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revision 1.71, Sat Oct 14 18:08:12 2006 UTC revision 1.101, Wed Sep 3 20:56:20 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 217  Line 218 
218  index will be created for each relation with at least one searchable field in it.  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.  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 250  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 294  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 328  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. "sort" is the key modifier for the sort command.  # 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, sort => "",  dataGen => "StringGen('A')" },  # index
345                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n", dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
346                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n", dataGen => "IntGen(0, 99999999)" },                                 indexMod =>   0, notes => "single ASCII character"},
347                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",  dataGen => "StringGen(IntGen(10,250))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
348                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",  dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
349                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n", dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
350                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g", dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
351                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n", dataGen => "IntGen(0, 1)" },                    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, sort => "",  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, sort => "",  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, sort => "",  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, sort => "",  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, sort => "",  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 357  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, $metaFileName);
420    
421  Create a new ERDB object.  Create a new ERDB object.
422    
# Line 390  Line 436 
436    
437  sub new {  sub new {
438      # Get the parameters.      # Get the parameters.
439      my ($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 404  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 445  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 506  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 524  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 563  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 597  Line 647 
647    
648  =head3 DumpMetaData  =head3 DumpMetaData
649    
650  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
651    
652  Return a dump of the metadata structure.  Return a dump of the metadata structure.
653    
# Line 610  Line 660 
660      return Data::Dumper::Dumper($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 629  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 678  Line 1062 
1062          # Push the result into the field list.          # Push the result into the field list.
1063          push @fieldList, $fieldString;          push @fieldList, $fieldString;
1064      }      }
     # If this is a root table, add the "new_record" flag. It defaults to 0, so  
     if ($rootFlag) {  
         push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";  
     }  
1065      # Convert the field list into a comma-delimited string.      # Convert the field list into a comma-delimited string.
1066      my $fieldThing = join(', ', @fieldList);      my $fieldThing = join(', ', @fieldList);
1067      # Insure the table is not already there.      # Insure the table is not already there.
# Line 692  Line 1072 
1072      my $estimation = undef;      my $estimation = undef;
1073      if ($estimatedRows) {      if ($estimatedRows) {
1074          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1075            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1076      }      }
1077      # Create the table.      # Create the table.
1078      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
# Line 706  Line 1087 
1087    
1088  =head3 VerifyFields  =head3 VerifyFields
1089    
1090  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>      my $count = $erdb->VerifyFields($relName, \@fieldList);
1091    
1092  Run through the list of proposed field values, insuring that all the character fields are  Run through the list of proposed field values, insuring that all the character fields are
1093  below the maximum length. If any fields are too long, they will be truncated in place.  below the maximum length. If any fields are too long, they will be truncated in place.
# Line 749  Line 1130 
1130              my $oldString = $fieldList->[$i];              my $oldString = $fieldList->[$i];
1131              if (length($oldString) > $maxLen) {              if (length($oldString) > $maxLen) {
1132                  # Here it's too big, so we truncate it.                  # Here it's too big, so we truncate it.
1133                  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);
1134                  $fieldList->[$i] = substr $oldString, 0, $maxLen;                  $fieldList->[$i] = substr $oldString, 0, $maxLen;
1135                  $retVal++;                  $retVal++;
1136              }              }
# Line 761  Line 1142 
1142    
1143  =head3 DigestFields  =head3 DigestFields
1144    
1145  C<< $erdb->DigestFields($relName, $fieldList); >>      $erdb->DigestFields($relName, $fieldList);
1146    
1147  Digest the strings in the field list that correspond to data type C<hash-string> in the  Digest the strings in the field list that correspond to data type C<hash-string> in the
1148  specified relation.  specified relation.
# Line 801  Line 1182 
1182    
1183  =head3 DigestKey  =head3 DigestKey
1184    
1185  C<< my $digested = $erdb->DigestKey($keyValue); >>      my $digested = $erdb->DigestKey($keyValue);
1186    
1187  Return the digested value of a symbolic key. The digested value can then be plugged into a  Return the digested value of a symbolic key. The digested value can then be plugged into a
1188  key-based search into a table with key-type hash-string.  key-based search into a table with key-type hash-string.
# Line 834  Line 1215 
1215    
1216  =head3 CreateIndex  =head3 CreateIndex
1217    
1218  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1219    
1220  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
1221  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
# Line 855  Line 1236 
1236      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
1237          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
1238          # Get the index's field list.          # Get the index's field list.
1239          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
1240            # Get a hash of the relation's field types.
1241            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1242            # We need to check for text fields so we can append a length limitation for them. To do
1243            # that, we need the relation's field list.
1244            my $relFields = $relationData->{Fields};
1245            for (my $i = 0; $i <= $#rawFields; $i++) {
1246                # Get the field type.
1247                my $field = $rawFields[$i];
1248                my $type = $types{$field};
1249                # Ask if it requires using prefix notation for the index.
1250                my $mod = $TypeTable{$type}->{indexMod};
1251                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1252                if ($mod) {
1253                    # Append the prefix length to the field name,
1254                    $rawFields[$i] .= "($mod)";
1255                }
1256            }
1257            my @fieldList = _FixNames(@rawFields);
1258          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
1259          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
1260          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
# Line 870  Line 1269 
1269      }      }
1270  }  }
1271    
1272    =head3 GetSecondaryFields
1273    
1274        my %fieldTuples = $erdb->GetSecondaryFields($entityName);
1275    
1276    This method will return a list of the name and type of each of the secondary
1277    fields for a specified entity. Secondary fields are stored in two-column tables
1278    in addition to the primary entity table. This enables the field to have no value
1279    or to have multiple values.
1280    
1281    =over 4
1282    
1283    =item entityName
1284    
1285    Name of the entity whose secondary fields are desired.
1286    
1287    =item RETURN
1288    
1289    Returns a hash mapping the field names to their field types.
1290    
1291    =back
1292    
1293    =cut
1294    
1295    sub GetSecondaryFields {
1296        # Get the parameters.
1297        my ($self, $entityName) = @_;
1298        # Declare the return variable.
1299        my %retVal = ();
1300        # Look for the entity.
1301        my $table = $self->GetFieldTable($entityName);
1302        # Loop through the fields, pulling out the secondaries.
1303        for my $field (sort keys %{$table}) {
1304            if ($table->{$field}->{relation} ne $entityName) {
1305                # Here we have a secondary field.
1306                $retVal{$field} = $table->{$field}->{type};
1307            }
1308        }
1309        # Return the result.
1310        return %retVal;
1311    }
1312    
1313    =head3 GetFieldRelationName
1314    
1315        my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1316    
1317    Return the name of the relation containing a specified field.
1318    
1319    =over 4
1320    
1321    =item objectName
1322    
1323    Name of the entity or relationship containing the field.
1324    
1325    =item fieldName
1326    
1327    Name of the relevant field in that entity or relationship.
1328    
1329    =item RETURN
1330    
1331    Returns the name of the database relation containing the field, or C<undef> if
1332    the field does not exist.
1333    
1334    =back
1335    
1336    =cut
1337    
1338    sub GetFieldRelationName {
1339        # Get the parameters.
1340        my ($self, $objectName, $fieldName) = @_;
1341        # Declare the return variable.
1342        my $retVal;
1343        # Get the object field table.
1344        my $table = $self->GetFieldTable($objectName);
1345        # Only proceed if the field exists.
1346        if (exists $table->{$fieldName}) {
1347            # Determine the name of the relation that contains this field.
1348            $retVal = $table->{$fieldName}->{relation};
1349        }
1350        # Return the result.
1351        return $retVal;
1352    }
1353    
1354    =head3 DeleteValue
1355    
1356        my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1357    
1358    Delete secondary field values from the database. This method can be used to delete all
1359    values of a specified field for a particular entity instance, or only a single value.
1360    
1361    Secondary fields are stored in two-column relations separate from an entity's primary
1362    table, and as a result a secondary field can legitimately have no value or multiple
1363    values. Therefore, it makes sense to talk about deleting secondary fields where it
1364    would not make sense for primary fields.
1365    
1366    =over 4
1367    
1368    =item entityName
1369    
1370    Name of the entity from which the fields are to be deleted.
1371    
1372    =item id
1373    
1374    ID of the entity instance to be processed. If the instance is not found, this
1375    method will have no effect. If C<undef> is specified, all values for all of
1376    the entity instances will be deleted.
1377    
1378    =item fieldName
1379    
1380    Name of the field whose values are to be deleted.
1381    
1382    =item fieldValue (optional)
1383    
1384    Value to be deleted. If not specified, then all values of the specified field
1385    will be deleted for the entity instance. If specified, then only the values which
1386    match this parameter will be deleted.
1387    
1388    =item RETURN
1389    
1390    Returns the number of rows deleted.
1391    
1392    =back
1393    
1394    =cut
1395    
1396    sub DeleteValue {
1397        # Get the parameters.
1398        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1399        # Declare the return value.
1400        my $retVal = 0;
1401        # We need to set up an SQL command to do the deletion. First, we
1402        # find the name of the field's relation.
1403        my $table = $self->GetFieldTable($entityName);
1404        my $field = $table->{$fieldName};
1405        my $relation = $field->{relation};
1406        # Make sure this is a secondary field.
1407        if ($relation eq $entityName) {
1408            Confess("Cannot delete values of $fieldName for $entityName.");
1409        } else {
1410            # Set up the SQL command to delete all values.
1411            my $sql = "DELETE FROM $relation";
1412            # Build the filter.
1413            my @filters = ();
1414            my @parms = ();
1415            # Check for a filter by ID.
1416            if (defined $id) {
1417                push @filters, "id = ?";
1418                push @parms, $id;
1419            }
1420            # Check for a filter by value.
1421            if (defined $fieldValue) {
1422                push @filters, "$fieldName = ?";
1423                push @parms, $fieldValue;
1424            }
1425            # Append the filters to the command.
1426            if (@filters) {
1427                $sql .= " WHERE " . join(" AND ", @filters);
1428            }
1429            # Execute the command.
1430            my $dbh = $self->{_dbh};
1431            $retVal = $dbh->SQL($sql, 0, @parms);
1432        }
1433        # Return the result.
1434        return $retVal;
1435    }
1436    
1437  =head3 LoadTables  =head3 LoadTables
1438    
1439  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>      my $stats = $erdb->LoadTables($directoryName, $rebuild);
1440    
1441  This method will load the database tables from a directory. The tables must already have been created  This method will load the database tables from a directory. The tables must already have been created
1442  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
# Line 932  Line 1496 
1496    
1497  =head3 GetTableNames  =head3 GetTableNames
1498    
1499  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1500    
1501  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1502    
# Line 949  Line 1513 
1513    
1514  =head3 GetEntityTypes  =head3 GetEntityTypes
1515    
1516  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1517    
1518  Return a list of the entity type names.  Return a list of the entity type names.
1519    
# Line 964  Line 1528 
1528      return sort keys %{$entityList};      return sort keys %{$entityList};
1529  }  }
1530    
1531    =head3 GetConnectingRelationships
1532    
1533        my @list = $erdb->GetConnectingRelationships($entityName);
1534    
1535    Return a list of the relationships connected to the specified entity.
1536    
1537    =over 4
1538    
1539    =item entityName
1540    
1541    Entity whose connected relationships are desired.
1542    
1543    =item RETURN
1544    
1545    Returns a list of the relationships that originate from the entity.
1546    If the entity is on the from end, it will return the relationship
1547    name. If the entity is on the to end it will return the converse of
1548    the relationship name.
1549    
1550    =back
1551    
1552    =cut
1553    
1554    sub GetConnectingRelationships {
1555        # Get the parameters.
1556        my ($self, $entityName) = @_;
1557        # Declare the return variable.
1558        my @retVal;
1559        # Get the relationship list.
1560        my $relationships = $self->{_metaData}->{Relationships};
1561        # Find the entity.
1562        my $entity = $self->{_metaData}->{Entities}->{$entityName};
1563        # Only proceed if the entity exists.
1564        if (! defined $entity) {
1565            Trace("Entity $entityName not found.") if T(3);
1566        } else {
1567            # Loop through the relationships.
1568            my @rels = keys %$relationships;
1569            Trace(scalar(@rels) . " relationships found in connection search.") if T(3);
1570            for my $relationshipName (@rels) {
1571                my $relationship = $relationships->{$relationshipName};
1572                if ($relationship->{from} eq $entityName) {
1573                    # Here we have a forward relationship.
1574                    push @retVal, $relationshipName;
1575                } elsif ($relationship->{to} eq $entityName) {
1576                    # Here we have a backward relationship. In this case, the
1577                    # converse relationship name is preferred if it exists.
1578                    my $converse = $relationship->{converse} || $relationshipName;
1579                    push @retVal, $converse;
1580                }
1581            }
1582        }
1583        # Return the result.
1584        return @retVal;
1585    }
1586    
1587    
1588    
1589    
1590    =head3 GetDataTypes
1591    
1592        my %types = ERDB::GetDataTypes();
1593    
1594    Return a table of ERDB data types. The table returned is a hash of hashes.
1595    The keys of the big hash are the datatypes. Each smaller hash has several
1596    values used to manage the data. The most interesting is the SQL type (key
1597    C<sqlType>) and the descriptive node (key C<notes>).
1598    
1599    Note that changing the values in the smaller hashes will seriously break
1600    things, so this data should be treated as read-only.
1601    
1602    =cut
1603    
1604    sub GetDataTypes {
1605        return %TypeTable;
1606    }
1607    
1608    
1609  =head3 IsEntity  =head3 IsEntity
1610    
1611  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1612    
1613  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1614    
# Line 993  Line 1635 
1635    
1636  =head3 Get  =head3 Get
1637    
1638  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1639    
1640  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
1641  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 1001  Line 1643 
1643  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
1644  $genus.  $genus.
1645    
1646  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1647    
1648  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
1649  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1650    
1651  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1652    
1653  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1654  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 1018  Line 1660 
1660  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
1661  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
1662    
1663  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1664    
1665  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
1666  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
# Line 1054  Line 1696 
1696  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
1697  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1698    
1699  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1700    
1701  Note that the case is important. Only an uppercase "ORDER BY" with a single space will  Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1702  be processed. The idea is to make it less likely to find the verb by accident.  be processed. The idea is to make it less likely to find the verb by accident.
# Line 1067  Line 1709 
1709  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by  be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1710  a positive number. So, for example  a positive number. So, for example
1711    
1712  C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>      "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1713    
1714  will only return the first ten genomes for the specified genus. The ORDER BY clause is not  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1715  required. For example, to just get the first 10 genomes in the B<Genome> table, you could  required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1716  use  use
1717    
1718  C<< "LIMIT 10" >>      "LIMIT 10"
1719    
1720  =item params  =item params
1721    
# Line 1094  Line 1736 
1736      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1737          $self->_SetupSQL($objectNames, $filterClause);          $self->_SetupSQL($objectNames, $filterClause);
1738      # Create the query.      # Create the query.
1739      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1740          ".* $suffix";          ".* $suffix";
1741      my $sth = $self->_GetStatementHandle($command, $params);      my $sth = $self->_GetStatementHandle($command, $params);
1742      # Now we create the relation map, which enables DBQuery to determine the order, name      # Now we create the relation map, which enables DBQuery to determine the order, name
# Line 1108  Line 1750 
1750      return $retVal;      return $retVal;
1751  }  }
1752    
1753    
1754    
1755  =head3 Search  =head3 Search
1756    
1757  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>      my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1758    
1759  Perform a full text search with filtering. The search will be against a specified object  Perform a full text search with filtering. The search will be against a specified object
1760  in the object name list. That object will get an extra field containing the search  in the object name list. That object will get an extra field containing the search
# Line 1121  Line 1765 
1765    
1766  =item searchExpression  =item searchExpression
1767    
1768  Boolean search expression for the text fields of the target object.  Boolean search expression for the text fields of the target object. The default mode for
1769    a Boolean search expression is OR, but we want the default to be AND, so we will
1770    add a C<+> operator to each word with no other operator before it.
1771    
1772  =item idx  =item idx
1773    
# Line 1158  Line 1804 
1804      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1805      # Declare the return variable.      # Declare the return variable.
1806      my $retVal;      my $retVal;
1807      # Create a safety copy of the parameter list.      # Create a safety copy of the parameter list. Note we have to be careful to insure
1808      my @myParams = @{$params};      # a parameter list exists before we copy it.
1809        my @myParams = ();
1810        if (defined $params) {
1811            @myParams = @{$params};
1812        }
1813      # Get the first object's structure so we have access to the searchable fields.      # Get the first object's structure so we have access to the searchable fields.
1814      my $object1Name = $objectNames->[$idx];      my $object1Name = $objectNames->[$idx];
1815      my $object1Structure = $self->_GetStructure($object1Name);      my $object1Structure = $self->_GetStructure($object1Name);
# Line 1171  Line 1821 
1821          my @fields = @{$object1Structure->{searchFields}};          my @fields = @{$object1Structure->{searchFields}};
1822          # Clean the search expression.          # Clean the search expression.
1823          my $actualKeywords = $self->CleanKeywords($searchExpression);          my $actualKeywords = $self->CleanKeywords($searchExpression);
1824            # Prefix a "+" to each uncontrolled word. This converts the default
1825            # search mode from OR to AND.
1826            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1827            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1828          # We need two match expressions, one for the filter clause and one in the          # We need two match expressions, one for the filter clause and one in the
1829          # query itself. Both will use a parameter mark, so we need to push the          # query itself. Both will use a parameter mark, so we need to push the
1830          # search expression onto the front of the parameter list twice.          # search expression onto the front of the parameter list twice.
# Line 1183  Line 1837 
1837              $self->_SetupSQL($objectNames, $filterClause, $matchClause);              $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1838          # Create the query. Note that the match clause is inserted at the front of          # Create the query. Note that the match clause is inserted at the front of
1839          # the select fields.          # the select fields.
1840          my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .          my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1841              ".* $suffix";              ".* $suffix";
1842          my $sth = $self->_GetStatementHandle($command, \@myParams);          my $sth = $self->_GetStatementHandle($command, \@myParams);
1843          # Now we create the relation map, which enables DBQuery to determine the order, name          # Now we create the relation map, which enables DBQuery to determine the order, name
# Line 1197  Line 1851 
1851    
1852  =head3 GetFlat  =head3 GetFlat
1853    
1854  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>      my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1855    
1856  This is a variation of L</GetAll> that asks for only a single field per record and  This is a variation of L</GetAll> that asks for only a single field per record and
1857  returns a single flattened list.  returns a single flattened list.
# Line 1248  Line 1902 
1902      return @retVal;      return @retVal;
1903  }  }
1904    
1905  =head3 Delete  =head3 SpecialFields
1906    
1907  C<< my $stats = $erdb->Delete($entityName, $objectID); >>      my %specials = $erdb->SpecialFields($entityName);
1908    
1909  Delete an entity instance from the database. The instance is deleted along with all entity and  Return a hash mapping special fields in the specified entity to the value of their
1910  relationship instances dependent on it. The idea of dependence here is recursive. An object is  C<special> attribute. This enables the subclass to get access to the special field
1911  always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  attributes without needed to plumb the internal ERDB data structures.
 relationship connected to a dependent entity or the "to" entity connected to a 1-to-many  
 dependent relationship.  
1912    
1913  =over 4  =over 4
1914    
1915  =item entityName  =item entityName
1916    
1917  Name of the entity type for the instance being deleted.  Name of the entity whose special fields are desired.
1918    
1919  =item objectID  =item RETURN
1920    
1921  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  Returns a hash. The keys of the hash are the special field names, and the values
1922    are the values from each special field's C<special> attribute.
1923    
1924    =back
1925    
1926    =cut
1927    
1928    sub SpecialFields {
1929        # Get the parameters.
1930        my ($self, $entityName) = @_;
1931        # Declare the return variable.
1932        my %retVal = ();
1933        # Find the entity's data structure.
1934        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1935        # Loop through its fields, adding each special field to the return hash.
1936        my $fieldHash = $entityData->{Fields};
1937        for my $fieldName (keys %{$fieldHash}) {
1938            my $fieldData = $fieldHash->{$fieldName};
1939            if (exists $fieldData->{special}) {
1940                $retVal{$fieldName} = $fieldData->{special};
1941            }
1942        }
1943        # Return the result.
1944        return %retVal;
1945    }
1946    
1947    =head3 Delete
1948    
1949        my $stats = $erdb->Delete($entityName, $objectID, %options);
1950    
1951    Delete an entity instance from the database. The instance is deleted along with all entity and
1952    relationship instances dependent on it. The definition of I<dependence> is recursive.
1953    
1954    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1955    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1956    dependent relationship.
1957    
1958    =over 4
1959    
1960    =item entityName
1961    
1962    Name of the entity type for the instance being deleted.
1963    
1964    =item objectID
1965    
1966    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1967  then it is presumed to by a LIKE pattern.  then it is presumed to by a LIKE pattern.
1968    
1969  =item testFlag  =item options
1970    
1971  If TRUE, the delete statements will be traced without being executed.  A hash detailing the options for this delete operation.
1972    
1973  =item RETURN  =item RETURN
1974    
# Line 1280  Line 1977 
1977    
1978  =back  =back
1979    
1980    The permissible options for this method are as follows.
1981    
1982    =over 4
1983    
1984    =item testMode
1985    
1986    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1987    
1988    =item keepRoot
1989    
1990    If TRUE, then the entity instances will not be deleted, only the dependent records.
1991    
1992    =back
1993    
1994  =cut  =cut
1995  #: Return Type $%;  #: Return Type $%;
1996  sub Delete {  sub Delete {
1997      # Get the parameters.      # Get the parameters.
1998      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1999      # Declare the return variable.      # Declare the return variable.
2000      my $retVal = Stats->new();      my $retVal = Stats->new();
2001      # Get the DBKernel object.      # Get the DBKernel object.
# Line 1301  Line 2012 
2012      # FROM-relationships and entities.      # FROM-relationships and entities.
2013      my @fromPathList = ();      my @fromPathList = ();
2014      my @toPathList = ();      my @toPathList = ();
2015      # This final hash is used to remember what work still needs to be done. We push paths      # This final list is used to remember what work still needs to be done. We push paths
2016      # onto the list, then pop them off to extend the paths. We prime it with the starting      # onto the list, then pop them off to extend the paths. We prime it with the starting
2017      # point. Note that we will work hard to insure that the last item on a path in the      # point. Note that we will work hard to insure that the last item on a path in the
2018      # TODO list is always an entity.      # to-do list is always an entity.
2019      my @todoList = ([$entityName]);      my @todoList = ([$entityName]);
2020      while (@todoList) {      while (@todoList) {
2021          # Get the current path.          # Get the current path.
# Line 1312  Line 2023 
2023          # Copy it into a list.          # Copy it into a list.
2024          my @stackedPath = @{$current};          my @stackedPath = @{$current};
2025          # 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.
2026          my $entityName = pop @stackedPath;          my $myEntityName = pop @stackedPath;
2027          # Add it to the alreadyFound list.          # Add it to the alreadyFound list.
2028          $alreadyFound{$entityName} = 1;          $alreadyFound{$myEntityName} = 1;
2029            # Figure out if we need to delete this entity.
2030            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
2031          # Get the entity data.          # Get the entity data.
2032          my $entityData = $self->_GetStructure($entityName);              my $entityData = $self->_GetStructure($myEntityName);
2033          # 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.  
2034          my $relations = $entityData->{Relations};          my $relations = $entityData->{Relations};
2035          for my $relation (keys %{$relations}) {          for my $relation (keys %{$relations}) {
2036              my @augmentedList = (@stackedPath, $relation);              my @augmentedList = (@stackedPath, $relation);
2037              push @fromPathList, \@augmentedList;              push @fromPathList, \@augmentedList;
2038          }          }
2039            }
2040          # Now we need to look for relationships connected to this entity.          # Now we need to look for relationships connected to this entity.
2041          my $relationshipList = $self->{_metaData}->{Relationships};          my $relationshipList = $self->{_metaData}->{Relationships};
2042          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
2043              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
2044              # Check the FROM field. We're only interested if it's us.              # Check the FROM field. We're only interested if it's us.
2045              if ($relationship->{from} eq $entityName) {              if ($relationship->{from} eq $myEntityName) {
2046                  # Add the path to this relationship.                  # Add the path to this relationship.
2047                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2048                  push @fromPathList, \@augmentedList;                  push @fromPathList, \@augmentedList;
2049                  # Check the arity. If it's MM we're done. If it's 1M                  # Check the arity. If it's MM we're done. If it's 1M
2050                  # and the target hasn't been seen yet, we want to                  # and the target hasn't been seen yet, we want to
# Line 1350  Line 2063 
2063              }              }
2064              # Now check the TO field. In this case only the relationship needs              # Now check the TO field. In this case only the relationship needs
2065              # deletion.              # deletion.
2066              if ($relationship->{to} eq $entityName) {              if ($relationship->{to} eq $myEntityName) {
2067                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2068                  push @toPathList, \@augmentedList;                  push @toPathList, \@augmentedList;
2069              }              }
2070          }          }
2071      }      }
2072      # Create the first qualifier for the WHERE clause. This selects the      # Create the first qualifier for the WHERE clause. This selects the
2073      # 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
2074      # 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
2075      # to the table containing the dependent records to delete.      # to the table containing the dependent records to delete.
2076      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
2077      # 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 1397  Line 2110 
2110                  }                  }
2111              }              }
2112              # Now we have our desired DELETE statement.              # Now we have our desired DELETE statement.
2113              if ($testFlag) {              if ($options{testMode}) {
2114                  # Here the user wants to trace without executing.                  # Here the user wants to trace without executing.
2115                  Trace($stmt) if T(0);                  Trace($stmt) if T(0);
2116              } else {              } else {
2117                  # 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
2118                  # if an error occurs, so we just go ahead and do it.                  # if an error occurs, so we just go ahead and do it.
2119                  Trace("Executing delete from $target using '$objectID'.") if T(3);                  Trace("Executing delete from $target using '$objectID'.") if T(3);
2120                  my $rv = $db->SQL($stmt, 0, $objectID);                  my $rv = $db->SQL($stmt, 0, $objectID);
# Line 1416  Line 2129 
2129      return $retVal;      return $retVal;
2130  }  }
2131    
2132    =head3 Disconnect
2133    
2134        $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2135    
2136    Disconnect an entity instance from all the objects to which it is related. This
2137    will delete each relationship instance that connects to the specified entity.
2138    
2139    =over 4
2140    
2141    =item relationshipName
2142    
2143    Name of the relationship whose instances are to be deleted.
2144    
2145    =item originEntityName
2146    
2147    Name of the entity that is to be disconnected.
2148    
2149    =item originEntityID
2150    
2151    ID of the entity that is to be disconnected.
2152    
2153    =back
2154    
2155    =cut
2156    
2157    sub Disconnect {
2158        # Get the parameters.
2159        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
2160        # Get the relationship descriptor.
2161        my $structure = $self->_GetStructure($relationshipName);
2162        # Insure we have a relationship.
2163        if (! exists $structure->{from}) {
2164            Confess("$relationshipName is not a relationship in the database.");
2165        } else {
2166            # Get the database handle.
2167            my $dbh = $self->{_dbh};
2168            # We'll set this value to 1 if we find our entity.
2169            my $found = 0;
2170            # Loop through the ends of the relationship.
2171            for my $dir ('from', 'to') {
2172                if ($structure->{$dir} eq $originEntityName) {
2173                    $found = 1;
2174                    # Here we want to delete all relationship instances on this side of the
2175                    # entity instance.
2176                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2177                    # We do this delete in batches to keep it from dragging down the
2178                    # server.
2179                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2180                    my $done = 0;
2181                    while (! $done) {
2182                        # Do the delete.
2183                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2184                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2185                        $done = ($rows == 0 || ! $limitClause);
2186                    }
2187                }
2188            }
2189            # Insure we found the entity on at least one end.
2190            if (! $found) {
2191                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2192            }
2193        }
2194    }
2195    
2196    =head3 DeleteRow
2197    
2198        $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2199    
2200    Delete a row from a relationship. In most cases, only the from-link and to-link are
2201    needed; however, for relationships with intersection data values can be specified
2202    for the other fields using a hash.
2203    
2204    =over 4
2205    
2206    =item relationshipName
2207    
2208    Name of the relationship from which the row is to be deleted.
2209    
2210    =item fromLink
2211    
2212    ID of the entity instance in the From direction.
2213    
2214    =item toLink
2215    
2216    ID of the entity instance in the To direction.
2217    
2218    =item values
2219    
2220    Reference to a hash of other values to be used for filtering the delete.
2221    
2222    =back
2223    
2224    =cut
2225    
2226    sub DeleteRow {
2227        # Get the parameters.
2228        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2229        # Create a hash of all the filter information.
2230        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2231        if (defined $values) {
2232            for my $key (keys %{$values}) {
2233                $filter{$key} = $values->{$key};
2234            }
2235        }
2236        # Build an SQL statement out of the hash.
2237        my @filters = ();
2238        my @parms = ();
2239        for my $key (keys %filter) {
2240            push @filters, _FixName($key) . " = ?";
2241            push @parms, $filter{$key};
2242        }
2243        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2244        my $command = "DELETE FROM $relationshipName WHERE " .
2245                      join(" AND ", @filters);
2246        # Execute it.
2247        my $dbh = $self->{_dbh};
2248        $dbh->SQL($command, undef, @parms);
2249    }
2250    
2251    =head3 DeleteLike
2252    
2253        my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2254    
2255    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2256    filter, only fields from the relationship itself can be used.
2257    
2258    =over 4
2259    
2260    =item relName
2261    
2262    Name of the relationship whose records are to be deleted.
2263    
2264    =item filter
2265    
2266    A filter clause (L</Get>-style) for the delete query.
2267    
2268    =item parms
2269    
2270    Reference to a list of parameters for the filter clause.
2271    
2272    =item RETURN
2273    
2274    Returns a count of the number of rows deleted.
2275    
2276    =back
2277    
2278    =cut
2279    
2280    sub DeleteLike {
2281        # Get the parameters.
2282        my ($self, $objectName, $filter, $parms) = @_;
2283        # Declare the return variable.
2284        my $retVal;
2285        # Insure the parms argument is an array reference if the caller left it off.
2286        if (! defined($parms)) {
2287            $parms = [];
2288        }
2289        # Insure we have a relationship. The main reason for this is if we delete an entity
2290        # instance we have to yank out a bunch of other stuff with it.
2291        if ($self->IsEntity($objectName)) {
2292            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2293        } else {
2294            # Create the SQL command suffix to get the desierd records.
2295            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2296            # Convert it to a DELETE command.
2297            my $command = "DELETE $suffix";
2298            # Execute the command.
2299            my $dbh = $self->{_dbh};
2300            my $result = $dbh->SQL($command, 0, @{$parms});
2301            # Check the results. Note we convert the "0D0" result to a real zero.
2302            # A failure causes an abnormal termination, so the caller isn't going to
2303            # worry about it.
2304            if (! defined $result) {
2305                Confess("Error deleting from $objectName: " . $dbh->errstr());
2306            } elsif ($result == 0) {
2307                $retVal = 0;
2308            } else {
2309                $retVal = $result;
2310            }
2311        }
2312        # Return the result count.
2313        return $retVal;
2314    }
2315    
2316  =head3 SortNeeded  =head3 SortNeeded
2317    
2318  C<< my $parms = $erdb->SortNeeded($relationName); >>      my $parms = $erdb->SortNeeded($relationName);
2319    
2320  Return the pipe command for the sort that should be applied to the specified  Return the pipe command for the sort that should be applied to the specified
2321  relation when creating the load file.  relation when creating the load file.
# Line 1466  Line 2363 
2363      } elsif (exists $relationshipTable->{$relationName}) {      } elsif (exists $relationshipTable->{$relationName}) {
2364          # Here we have a relationship. We sort using the FROM index.          # Here we have a relationship. We sort using the FROM index.
2365          my $relationshipData = $relationshipTable->{$relationName};          my $relationshipData = $relationshipTable->{$relationName};
2366          my $index = $relationData->{Indexes}->{"idx${relationName}From"};          my $index = $relationData->{Indexes}->{idxFrom};
2367          push @keyNames, @{$index->{IndexFields}};          push @keyNames, @{$index->{IndexFields}};
2368      } else {      } else {
2369          # Here we have a secondary entity relation, so we have a sort on the ID field.          # Here we have a secondary entity relation, so we have a sort on the ID field.
# Line 1474  Line 2371 
2371      }      }
2372      # Now we parse the key names into sort parameters. First, we prime the return      # Now we parse the key names into sort parameters. First, we prime the return
2373      # string.      # string.
2374      my $retVal = "sort -t\"\t\" ";      my $retVal = "sort -S 1G -T\"$FIG_Config::temp\" -t\"\t\" ";
2375      # Get the relation's field list.      # Get the relation's field list.
2376      my @fields = @{$relationData->{Fields}};      my @fields = @{$relationData->{Fields}};
2377      # Loop through the keys.      # Loop through the keys.
# Line 1504  Line 2401 
2401                  # will stop the inner loop. Note that the field number is                  # will stop the inner loop. Note that the field number is
2402                  # 1-based in the sort command, so we have to increment the                  # 1-based in the sort command, so we have to increment the
2403                  # index.                  # index.
2404                  $fieldSpec = ($i + 1) . $modifier;                  my $realI = $i + 1;
2405                    $fieldSpec = "$realI,$realI$modifier";
2406              }              }
2407          }          }
2408          # Add this field to the sort command.          # Add this field to the sort command.
# Line 1516  Line 2414 
2414    
2415  =head3 GetList  =head3 GetList
2416    
2417  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>      my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2418    
2419  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
2420  specified filter clause.  specified filter clause.
# Line 1544  Line 2442 
2442  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
2443  particular genus and sorts them by species name.  particular genus and sorts them by species name.
2444    
2445  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
2446    
2447  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
2448  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
# Line 1556  Line 2454 
2454    
2455  =item RETURN  =item RETURN
2456    
2457  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2458    
2459  =back  =back
2460    
# Line 1579  Line 2477 
2477    
2478  =head3 GetCount  =head3 GetCount
2479    
2480  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2481    
2482  Return the number of rows found by a specified query. This method would  Return the number of rows found by a specified query. This method would
2483  normally be used to count the records in a single table. For example, in a  normally be used to count the records in a single table. For example, in a
# Line 1672  Line 2570 
2570    
2571  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
2572    
2573  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $sentence = $erdb->ComputeObjectSentence($objectName);
2574    
2575  Check an object name, and if it is a relationship convert it to a relationship sentence.  Check an object name, and if it is a relationship convert it to a relationship sentence.
2576    
# Line 1707  Line 2605 
2605    
2606  =head3 DumpRelations  =head3 DumpRelations
2607    
2608  C<< $erdb->DumpRelations($outputDirectory); >>      $erdb->DumpRelations($outputDirectory);
2609    
2610  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
2611  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 1749  Line 2647 
2647    
2648  =head3 InsertValue  =head3 InsertValue
2649    
2650  C<< $erdb->InsertValue($entityID, $fieldName, $value); >>      $erdb->InsertValue($entityID, $fieldName, $value);
2651    
2652  This method will insert a new value into the database. The value must be one  This method will insert a new value into the database. The value must be one
2653  associated with a secondary relation, since primary values cannot be inserted:  associated with a secondary relation, since primary values cannot be inserted:
# Line 1812  Line 2710 
2710    
2711  =head3 InsertObject  =head3 InsertObject
2712    
2713  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>      $erdb->InsertObject($objectType, \%fieldHash);
2714    
2715  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2716  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 1821  Line 2719 
2719  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2720  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
2721    
2722  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>      $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2723    
2724  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2725  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2726    
2727  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>      $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2728    
2729  =over 4  =over 4
2730    
# Line 1838  Line 2736 
2736    
2737  Hash of field names to values.  Hash of field names to values.
2738    
 =item RETURN  
   
 Returns 1 if successful, 0 if an error occurred.  
   
2739  =back  =back
2740    
2741  =cut  =cut
# Line 1899  Line 2793 
2793                  push @missing, $fieldName;                  push @missing, $fieldName;
2794              }              }
2795          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
         }  
2796          # Only proceed if there are no missing fields.          # Only proceed if there are no missing fields.
2797          if (@missing > 0) {          if (@missing > 0) {
2798              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
# Line 1940  Line 2829 
2829                  $retVal = $sth->execute(@parameterList);                  $retVal = $sth->execute(@parameterList);
2830                  if (!$retVal) {                  if (!$retVal) {
2831                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2832                      Trace("Insert error: $errorString.") if T(0);                      Confess("Error inserting into $relationName: $errorString");
2833                    } else {
2834                        Trace("Insert successful using $parameterList[0].") if T(3);
2835                  }                  }
2836              }              }
2837          }          }
2838      }      }
2839      # Return the success indicator.      # Return a 1 for backward compatability.
2840      return $retVal;      return 1;
2841    }
2842    
2843    =head3 UpdateEntity
2844    
2845        $erdb->UpdateEntity($entityName, $id, \%fields);
2846    
2847    Update the values of an entity. This is an unprotected update, so it should only be
2848    done if the database resides on a database server.
2849    
2850    =over 4
2851    
2852    =item entityName
2853    
2854    Name of the entity to update. (This is the entity type.)
2855    
2856    =item id
2857    
2858    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2859    
2860    =item fields
2861    
2862    Reference to a hash mapping field names to their new values. All of the fields named
2863    must be in the entity's primary relation, and they cannot any of them be the ID field.
2864    
2865    =back
2866    
2867    =cut
2868    
2869    sub UpdateEntity {
2870        # Get the parameters.
2871        my ($self, $entityName, $id, $fields) = @_;
2872        # Get a list of the field names being updated.
2873        my @fieldList = keys %{$fields};
2874        # Verify that the fields exist.
2875        my $checker = $self->GetFieldTable($entityName);
2876        for my $field (@fieldList) {
2877            if ($field eq 'id') {
2878                Confess("Cannot update the ID field for entity $entityName.");
2879            } elsif ($checker->{$field}->{relation} ne $entityName) {
2880                Confess("Cannot find $field in primary relation of $entityName.");
2881            }
2882        }
2883        # Build the SQL statement.
2884        my @sets = ();
2885        my @valueList = ();
2886        for my $field (@fieldList) {
2887            push @sets, _FixName($field) . " = ?";
2888            push @valueList, $fields->{$field};
2889        }
2890        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2891        # Add the ID to the list of binding values.
2892        push @valueList, $id;
2893        # Call SQL to do the work.
2894        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2895        # Check for errors.
2896        if ($rows == 0) {
2897            Confess("Entity $id of type $entityName not found.");
2898        }
2899  }  }
2900    
2901  =head3 LoadTable  =head3 LoadTable
2902    
2903  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      my $results = $erdb->LoadTable($fileName, $relationName, %options);
2904    
2905  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2906  first.  first.
# Line 1966  Line 2915 
2915    
2916  Name of the relation to be loaded. This is the same as the table name.  Name of the relation to be loaded. This is the same as the table name.
2917    
2918  =item truncateFlag  =item options
2919    
2920  TRUE if the table should be dropped and re-created, else FALSE  A hash of load options.
2921    
2922  =item RETURN  =item RETURN
2923    
# Line 1976  Line 2925 
2925    
2926  =back  =back
2927    
2928    The permissible options are as follows.
2929    
2930    =over 4
2931    
2932    =item truncate
2933    
2934    If TRUE, then the table will be erased before loading.
2935    
2936    =item mode
2937    
2938    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2939    This option is only applicable to a MySQL database.
2940    
2941    =item partial
2942    
2943    If TRUE, then it is assumed that this is a partial load, and the table will not
2944    be analyzed and compacted at the end.
2945    
2946    =back
2947    
2948  =cut  =cut
2949  sub LoadTable {  sub LoadTable {
2950      # Get the parameters.      # Get the parameters.
2951      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $fileName, $relationName, %options) = @_;
2952      # Create the statistical return object.      # Create the statistical return object.
2953      my $retVal = _GetLoadStats();      my $retVal = _GetLoadStats();
2954      # Trace the fact of the load.      # Trace the fact of the load.
# Line 1991  Line 2960 
2960      # Get the relation data.      # Get the relation data.
2961      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
2962      # Check the truncation flag.      # Check the truncation flag.
2963      if ($truncateFlag) {      if ($options{truncate}) {
2964          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2965          # Compute the row count estimate. We take the size of the load file,          # Compute the row count estimate. We take the size of the load file,
2966          # divide it by the estimated row size, and then multiply by 1.5 to          # divide it by the estimated row size, and then multiply by 2 to
2967          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2968          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2969          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2970          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 8 / $rowSize;
2971            if ($estimate < 1000) {
2972                $estimate = 1000;
2973            }
2974          # Re-create the table without its index.          # Re-create the table without its index.
2975          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2976          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 2014  Line 2986 
2986      # Load the table.      # Load the table.
2987      my $rv;      my $rv;
2988      eval {      eval {
2989          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
2990      };      };
2991      if (!defined $rv) {      if (!defined $rv) {
2992          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
2993          $retVal->AddMessage("Table load failed for $relationName using $fileName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2994          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
2995      } else {      } else {
2996          # Here we successfully loaded the table.          # Here we successfully loaded the table.
2997          $retVal->Add("tables");          $retVal->Add("tables");
2998          my $size = -s $fileName;          my $size = -s $fileName;
2999          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
3000            $retVal->Add("bytes", $size);
3001          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
3002          if ($truncateFlag) {          if ($options{truncate}) {
3003              # Indexes are created here for PostGres. For PostGres, indexes are              # Indexes are created here for PostGres. For PostGres, indexes are
3004              # best built at the end. For MySQL, the reverse is true.              # best built at the end. For MySQL, the reverse is true.
3005              if (! $dbh->{_preIndex}) {              if (! $dbh->{_preIndex}) {
# Line 2040  Line 3013 
3013              # The full-text index (if any) is always built last, even for MySQL.              # The full-text index (if any) is always built last, even for MySQL.
3014              # First we need to see if this table has a full-text index. Only              # First we need to see if this table has a full-text index. Only
3015              # primary relations are allowed that privilege.              # primary relations are allowed that privilege.
3016                Trace("Checking for full-text index on $relationName.") if T(2);
3017              if ($self->_IsPrimary($relationName)) {              if ($self->_IsPrimary($relationName)) {
3018                  # Get the relation's entity/relationship structure.                  $self->CreateSearchIndex($relationName);
                 my $structure = $self->_GetStructure($relationName);  
                 # Check for a searchable fields list.  
                 if (exists $structure->{searchFields}) {  
                     # Here we know that we need to create a full-text search index.  
                     # Get an SQL-formatted field name list.  
                     my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));  
                     # Create the index.  
                     $dbh->create_index(tbl => $relationName, idx => "search_idx_$relationName",  
                                        flds => $fields, kind => 'fulltext');  
                 }  
3019              }              }
3020          }          }
3021      }      }
3022      # Analyze the table to improve performance.      # Analyze the table to improve performance.
3023        if (! $options{partial}) {
3024      Trace("Analyzing and compacting $relationName.") if T(3);      Trace("Analyzing and compacting $relationName.") if T(3);
3025      $dbh->vacuum_it($relationName);          $self->Analyze($relationName);
3026        }
3027      Trace("$relationName load completed.") if T(3);      Trace("$relationName load completed.") if T(3);
3028      # Return the statistics.      # Return the statistics.
3029      return $retVal;      return $retVal;
3030  }  }
3031    
3032  =head3 GenerateEntity  =head3 Analyze
3033    
3034  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>      $erdb->Analyze($tableName);
3035    
3036  Generate the data for a new entity instance. This method creates a field hash suitable for  Analyze and compact a table in the database. This is useful after a load
3037  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  to improve the performance of the indexes.
 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.  
3038    
3039  =over 4  =over 4
3040    
3041  =item id  =item tableName
   
 ID to assign to the new entity.  
   
 =item type  
3042    
3043  Type name for the new entity.  Name of the table to be analyzed and compacted.
   
 =item values  
   
 Hash containing additional values that might be needed by the data generation methods (optional).  
3044    
3045  =back  =back
3046    
3047  =cut  =cut
3048    
3049  sub GenerateEntity {  sub Analyze {
3050      # Get the parameters.      # Get the parameters.
3051      my ($self, $id, $type, $values) = @_;      my ($self, $tableName) = @_;
3052      # Create the return hash.      # Analyze the table.
3053      my $this = { id => $id };      $self->{_dbh}->vacuum_it($tableName);
     # Get the metadata structure.  
     my $metadata = $self->{_metaData};  
     # Get this entity's list of fields.  
     if (!exists $metadata->{Entities}->{$type}) {  
         Confess("Unrecognized entity type $type in GenerateEntity.");  
     } else {  
         my $entity = $metadata->{Entities}->{$type};  
         my $fields = $entity->{Fields};  
         # Generate data from the fields.  
         _GenerateFields($this, $fields, $type, $values);  
     }  
     # Return the hash created.  
     return $this;  
3054  }  }
3055    
3056  =head3 GetEntity  =head3 TruncateTable
3057    
3058  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      $erdb->TruncateTable($table);
3059    
3060  Return an object describing the entity instance with a specified ID.  Delete all rows from a table quickly. This uses the built-in SQL
3061    C<TRUNCATE> statement, which effectively drops and re-creates a table
3062    with all its settings intact.
3063    
3064  =over 4  =over 4
3065    
3066  =item entityType  =item table
   
 Entity type name.  
   
 =item ID  
   
 ID of the desired entity.  
   
 =item RETURN  
3067    
3068  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Name of the table to be cleared.
 instance is found with the specified key.  
3069    
3070  =back  =back
3071    
3072  =cut  =cut
3073    
3074  sub GetEntity {  sub TruncateTable {
3075      # Get the parameters.      # Get the parameters.
3076      my ($self, $entityType, $ID) = @_;      my ($self, $table) = @_;
3077      # Create a query.      # Get the database handle.
3078      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);      my $dbh = $self->{_dbh};
3079      # Get the first (and only) object.      # Execute a truncation comment.
3080      my $retVal = $query->Fetch();      $dbh->SQL("TRUNCATE TABLE $table");
     # Return the result.  
     return $retVal;  
3081  }  }
3082    
 =head3 GetChoices  
3083    
3084  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>  =head3 CreateSearchIndex
3085    
3086  Return a list of all the values for the specified field that are represented in the      $erdb->CreateSearchIndex($objectName);
 specified entity.  
3087    
3088  Note that if the field is not indexed, then this will be a very slow operation.  Check for a full-text search index on the specified entity or relationship object, and
3089    if one is required, rebuild it.
3090    
3091  =over 4  =over 4
3092    
3093  =item entityName  =item objectName
3094    
3095  Name of an entity in the database.  Name of the entity or relationship to be indexed.
3096    
3097  =item fieldName  =back
3098    
3099  Name of a field belonging to the entity. This is a raw field name without  =cut
 the standard parenthesized notation used in most calls.  
3100    
3101  =item RETURN  sub CreateSearchIndex {
3102        # Get the parameters.
3103        my ($self, $objectName) = @_;
3104        # Get the relation's entity/relationship structure.
3105        my $structure = $self->_GetStructure($objectName);
3106        # Get the database handle.
3107        my $dbh = $self->{_dbh};
3108        Trace("Checking for search fields in $objectName.") if T(3);
3109        # Check for a searchable fields list.
3110        if (exists $structure->{searchFields}) {
3111            # Here we know that we need to create a full-text search index.
3112            # Get an SQL-formatted field name list.
3113            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
3114            # Create the index. If it already exists, it will be dropped.
3115            $dbh->create_index(tbl => $objectName, idx => "search_idx",
3116                               flds => $fields, kind => 'fulltext');
3117            Trace("Index created for $fields in $objectName.") if T(2);
3118        }
3119    }
3120    
3121  Returns a list of the distinct values for the specified field in the database.  =head3 DropRelation
3122    
3123        $erdb->DropRelation($relationName);
3124    
3125    Physically drop a relation from the database.
3126    
3127    =over 4
3128    
3129    =item relationName
3130    
3131    Name of the relation to drop. If it does not exist, this method will have
3132    no effect.
3133    
3134  =back  =back
3135    
3136  =cut  =cut
3137    
3138  sub GetChoices {  sub DropRelation {
3139      # Get the parameters.      # Get the parameters.
3140      my ($self, $entityName, $fieldName) = @_;      my ($self, $relationName) = @_;
3141      # Declare the return variable.      # Get the database handle.
3142      my @retVal;      my $dbh = $self->{_dbh};
3143      # Get the entity data structure.      # Drop the relation. The method used here has no effect if the relation
3144      my $entityData = $self->_GetStructure($entityName);      # does not exist.
3145      # Get the field.      Trace("Invoking DB Kernel to drop $relationName.") if T(3);
3146        $dbh->drop_table(tbl => $relationName);
3147    }
3148    
3149    =head3 MatchSqlPattern
3150    
3151        my $matched = ERDB::MatchSqlPattern($value, $pattern);
3152    
3153    Determine whether or not a specified value matches an SQL pattern. An SQL
3154    pattern has two wild card characters: C<%> that matches multiple characters,
3155    and C<_> that matches a single character. These can be escaped using a
3156    backslash (C<\>). We pull this off by converting the SQL pattern to a
3157    PERL regular expression. As per SQL rules, the match is case-insensitive.
3158    
3159    =over 4
3160    
3161    =item value
3162    
3163    Value to be matched against the pattern. Note that an undefined or empty
3164    value will not match anything.
3165    
3166    =item pattern
3167    
3168    SQL pattern against which to match the value. An undefined or empty pattern will
3169    match everything.
3170    
3171    =item RETURN
3172    
3173    Returns TRUE if the value and pattern match, else FALSE.
3174    
3175    =back
3176    
3177    =cut
3178    
3179    sub MatchSqlPattern {
3180        # Get the parameters.
3181        my ($value, $pattern) = @_;
3182        # Declare the return variable.
3183        my $retVal;
3184        # Insure we have a pattern.
3185        if (! defined($pattern) || $pattern eq "") {
3186            $retVal = 1;
3187        } else {
3188            # Break the pattern into pieces around the wildcard characters. Because we
3189            # use parentheses in the split function's delimiter expression, we'll get
3190            # list elements for the delimiters as well as the rest of the string.
3191            my @pieces = split /([_%]|\\[_%])/, $pattern;
3192            # Check some fast special cases.
3193            if ($pattern eq '%') {
3194                # A null pattern matches everything.
3195                $retVal = 1;
3196            } elsif (@pieces == 1) {
3197                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
3198                $retVal = (lc($value) eq lc($pattern));
3199            } elsif (@pieces == 2 && $pieces[1] eq '%') {
3200                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
3201                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
3202            } else {
3203                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
3204                my $realPattern = "";
3205                for my $piece (@pieces) {
3206                    # Determine the type of piece.
3207                    if ($piece eq "") {
3208                        # Empty pieces are ignored.
3209                    } elsif ($piece eq "%") {
3210                        # Here we have a multi-character wildcard. Note that it can match
3211                        # zero or more characters.
3212                        $realPattern .= ".*"
3213                    } elsif ($piece eq "_") {
3214                        # Here we have a single-character wildcard.
3215                        $realPattern .= ".";
3216                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
3217                        # This is an escape sequence (which is a rare thing, actually).
3218                        $realPattern .= substr($piece, 1, 1);
3219                    } else {
3220                        # Here we have raw text.
3221                        $realPattern .= quotemeta($piece);
3222                    }
3223                }
3224                # Do the match.
3225                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
3226            }
3227        }
3228        # Return the result.
3229        return $retVal;
3230    }
3231    
3232    =head3 GetEntity
3233    
3234        my $entityObject = $erdb->GetEntity($entityType, $ID);
3235    
3236    Return an object describing the entity instance with a specified ID.
3237    
3238    =over 4
3239    
3240    =item entityType
3241    
3242    Entity type name.
3243    
3244    =item ID
3245    
3246    ID of the desired entity.
3247    
3248    =item RETURN
3249    
3250    Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
3251    instance is found with the specified key.
3252    
3253    =back
3254    
3255    =cut
3256    
3257    sub GetEntity {
3258        # Get the parameters.
3259        my ($self, $entityType, $ID) = @_;
3260        # Create a query.
3261        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3262        # Get the first (and only) object.
3263        my $retVal = $query->Fetch();
3264        if (T(3)) {
3265            if ($retVal) {
3266                Trace("Entity $entityType \"$ID\" found.");
3267            } else {
3268                Trace("Entity $entityType \"$ID\" not found.");
3269            }
3270        }
3271        # Return the result.
3272        return $retVal;
3273    }
3274    
3275    =head3 GetChoices
3276    
3277        my @values = $erdb->GetChoices($entityName, $fieldName);
3278    
3279    Return a list of all the values for the specified field that are represented in the
3280    specified entity.
3281    
3282    Note that if the field is not indexed, then this will be a very slow operation.
3283    
3284    =over 4
3285    
3286    =item entityName
3287    
3288    Name of an entity in the database.
3289    
3290    =item fieldName
3291    
3292    Name of a field belonging to the entity. This is a raw field name without
3293    the standard parenthesized notation used in most calls.
3294    
3295    =item RETURN
3296    
3297    Returns a list of the distinct values for the specified field in the database.
3298    
3299    =back
3300    
3301    =cut
3302    
3303    sub GetChoices {
3304        # Get the parameters.
3305        my ($self, $entityName, $fieldName) = @_;
3306        # Declare the return variable.
3307        my @retVal;
3308        # Get the entity data structure.
3309        my $entityData = $self->_GetStructure($entityName);
3310        # Get the field.
3311      my $fieldHash = $entityData->{Fields};      my $fieldHash = $entityData->{Fields};
3312      if (! exists $fieldHash->{$fieldName}) {      if (! exists $fieldHash->{$fieldName}) {
3313          Confess("$fieldName not found in $entityName.");          Confess("$fieldName not found in $entityName.");
# Line 2214  Line 3329 
3329    
3330  =head3 GetEntityValues  =head3 GetEntityValues
3331    
3332  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3333    
3334  Return a list of values from a specified entity instance. If the entity instance  Return a list of values from a specified entity instance. If the entity instance
3335  does not exist, an empty list is returned.  does not exist, an empty list is returned.
# Line 2258  Line 3373 
3373    
3374  =head3 GetAll  =head3 GetAll
3375    
3376  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3377    
3378  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
3379  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 2272  Line 3387 
3387  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
3388  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
3389  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
3390  feature ID followed by all of its aliases.  feature ID followed by all of its essentiality determinations.
3391    
3392  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)']);
3393    
3394  =over 4  =over 4
3395    
# Line 2299  Line 3414 
3414    
3415  List of the fields to be returned in each element of the list returned.  List of the fields to be returned in each element of the list returned.
3416    
3417  =item count  =item count
3418    
3419    Maximum number of records to return. If omitted or 0, all available records will be returned.
3420    
3421    =item RETURN
3422    
3423    Returns a list of list references. Each element of the return list contains the values for the
3424    fields specified in the B<fields> parameter.
3425    
3426    =back
3427    
3428    =cut
3429    #: Return Type @@;
3430    sub GetAll {
3431        # Get the parameters.
3432        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3433        # Translate the parameters from a list reference to a list. If the parameter
3434        # list is a scalar we convert it into a singleton list.
3435        my @parmList = ();
3436        if (ref $parameterList eq "ARRAY") {
3437            Trace("GetAll parm list is an array.") if T(4);
3438            @parmList = @{$parameterList};
3439        } else {
3440            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3441            push @parmList, $parameterList;
3442        }
3443        # Insure the counter has a value.
3444        if (!defined $count) {
3445            $count = 0;
3446        }
3447        # Add the row limit to the filter clause.
3448        if ($count > 0) {
3449            $filterClause .= " LIMIT $count";
3450        }
3451        # Create the query.
3452        my $query = $self->Get($objectNames, $filterClause, \@parmList);
3453        # Set up a counter of the number of records read.
3454        my $fetched = 0;
3455        # Loop through the records returned, extracting the fields. Note that if the
3456        # counter is non-zero, we stop when the number of records read hits the count.
3457        my @retVal = ();
3458        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3459            my @rowData = $row->Values($fields);
3460            push @retVal, \@rowData;
3461            $fetched++;
3462        }
3463        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3464        # Return the resulting list.
3465        return @retVal;
3466    }
3467    
3468    =head3 Exists
3469    
3470        my $found = $sprout->Exists($entityName, $entityID);
3471    
3472    Return TRUE if an entity exists, else FALSE.
3473    
3474    =over 4
3475    
3476    =item entityName
3477    
3478    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3479    
3480    =item entityID
3481    
3482    ID of the entity instance whose existence is to be checked.
3483    
3484    =item RETURN
3485    
3486    Returns TRUE if the entity instance exists, else FALSE.
3487    
3488    =back
3489    
3490    =cut
3491    #: Return Type $;
3492    sub Exists {
3493        # Get the parameters.
3494        my ($self, $entityName, $entityID) = @_;
3495        # Check for the entity instance.
3496        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3497        my $testInstance = $self->GetEntity($entityName, $entityID);
3498        # Return an existence indicator.
3499        my $retVal = ($testInstance ? 1 : 0);
3500        return $retVal;
3501    }
3502    
3503    =head3 EstimateRowSize
3504    
3505        my $rowSize = $erdb->EstimateRowSize($relName);
3506    
3507    Estimate the row size of the specified relation. The estimated row size is computed by adding
3508    up the average length for each data type.
3509    
3510    =over 4
3511    
3512    =item relName
3513    
3514    Name of the relation whose estimated row size is desired.
3515    
3516    =item RETURN
3517    
3518    Returns an estimate of the row size for the specified relation.
3519    
3520    =back
3521    
3522    =cut
3523    #: Return Type $;
3524    sub EstimateRowSize {
3525        # Get the parameters.
3526        my ($self, $relName) = @_;
3527        # Declare the return variable.
3528        my $retVal = 0;
3529        # Find the relation descriptor.
3530        my $relation = $self->_FindRelation($relName);
3531        # Get the list of fields.
3532        for my $fieldData (@{$relation->{Fields}}) {
3533            # Get the field type and add its length.
3534            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3535            $retVal += $fieldLen;
3536        }
3537        # Return the result.
3538        return $retVal;
3539    }
3540    
3541    =head3 GetFieldTable
3542    
3543        my $fieldHash = $self->GetFieldTable($objectnName);
3544    
3545    Get the field structure for a specified entity or relationship.
3546    
3547    =over 4
3548    
3549    =item objectName
3550    
3551    Name of the desired entity or relationship.
3552    
3553    =item RETURN
3554    
3555    The table containing the field descriptors for the specified object.
3556    
3557    =back
3558    
3559    =cut
3560    
3561    sub GetFieldTable {
3562        # Get the parameters.
3563        my ($self, $objectName) = @_;
3564        # Get the descriptor from the metadata.
3565        my $objectData = $self->_GetStructure($objectName);
3566        # Return the object's field table.
3567        return $objectData->{Fields};
3568    }
3569    
3570    =head3 SplitKeywords
3571    
3572        my @keywords = ERDB::SplitKeywords($keywordString);
3573    
3574    This method returns a list of the positive keywords in the specified
3575    keyword string. All of the operators will have been stripped off,
3576    and if the keyword is preceded by a minus operator (C<->), it will
3577    not be in the list returned. The idea here is to get a list of the
3578    keywords the user wants to see. The list will be processed to remove
3579    duplicates.
3580    
3581    It is possible to create a string that confuses this method. For example
3582    
3583        frog toad -frog
3584    
3585    would return both C<frog> and C<toad>. If this is a problem we can deal
3586    with it later.
3587    
3588    =over 4
3589    
3590    =item keywordString
3591    
3592    The keyword string to be parsed.
3593    
3594    =item RETURN
3595    
3596    Returns a list of the words in the keyword string the user wants to
3597    see.
3598    
3599    =back
3600    
3601    =cut
3602    
3603    sub SplitKeywords {
3604        # Get the parameters.
3605        my ($keywordString) = @_;
3606        # Make a safety copy of the string. (This helps during debugging.)
3607        my $workString = $keywordString;
3608        # Convert operators we don't care about to spaces.
3609        $workString =~ tr/+"()<>/ /;
3610        # Split the rest of the string along space boundaries. Note that we
3611        # eliminate any words that are zero length or begin with a minus sign.
3612        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3613        # Use a hash to remove duplicates.
3614        my %words = map { $_ => 1 } @wordList;
3615        # Return the result.
3616        return sort keys %words;
3617    }
3618    
3619    =head3 ValidateFieldName
3620    
3621        my $okFlag = ERDB::ValidateFieldName($fieldName);
3622    
3623    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3624    be hyphenated words subject to certain restrictions.
3625    
3626    =over 4
3627    
3628    =item fieldName
3629    
3630    Field name to be validated.
3631    
3632    =item RETURN
3633    
3634    Returns TRUE if the field name is valid, else FALSE.
3635    
3636    =back
3637    
3638    =cut
3639    
3640    sub ValidateFieldName {
3641        # Get the parameters.
3642        my ($fieldName) = @_;
3643        # Declare the return variable. The field name is valid until we hear
3644        # differently.
3645        my $retVal = 1;
3646        # Compute the maximum name length.
3647        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3648        # Look for bad stuff in the name.
3649        if ($fieldName =~ /--/) {
3650            # Here we have a doubled minus sign.
3651            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3652            $retVal = 0;
3653        } elsif ($fieldName !~ /^[A-Za-z]/) {
3654            # Here the field name is missing the initial letter.
3655            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3656            $retVal = 0;
3657        } elsif (length($fieldName) > $maxLen) {
3658            # Here the field name is too long.
3659            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3660        } else {
3661            # Strip out the minus signs. Everything remaining must be a letter,
3662            # underscore, or digit.
3663            my $strippedName = $fieldName;
3664            $strippedName =~ s/-//g;
3665            if ($strippedName !~ /^(\w|\d)+$/) {
3666                Trace("Field name $fieldName contains illegal characters.") if T(1);
3667                $retVal = 0;
3668            }
3669        }
3670        # Return the result.
3671        return $retVal;
3672    }
3673    
3674    =head3 ReadMetaXML
3675    
3676        my $rawMetaData = ERDB::ReadDBD($fileName);
3677    
3678    This method reads a raw database definition XML file and returns it.
3679    Normally, the metadata used by the ERDB system has been processed and
3680    modified to make it easier to load and retrieve the data; however,
3681    this method can be used to get the data in its raw form.
3682    
3683    =over 4
3684    
3685    =item fileName
3686    
3687    Name of the XML file to read.
3688    
3689    =item RETURN
3690    
3691    Returns a hash reference containing the raw XML data from the specified file.
3692    
3693    =back
3694    
3695    =cut
3696    
3697    sub ReadMetaXML {
3698        # Get the parameters.
3699        my ($fileName) = @_;
3700        # Read the XML.
3701        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3702        Trace("XML metadata loaded from file $fileName.") if T(1);
3703        # Return the result.
3704        return $retVal;
3705    }
3706    
3707    =head3 GetEntityFieldHash
3708    
3709        my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3710    
3711    Get the field hash of the named entity in the specified raw XML structure.
3712    The field hash may not exist, in which case we need to create it.
3713    
3714    =over 4
3715    
3716    =item structure
3717    
3718    Raw XML structure defininng the database. This is not the run-time XML used by
3719    an ERDB object, since that has all sorts of optimizations built-in.
3720    
3721    =item entityName
3722    
3723    Name of the entity whose field structure is desired.
3724    
3725    =item RETURN
3726    
3727    Returns the field hash used to define the entity's fields.
3728    
3729    =back
3730    
3731    =cut
3732    
3733    sub GetEntityFieldHash {
3734        # Get the parameters.
3735        my ($structure, $entityName) = @_;
3736        # Get the entity structure.
3737        my $entityData = $structure->{Entities}->{$entityName};
3738        # Look for a field structure.
3739        my $retVal = $entityData->{Fields};
3740        # If it doesn't exist, create it.
3741        if (! defined($retVal)) {
3742            $entityData->{Fields} = {};
3743            $retVal = $entityData->{Fields};
3744        }
3745        # Return the result.
3746        return $retVal;
3747    }
3748    
3749    =head3 WriteMetaXML
3750    
3751        ERDB::WriteMetaXML($structure, $fileName);
3752    
3753    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3754    used to update the database definition. It must be used with care, however, since it
3755    will only work on a raw structure, not on the processed structure created by an ERDB
3756    constructor.
3757    
3758    =over 4
3759    
3760    =item structure
3761    
3762  Maximum number of records to return. If omitted or 0, all available records will be returned.  XML structure to be written to the file.
3763    
3764  =item RETURN  =item fileName
3765    
3766  Returns a list of list references. Each element of the return list contains the values for the  Name of the output file to which the updated XML should be stored.
 fields specified in the B<fields> parameter.  
3767    
3768  =back  =back
3769    
3770  =cut  =cut
3771  #: Return Type @@;  
3772  sub GetAll {  sub WriteMetaXML {
3773      # Get the parameters.      # Get the parameters.
3774      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      my ($structure, $fileName) = @_;
3775      # Translate the parameters from a list reference to a list. If the parameter      # Compute the output.
3776      # list is a scalar we convert it into a singleton list.      my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3777      my @parmList = ();      # Write it to the file.
3778      if (ref $parameterList eq "ARRAY") {      my $xmlOut = Open(undef, ">$fileName");
3779          Trace("GetAll parm list is an array.") if T(4);      print $xmlOut $fileString;
         @parmList = @{$parameterList};  
     } else {  
         Trace("GetAll parm list is a scalar: $parameterList.") if T(4);  
         push @parmList, $parameterList;  
     }  
     # Insure the counter has a value.  
     if (!defined $count) {  
         $count = 0;  
     }  
     # Add the row limit to the filter clause.  
     if ($count > 0) {  
         $filterClause .= " LIMIT $count";  
     }  
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, \@parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
     # Loop through the records returned, extracting the fields. Note that if the  
     # counter is non-zero, we stop when the number of records read hits the count.  
     my @retVal = ();  
     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
         my @rowData = $row->Values($fields);  
         push @retVal, \@rowData;  
         $fetched++;  
     }  
     Trace("$fetched rows returned in GetAll.") if T(SQL => 4);  
     # Return the resulting list.  
     return @retVal;  
3780  }  }
3781    
 =head3 Exists  
   
 C<< my $found = $sprout->Exists($entityName, $entityID); >>  
3782    
3783  Return TRUE if an entity exists, else FALSE.  =head3 HTMLNote
3784    
3785  =over 4  Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3786    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3787    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3788    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3789    
3790  =item entityName      my $realHtml = ERDB::HTMLNote($dataString);
3791    
3792  Name of the entity type (e.g. C<Feature>) relevant to the existence check.  =over 4
3793    
3794  =item entityID  =item dataString
3795    
3796  ID of the entity instance whose existence is to be checked.  String to convert to HTML.
3797    
3798  =item RETURN  =item RETURN
3799    
3800  Returns TRUE if the entity instance exists, else FALSE.  An HTML string derived from the input string.
3801    
3802  =back  =back
3803    
3804  =cut  =cut
3805  #: Return Type $;  
3806  sub Exists {  sub HTMLNote {
3807      # Get the parameters.      # Get the parameter.
3808      my ($self, $entityName, $entityID) = @_;      my ($dataString) = @_;
3809      # Check for the entity instance.      # HTML-escape the text.
3810      Trace("Checking existence of $entityName with ID=$entityID.") if T(4);      my $retVal = CGI::escapeHTML($dataString);
3811      my $testInstance = $self->GetEntity($entityName, $entityID);      # Substitute the bulletin board codes.
3812      # Return an existence indicator.      $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3813      my $retVal = ($testInstance ? 1 : 0);      $retVal =~ s!\[p\]!</p><p>!g;
3814        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3815        $retVal =~ s!\[/link\]!</a>!g;
3816        # Return the result.
3817      return $retVal;      return $retVal;
3818  }  }
3819    
3820  =head3 EstimateRowSize  =head3 WikiNote
3821    
3822  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3823    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3824    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3825    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3826    
3827  Estimate the row size of the specified relation. The estimated row size is computed by adding      my $wikiText = ERDB::WikiNote($dataString);
 up the average length for each data type.  
3828    
3829  =over 4  =over 4
3830    
3831  =item relName  =item dataString
3832    
3833  Name of the relation whose estimated row size is desired.  String to convert to Wiki text.
3834    
3835  =item RETURN  =item RETURN
3836    
3837  Returns an estimate of the row size for the specified relation.  An Wiki text string derived from the input string.
3838    
3839  =back  =back
3840    
3841  =cut  =cut
3842  #: Return Type $;  
3843  sub EstimateRowSize {  sub WikiNote {
3844      # Get the parameters.      # Get the parameter.
3845      my ($self, $relName) = @_;      my ($dataString) = @_;
3846      # Declare the return variable.      # HTML-escape the text.
3847      my $retVal = 0;      my $retVal = CGI::escapeHTML($dataString);
3848      # Find the relation descriptor.      # Substitute the bulletin board codes.
3849      my $relation = $self->_FindRelation($relName);      my $italic = WikiTools::ItalicCode();
3850      # Get the list of fields.      $retVal =~ s/\[\/?i\]/$italic/g;
3851      for my $fieldData (@{$relation->{Fields}}) {      my $bold = WikiTools::BoldCode();
3852          # Get the field type and add its length.      $retVal =~ s/\[\/?b\]/$bold/g;
3853          my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};      # Paragraph breaks are the same no matter which Wiki you're using.
3854          $retVal += $fieldLen;      $retVal =~ s!\[p\]!\n\n!g;
3855        # Now we do the links, which are complicated by the need to know two
3856        # things: the target URL and the text.
3857        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3858            # Replace the matched string with the Wiki markup for links. Note that
3859            # $-[0] is the starting position of the match for the entire expression,
3860            # and $+[0] is past the ending position.
3861            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3862      }      }
3863      # Return the result.      # Return the result.
3864      return $retVal;      return $retVal;
3865  }  }
3866    
3867  =head3 GetFieldTable  =head3 BeginTran
3868    
3869  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>      $erdb->BeginTran();
3870    
3871  Get the field structure for a specified entity or relationship.  Start a database transaction.
3872    
3873    =cut
3874    
3875    sub BeginTran {
3876        my ($self) = @_;
3877        $self->{_dbh}->begin_tran();
3878    
3879    }
3880    
3881    =head3 CommitTran
3882    
3883        $erdb->CommitTran();
3884    
3885    Commit an active database transaction.
3886    
3887    =cut
3888    
3889    sub CommitTran {
3890        my ($self) = @_;
3891        $self->{_dbh}->commit_tran();
3892    }
3893    
3894    =head3 RollbackTran
3895    
3896        $erdb->RollbackTran();
3897    
3898    Roll back an active database transaction.
3899    
3900    =cut
3901    
3902    sub RollbackTran {
3903        my ($self) = @_;
3904        $self->{_dbh}->roll_tran();
3905    }
3906    
3907    =head3 UpdateField
3908    
3909        my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3910    
3911    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3912    returned.
3913    
3914  =over 4  =over 4
3915    
3916  =item objectName  =item fieldName
3917    
3918  Name of the desired entity or relationship.  Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3919    
3920    =item oldValue
3921    
3922    Value to be modified. All occurrences of this value in the named field will be replaced by the
3923    new value.
3924    
3925    =item newValue
3926    
3927    New value to be substituted for the old value when it's found.
3928    
3929    =item filter
3930    
3931    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3932    
3933    =item parms
3934    
3935    Reference to a list of parameter values in the filter.
3936    
3937  =item RETURN  =item RETURN
3938    
3939  The table containing the field descriptors for the specified object.  Returns the number of rows modified.
3940    
3941  =back  =back
3942    
3943  =cut  =cut
3944    
3945  sub GetFieldTable {  sub UpdateField {
3946      # Get the parameters.      # Get the parameters.
3947      my ($self, $objectName) = @_;      my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3948      # Get the descriptor from the metadata.      # Get the object and field names from the field name parameter.
3949      my $objectData = $self->_GetStructure($objectName);      $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3950      # Return the object's field table.      my $objectName = $1;
3951      return $objectData->{Fields};      my $realFieldName = _FixName($2);
3952        # Add the old value to the filter. Note we allow the possibility that no
3953        # filter was specified.
3954        my $realFilter = "$fieldName = ?";
3955        if ($filter) {
3956            $realFilter .= " AND $filter";
3957        }
3958        # Format the query filter.
3959        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3960            $self->_SetupSQL([$objectName], $realFilter);
3961        # Create the query. Since there is only one object name, the mapped-name data is not
3962        # necessary. Neither is the FROM clause.
3963        $suffix =~ s/^FROM.+WHERE\s+//;
3964        # Create the update statement.
3965        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3966        # Get the database handle.
3967        my $dbh = $self->{_dbh};
3968        # Add the old and new values to the parameter list. Note we allow the possibility that
3969        # there are no user-supplied parameters.
3970        my @params = ($newValue, $oldValue);
3971        if (defined $parms) {
3972            push @params, @{$parms};
3973        }
3974        # Execute the update.
3975        my $retVal = $dbh->SQL($command, 0, @params);
3976        # Make the funky zero a real zero.
3977        if ($retVal == 0) {
3978            $retVal = 0;
3979        }
3980        # Return the result.
3981        return $retVal;
3982  }  }
3983    
3984    
3985  =head2 Data Mining Methods  =head2 Data Mining Methods
3986    
3987  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3988    
3989  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3990    
3991  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
3992  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 2517  Line 4047 
4047    
4048  =head3 FindColumn  =head3 FindColumn
4049    
4050  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
4051    
4052  Return the location a desired column in a data mining header line. The data  Return the location a desired column in a data mining header line. The data
4053  mining header line is a tab-separated list of column names. The column  mining header line is a tab-separated list of column names. The column
# Line 2575  Line 4105 
4105    
4106  =head3 ParseColumns  =head3 ParseColumns
4107    
4108  C<< my @columns = ERDB::ParseColumns($line); >>      my @columns = ERDB::ParseColumns($line);
4109    
4110  Convert the specified data line to a list of columns.  Convert the specified data line to a list of columns.
4111    
# Line 2607  Line 4137 
4137    
4138  =head2 Virtual Methods  =head2 Virtual Methods
4139    
4140    =head3 _CreatePPOIndex
4141    
4142        my $index = ERDB::_CreatePPOIndex($indexObject);
4143    
4144    Convert the XML for an ERDB index to the XML structure for a PPO
4145    index.
4146    
4147    =over 4
4148    
4149    =item indexObject
4150    
4151    ERDB XML structure for an index.
4152    
4153    =item RETURN
4154    
4155    PPO XML structure for the same index.
4156    
4157    =back
4158    
4159    =cut
4160    
4161    sub _CreatePPOIndex {
4162        # Get the parameters.
4163        my ($indexObject) = @_;
4164        # The incoming index contains a list of the index fields in the IndexFields
4165        # member. We loop through it to create the index tags.
4166        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
4167        # Wrap the fields in attribute tags.
4168        my $retVal = { attribute => \@fields };
4169        # Return the result.
4170        return $retVal;
4171    }
4172    
4173    =head3 _CreatePPOField
4174    
4175        my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
4176    
4177    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
4178    
4179    =over 4
4180    
4181    =item fieldName
4182    
4183    Name of the scalar field.
4184    
4185    =item fieldObject
4186    
4187    ERDB XML structure describing the field.
4188    
4189    =item RETURN
4190    
4191    Returns a PPO XML structure for the same field.
4192    
4193    =back
4194    
4195    =cut
4196    
4197    sub _CreatePPOField {
4198        # Get the parameters.
4199        my ($fieldName, $fieldObject) = @_;
4200        # Get the field type.
4201        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
4202        # Fix up the field name.
4203        $fieldName = _FixName($fieldName);
4204        # Build the scalar tag.
4205        my $retVal = { label => $fieldName, type => $type };
4206        # Return the result.
4207        return $retVal;
4208    }
4209    
4210  =head3 CleanKeywords  =head3 CleanKeywords
4211    
4212  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>      my $cleanedString = $erdb->CleanKeywords($searchExpression);
4213    
4214  Clean up a search expression or keyword list. This is a virtual method that may  Clean up a search expression or keyword list. This is a virtual method that may
4215  be overridden by the subclass. The base-class method removes extra spaces  be overridden by the subclass. The base-class method removes extra spaces
# Line 2644  Line 4244 
4244      return $retVal;      return $retVal;
4245  }  }
4246    
4247    =head3 GetSourceObject
4248    
4249        my $source = $erdb->GetSourceObject($entityName);
4250    
4251    Return the object to be used in loading special attributes of the specified entity. The
4252    algorithm for loading special attributes is stored in the C<DataGen> elements of the
4253    XML
4254    
4255  =head2 Internal Utility Methods  =head2 Internal Utility Methods
4256    
4257  =head3 _RelationMap  =head3 _RelationMap
4258    
4259  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>      my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
4260    
4261  Create the relation map for an SQL query. The relation map is used by B<DBObject>  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
4262  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
4263    
4264  =over 4  =over 4
# Line 2667  Line 4275 
4275  =item RETURN  =item RETURN
4276    
4277  Returns a list of 2-tuples. Each tuple consists of an object name as used in the  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
4278  query followed by the actual name of that object. This enables the B<DBObject> to  query followed by the actual name of that object. This enables the B<ERDBObject> to
4279  determine the order of the tables in the query and which object name belongs to each  determine the order of the tables in the query and which object name belongs to each
4280  mapped object name. Most of the time these two values are the same; however, if a  mapped object name. Most of the time these two values are the same; however, if a
4281  relation occurs twice in the query, the relation name in the field list and WHERE  relation occurs twice in the query, the relation name in the field list and WHERE
# Line 2961  Line 4569 
4569  sub _GetStatementHandle {  sub _GetStatementHandle {
4570      # Get the parameters.      # Get the parameters.
4571      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4572        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4573      # Trace the query.      # Trace the query.
4574      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4575      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 2969  Line 4578 
4578      # Prepare the command.      # Prepare the command.
4579      my $sth = $dbh->prepare_command($command);      my $sth = $dbh->prepare_command($command);
4580      # Execute it with the parameters bound in.      # Execute it with the parameters bound in.
4581      $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
4582      # Return the statement handle.      # Return the statement handle.
4583      return $sth;      return $sth;
4584  }  }
# Line 2986  Line 4595 
4595      return Stats->new();      return Stats->new();
4596  }  }
4597    
 =head3 _GenerateFields  
   
 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;  
             }  
         }  
     }  
 }  
   
4598  =head3 _DumpRelation  =head3 _DumpRelation
4599    
4600  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.
4601    
4602  This is an instance method.  This is an instance method.
4603    
# Line 3207  Line 4742 
4742          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
4743              # Loop through the object's fields.              # Loop through the object's fields.
4744              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
4745                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
4746                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
4747                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($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";  
4748                          $retVal = 0;                          $retVal = 0;
4749                      }                      }
4750                  }                  }
4751              }              }
4752          }          }
     }  
4753      # If an error was found, fail.      # If an error was found, fail.
4754      if ($retVal  == 0) {      if ($retVal  == 0) {
4755          Confess("Errors found in field names.");          Confess("Errors found in field names.");
# Line 3286  Line 4807 
4807      # be a null string.      # be a null string.
4808      if ($fileName ne "") {      if ($fileName ne "") {
4809          # Load the relation from the file.          # Load the relation from the file.
4810          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4811      } elsif ($rebuild) {      } elsif ($rebuild) {
4812          # 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.
4813          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 3295  Line 4816 
4816      return $retVal;      return $retVal;
4817  }  }
4818    
4819    
4820  =head3 _LoadMetaData  =head3 _LoadMetaData
4821    
4822        my $metadata = ERDB::_LoadMetaData($filename);
4823    
4824  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.
4825  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
4826  load or use the database. The schema for the XML file is F<ERDatabase.xml>.  load or use the database. The schema for the XML file is F<ERDatabase.xml>.
# Line 3320  Line 4844 
4844  sub _LoadMetaData {  sub _LoadMetaData {
4845      # Get the parameters.      # Get the parameters.
4846      my ($filename) = @_;      my ($filename) = @_;
4847      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4848      # 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
4849      # get the exact structure we want.      # get the exact structure we want.
4850      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 $filename.") if T(1);  
4851      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
4852      # the method below will fail.      # the method below will fail.
4853      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 3459  Line 4970 
4970              if ($found == 0) {              if ($found == 0) {
4971                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4972              }              }
4973              # Now we need to convert the relation's index list to an index table. We begin by creating              # Attach all the indexes to the relation.
4974              # an empty table in the relation structure.              _ProcessIndexes($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++;  
             }  
4975          }          }
4976          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4977          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 3483  Line 4985 
4985          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4986          # Format a description for the FROM field.          # Format a description for the FROM field.
4987          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4988          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].";
4989          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4990          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4991          # Add the FROM field.          # Add the FROM field.
# Line 3493  Line 4995 
4995                                                      PrettySort => 1});                                                      PrettySort => 1});
4996          # Format a description for the TO field.          # Format a description for the TO field.
4997          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4998          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].";
4999          # Get the TO entity's key type.          # Get the TO entity's key type.
5000          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
5001          # Add the TO field.          # Add the TO field.
# Line 3505  Line 5007 
5007          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
5008                               Indexes => { } };                               Indexes => { } };
5009          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
5010    
5011            # Add the alternate indexes (if any). This MUST be done before the FROM and
5012            # TO indexes, because it erases the relation's index list.
5013            if (exists $relationshipStructure->{Indexes}) {
5014                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
5015            }
5016            # Add the relation to the master table.
5017          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
5018          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
5019          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
5020          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
5021      }      }
5022      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 3664  Line 5172 
5172          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
5173      }      }
5174      # Add the index to the relation.      # Add the index to the relation.
5175      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
5176    }
5177    
5178    =head3 _ProcessIndexes
5179    
5180        ERDB::_ProcessIndexes($indexList, $relation);
5181    
5182    Build the data structures for the specified indexes in the specified relation.
5183    
5184    =over 4
5185    
5186    =item indexList
5187    
5188    Reference to a list of indexes. Each index is a hash reference containing an optional
5189    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
5190    to a list of index field structures. An index field structure, in turn, is a reference
5191    to a hash that contains a C<name> attribute for the field name and an C<order>
5192    attribute that specifies either C<ascending> or C<descending>. In this sense the
5193    index list encapsulates the XML C<Indexes> structure in the database definition.
5194    
5195    =item relation
5196    
5197    The structure that describes the current relation. The new index descriptors will
5198    be stored in the structure's C<Indexes> member. Any previous data in the structure
5199    will be lost.
5200    
5201    =back
5202    
5203    =cut
5204    
5205    sub _ProcessIndexes {
5206        # Get the parameters.
5207        my ($indexList, $relation) = @_;
5208        # Now we need to convert the relation's index list to an index table. We begin by creating
5209        # an empty table in the relation structure.
5210        $relation->{Indexes} = { };
5211        # Loop through the indexes.
5212        my $count = 0;
5213        for my $index (@{$indexList}) {
5214            # Add this index to the index table.
5215            _AddIndex("idx$count", $relation, $index);
5216            # Increment the counter so that the next index has a different name.
5217            $count++;
5218        }
5219  }  }
5220    
5221  =head3 _AddIndex  =head3 _AddIndex
# Line 3763  Line 5314 
5314              my $type = $fieldData->{type};              my $type = $fieldData->{type};
5315              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
5316              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
             # Plug in a data generator if we need one.  
             if (!exists $fieldData->{DataGen}) {  
                 # The data generator will use the default for the field's type.  
                 $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };  
             }  
5317              # Check for searchability.              # Check for searchability.
5318              if ($fieldData->{searchable}) {              if ($fieldData->{searchable}) {
5319                  # Only allow this for a primary relation.                  # Only allow this for a primary relation.
# Line 3777  Line 5323 
5323                      push @textFields, $fieldName;                      push @textFields, $fieldName;
5324                  }                  }
5325              }              }
             # Plug in the defaults for the optional data generation parameters.  
             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
5326              # Add the PrettySortValue.              # Add the PrettySortValue.
5327              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
5328          }          }
# Line 4010  Line 5554 
5554      return $retVal;      return $retVal;
5555  }  }
5556    
5557  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5558    
5559  =head3 _ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5560    
# Line 4042  Line 5586 
5586      # Get the parameters.      # Get the parameters.
5587      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5588      # Format the relationship sentence.      # Format the relationship sentence.
5589      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5590      # Compute the arity.      # Compute the arity.
5591      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5592      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 4087  Line 5631 
5631      return $result;      return $result;
5632  }  }
5633    
5634    =head3 _WikiRelationTable
5635    
5636    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5637    table with three columns-- the field name, the field type, and the field description.
5638    
5639    This is a static method.
5640    
5641    =over 4
5642    
5643    =item relationName
5644    
5645    Name of the relation being formatted.
5646    
5647    =item relationData
5648    
5649    Hash containing the relation's fields and indexes.
5650    
5651    =item RETURN
5652    
5653    Returns a Wiki string that can be used to display the relation name and all of its fields.
5654    
5655    =back
5656    
5657    =cut
5658    
5659    sub _WikiRelationTable {
5660        # Get the parameters.
5661        my ($relationName, $relationData) = @_;
5662        # We'll create a list of lists in here, then call WikiTools::Table to
5663        # convert it into a table.
5664        my @rows = ();
5665        # Push in the header row.
5666        push @rows, [qw(Field Type Description)];
5667        # Loop through the fields.
5668        for my $field (@{$relationData->{Fields}}) {
5669            # Create this field's row. We always have a name and type.
5670            my @row = ($field->{name}, $field->{type});
5671            # If we have a description, add it as the third column.
5672            if (exists $field->{Notes}) {
5673                push @row, WikiNote($field->{Notes}->{content});
5674            }
5675            # Push this row onto the table list.
5676            push @rows, \@row;
5677        }
5678        # Store the rows as a Wiki table with a level-4 heading.
5679        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5680                          WikiTools::Table(@rows));
5681        # Now we show the relation's indexes. These are formatted as another
5682        # table.
5683        @rows = ();
5684        # Push in the header row.
5685        push @rows, [qw(Index Unique Fields Notes)];
5686        # Get the index hash.
5687        my $indexTable = $relationData->{Indexes};
5688        # Loop through the indexes. For an entity, there is always at least one index.
5689        # For a relationship, there are at least two. The upshot is we don't need to
5690        # worry about accidentally generating a frivolous table here.
5691        for my $indexName (sort keys %$indexTable) {
5692            my $indexData = $indexTable->{$indexName};
5693            # Determine whether or not the index is unique.
5694            my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
5695                          "yes" : "");
5696            # Get the field list.
5697            my $fields = join(', ', @{$indexData->{IndexFields}});
5698            # Get the note text.
5699            my $description = "";
5700            if (my $note = $indexData->{Notes}) {
5701                $description = WikiNote($note->{content});
5702            }
5703            # Format this row.
5704            my @row = ($indexName, $unique, $fields, $description);
5705            push @rows, \@row;
5706        }
5707        # Add the index list to the result.
5708        $retVal .= "\n\n" . WikiTools::Table(@rows);
5709    }
5710    
5711  =head3 _ShowRelationTable  =head3 _ShowRelationTable
5712    
5713  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
# Line 4137  Line 5758 
5758          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
5759          # Add any note text.          # Add any note text.
5760          if (my $note = $indexData->{Notes}) {          if (my $note = $indexData->{Notes}) {
5761              $htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";              $htmlString .= "<li>" . HTMLNote($note->{content}) . "</li>\n";
5762          }          }
5763          # Add the fiield list.          # Add the fiield list.
5764          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
# Line 4203  Line 5824 
5824      # Compute the number of columns.      # Compute the number of columns.
5825      my $colCount = @colNames;      my $colCount = @colNames;
5826      # Generate the title row.      # Generate the title row.
5827      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";
5828      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
5829      $htmlString .= "<tr>";      $htmlString .= "<tr>";
5830      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 4222  Line 5843 
5843  =cut  =cut
5844    
5845  sub _CloseTable {  sub _CloseTable {
5846      return "</table></p>\n";      return "</table>\n";
5847  }  }
5848    
5849  =head3 _ShowField  =head3 _ShowField
# Line 4252  Line 5873 
5873      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>";
5874      # If we have content, add it as a third column.      # If we have content, add it as a third column.
5875      if (exists $fieldData->{Notes}) {      if (exists $fieldData->{Notes}) {
5876          $htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";          $htmlString .= "<td>" . HTMLNote($fieldData->{Notes}->{content}) . "</td>";
5877      }      }
5878      # Close off the row.      # Close off the row.
5879      $htmlString .= "</tr>\n";      $htmlString .= "</tr>\n";
# Line 4260  Line 5881 
5881      return $htmlString;      return $htmlString;
5882  }  }
5883    
5884  =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  
   
 C<< my $char = RandChar($sourceString); >>  
   
 Select a random character from a string.  
   
 =over 4  
   
 =item sourceString  
   
 String from which the random character should be selected.  
   
 =item RETURN  
   
 Returns a single character from the incoming string.  
   
 =back  
   
 =cut  
   
 sub RandChar {  
     # Get the parameter.  
     my ($sourceString) = @_;  
     # Select a random character.  
     my $retVal = IntGen(0, (length $sourceString) - 1);  
     # Return it.  
     return substr($sourceString, $retVal, 1);  
 }  
   
 =head3 RandChars  
   
 C<< my $string = RandChars($sourceString, $length); >>  
   
 Create a string from characters taken from a source string.  
   
 =over 4  
   
 =item sourceString  
   
 String from which the random characters should be selected.  
   
 =item length  
   
 Number of characters to put in the output string.  
   
 =item RETURN  
   
 Returns a string of the specified length consisting of characters taken from the  
 source string.  
   
 =back  
   
 =cut  
   
 sub RandChars {  
     # Get the parameters.  
     my ($sourceString, $length) = @_;  
     # Call RandChar repeatedly to generate the string.  
     my $retVal = "";  
     for (my $i = 0; $i < $length; $i++) {  
         $retVal .= RandChar($sourceString);  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 RandParam  
   
 C<< my $value = RandParam($parm1, $parm2, ... $parmN); >>  
   
 Return a randomly-selected value from the parameter list.  
   
 =over 4  
   
 =item parm1, parm2, ... parmN  
   
 List of values of which one will be selected.  
   
 =item RETURN  
   
 Returns a randomly-chosen value from the specified list.  
   
 =back  
   
 =cut  
   
 sub RandParam {  
     # Get the parameter.  
     my @parms = @_;  
     # Choose a random parameter from the list.  
     my $chosenIndex = IntGen(0, $#parms);  
     return $parms[$chosenIndex];  
 }  
   
 =head3 StringGen  
5885    
5886  C<< my $string = StringGen($pattern1, $pattern2, ... $patternN); >>      my @noteParagraphs = _ObjectNotes($objectData);
5887    
5888  Returns a random string derived from a randomly-chosen format pattern. The pattern  Return a list of the notes and asides for an entity or relationship in
5889  can either be a number (indicating the number of characters desired, or the letter  Wiki format.
 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.  
5890    
5891  =over 4  =over 4
5892    
5893  =item pattern1, pattern2, ... patternN  =item objectData
5894    
5895  List of patterns to be used to generate string values.  The metadata for the desired entity or relationship.
5896    
5897  =item RETURN  =item RETURN
5898    
5899  A single string generated from a pattern.  Returns a list of text paragraphs in Wiki markup form.
5900    
5901  =back  =back
5902    
5903  =cut  =cut
5904    
5905  sub StringGen {  sub _ObjectNotes {
5906      # Get the parameters.      # Get the parameters.
5907      my @patterns = @_;      my ($objectData) = @_;
     # Choose the appropriate pattern.  
     my $chosenPattern = RandParam(@patterns);  
5908      # Declare the return variable.      # Declare the return variable.
5909      my $retVal = "";      my @retVal;
5910      # Determine whether this is a count or a picture pattern.      # Loop through the types of notes.
5911      if ($chosenPattern =~ m/^\d+/) {      for my $noteType (qw(Notes Asides)) {
5912          # Here we have a count. Get the string of source characters.          my $text = $objectData->{$noteType};
5913          my $letterString = $PictureTable{'X'};          if ($text) {
5914          my $stringLen = length $letterString;              push @retVal, "", WikiNote($text->{content});
         # Save the number of characters we have to generate.  
         my $charsLeft = $chosenPattern;  
         # Loop until the return variable is full.  
         while ($charsLeft > 0) {  
             # Generate a random position in the soruce string.  
             my $stringIndex = IntGen(0, $stringLen - 1);  
             # Compute the number of characters to pull out of the source string.  
             my $chunkSize = $stringLen - $stringIndex;  
             if ($chunkSize > $charsLeft) { $chunkSize = $charsLeft; }  
             # Stuff this chunk into the return value.  
             $retVal .= substr($letterString, $stringIndex, $chunkSize);  
             # Record the data moved.  
             $charsLeft -= $chunkSize;  
         }  
     } elsif ($chosenPattern =~ m/^P/) {  
         # Here we have a picture string. We will move through the picture one  
         # character at a time generating data.  
         for (my $i = 1; $i < length $chosenPattern; $i++) {  
             # Get this picture character.  
             my $chr = substr($chosenPattern, $i, 1);  
             # Check to see if the picture char is one we recognize.  
             if (exists $PictureTable{$chr}) {  
                 # Choose a random character from the available values for this  
                 # picture character.  
                 $retVal .= RandChar($PictureTable{$chr});  
             } else {  
                 # Copy in the picture character as a literal.  
                 $retVal .= $chr;  
             }  
         }  
     } else {  
         # Here we have neither a picture string or a letter count, so we treat  
         # the string as a literal.  
         $retVal = $chosenPattern;  
5915      }      }
     # Return the string formed.  
     return $retVal;  
5916  }  }
   
 =head3 DateGen  
   
 C<< my $date = DateGen($startDayOffset, $endDayOffset, $minutes); >>  
   
 Return a numeric timestamp within the specified range of days with the specified minute  
 value. The range of days is specified relevant to the current day. Thus, the call  
   
 C<< my $date = DateGen(-1, 5, 720); >>  
   
 will return a timestamp at noon (72 minutes past midnight) sometime during the week that  
 began on the preceding day. If you want a random minute of the day, simply combine with  
 a call to L</IntGen>, as follows.  
   
 C<< my $date = DateGen(-1, 5, IntGen(0, 1439)); >>  
   
 =over 4  
   
 =item startDayOffset  
   
 The earliest day that can be returned, relative to the current day.  
   
 =item endDayOffset  
   
 The latest day that can be returned, related to the current day.  
   
 =item minutes  
   
 Number of minutes into the selected day that should be used.  
   
 =back  
   
 =cut  
   
 sub DateGen {  
     # Get the parameters.  
     my ($startDayOffset, $endDayOffset, $minutes) = @_;  
     # Get midnight of the current day.  
     my $now = time();  
     my ($sec, $min, $hour) = localtime($now);  
     my $today = $now - (($hour * 60 + $min) * 60 + $sec);  
     # Compute the day we want.  
     my $newDay = IntGen($startDayOffset, $endDayOffset) * 86400 + $today;  
     # Add the minutes.  
     my $retVal = $newDay + $minutes * 60;  
5917      # Return the result.      # Return the result.
     return $retVal;  
 }  
   
 =head3 FloatGen  
   
 C<< my $number = FloatGen($min, $max); >>  
   
 Return a random floating-point number greater than or equal to the specified minimum and  
 less than the specified maximum.  
   
 =over 4  
   
 =item min  
   
 Minimum permissible value for the number returned.  
   
 =item max  
   
 Maximum permissible value for the number returned.  
   
 =item RETURN  
   
 Returns a floating-point number anywhere in the specified range.  
   
 =back  
   
 =cut  
   
 sub FloatGen {  
     # Get the parameters.  
     my ($min, $max) = @_;  
     # Generate the result.  
     my $retVal = rand($max - $min) + $min;  
     return $retVal;  
 }  
   
 =head3 ListGen  
   
 C<< my @list = ListGen($pattern, $count); >>  
   
 Return a list containing a fixed number of randomly-generated strings.  
   
 =over 4  
   
 =item pattern  
   
 A pattern (in the form expected by L</StringGen>) that should be used to generate the  
 strings in the list.  
   
 =item count  
   
 The number of list entries to generate.  
   
 =item RETURN  
   
 Returns a list consisting of the specified number of strings.  
   
 =back  
   
 =cut  
   
 sub ListGen {  
     # Get the parameters.  
     my ($pattern, $count) = @_;  
     # Generate the list.  
     my @retVal = ();  
     for (my $i = 0; $i < $count; $i++) {  
         push @retVal, StringGen($pattern);  
     }  
     # Return it.  
5918      return @retVal;      return @retVal;
5919  }  }
5920    

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