
2884    
2885    =item mode
2886    
2887    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2888    This option is only applicable to a MySQL database.
2889    
2890    =item partial
2891    
2892    If TRUE, then it is assumed that this is a partial load, and the table will not
2893    be analyzed and compacted at the end.
2894    
2895    =back
2896    
2897  =cut  =cut
2898  sub LoadTable {  sub LoadTable {
2899      # Get the parameters.      # Get the parameters.
2900      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $fileName, $relationName, %options) = @_;
2901      # Create the statistical return object.      # Create the statistical return object.
2902      my $retVal = _GetLoadStats();      my $retVal = _GetLoadStats();
2903      # Trace the fact of the load.      # Trace the fact of the load.
# Line 1725  Line 2909 
2909      # Get the relation data.      # Get the relation data.
2910      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
2911      # Check the truncation flag.      # Check the truncation flag.
2912      if ($truncateFlag) {      if ($options{truncate}) {
2913          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2914          # Compute the row count estimate. We take the size of the load file,          # Compute the row count estimate. We take the size of the load file,
2915          # divide it by the estimated row size, and then multiply by 1.5 to          # divide it by the estimated row size, and then multiply by 2 to
2916          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2917          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2918          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2919          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 8 / $rowSize;
2920            if ($estimate < 1000) {
2921                $estimate = 1000;
2922            }
2923          # Re-create the table without its index.          # Re-create the table without its index.
2924          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2925          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 1748  Line 2935 
2935      # Load the table.      # Load the table.
2936      my $rv;      my $rv;
2937      eval {      eval {
2938          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
2939      };      };
2940      if (!defined $rv) {      if (!defined $rv) {
2941          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
2942          $retVal->AddMessage("Table load failed for $relationName using $fileName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2943          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
2944      } else {      } else {
2945          # Here we successfully loaded the table.          # Here we successfully loaded the table.
2946          $retVal->Add("tables");          $retVal->Add("tables");
2947          my $size = -s $fileName;          my $size = -s $fileName;
2948          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
2949            $retVal->Add("bytes", $size);
2950          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
2951          if ($truncateFlag && ! $dbh->{_preIndex}) {          if ($options{truncate}) {
2952                # Indexes are created here for PostGres. For PostGres, indexes are
2953                # best built at the end. For MySQL, the reverse is true.
2954                if (! $dbh->{_preIndex}) {
2955              eval {              eval {
2956                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
2957              };              };
# Line 1768  Line 2959 
2959                  $retVal->AddMessage($@);                  $retVal->AddMessage($@);
2960              }              }
2961          }          }
2962                # The full-text index (if any) is always built last, even for MySQL.
2963                # First we need to see if this table has a full-text index. Only
2964                # primary relations are allowed that privilege.
2965                Trace("Checking for full-text index on $relationName.") if T(2);
2966                if ($self->_IsPrimary($relationName)) {
2967                    $self->CreateSearchIndex($relationName);
2968                }
2969            }
2970      }      }
2971      # Analyze the table to improve performance.      # Analyze the table to improve performance.
2972        if (! $options{partial}) {
2973            Trace("Analyzing and compacting $relationName.") if T(3);
2974      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
2975        }
2976        Trace("$relationName load completed.") if T(3);
2977      # Return the statistics.      # Return the statistics.
2978      return $retVal;      return $retVal;
2979  }  }
2980    
2981  =head3 GenerateEntity  =head3 CreateSearchIndex
2982    
2983  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>      $erdb->CreateSearchIndex($objectName);
2984    
2985  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
2986  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.  
2987    
2988  =over 4  =over 4
2989    
2990  =item id  =item objectName
2991    
2992  ID to assign to the new entity.  Name of the entity or relationship to be indexed.
2993    
2994  =item type  =back
2995    
2996  Type name for the new entity.  =cut
2997    
2998  =item values  sub CreateSearchIndex {
2999        # Get the parameters.
3000        my ($self, $objectName) = @_;
3001        # Get the relation's entity/relationship structure.
3002        my $structure = $self->_GetStructure($objectName);
3003        # Get the database handle.
3004        my $dbh = $self->{_dbh};
3005        Trace("Checking for search fields in $objectName.") if T(3);
3006        # Check for a searchable fields list.
3007        if (exists $structure->{searchFields}) {
3008            # Here we know that we need to create a full-text search index.
3009            # Get an SQL-formatted field name list.
3010            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
3011            # Create the index. If it already exists, it will be dropped.
3012            $dbh->create_index(tbl => $objectName, idx => "search_idx",
3013                               flds => $fields, kind => 'fulltext');
3014            Trace("Index created for $fields in $objectName.") if T(2);
3015        }
3016    }
3017    
3018    =head3 DropRelation
3019    
3020        $erdb->DropRelation($relationName);
3021    
3022    Physically drop a relation from the database.
3023    
3024  Hash containing additional values that might be needed by the data generation methods (optional).  =over 4
3025    
3026    =item relationName
3027    
3028    Name of the relation to drop. If it does not exist, this method will have
3029    no effect.
3030    
3031  =back  =back
3032    
3033  =cut  =cut
3034    
3035  sub GenerateEntity {  sub DropRelation {
3036      # Get the parameters.      # Get the parameters.
3037      my ($self, $id, $type, $values) = @_;      my ($self, $relationName) = @_;
3038      # Create the return hash.      # Get the database handle.
3039      my $this = { id => $id };      my $dbh = $self->{_dbh};
3040      # Get the metadata structure.      # Drop the relation. The method used here has no effect if the relation
3041      my $metadata = $self->{_metaData};      # does not exist.
3042      # Get this entity's list of fields.      Trace("Invoking DB Kernel to drop $relationName.") if T(3);
3043      if (!exists $metadata->{Entities}->{$type}) {      $dbh->drop_table(tbl => $relationName);
3044          Confess("Unrecognized entity type $type in GenerateEntity.");  }
3045      } else {  
3046          my $entity = $metadata->{Entities}->{$type};  =head3 MatchSqlPattern
3047          my $fields = $entity->{Fields};  
3048          # Generate data from the fields.      my $matched = ERDB::MatchSqlPattern($value, $pattern);
3049          _GenerateFields($this, $fields, $type, $values);  
3050    Determine whether or not a specified value matches an SQL pattern. An SQL
3051    pattern has two wild card characters: C<%> that matches multiple characters,
3052    and C<_> that matches a single character. These can be escaped using a
3053    backslash (C<\>). We pull this off by converting the SQL pattern to a
3054    PERL regular expression. As per SQL rules, the match is case-insensitive.
3055    
3056    =over 4
3057    
3058    =item value
3059    
3060    Value to be matched against the pattern. Note that an undefined or empty
3061    value will not match anything.
3062    
3063    =item pattern
3064    
3065    SQL pattern against which to match the value. An undefined or empty pattern will
3066    match everything.
3067    
3068    =item RETURN
3069    
3070    Returns TRUE if the value and pattern match, else FALSE.
3071    
3072    =back
3073    
3074    =cut
3075    
3076    sub MatchSqlPattern {
3077        # Get the parameters.
3078        my ($value, $pattern) = @_;
3079        # Declare the return variable.
3080        my $retVal;
3081        # Insure we have a pattern.
3082        if (! defined($pattern) || $pattern eq "") {
3083            $retVal = 1;
3084        } else {
3085            # Break the pattern into pieces around the wildcard characters. Because we
3086            # use parentheses in the split function's delimiter expression, we'll get
3087            # list elements for the delimiters as well as the rest of the string.
3088            my @pieces = split /([_%]|\\[_%])/, $pattern;
3089            # Check some fast special cases.
3090            if ($pattern eq '%') {
3091                # A null pattern matches everything.
3092                $retVal = 1;
3093            } elsif (@pieces == 1) {
3094                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
3095                $retVal = (lc($value) eq lc($pattern));
3096            } elsif (@pieces == 2 && $pieces[1] eq '%') {
3097                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
3098                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
3099            } else {
3100                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
3101                my $realPattern = "";
3102                for my $piece (@pieces) {
3103                    # Determine the type of piece.
3104                    if ($piece eq "") {
3105                        # Empty pieces are ignored.
3106                    } elsif ($piece eq "%") {
3107                        # Here we have a multi-character wildcard. Note that it can match
3108                        # zero or more characters.
3109                        $realPattern .= ".*"
3110                    } elsif ($piece eq "_") {
3111                        # Here we have a single-character wildcard.
3112                        $realPattern .= ".";
3113                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
3114                        # This is an escape sequence (which is a rare thing, actually).
3115                        $realPattern .= substr($piece, 1, 1);
3116                    } else {
3117                        # Here we have raw text.
3118                        $realPattern .= quotemeta($piece);
3119                    }
3120                }
3121                # Do the match.
3122                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
3123            }
3124      }      }
3125      # Return the hash created.      # Return the result.
3126      return $this;      return $retVal;
3127  }  }
3128    
3129  =head3 GetEntity  =head3 GetEntity
3130    
3131  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $entityObject = $erdb->GetEntity($entityType, $ID);
3132    
3133  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
3134    
# Line 1851  Line 3144 
3144    
3145  =item RETURN  =item RETURN
3146    
3147  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
3148  instance is found with the specified key.  instance is found with the specified key.
3149    
3150  =back  =back
# Line 1869  Line 3162 
3162      return $retVal;      return $retVal;
3163  }  }
3164    
3165    =head3 GetChoices
3166    
3167        my @values = $erdb->GetChoices($entityName, $fieldName);
3168    
3169    Return a list of all the values for the specified field that are represented in the
3170    specified entity.
3171    
3172    Note that if the field is not indexed, then this will be a very slow operation.
3173    
3174    =over 4
3175    
3176    =item entityName
3177    
3178    Name of an entity in the database.
3179    
3180    =item fieldName
3181    
3182    Name of a field belonging to the entity. This is a raw field name without
3183    the standard parenthesized notation used in most calls.
3184    
3185    =item RETURN
3186    
3187    Returns a list of the distinct values for the specified field in the database.
3188    
3189    =back
3190    
3191    =cut
3192    
3193    sub GetChoices {
3194        # Get the parameters.
3195        my ($self, $entityName, $fieldName) = @_;
3196        # Declare the return variable.
3197        my @retVal;
3198        # Get the entity data structure.
3199        my $entityData = $self->_GetStructure($entityName);
3200        # Get the field.
3201        my $fieldHash = $entityData->{Fields};
3202        if (! exists $fieldHash->{$fieldName}) {
3203            Confess("$fieldName not found in $entityName.");
3204        } else {
3205            # Get the name of the relation containing the field.
3206            my $relation = $fieldHash->{$fieldName}->{relation};
3207            # Fix up the field name.
3208            my $realName = _FixName($fieldName);
3209            # Get the database handle.
3210            my $dbh = $self->{_dbh};
3211            # Query the database.
3212            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
3213            # Clean the results. They are stored as a list of lists, and we just want the one list.
3214            @retVal = sort map { $_->[0] } @{$results};
3215        }
3216        # Return the result.
3217        return @retVal;
3218    }
3219    
3220  =head3 GetEntityValues  =head3 GetEntityValues
3221    
3222  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3223    
3224  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance. If the entity instance
3225    does not exist, an empty list is returned.
3226    
3227  =over 4  =over 4
3228    
# Line 1914  Line 3263 
3263    
3264  =head3 GetAll  =head3 GetAll
3265    
3266  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3267    
3268  Return a list of values taken from the objects returned by a query. The first three  Return a list of values taken from the objects returned by a query. The first three
3269  parameters correspond to the parameters of the L</Get> method. The final parameter is  parameters correspond to the parameters of the L</Get> method. The final parameter is
# Line 1928  Line 3277 
3277  fields specified returns multiple values, they are flattened in with the rest. For  fields specified returns multiple values, they are flattened in with the rest. For
3278  example, the following call will return a list of the features in a particular  example, the following call will return a list of the features in a particular
3279  spreadsheet cell, and each feature will be represented by a list containing the  spreadsheet cell, and each feature will be represented by a list containing the
3280  feature ID followed by all of its aliases.  feature ID followed by all of its essentiality determinations.
3281    
3282  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)']);
3283    
3284  =over 4  =over 4
3285    
# Line 2001  Line 3350 
3350          push @retVal, \@rowData;          push @retVal, \@rowData;
3351          $fetched++;          $fetched++;
3352      }      }
3353        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3354      # Return the resulting list.      # Return the resulting list.
3355      return @retVal;      return @retVal;
3356  }  }
3357    
3358    =head3 Exists
3359    
3360        my $found = $sprout->Exists($entityName, $entityID);
3361    
3362    Return TRUE if an entity exists, else FALSE.
3363    
3364    =over 4
3365    
3366    =item entityName
3367    
3368    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3369    
3370    =item entityID
3371    
3372    ID of the entity instance whose existence is to be checked.
3373    
3374    =item RETURN
3375    
3376    Returns TRUE if the entity instance exists, else FALSE.
3377    
3378    =back
3379    
3380    =cut
3381    #: Return Type $;
3382    sub Exists {
3383        # Get the parameters.
3384        my ($self, $entityName, $entityID) = @_;
3385        # Check for the entity instance.
3386        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3387        my $testInstance = $self->GetEntity($entityName, $entityID);
3388        # Return an existence indicator.
3389        my $retVal = ($testInstance ? 1 : 0);
3390        return $retVal;
3391    }
3392    
3393  =head3 EstimateRowSize  =head3 EstimateRowSize
3394    
3395  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>      my $rowSize = $erdb->EstimateRowSize($relName);
3396    
3397  Estimate the row size of the specified relation. The estimated row size is computed by adding  Estimate the row size of the specified relation. The estimated row size is computed by adding
3398  up the average length for each data type.  up the average length for each data type.
# Line 2018  Line 3403 
3403    
3404  Name of the relation whose estimated row size is desired.  Name of the relation whose estimated row size is desired.
3405    
3406  =item RETURN  =item RETURN
3407    
3408    Returns an estimate of the row size for the specified relation.
3409    
3410    =back
3411    
3412    =cut
3413    #: Return Type $;
3414    sub EstimateRowSize {
3415        # Get the parameters.
3416        my ($self, $relName) = @_;
3417        # Declare the return variable.
3418        my $retVal = 0;
3419        # Find the relation descriptor.
3420        my $relation = $self->_FindRelation($relName);
3421        # Get the list of fields.
3422        for my $fieldData (@{$relation->{Fields}}) {
3423            # Get the field type and add its length.
3424            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3425            $retVal += $fieldLen;
3426        }
3427        # Return the result.
3428        return $retVal;
3429    }
3430    
3431    =head3 GetFieldTable
3432    
3433        my $fieldHash = $self->GetFieldTable($objectnName);
3434    
3435    Get the field structure for a specified entity or relationship.
3436    
3437    =over 4
3438    
3439    =item objectName
3440    
3441    Name of the desired entity or relationship.
3442    
3443    =item RETURN
3444    
3445    The table containing the field descriptors for the specified object.
3446    
3447    =back
3448    
3449    =cut
3450    
3451    sub GetFieldTable {
3452        # Get the parameters.
3453        my ($self, $objectName) = @_;
3454        # Get the descriptor from the metadata.
3455        my $objectData = $self->_GetStructure($objectName);
3456        # Return the object's field table.
3457        return $objectData->{Fields};
3458    }
3459    
3460    =head3 SplitKeywords
3461    
3462        my @keywords = ERDB::SplitKeywords($keywordString);
3463    
3464    This method returns a list of the positive keywords in the specified
3465    keyword string. All of the operators will have been stripped off,
3466    and if the keyword is preceded by a minus operator (C<->), it will
3467    not be in the list returned. The idea here is to get a list of the
3468    keywords the user wants to see. The list will be processed to remove
3469    duplicates.
3470    
3471    It is possible to create a string that confuses this method. For example
3472    
3473        frog toad -frog
3474    
3475    would return both C<frog> and C<toad>. If this is a problem we can deal
3476    with it later.
3477    
3478    =over 4
3479    
3480    =item keywordString
3481    
3482    The keyword string to be parsed.
3483    
3484    =item RETURN
3485    
3486    Returns a list of the words in the keyword string the user wants to
3487    see.
3488    
3489    =back
3490    
3491    =cut
3492    
3493    sub SplitKeywords {
3494        # Get the parameters.
3495        my ($keywordString) = @_;
3496        # Make a safety copy of the string. (This helps during debugging.)
3497        my $workString = $keywordString;
3498        # Convert operators we don't care about to spaces.
3499        $workString =~ tr/+"()<>/ /;
3500        # Split the rest of the string along space boundaries. Note that we
3501        # eliminate any words that are zero length or begin with a minus sign.
3502        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3503        # Use a hash to remove duplicates.
3504        my %words = map { $_ => 1 } @wordList;
3505        # Return the result.
3506        return sort keys %words;
3507    }
3508    
3509    =head3 ValidateFieldName
3510    
3511        my $okFlag = ERDB::ValidateFieldName($fieldName);
3512    
3513    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3514    be hyphenated words subject to certain restrictions.
3515    
3516    =over 4
3517    
3518    =item fieldName
3519    
3520    Field name to be validated.
3521    
3522    =item RETURN
3523    
3524    Returns TRUE if the field name is valid, else FALSE.
3525    
3526    =back
3527    
3528    =cut
3529    
3530    sub ValidateFieldName {
3531        # Get the parameters.
3532        my ($fieldName) = @_;
3533        # Declare the return variable. The field name is valid until we hear
3534        # differently.
3535        my $retVal = 1;
3536        # Compute the maximum name length.
3537        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3538        # Look for bad stuff in the name.
3539        if ($fieldName =~ /--/) {
3540            # Here we have a doubled minus sign.
3541            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3542            $retVal = 0;
3543        } elsif ($fieldName !~ /^[A-Za-z]/) {
3544            # Here the field name is missing the initial letter.
3545            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3546            $retVal = 0;
3547        } elsif (length($fieldName) > $maxLen) {
3548            # Here the field name is too long.
3549            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3550        } else {
3551            # Strip out the minus signs. Everything remaining must be a letter,
3552            # underscore, or digit.
3553            my $strippedName = $fieldName;
3554            $strippedName =~ s/-//g;
3555            if ($strippedName !~ /^(\w|\d)+$/) {
3556                Trace("Field name $fieldName contains illegal characters.") if T(1);
3557                $retVal = 0;
3558            }
3559        }
3560        # Return the result.
3561        return $retVal;
3562    }
3563    
3564    =head3 ReadMetaXML
3565    
3566        my $rawMetaData = ERDB::ReadDBD($fileName);
3567    
3568    This method reads a raw database definition XML file and returns it.
3569    Normally, the metadata used by the ERDB system has been processed and
3570    modified to make it easier to load and retrieve the data; however,
3571    this method can be used to get the data in its raw form.
3572    
3573    =over 4
3574    
3575    =item fileName
3576    
3577    Name of the XML file to read.
3578    
3579    =item RETURN
3580    
3581    Returns a hash reference containing the raw XML data from the specified file.
3582    
3583    =back
3584    
3585    =cut
3586    
3587    sub ReadMetaXML {
3588        # Get the parameters.
3589        my ($fileName) = @_;
3590        # Read the XML.
3591        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3592        Trace("XML metadata loaded from file $fileName.") if T(1);
3593        # Return the result.
3594        return $retVal;
3595    }
3596    
3597    =head3 GetEntityFieldHash
3598    
3599        my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3600    
3601    Get the field hash of the named entity in the specified raw XML structure.
3602    The field hash may not exist, in which case we need to create it.
3603    
3604    =over 4
3605    
3606    =item structure
3607    
3608    Raw XML structure defininng the database. This is not the run-time XML used by
3609    an ERDB object, since that has all sorts of optimizations built-in.
3610    
3611    =item entityName
3612    
3613    Name of the entity whose field structure is desired.
3614    
3615    =item RETURN
3616    
3617    Returns the field hash used to define the entity's fields.
3618    
3619    =back
3620    
3621    =cut
3622    
3623    sub GetEntityFieldHash {
3624        # Get the parameters.
3625        my ($structure, $entityName) = @_;
3626        # Get the entity structure.
3627        my $entityData = $structure->{Entities}->{$entityName};
3628        # Look for a field structure.
3629        my $retVal = $entityData->{Fields};
3630        # If it doesn't exist, create it.
3631        if (! defined($retVal)) {
3632            $entityData->{Fields} = {};
3633            $retVal = $entityData->{Fields};
3634        }
3635        # Return the result.
3636        return $retVal;
3637    }
3638    
3639    =head3 WriteMetaXML
3640    
3641        ERDB::WriteMetaXML($structure, $fileName);
3642    
3643    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3644    used to update the database definition. It must be used with care, however, since it
3645    will only work on a raw structure, not on the processed structure created by an ERDB
3646    constructor.
3647    
3648    =over 4
3649    
3650    =item structure
3651    
3652    XML structure to be written to the file.
3653    
3654    =item fileName
3655    
3656    Name of the output file to which the updated XML should be stored.
3657    
3658    =back
3659    
3660    =cut
3661    
3662    sub WriteMetaXML {
3663        # Get the parameters.
3664        my ($structure, $fileName) = @_;
3665        # Compute the output.
3666        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3667        # Write it to the file.
3668        my $xmlOut = Open(undef, ">$fileName");
3669        print $xmlOut $fileString;
3670    }
3671    
3672    
3673    =head3 HTMLNote
3674    
3675    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3676    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3677    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3678    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3679    
3680        my $realHtml = ERDB::HTMLNote($dataString);
3681    
3682    =over 4
3683    
3684    =item dataString
3685    
3686    String to convert to HTML.
3687    
3688    =item RETURN
3689    
3690    An HTML string derived from the input string.
3691    
3692    =back
3693    
3694    =cut
3695    
3696    sub HTMLNote {
3697        # Get the parameter.
3698        my ($dataString) = @_;
3699        # HTML-escape the text.
3700        my $retVal = CGI::escapeHTML($dataString);
3701        # Substitute the bulletin board codes.
3702        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3703        $retVal =~ s!\[p\]!</p><p>!g;
3704        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3705        $retVal =~ s!\[/link\]!</a>!g;
3706        # Return the result.
3707        return $retVal;
3708    }
3709    
3710    =head3 WikiNote
3711    
3712    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3713    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3714    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3715    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3716    
3717        my $wikiText = ERDB::WikiNote($dataString);
3718    
3719    =over 4
3720    
3721    =item dataString
3722    
3723    String to convert to Wiki text.
3724    
3725    =item RETURN
3726    
3727    An Wiki text string derived from the input string.
3728    
3729    =back
3730    
3731    =cut
3732    
3733    sub WikiNote {
3734        # Get the parameter.
3735        my ($dataString) = @_;
3736        # HTML-escape the text.
3737        my $retVal = CGI::escapeHTML($dataString);
3738        # Substitute the bulletin board codes.
3739        my $italic = WikiTools::ItalicCode();
3740        $retVal =~ s/\[\/?i\]/$italic/g;
3741        my $bold = WikiTools::BoldCode();
3742        $retVal =~ s/\[\/?b\]/$bold/g;
3743        # Paragraph breaks are the same no matter which Wiki you're using.
3744        $retVal =~ s!\[p\]!\n\n!g;
3745        # Now we do the links, which are complicated by the need to know two
3746        # things: the target URL and the text.
3747        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3748            # Replace the matched string with the Wiki markup for links. Note that
3749            # $-[0] is the starting position of the match for the entire expression,
3750            # and $+[0] is past the ending position.
3751            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3752        }
3753        # Return the result.
3754        return $retVal;
3755    }
3756    
3757    =head3 BeginTran
3758    
3759        $erdb->BeginTran();
3760    
3761    Start a database transaction.
3762    
3763    =cut
3764    
3765    sub BeginTran {
3766        my ($self) = @_;
3767        $self->{_dbh}->begin_tran();
3768    
3769    }
3770    
3771    =head3 CommitTran
3772    
3773        $erdb->CommitTran();
3774    
3775    Commit an active database transaction.
3776    
3777    =cut
3778    
3779    sub CommitTran {
3780        my ($self) = @_;
3781        $self->{_dbh}->commit_tran();
3782    }
3783    
3784    =head3 RollbackTran
3785    
3786        $erdb->RollbackTran();
3787    
3788    Roll back an active database transaction.
3789    
3790    =cut
3791    
3792    sub RollbackTran {
3793        my ($self) = @_;
3794        $self->{_dbh}->roll_tran();
3795    }
3796    
3797    =head3 UpdateField
3798    
3799        my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3800    
3801    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3802    returned.
3803    
3804    =over 4
3805    
3806    =item fieldName
3807    
3808  Returns an estimate of the row size for the specified relation.  Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3809    
3810  =back  =item oldValue
3811    
3812  =cut  Value to be modified. All occurrences of this value in the named field will be replaced by the
3813  #: Return Type $;  new value.
 sub EstimateRowSize {  
     # Get the parameters.  
     my ($self, $relName) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Find the relation descriptor.  
     my $relation = $self->_FindRelation($relName);  
     # Get the list of fields.  
     for my $fieldData (@{$relation->{Fields}}) {  
         # Get the field type and add its length.  
         my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};  
         $retVal += $fieldLen;  
     }  
     # Return the result.  
     return $retVal;  
 }  
3814    
3815  =head3 GetFieldTable  =item newValue
3816    
3817  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>  New value to be substituted for the old value when it's found.
3818    
3819  Get the field structure for a specified entity or relationship.  =item filter
3820    
3821  =over 4  A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3822    
3823  =item objectName  =item parms
3824    
3825  Name of the desired entity or relationship.  Reference to a list of parameter values in the filter.
3826    
3827  =item RETURN  =item RETURN
3828    
3829  The table containing the field descriptors for the specified object.  Returns the number of rows modified.
3830    
3831  =back  =back
3832    
3833  =cut  =cut
3834    
3835  sub GetFieldTable {  sub UpdateField {
3836      # Get the parameters.      # Get the parameters.
3837      my ($self, $objectName) = @_;      my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3838      # Get the descriptor from the metadata.      # Get the object and field names from the field name parameter.
3839      my $objectData = $self->_GetStructure($objectName);      $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3840      # Return the object's field table.      my $objectName = $1;
3841      return $objectData->{Fields};      my $realFieldName = _FixName($2);
3842        # Add the old value to the filter. Note we allow the possibility that no
3843        # filter was specified.
3844        my $realFilter = "$fieldName = ?";
3845        if ($filter) {
3846            $realFilter .= " AND $filter";
3847        }
3848        # Format the query filter.
3849        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3850            $self->_SetupSQL([$objectName], $realFilter);
3851        # Create the query. Since there is only one object name, the mapped-name data is not
3852        # necessary. Neither is the FROM clause.
3853        $suffix =~ s/^FROM.+WHERE\s+//;
3854        # Create the update statement.
3855        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3856        # Get the database handle.
3857        my $dbh = $self->{_dbh};
3858        # Add the old and new values to the parameter list. Note we allow the possibility that
3859        # there are no user-supplied parameters.
3860        my @params = ($newValue, $oldValue);
3861        if (defined $parms) {
3862            push @params, @{$parms};
3863        }
3864        # Execute the update.
3865        my $retVal = $dbh->SQL($command, 0, @params);
3866        # Make the funky zero a real zero.
3867        if ($retVal == 0) {
3868            $retVal = 0;
3869        }
3870        # Return the result.
3871        return $retVal;
3872  }  }
3873    
3874    
3875  =head2 Data Mining Methods  =head2 Data Mining Methods
3876    
3877  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3878    
3879  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3880    
3881  Return a list of the useful attributes that would be returned by a B<Cross> call  Return a list of the useful attributes that would be returned by a B<Cross> call
3882  from an entity of the source entity type through the specified relationship. This  from an entity of the source entity type through the specified relationship. This
# Line 2137  Line 3937 
3937    
3938  =head3 FindColumn  =head3 FindColumn
3939    
3940  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
3941    
3942  Return the location a desired column in a data mining header line. The data  Return the location a desired column in a data mining header line. The data
3943  mining header line is a tab-separated list of column names. The column  mining header line is a tab-separated list of column names. The column
# Line 2195  Line 3995 
3995    
3996  =head3 ParseColumns  =head3 ParseColumns
3997    
3998  C<< my @columns = ERDB->ParseColumns($line); >>      my @columns = ERDB::ParseColumns($line);
3999    
4000  Convert the specified data line to a list of columns.  Convert the specified data line to a list of columns.
4001    
# Line 2216  Line 4016 
4016    
4017  sub ParseColumns {  sub ParseColumns {
4018      # Get the parameters.      # Get the parameters.
4019      my ($self, $line) = @_;      my ($line) = @_;
4020      # Chop off the line-end.      # Chop off the line-end.
4021      chomp $line;      chomp $line;
4022      # Split it into a list.      # Split it into a list.
# Line 2225  Line 4025 
4025      return @retVal;      return @retVal;
4026  }  }
4027    
4028    =head2 Virtual Methods
4029    
4030    =head3 _CreatePPOIndex
4031    
4032        my $index = ERDB::_CreatePPOIndex($indexObject);
4033    
4034    Convert the XML for an ERDB index to the XML structure for a PPO
4035    index.
4036    
4037    =over 4
4038    
4039    =item indexObject
4040    
4041    ERDB XML structure for an index.
4042    
4043    =item RETURN
4044    
4045    PPO XML structure for the same index.
4046    
4047    =back
4048    
4049    =cut
4050    
4051    sub _CreatePPOIndex {
4052        # Get the parameters.
4053        my ($indexObject) = @_;
4054        # The incoming index contains a list of the index fields in the IndexFields
4055        # member. We loop through it to create the index tags.
4056        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
4057        # Wrap the fields in attribute tags.
4058        my $retVal = { attribute => \@fields };
4059        # Return the result.
4060        return $retVal;
4061    }
4062    
4063    =head3 _CreatePPOField
4064    
4065        my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
4066    
4067    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
4068    
4069    =over 4
4070    
4071    =item fieldName
4072    
4073    Name of the scalar field.
4074    
4075    =item fieldObject
4076    
4077    ERDB XML structure describing the field.
4078    
4079    =item RETURN
4080    
4081    Returns a PPO XML structure for the same field.
4082    
4083    =back
4084    
4085    =cut
4086    
4087    sub _CreatePPOField {
4088        # Get the parameters.
4089        my ($fieldName, $fieldObject) = @_;
4090        # Get the field type.
4091        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
4092        # Fix up the field name.
4093        $fieldName = _FixName($fieldName);
4094        # Build the scalar tag.
4095        my $retVal = { label => $fieldName, type => $type };
4096        # Return the result.
4097        return $retVal;
4098    }
4099    
4100    =head3 CleanKeywords
4101    
4102        my $cleanedString = $erdb->CleanKeywords($searchExpression);
4103    
4104    Clean up a search expression or keyword list. This is a virtual method that may
4105    be overridden by the subclass. The base-class method removes extra spaces
4106    and converts everything to lower case.
4107    
4108    =over 4
4109    
4110    =item searchExpression
4111    
4112    Search expression or keyword list to clean. Note that a search expression may
4113    contain boolean operators which need to be preserved. This includes leading
4114    minus signs.
4115    
4116    =item RETURN
4117    
4118    Cleaned expression or keyword list.
4119    
4120    =back
4121    
4122    =cut
4123    
4124    sub CleanKeywords {
4125        # Get the parameters.
4126        my ($self, $searchExpression) = @_;
4127        # Lower-case the expression and copy it into the return variable. Note that we insure we
4128        # don't accidentally end up with an undefined value.
4129        my $retVal = lc($searchExpression || "");
4130        # Remove extra spaces.
4131        $retVal =~ s/\s+/ /g;
4132        $retVal =~ s/(^\s+)|(\s+$)//g;
4133        # Return the result.
4134        return $retVal;
4135    }
4136    
4137    =head3 GetSourceObject
4138    
4139        my $source = $erdb->GetSourceObject($entityName);
4140    
4141    Return the object to be used in loading special attributes of the specified entity. The
4142    algorithm for loading special attributes is stored in the C<DataGen> elements of the
4143    XML
4144    
4145  =head2 Internal Utility Methods  =head2 Internal Utility Methods
4146    
4147  =head3 SetupSQL  =head3 _RelationMap
4148    
4149        my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
4150    
4151    Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
4152    to determine how to interpret the results of the query.
4153    
4154    =over 4
4155    
4156    =item mappedNameHashRef
4157    
4158    Reference to a hash that maps modified object names to real object names.
4159    
4160    =item mappedNameListRef
4161    
4162    Reference to a list of modified object names in the order they appear in the
4163    SELECT list.
4164    
4165    =item RETURN
4166    
4167    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
4168    query followed by the actual name of that object. This enables the B<ERDBObject> to
4169    determine the order of the tables in the query and which object name belongs to each
4170    mapped object name. Most of the time these two values are the same; however, if a
4171    relation occurs twice in the query, the relation name in the field list and WHERE
4172    clause will use a mapped name (generally the actual relation name with a numeric
4173    suffix) that does not match the actual relation name.
4174    
4175    =back
4176    
4177    =cut
4178    
4179    sub _RelationMap {
4180        # Get the parameters.
4181        my ($mappedNameHashRef, $mappedNameListRef) = @_;
4182        # Declare the return variable.
4183        my @retVal = ();
4184        # Build the map.
4185        for my $mappedName (@{$mappedNameListRef}) {
4186            push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
4187        }
4188        # Return it.
4189        return @retVal;
4190    }
4191    
4192    
4193    =head3 _SetupSQL
4194    
4195  Process a list of object names and a filter clause so that they can be used to  Process a list of object names and a filter clause so that they can be used to
4196  build an SQL statement. This method takes in a reference to a list of object names  build an SQL statement. This method takes in a reference to a list of object names
# Line 2247  Line 4210 
4210  A string containing the WHERE clause for the query (without the C<WHERE>) and also  A string containing the WHERE clause for the query (without the C<WHERE>) and also
4211  optionally the C<ORDER BY> and C<LIMIT> clauses.  optionally the C<ORDER BY> and C<LIMIT> clauses.
4212    
4213    =item matchClause
4214    
4215    An optional full-text search clause. If specified, it will be inserted at the
4216    front of the WHERE clause. It should already be SQL-formatted; that is, the
4217    field names should be in the form I<table>C<.>I<fieldName>.
4218    
4219  =item RETURN  =item RETURN
4220    
4221  Returns a three-element list. The first element is the SQL statement suffix, beginning  Returns a three-element list. The first element is the SQL statement suffix, beginning
# Line 2259  Line 4228 
4228  =cut  =cut
4229    
4230  sub _SetupSQL {  sub _SetupSQL {
4231      my ($self, $objectNames, $filterClause) = @_;      my ($self, $objectNames, $filterClause, $matchClause) = @_;
4232      # Adjust the list of object names to account for multiple occurrences of the      # Adjust the list of object names to account for multiple occurrences of the
4233      # same object. We start with a hash table keyed on object name that will      # same object. We start with a hash table keyed on object name that will
4234      # return the object suffix. The first time an object is encountered it will      # return the object suffix. The first time an object is encountered it will
# Line 2308  Line 4277 
4277      # FROM name1, name2, ... nameN      # FROM name1, name2, ... nameN
4278      #      #
4279      my $suffix = "FROM " . join(', ', @fromList);      my $suffix = "FROM " . join(', ', @fromList);
4280        # Now for the WHERE. First, we need a place for the filter string.
4281        my $filterString = "";
4282        # We will also keep a list of conditions to add to the WHERE clause in order to link
4283        # entities and relationships as well as primary relations to secondary ones.
4284        my @joinWhere = ();
4285      # Check for a filter clause.      # Check for a filter clause.
4286      if ($filterClause) {      if ($filterClause) {
4287          # Here we have one, so we convert its field names and add it to the query. First,          # Here we have one, so we convert its field names and add it to the query. First,
4288          # We create a copy of the filter string we can work with.          # We create a copy of the filter string we can work with.
4289          my $filterString = $filterClause;          $filterString = $filterClause;
4290          # Next, we sort the object names by length. This helps protect us from finding          # Next, we sort the object names by length. This helps protect us from finding
4291          # object names inside other object names when we're doing our search and replace.          # object names inside other object names when we're doing our search and replace.
4292          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;          my @sortedNames = sort { length($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 = ();  
4293          # The final preparatory step is to create a hash table of relation names. The          # The final preparatory step is to create a hash table of relation names. The
4294          # table begins with the relation names already in the SELECT command. We may          # table begins with the relation names already in the SELECT command. We may
4295          # need to add relations later if there is filtering on a field in a secondary          # need to add relations later if there is filtering on a field in a secondary
# Line 2386  Line 4357 
4357                  }                  }
4358              }              }
4359          }          }
4360        }
4361          # The next step is to join the objects together. We only need to do this if there          # The next step is to join the objects together. We only need to do this if there
4362          # is more than one object in the object list. We start with the first object and          # is more than one object in the object list. We start with the first object and
4363          # run through the objects after it. Note also that we make a safety copy of the          # run through the objects after it. Note also that we make a safety copy of the
4364          # list before running through it.      # list before running through it, because we shift off the first object before
4365        # processing the rest.
4366          my @mappedObjectList = @mappedNameList;          my @mappedObjectList = @mappedNameList;
4367          my $lastMappedObject = shift @mappedObjectList;          my $lastMappedObject = shift @mappedObjectList;
4368          # Get the join table.          # Get the join table.
# Line 2418  Line 4391 
4391          # here is we want the filter clause to be empty if there's no WHERE filter.          # here is we want the filter clause to be empty if there's no WHERE filter.
4392          # We'll put the ORDER BY / LIMIT clauses in the following variable.          # We'll put the ORDER BY / LIMIT clauses in the following variable.
4393          my $orderClause = "";          my $orderClause = "";
4394        # This is only necessary if we have a filter string in which the ORDER BY
4395        # and LIMIT clauses can live.
4396        if ($filterString) {
4397          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
4398          # operator so that we find the first occurrence of either verb.          # operator so that we find the first occurrence of either verb.
4399          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
# Line 2426  Line 4402 
4402              $orderClause = $2 . substr($filterString, $pos);              $orderClause = $2 . substr($filterString, $pos);
4403              $filterString = $1;              $filterString = $1;
4404          }          }
4405          # Add the filter and the join clauses (if any) to the SELECT command.      }
4406        # All the things that are supposed to be in the WHERE clause of the
4407        # SELECT command need to be put into @joinWhere so we can string them
4408        # together. We begin with the match clause. This is important,
4409        # because the match clause's parameter mark must precede any parameter
4410        # marks in the filter string.
4411        if ($matchClause) {
4412            push @joinWhere, $matchClause;
4413        }
4414        # Add the filter string. We put it in parentheses to avoid operator
4415        # precedence problems with the match clause or the joins.
4416          if ($filterString) {          if ($filterString) {
4417              Trace("Filter string is \"$filterString\".") if T(4);              Trace("Filter string is \"$filterString\".") if T(4);
4418              push @joinWhere, "($filterString)";              push @joinWhere, "($filterString)";
4419          }          }
4420        # String it all together into a big filter clause.
4421          if (@joinWhere) {          if (@joinWhere) {
4422              $suffix .= " WHERE " . join(' AND ', @joinWhere);              $suffix .= " WHERE " . join(' AND ', @joinWhere);
4423          }          }
4424          # Add the sort or limit clause (if any) to the SELECT command.      # Add the sort or limit clause (if any).
4425          if ($orderClause) {          if ($orderClause) {
4426              $suffix .= " $orderClause";              $suffix .= " $orderClause";
4427          }          }
     }  
4428      # Return the suffix, the mapped name list, and the mapped name hash.      # Return the suffix, the mapped name list, and the mapped name hash.
4429      return ($suffix, \@mappedNameList, \%mappedNameHash);      return ($suffix, \@mappedNameList, \%mappedNameHash);
4430  }  }
4431    
4432  =head3 GetStatementHandle  =head3 _GetStatementHandle
4433    
4434  This method will prepare and execute an SQL query, returning the statement handle.  This method will prepare and execute an SQL query, returning the statement handle.
4435  The main reason for doing this here is so that everybody who does SQL queries gets  The main reason for doing this here is so that everybody who does SQL queries gets
# Line 2473  Line 4459 
4459  sub _GetStatementHandle {  sub _GetStatementHandle {
4460      # Get the parameters.      # Get the parameters.
4461      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4462        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4463      # Trace the query.      # Trace the query.
4464      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4465      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 2481  Line 4468 
4468      # Prepare the command.      # Prepare the command.
4469      my $sth = $dbh->prepare_command($command);      my $sth = $dbh->prepare_command($command);
4470      # Execute it with the parameters bound in.      # Execute it with the parameters bound in.
4471      $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
4472      # Return the statement handle.      # Return the statement handle.
4473      return $sth;      return $sth;
4474  }  }
4475    
4476  =head3 GetLoadStats  =head3 _GetLoadStats
4477    
4478  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
4479    
# Line 2498  Line 4485 
4485      return Stats->new();      return Stats->new();
4486  }  }
4487    
4488  =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  
4489    
4490  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.
4491    
4492  This is an instance method.  This is an instance method.
4493    
# Line 2622  Line 4535 
4535      close DTXOUT;      close DTXOUT;
4536  }  }
4537    
4538  =head3 GetStructure  =head3 _GetStructure
4539    
4540  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
4541    
# Line 2661  Line 4574 
4574      return $retVal;      return $retVal;
4575  }  }
4576    
4577  =head3 GetRelationTable  
4578    
4579    =head3 _GetRelationTable
4580    
4581  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
4582    
# Line 2690  Line 4605 
4605      return $objectData->{Relations};      return $objectData->{Relations};
4606  }  }
4607    
4608  =head3 ValidateFieldNames  =head3 _ValidateFieldNames
4609    
4610  Determine whether or not the field names are valid. A description of the problems with the names  Determine whether or not the field names are valid. A description of the problems with the names
4611  will be written to the standard error output. If there is an error, this method will abort. This is  will be written to the standard error output. If there is an error, this method will abort. This is
# Line 2717  Line 4632 
4632          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
4633              # Loop through the object's fields.              # Loop through the object's fields.
4634              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
4635                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
4636                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
4637                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($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";  
4638                          $retVal = 0;                          $retVal = 0;
4639                      }                      }
4640                  }                  }
4641              }              }
4642          }          }
     }  
4643      # If an error was found, fail.      # If an error was found, fail.
4644      if ($retVal  == 0) {      if ($retVal  == 0) {
4645          Confess("Errors found in field names.");          Confess("Errors found in field names.");
4646      }      }
4647  }  }
4648    
4649  =head3 LoadRelation  =head3 _LoadRelation
4650    
4651  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
4652  file with the same name as the relation exists in the specified directory.  file with the same name as the relation exists in the specified directory.
# Line 2796  Line 4697 
4697      # be a null string.      # be a null string.
4698      if ($fileName ne "") {      if ($fileName ne "") {
4699          # Load the relation from the file.          # Load the relation from the file.
4700          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4701      } elsif ($rebuild) {      } elsif ($rebuild) {
4702          # Here we are rebuilding, but no file exists, so we just re-create the table.          # Here we are rebuilding, but no file exists, so we just re-create the table.
4703          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 2805  Line 4706 
4706      return $retVal;      return $retVal;
4707  }  }
4708    
4709  =head3 LoadMetaData  
4710    =head3 _LoadMetaData
4711    
4712        my $metadata = ERDB::_LoadMetaData($filename);
4713    
4714  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4715  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 2830  Line 4734 
4734  sub _LoadMetaData {  sub _LoadMetaData {
4735      # Get the parameters.      # Get the parameters.
4736      my ($filename) = @_;      my ($filename) = @_;
4737      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4738      # Slurp the XML file into a variable. Extensive use of options is used to insure we      # Slurp the XML file into a variable. Extensive use of options is used to insure we
4739      # get the exact structure we want.      # get the exact structure we want.
4740      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 $filename.") if T(1);  
4741      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
4742      # the method below will fail.      # the method below will fail.
4743      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 2969  Line 4860 
4860              if ($found == 0) {              if ($found == 0) {
4861                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4862              }              }
4863              # Now we need to convert the relation's index list to an index table. We begin by creating              # Attach all the indexes to the relation.
4864              # an empty table in the relation structure.              _ProcessIndexes($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++;  
             }  
4865          }          }
4866          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4867          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 2993  Line 4875 
4875          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4876          # Format a description for the FROM field.          # Format a description for the FROM field.
4877          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4878          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].";
4879          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4880          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4881          # Add the FROM field.          # Add the FROM field.
# Line 3003  Line 4885 
4885                                                      PrettySort => 1});                                                      PrettySort => 1});
4886          # Format a description for the TO field.          # Format a description for the TO field.
4887          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4888          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].";
4889          # Get the TO entity's key type.          # Get the TO entity's key type.
4890          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4891          # Add the TO field.          # Add the TO field.
# Line 3015  Line 4897 
4897          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
4898                               Indexes => { } };                               Indexes => { } };
4899          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
4900    
4901            # Add the alternate indexes (if any). This MUST be done before the FROM and
4902            # TO indexes, because it erases the relation's index list.
4903            if (exists $relationshipStructure->{Indexes}) {
4904                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
4905            }
4906            # Add the relation to the master table.
4907          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
4908          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
4909          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
4910          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
4911      }      }
4912      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 3117  Line 5005 
5005          # joins, the direction makes a difference with the recursive joins. This can give          # joins, the direction makes a difference with the recursive joins. This can give
5006          # rise to situations where we can't create the path we want; however, it is always          # rise to situations where we can't create the path we want; however, it is always
5007          # possible to get the same effect using multiple queries.          # possible to get the same effect using multiple queries.
5008          for my $relationshipName (@bothList) {          for my $relationshipName (@bothList) {
5009              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
5010              # Join to the entity from each direction.              # Join to the entity from each direction.
5011              $joinTable{"$entityName/$relationshipName"} =              $joinTable{"$entityName/$relationshipName"} =
5012                  "$entityName.id = $relationshipName.from_link";                  "$entityName.id = $relationshipName.from_link";
5013              $joinTable{"$relationshipName/$entityName"} =              $joinTable{"$relationshipName/$entityName"} =
5014                  "$relationshipName.to_link = $entityName.id";                  "$relationshipName.to_link = $entityName.id";
         }  
     }  
     # Add the join table to the structure.  
     $metadata->{Joins} = \%joinTable;  
     # Return the slurped and fixed-up structure.  
     return $metadata;  
 }  
   
 =head3 SortNeeded  
   
 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;  
5015          }          }
5016      }      }
5017      # Return the result.      # Add the join table to the structure.
5018      return $retVal;      $metadata->{Joins} = \%joinTable;
5019        # Return the slurped and fixed-up structure.
5020        return $metadata;
5021  }  }
5022    
5023  =head3 CreateRelationshipIndex  =head3 _CreateRelationshipIndex
5024    
5025  Create an index for a relationship's relation.  Create an index for a relationship's relation.
5026    
# Line 3214  Line 5062 
5062          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
5063      }      }
5064      # Add the index to the relation.      # Add the index to the relation.
5065      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
5066    }
5067    
5068    =head3 _ProcessIndexes
5069    
5070        ERDB::_ProcessIndexes($indexList, $relation);
5071    
5072    Build the data structures for the specified indexes in the specified relation.
5073    
5074    =over 4
5075    
5076    =item indexList
5077    
5078    Reference to a list of indexes. Each index is a hash reference containing an optional
5079    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
5080    to a list of index field structures. An index field structure, in turn, is a reference
5081    to a hash that contains a C<name> attribute for the field name and an C<order>
5082    attribute that specifies either C<ascending> or C<descending>. In this sense the
5083    index list encapsulates the XML C<Indexes> structure in the database definition.
5084    
5085    =item relation
5086    
5087    The structure that describes the current relation. The new index descriptors will
5088    be stored in the structure's C<Indexes> member. Any previous data in the structure
5089    will be lost.
5090    
5091    =back
5092    
5093    =cut
5094    
5095    sub _ProcessIndexes {
5096        # Get the parameters.
5097        my ($indexList, $relation) = @_;
5098        # Now we need to convert the relation's index list to an index table. We begin by creating
5099        # an empty table in the relation structure.
5100        $relation->{Indexes} = { };
5101        # Loop through the indexes.
5102        my $count = 0;
5103        for my $index (@{$indexList}) {
5104            # Add this index to the index table.
5105            _AddIndex("idx$count", $relation, $index);
5106            # Increment the counter so that the next index has a different name.
5107            $count++;
5108        }
5109  }  }
5110    
5111  =head3 AddIndex  =head3 _AddIndex
5112    
5113  Add an index to a relation structure.  Add an index to a relation structure.
5114    
# Line 3263  Line 5154 
5154      $relationStructure->{Indexes}->{$indexName} = $newIndex;      $relationStructure->{Indexes}->{$indexName} = $newIndex;
5155  }  }
5156    
5157  =head3 FixupFields  =head3 _FixupFields
5158    
5159  This method fixes the field list for an entity or relationship. It will add the caller-specified  This method fixes the field list for an entity or relationship. It will add the caller-specified
5160  relation name to fields that do not have a name and set the C<PrettySort> value as specified.  relation name to fields that do not have a name and set the C<PrettySort> value as specified.
# Line 3301  Line 5192 
5192          # Here it doesn't, so we create a new one.          # Here it doesn't, so we create a new one.
5193          $structure->{Fields} = { };          $structure->{Fields} = { };
5194      } else {      } else {
5195          # 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
5196            # create a list for stashing them.
5197            my @textFields = ();
5198            # Loop through the fields.
5199          my $fieldStructures = $structure->{Fields};          my $fieldStructures = $structure->{Fields};
5200          for my $fieldName (keys %{$fieldStructures}) {          for my $fieldName (keys %{$fieldStructures}) {
5201              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
# Line 3310  Line 5204 
5204              my $type = $fieldData->{type};              my $type = $fieldData->{type};
5205              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
5206              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
5207              # Plug in a data generator if we need one.              # Check for searchability.
5208              if (!exists $fieldData->{DataGen}) {              if ($fieldData->{searchable}) {
5209                  # The data generator will use the default for the field's type.                  # Only allow this for a primary relation.
5210                  $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };                  if ($fieldData->{relation} ne $defaultRelationName) {
5211                        Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
5212                    } else {
5213                        push @textFields, $fieldName;
5214                    }
5215              }              }
             # Plug in the defaults for the optional data generation parameters.  
             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
5216              # Add the PrettySortValue.              # Add the PrettySortValue.
5217              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
5218          }          }
5219            # If there are searchable fields, remember the fact.
5220            if (@textFields) {
5221                $structure->{searchFields} = \@textFields;
5222            }
5223      }      }
5224  }  }
5225    
5226  =head3 FixName  =head3 _FixName
5227    
5228  Fix the incoming field name so that it is a legal SQL column name.  Fix the incoming field name so that it is a legal SQL column name.
5229    
# Line 3352  Line 5252 
5252      return $fieldName;      return $fieldName;
5253  }  }
5254    
5255  =head3 FixNames  =head3 _FixNames
5256    
5257  Fix all the field names in a list.  Fix all the field names in a list.
5258    
# Line 3383  Line 5283 
5283      return @result;      return @result;
5284  }  }
5285    
5286  =head3 AddField  =head3 _AddField
5287    
5288  Add a field to a field list.  Add a field to a field list.
5289    
# Line 3418  Line 5318 
5318      $fieldList->{$fieldName} = $fieldStructure;      $fieldList->{$fieldName} = $fieldStructure;
5319  }  }
5320    
5321  =head3 ReOrderRelationTable  =head3 _ReOrderRelationTable
5322    
5323  This method will take a relation table and re-sort it according to the implicit ordering of the  This method will take a relation table and re-sort it according to the implicit ordering of the
5324  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
# Line 3479  Line 5379 
5379    
5380  }  }
5381    
5382  =head3 IsPrimary  =head3 _IsPrimary
5383    
5384  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
5385  if it has the same name as an entity or relationship.  if it has the same name as an entity or relationship.
# Line 3515  Line 5415 
5415      return $retVal;      return $retVal;
5416  }  }
5417    
5418  =head3 FindRelation  =head3 _FindRelation
5419    
5420  Return the descriptor for the specified relation.  Return the descriptor for the specified relation.
5421    
# Line 3544  Line 5444 
5444      return $retVal;      return $retVal;
5445  }  }
5446    
5447  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5448    
5449  =head3 ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5450    
5451  The relationship sentence consists of the relationship name between the names of the  The relationship sentence consists of the relationship name between the names of the
5452  two related entities and an arity indicator.  two related entities and an arity indicator.
# Line 3576  Line 5476 
5476      # Get the parameters.      # Get the parameters.
5477      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5478      # Format the relationship sentence.      # Format the relationship sentence.
5479      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5480      # Compute the arity.      # Compute the arity.
5481      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5482      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 3584  Line 5484 
5484      return $result;      return $result;
5485  }  }
5486    
5487  =head3 ComputeRelationshipHeading  =head3 _ComputeRelationshipHeading
5488    
5489  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
5490  names hyperlinked to the appropriate entity sections of the document.  names hyperlinked to the appropriate entity sections of the document.
# Line 3621  Line 5521 
5521      return $result;      return $result;
5522  }  }
5523    
5524  =head3 ShowRelationTable  =head3 _WikiRelationTable
5525    
5526    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5527    table with three columns-- the field name, the field type, and the field description.
5528    
5529    This is a static method.
5530    
5531    =over 4
5532    
5533    =item relationName
5534    
5535    Name of the relation being formatted.
5536    
5537    =item relationData
5538    
5539    Hash containing the relation's fields and indexes.
5540    
5541    =item RETURN
5542    
5543    Returns a Wiki string that can be used to display the relation name and all of its fields.
5544    
5545    =back
5546    
5547    =cut
5548    
5549    sub _WikiRelationTable {
5550        # Get the parameters.
5551        my ($relationName, $relationData) = @_;
5552        # We'll create a list of lists in here, then call WikiTools::Table to
5553        # convert it into a table.
5554        my @rows = ();
5555        # Push in the header row.
5556        push @rows, [qw(Field Type Description)];
5557        # Loop through the fields.
5558        for my $field (@{$relationData->{Fields}}) {
5559            # Create this field's row. We always have a name and type.
5560            my @row = ($field->{name}, $field->{type});
5561            # If we have a description, add it as the third column.
5562            if (exists $field->{Notes}) {
5563                push @row, WikiNote($field->{Notes}->{content});
5564            }
5565            # Push this row onto the table list.
5566            push @rows, \@row;
5567        }
5568        # Store the rows as a Wiki table with a level-4 heading.
5569        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5570                          WikiTools::Table(@rows));
5571        # Now we show the relation's indexes. These are formatted as another
5572        # table.
5573        @rows = ();
5574        # Push in the header row.
5575        push @rows, [qw(Index Unique Fields Notes)];
5576        # Get the index hash.
5577        my $indexTable = $relationData->{Indexes};
5578        # Loop through the indexes. For an entity, there is always at least one index.
5579        # For a relationship, there are at least two. The upshot is we don't need to
5580        # worry about accidentally generating a frivolous table here.
5581        for my $indexName (sort keys %$indexTable) {
5582            my $indexData = $indexTable->{$indexName};
5583            # Determine whether or not the index is unique.
5584            my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
5585                          "yes" : "");
5586            # Get the field list.
5587            my $fields = join(', ', @{$indexData->{IndexFields}});
5588            # Get the note text.
5589            my $description = "";
5590            if (my $note = $indexData->{Notes}) {
5591                $description = WikiNote($note->{content});
5592            }
5593            # Format this row.
5594            my @row = ($indexName, $unique, $fields, $description);
5595            push @rows, \@row;
5596        }
5597        # Add the index list to the result.
5598        $retVal .= "\n\n" . WikiTools::Table(@rows);
5599    }
5600    
5601    =head3 _ShowRelationTable
5602    
5603  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
5604  table with three columns-- the field name, the field type, and the field description.  table with three columns-- the field name, the field type, and the field description.
# Line 3671  Line 5648 
5648          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
5649          # Add any note text.          # Add any note text.
5650          if (my $note = $indexData->{Notes}) {          if (my $note = $indexData->{Notes}) {
5651              $htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";              $htmlString .= "<li>" . HTMLNote($note->{content}) . "</li>\n";
5652          }          }
5653          # Add the fiield list.          # Add the fiield list.
5654          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
# Line 3682  Line 5659 
5659      $htmlString .= "</ul>\n";      $htmlString .= "</ul>\n";
5660  }  }
5661    
5662  =head3 OpenFieldTable  =head3 _OpenFieldTable
5663    
5664  This method creates the header string for the field table generated by L</ShowMetaData>.  This method creates the header string for the field table generated by L</ShowMetaData>.
5665    
# Line 3707  Line 5684 
5684      return _OpenTable($tablename, 'Field', 'Type', 'Description');      return _OpenTable($tablename, 'Field', 'Type', 'Description');
5685  }  }
5686    
5687  =head3 OpenTable  =head3 _OpenTable
5688    
5689  This method creates the header string for an HTML table.  This method creates the header string for an HTML table.
5690    
# Line 3737  Line 5714 
5714      # Compute the number of columns.      # Compute the number of columns.
5715      my $colCount = @colNames;      my $colCount = @colNames;
5716      # Generate the title row.      # Generate the title row.
5717      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";
5718      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
5719      $htmlString .= "<tr>";      $htmlString .= "<tr>";
5720      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 3747  Line 5724 
5724      return $htmlString;      return $htmlString;
5725  }  }
5726    
5727  =head3 CloseTable  =head3 _CloseTable
5728    
5729  This method returns the HTML for closing a table.  This method returns the HTML for closing a table.
5730    
# Line 3756  Line 5733 
5733  =cut  =cut
5734    
5735  sub _CloseTable {  sub _CloseTable {
5736      return "</table></p>\n";      return "</table>\n";
5737  }  }
5738    
5739  =head3 ShowField  =head3 _ShowField
5740    
5741  This method returns the HTML for displaying a row of field information in a field table.  This method returns the HTML for displaying a row of field information in a field table.
5742    
# Line 3786  Line 5763 
5763      my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";      my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";
5764      # If we have content, add it as a third column.      # If we have content, add it as a third column.
5765      if (exists $fieldData->{Notes}) {      if (exists $fieldData->{Notes}) {
5766          $htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";          $htmlString .= "<td>" . HTMLNote($fieldData->{Notes}->{content}) . "</td>";
5767      }      }
5768      # Close off the row.      # Close off the row.
5769      $htmlString .= "</tr>\n";      $htmlString .= "</tr>\n";
# Line 3794  Line 5771 
5771      return $htmlString;      return $htmlString;
5772  }  }
5773    
5774  =head3 HTMLNote  =head3 _ObjectNotes
   
 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  
5775    
5776  C<< my $char = RandChar($sourceString); >>      my @noteParagraphs = _ObjectNotes($objectData);
5777    
5778  Select a random character from a string.  Return a list of the notes and asides for an entity or relationship in
5779    Wiki format.
5780    
5781  =over 4  =over 4
5782    
5783  =item sourceString  =item objectData
5784    
5785  String from which the random character should be selected.  The metadata for the desired entity or relationship.
5786    
5787  =item RETURN  =item RETURN
5788    
5789  Returns a single character from the incoming string.  Returns a list of text paragraphs in Wiki markup form.
5790    
5791  =back  =back
5792    
5793  =cut  =cut
5794    
5795  sub RandChar {  sub _ObjectNotes {
     # Get the parameter.  
     my ($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 {  
5796      # Get the parameters.      # Get the parameters.
5797      my @patterns = @_;      my ($objectData) = @_;
     # Choose the appropriate pattern.  
     my $chosenPattern = RandParam(@patterns);  
5798      # Declare the return variable.      # Declare the return variable.
5799      my $retVal = "";      my @retVal;
5800      # Determine whether this is a count or a picture pattern.      # Loop through the types of notes.