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revision 1.69, Fri Sep 29 15:06:17 2006 UTC revision 1.100, Tue Aug 12 06:07:06 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 190  Line 191 
191    
192  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
194  with the respect to field names, so a best practice is to use lower-case letters only.  with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198  =item type  =item type
199    
# Line 209  Line 212 
212  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
213  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227  =back  =back
228    
229  =head3 Indexes  =head3 Indexes
230    
231  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
232  be from the primary relation. The alternate indexes assist in ordering results  index must all be from the same relation. The alternate indexes assist in searching
233  from a query. A relationship can have up to two indexes-- a I<to-index> and a  on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
234  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
235  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
237  the genomes of a contig. A relationship's index must specify only fields in  the genomes of a contig. In addition, it can have zero or more alternate
238    indexes. A relationship's index must specify only fields in
239  the relationship.  the relationship.
240    
241  The indexes for an entity must be listed inside the B<Indexes> tag. The from-index  The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
242  of a relationship is specified using the B<FromIndex> tag; the to-index is specified  The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
243  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
244    
245  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
246  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 242  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 286  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 320  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 349  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, $metaFileName);
420    
421  Create a new ERDB object.  Create a new ERDB object.
422    
# Line 382  Line 436 
436    
437  sub new {  sub new {
438      # Get the parameters.      # Get the parameters.
439      my ($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 396  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 437  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 498  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 516  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 555  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 589  Line 647 
647    
648  =head3 DumpMetaData  =head3 DumpMetaData
649    
650  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
651    
652  Return a dump of the metadata structure.  Return a dump of the metadata structure.
653    
# Line 602  Line 660 
660      return Data::Dumper::Dumper($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 621  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 670  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 684  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);
1079      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
1080      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
1081      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
1082        # index will not be built until the table has been loaded.
1083      if ($indexFlag) {      if ($indexFlag) {
1084          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
1085      }      }
# Line 697  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 740  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 752  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 792  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 825  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 846  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} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1261          # Create the index.          # Create the index.
1262          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1263                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
1264          if ($rv) {          if ($rv) {
1265              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1266          } else {          } else {
# Line 861  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 923  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 940  Line 1513 
1513    
1514  =head3 GetEntityTypes  =head3 GetEntityTypes
1515    
1516  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1517    
1518  Return a list of the entity type names.  Return a list of the entity type names.
1519    
# Line 955  Line 1528 
1528      return sort keys %{$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 984  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 992  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 1009  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 1045  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 1058  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 1085  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 1099  Line 1750 
1750      return $retVal;      return $retVal;
1751  }  }
1752    
 =head3 GetFlat  
1753    
 C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>  
1754    
1755  This is a variation of L</GetAll> that asks for only a single field per record and  =head3 Search
1756  returns a single flattened list.  
1757        my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1758    
1759    Perform a full text search with filtering. The search will be against a specified object
1760    in the object name list. That object will get an extra field containing the search
1761    relevance. Note that except for the search expression, the parameters of this method are
1762    the same as those for L</Get> and follow the same rules.
1763    
1764  =over 4  =over 4
1765    
1766  =item objectNames  =item searchExpression
1767    
1768  List containing the names of the entity and relationship objects to be retrieved.  Boolean search expression for the text fields of the target object. The default mode for
1769    a Boolean search expression is OR, but we want the default to be AND, so we will
1770    add a C<+> operator to each word with no other operator before it.
1771    
1772  =item filterClause  =item idx
1773    
1774    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1775    
1776    =item objectNames
1777    
1778    List containing the names of the entity and relationship objects to be retrieved.
1779    
1780    =item filterClause
1781    
1782    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1783    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1784    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1785    in the filter clause should be added to the parameter list as additional parameters. The
1786    fields in a filter clause can come from primary entity relations, relationship relations,
1787    or secondary entity relations; however, all of the entities and relationships involved must
1788    be included in the list of object names.
1789    
1790    =item params
1791    
1792    Reference to a list of parameter values to be substituted into the filter clause.
1793    
1794    =item RETURN
1795    
1796    Returns a query object for the specified search.
1797    
1798    =back
1799    
1800    =cut
1801    
1802    sub Search {
1803        # Get the parameters.
1804        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1805        # Declare the return variable.
1806        my $retVal;
1807        # Create a safety copy of the parameter list. Note we have to be careful to insure
1808        # 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.
1814        my $object1Name = $objectNames->[$idx];
1815        my $object1Structure = $self->_GetStructure($object1Name);
1816        # Get the field list.
1817        if (! exists $object1Structure->{searchFields}) {
1818            Confess("No searchable index for $object1Name.");
1819        } else {
1820            # Get the field list.
1821            my @fields = @{$object1Structure->{searchFields}};
1822            # Clean the search expression.
1823            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
1829            # 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.
1831            unshift @myParams, $actualKeywords, $actualKeywords;
1832            # Build the match expression.
1833            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1834            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1835            # Process the SQL stuff.
1836            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1837                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1838            # Create the query. Note that the match clause is inserted at the front of
1839            # the select fields.
1840            my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1841                ".* $suffix";
1842            my $sth = $self->_GetStatementHandle($command, \@myParams);
1843            # Now we create the relation map, which enables DBQuery to determine the order, name
1844            # and mapped name for each object in the query.
1845            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1846            # Return the statement object.
1847            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1848        }
1849        return $retVal;
1850    }
1851    
1852    =head3 GetFlat
1853    
1854        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
1857    returns a single flattened list.
1858    
1859    =over 4
1860    
1861    =item objectNames
1862    
1863    List containing the names of the entity and relationship objects to be retrieved.
1864    
1865    =item filterClause
1866    
1867  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1868  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
# Line 1152  Line 1902 
1902      return @retVal;      return @retVal;
1903  }  }
1904    
1905    =head3 SpecialFields
1906    
1907        my %specials = $erdb->SpecialFields($entityName);
1908    
1909    Return a hash mapping special fields in the specified entity to the value of their
1910    C<special> attribute. This enables the subclass to get access to the special field
1911    attributes without needed to plumb the internal ERDB data structures.
1912    
1913    =over 4
1914    
1915    =item entityName
1916    
1917    Name of the entity whose special fields are desired.
1918    
1919    =item RETURN
1920    
1921    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  =head3 Delete
1948    
1949  C<< my $stats = $erdb->Delete($entityName, $objectID); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1950    
1951  Delete an entity instance from the database. The instance is deleted along with all entity and  Delete an entity instance from the database. The instance is deleted along with all entity and
1952  relationship instances dependent on it. The idea of dependence here is recursive. An object is  relationship instances dependent on it. The definition of I<dependence> is recursive.
1953  always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  
1954  relationship connected to a dependent entity or the "to" entity connected to a 1-to-many  An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1955    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1956  dependent relationship.  dependent relationship.
1957    
1958  =over 4  =over 4
# Line 1173  Line 1966 
1966  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
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 1184  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 $retVal = Stats->new();
2001      # Get the DBKernel object.      # Get the DBKernel object.
# Line 1205  Line 2012 
2012      # FROM-relationships and entities.      # FROM-relationships and entities.
2013      my @fromPathList = ();      my @fromPathList = ();
2014      my @toPathList = ();      my @toPathList = ();
2015      # This final hash is used to remember what work still needs to be done. We push paths      # This final list is used to remember what work still needs to be done. We push paths
2016      # onto the list, then pop them off to extend the paths. We prime it with the starting      # onto the list, then pop them off to extend the paths. We prime it with the starting
2017      # point. Note that we will work hard to insure that the last item on a path in the      # point. Note that we will work hard to insure that the last item on a path in the
2018      # TODO list is always an entity.      # to-do list is always an entity.
2019      my @todoList = ([$entityName]);      my @todoList = ([$entityName]);
2020      while (@todoList) {      while (@todoList) {
2021          # Get the current path.          # Get the current path.
# Line 1216  Line 2023 
2023          # Copy it into a list.          # Copy it into a list.
2024          my @stackedPath = @{$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, $relationshipName);
2048                  push @fromPathList, \@augmentedList;                  push @fromPathList, \@augmentedList;
2049                  # Check the arity. If it's MM we're done. If it's 1M                  # Check the arity. If it's MM we're done. If it's 1M
2050                  # and the target hasn't been seen yet, we want to                  # and the target hasn't been seen yet, we want to
# Line 1254  Line 2063 
2063              }              }
2064              # Now check the TO field. In this case only the relationship needs              # Now check the TO field. In this case only the relationship needs
2065              # deletion.              # deletion.
2066              if ($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 1301  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 1320  Line 2129 
2129      return $retVal;      return $retVal;
2130  }  }
2131    
2132  =head3 GetList  =head3 Disconnect
   
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>  
2133    
2134  Return a list of object descriptors for the specified objects as determined by the      $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
 specified filter clause.  
2135    
2136  This method is essentially the same as L</Get> except it returns a list of objects rather  Disconnect an entity instance from all the objects to which it is related. This
2137  than a query object that can be used to get the results one record at a time.  will delete each relationship instance that connects to the specified entity.
2138    
2139  =over 4  =over 4
2140    
2141  =item objectNames  =item relationshipName
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  
 specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  
 in the filter clause should be added to the parameter list as additional parameters. The  
 fields in a filter clause can come from primary entity relations, relationship relations,  
 or secondary entity relations; however, all of the entities and relationships involved must  
 be included in the list of object names.  
   
 The filter clause can also specify a sort order. To do this, simply follow the filter string  
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
   
 C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  
2142    
2143  The rules for field references in a sort order are the same as those for field references in the  Name of the relationship whose instances are to be deleted.
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
2144    
2145  =item params  =item originEntityName
2146    
2147  Reference to a list of parameter values to be substituted into the filter clause.  Name of the entity that is to be disconnected.
2148    
2149  =item RETURN  =item originEntityID
2150    
2151  Returns a list of B<DBObject>s that satisfy the query conditions.  ID of the entity that is to be disconnected.
2152    
2153  =back  =back
2154    
2155  =cut  =cut
2156  #: Return Type @%  
2157  sub GetList {  sub Disconnect {
2158      # Get the parameters.      # Get the parameters.
2159      my ($self, $objectNames, $filterClause, $params) = @_;      my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
2160      # Declare the return variable.      # Get the relationship descriptor.
2161      my @retVal = ();      my $structure = $self->_GetStructure($relationshipName);
2162      # Perform the query.      # Insure we have a relationship.
2163      my $query = $self->Get($objectNames, $filterClause, $params);      if (! exists $structure->{from}) {
2164      # Loop through the results.          Confess("$relationshipName is not a relationship in the database.");
2165      while (my $object = $query->Fetch) {      } else {
2166          push @retVal, $object;          # 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      }      }
     # Return the result.  
     return @retVal;  
2194  }  }
2195    
2196  =head3 GetCount  =head3 DeleteRow
2197    
2198  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>      $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2199    
2200  Return the number of rows found by a specified query. This method would  Delete a row from a relationship. In most cases, only the from-link and to-link are
2201  normally be used to count the records in a single table. For example, in a  needed; however, for relationships with intersection data values can be specified
2202  genetics database  for the other fields using a hash.
2203    
2204      my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);  =over 4
2205    
2206  would return the number of genomes for the genus I<homo>. It is conceivable, however,  =item relationshipName
 to use it to return records based on a join. For example,  
2207    
2208      my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',  Name of the relationship from which the row is to be deleted.
                                 ['homo %']);  
2209    
2210  would return the number of features for genomes in the genus I<homo>. Note that  =item fromLink
 only the rows from the first table are counted. If the above command were  
2211    
2212      my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',  ID of the entity instance in the From direction.
                                 ['homo %']);  
2213    
2214  it would return the number of genomes, not the number of genome/feature pairs.  =item toLink
2215    
2216    ID of the entity instance in the To direction.
2217    
2218    =item values
2219    
2220    Reference to a hash of other values to be used for filtering the delete.
2221    
2222    =back
2223    
2224    =cut
2225    
2226    sub DeleteRow {
2227        # Get the parameters.
2228        my ($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, $filter, \@parms);
2254    
2255    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2256    filter, only fields from the relationship itself can be used.
2257    
2258  =over 4  =over 4
2259    
2260  =item objectNames  =item relName
2261    
2262  Reference to a list of the objects (entities and relationships) included in the  Name of the relationship whose records are to be deleted.
 query.  
2263    
2264  =item filter  =item filter
2265    
2266  A filter clause for restricting the query. The rules are the same as for the L</Get>  A filter clause (L</Get>-style) for the delete query.
 method.  
2267    
2268  =item params  =item parms
2269    
2270  Reference to a list of the parameter values to be substituted for the parameter marks  Reference to a list of parameters for the filter clause.
 in the filter.  
2271    
2272  =item RETURN  =item RETURN
2273    
2274  Returns a count of the number of records in the first table that would satisfy  Returns a count of the number of rows deleted.
 the query.  
2275    
2276  =back  =back
2277    
2278  =cut  =cut
2279    
2280  sub GetCount {  sub DeleteLike {
2281      # Get the parameters.      # Get the parameters.
2282      my ($self, $objectNames, $filter, $params) = @_;      my ($self, $objectName, $filter, $parms) = @_;
     # Insure the params argument is an array reference if the caller left it off.  
     if (! defined($params)) {  
         $params = [];  
     }  
2283      # Declare the return variable.      # Declare the return variable.
2284      my $retVal;      my $retVal;
2285      # Find out if we're counting an entity or a relationship.      # Insure the parms argument is an array reference if the caller left it off.
2286      my $countedField;      if (! defined($parms)) {
2287      if ($self->IsEntity($objectNames->[0])) {          $parms = [];
2288          $countedField = "id";      }
2289        # Insure we have a relationship. The main reason for this is if we delete an entity
2290        # instance we have to yank out a bunch of other stuff with it.
2291        if ($self->IsEntity($objectName)) {
2292            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2293      } else {      } else {
2294          # For a relationship we count the to-link because it's usually more          # Create the SQL command suffix to get the desierd records.
2295          # numerous. Note we're automatically converting to the SQL form          my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2296          # of the field name (to_link vs. to-link).          # Convert it to a DELETE command.
2297          $countedField = "to_link";          my $command = "DELETE $suffix";
2298      }          # Execute the command.
2299      # Create the SQL command suffix to get the desired records.          my $dbh = $self->{_dbh};
2300      my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,          my $result = $dbh->SQL($command, 0, @{$parms});
2301                                                                              $filter);          # Check the results. Note we convert the "0D0" result to a real zero.
2302      # Prefix it with text telling it we want a record count.          # A failure causes an abnormal termination, so the caller isn't going to
2303      my $firstObject = $mappedNameListRef->[0];          # worry about it.
2304      my $command = "SELECT COUNT($firstObject.$countedField) $suffix";          if (! defined $result) {
2305      # Prepare and execute the command.              Confess("Error deleting from $objectName: " . $dbh->errstr());
2306      my $sth = $self->_GetStatementHandle($command, $params);          } elsif ($result == 0) {
2307      # Get the count value.              $retVal = 0;
     ($retVal) = $sth->fetchrow_array();  
     # Check for a problem.  
     if (! defined($retVal)) {  
         if ($sth->err) {  
             # Here we had an SQL error.  
             Confess("Error retrieving row count: " . $sth->errstr());  
2308          } else {          } else {
2309              # Here we have no result.              $retVal = $result;
             Confess("No result attempting to retrieve row count.");  
2310          }          }
2311      }      }
2312      # Return the result.      # Return the result count.
2313      return $retVal;      return $retVal;
2314  }  }
2315    
2316  =head3 ComputeObjectSentence  =head3 SortNeeded
2317    
2318  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my $parms = $erdb->SortNeeded($relationName);
2319    
2320  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return the pipe command for the sort that should be applied to the specified
2321    relation when creating the load file.
2322    
2323    For example, if the load file should be sorted ascending by the first
2324    field, this method would return
2325    
2326        sort -k1 -t"\t"
2327    
2328    If the first field is numeric, the method would return
2329    
2330        sort -k1n -t"\t"
2331    
2332    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2333    keys using a sort.
2334    
2335  =over 4  =over 4
2336    
2337  =item objectName  =item relationName
2338    
2339  Name of the entity or relationship.  Name of the relation to be examined.
2340    
2341  =item RETURN  =item
2342    
2343  Returns a string containing the entity name or a relationship sentence.  Returns the sort command to use for sorting the relation, suitable for piping.
2344    
2345  =back  =back
2346    
2347  =cut  =cut
2348    #: Return Type $;
2349  sub ComputeObjectSentence {  sub SortNeeded {
2350        # Get the parameters.
2351        my ($self, $relationName) = @_;
2352        # Declare a descriptor to hold the names of the key fields.
2353        my @keyNames = ();
2354        # Get the relation structure.
2355        my $relationData = $self->_FindRelation($relationName);
2356        # Find out if the relation is a primary entity relation,
2357        # a relationship relation, or a secondary entity relation.
2358        my $entityTable = $self->{_metaData}->{Entities};
2359        my $relationshipTable = $self->{_metaData}->{Relationships};
2360        if (exists $entityTable->{$relationName}) {
2361            # Here we have a primary entity relation.
2362            push @keyNames, "id";
2363        } elsif (exists $relationshipTable->{$relationName}) {
2364            # Here we have a relationship. We sort using the FROM index.
2365            my $relationshipData = $relationshipTable->{$relationName};
2366            my $index = $relationData->{Indexes}->{idxFrom};
2367            push @keyNames, @{$index->{IndexFields}};
2368        } else {
2369            # Here we have a secondary entity relation, so we have a sort on the ID field.
2370            push @keyNames, "id";
2371        }
2372        # Now we parse the key names into sort parameters. First, we prime the return
2373        # string.
2374        my $retVal = "sort -T\"$FIG_Config::temp\" -t\"\t\" ";
2375        # Get the relation's field list.
2376        my @fields = @{$relationData->{Fields}};
2377        # Loop through the keys.
2378        for my $keyData (@keyNames) {
2379            # Get the key and the ordering.
2380            my ($keyName, $ordering);
2381            if ($keyData =~ /^([^ ]+) DESC/) {
2382                ($keyName, $ordering) = ($1, "descending");
2383            } else {
2384                ($keyName, $ordering) = ($keyData, "ascending");
2385            }
2386            # Find the key's position and type.
2387            my $fieldSpec;
2388            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2389                my $thisField = $fields[$i];
2390                if ($thisField->{name} eq $keyName) {
2391                    # Get the sort modifier for this field type. The modifier
2392                    # decides whether we're using a character, numeric, or
2393                    # floating-point sort.
2394                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2395                    # If the index is descending for this field, denote we want
2396                    # to reverse the sort order on this field.
2397                    if ($ordering eq 'descending') {
2398                        $modifier .= "r";
2399                    }
2400                    # Store the position and modifier into the field spec, which
2401                    # will stop the inner loop. Note that the field number is
2402                    # 1-based in the sort command, so we have to increment the
2403                    # index.
2404                    my $realI = $i + 1;
2405                    $fieldSpec = "$realI,$realI$modifier";
2406                }
2407            }
2408            # Add this field to the sort command.
2409            $retVal .= " -k$fieldSpec";
2410        }
2411        # Return the result.
2412        return $retVal;
2413    }
2414    
2415    =head3 GetList
2416    
2417        my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2418    
2419    Return a list of object descriptors for the specified objects as determined by the
2420    specified filter clause.
2421    
2422    This method is essentially the same as L</Get> except it returns a list of objects rather
2423    than a query object that can be used to get the results one record at a time.
2424    
2425    =over 4
2426    
2427    =item objectNames
2428    
2429    List containing the names of the entity and relationship objects to be retrieved.
2430    
2431    =item filterClause
2432    
2433    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2434    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2435    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2436    in the filter clause should be added to the parameter list as additional parameters. The
2437    fields in a filter clause can come from primary entity relations, relationship relations,
2438    or secondary entity relations; however, all of the entities and relationships involved must
2439    be included in the list of object names.
2440    
2441    The filter clause can also specify a sort order. To do this, simply follow the filter string
2442    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.
2444    
2445        "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
2448    filter clause in general; however, odd things may happen if a sort field is from a secondary
2449    relation.
2450    
2451    =item params
2452    
2453    Reference to a list of parameter values to be substituted into the filter clause.
2454    
2455    =item RETURN
2456    
2457    Returns a list of B<ERDBObject>s that satisfy the query conditions.
2458    
2459    =back
2460    
2461    =cut
2462    #: Return Type @%
2463    sub GetList {
2464        # Get the parameters.
2465        my ($self, $objectNames, $filterClause, $params) = @_;
2466        # Declare the return variable.
2467        my @retVal = ();
2468        # Perform the query.
2469        my $query = $self->Get($objectNames, $filterClause, $params);
2470        # Loop through the results.
2471        while (my $object = $query->Fetch) {
2472            push @retVal, $object;
2473        }
2474        # Return the result.
2475        return @retVal;
2476    }
2477    
2478    =head3 GetCount
2479    
2480        my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2481    
2482    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
2484    genetics database
2485    
2486        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2487    
2488    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2489    to use it to return records based on a join. For example,
2490    
2491        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2492                                    ['homo %']);
2493    
2494    would return the number of features for genomes in the genus I<homo>. Note that
2495    only the rows from the first table are counted. If the above command were
2496    
2497        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2498                                    ['homo %']);
2499    
2500    it would return the number of genomes, not the number of genome/feature pairs.
2501    
2502    =over 4
2503    
2504    =item objectNames
2505    
2506    Reference to a list of the objects (entities and relationships) included in the
2507    query.
2508    
2509    =item filter
2510    
2511    A filter clause for restricting the query. The rules are the same as for the L</Get>
2512    method.
2513    
2514    =item params
2515    
2516    Reference to a list of the parameter values to be substituted for the parameter marks
2517    in the filter.
2518    
2519    =item RETURN
2520    
2521    Returns a count of the number of records in the first table that would satisfy
2522    the query.
2523    
2524    =back
2525    
2526    =cut
2527    
2528    sub GetCount {
2529        # Get the parameters.
2530        my ($self, $objectNames, $filter, $params) = @_;
2531        # Insure the params argument is an array reference if the caller left it off.
2532        if (! defined($params)) {
2533            $params = [];
2534        }
2535        # Declare the return variable.
2536        my $retVal;
2537        # Find out if we're counting an entity or a relationship.
2538        my $countedField;
2539        if ($self->IsEntity($objectNames->[0])) {
2540            $countedField = "id";
2541        } else {
2542            # For a relationship we count the to-link because it's usually more
2543            # numerous. Note we're automatically converting to the SQL form
2544            # of the field name (to_link vs. to-link).
2545            $countedField = "to_link";
2546        }
2547        # Create the SQL command suffix to get the desired records.
2548        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2549                                                                                $filter);
2550        # Prefix it with text telling it we want a record count.
2551        my $firstObject = $mappedNameListRef->[0];
2552        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2553        # Prepare and execute the command.
2554        my $sth = $self->_GetStatementHandle($command, $params);
2555        # Get the count value.
2556        ($retVal) = $sth->fetchrow_array();
2557        # Check for a problem.
2558        if (! defined($retVal)) {
2559            if ($sth->err) {
2560                # Here we had an SQL error.
2561                Confess("Error retrieving row count: " . $sth->errstr());
2562            } else {
2563                # Here we have no result.
2564                Confess("No result attempting to retrieve row count.");
2565            }
2566        }
2567        # Return the result.
2568        return $retVal;
2569    }
2570    
2571    =head3 ComputeObjectSentence
2572    
2573        my $sentence = $erdb->ComputeObjectSentence($objectName);
2574    
2575    Check an object name, and if it is a relationship convert it to a relationship sentence.
2576    
2577    =over 4
2578    
2579    =item objectName
2580    
2581    Name of the entity or relationship.
2582    
2583    =item RETURN
2584    
2585    Returns a string containing the entity name or a relationship sentence.
2586    
2587    =back
2588    
2589    =cut
2590    
2591    sub ComputeObjectSentence {
2592      # Get the parameters.      # Get the parameters.
2593      my ($self, $objectName) = @_;      my ($self, $objectName) = @_;
2594      # Set the default return value.      # Set the default return value.
# Line 1513  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 1555  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 1618  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 1627  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 1644  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 1705  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 1746  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 LoadTable  =head3 UpdateEntity
2844    
2845  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      $erdb->UpdateEntity($entityName, $id, \%fields);
2846    
2847  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Update the values of an entity. This is an unprotected update, so it should only be
2848  first.  done if the database resides on a database server.
2849    
2850  =over 4  =over 4
2851    
2852  =item fileName  =item entityName
   
 Name of the file from which the table data should be loaded.  
   
 =item relationName  
2853    
2854  Name of the relation to be loaded. This is the same as the table name.  Name of the entity to update. (This is the entity type.)
2855    
2856  =item truncateFlag  =item id
2857    
2858  TRUE if the table should be dropped and re-created, else FALSE  ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2859    
2860  =item RETURN  =item fields
2861    
2862  Returns a statistical object containing a list of the error messages.  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  =back
2866    
2867  =cut  =cut
2868  sub LoadTable {  
2869    sub UpdateEntity {
2870      # Get the parameters.      # Get the parameters.
2871      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $entityName, $id, $fields) = @_;
2872      # Create the statistical return object.      # Get a list of the field names being updated.
2873        my @fieldList = keys %{$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
2902    
2903        my $results = $erdb->LoadTable($fileName, $relationName, %options);
2904    
2905    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2906    first.
2907    
2908    =over 4
2909    
2910    =item fileName
2911    
2912    Name of the file from which the table data should be loaded.
2913    
2914    =item relationName
2915    
2916    Name of the relation to be loaded. This is the same as the table name.
2917    
2918    =item options
2919    
2920    A hash of load options.
2921    
2922    =item RETURN
2923    
2924    Returns a statistical object containing a list of the error messages.
2925    
2926    =back
2927    
2928    The permissible options are as follows.
2929    
2930    =over 4
2931    
2932    =item truncate
2933    
2934    If TRUE, then the table will be erased before loading.
2935    
2936    =item mode
2937    
2938    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2939    This option is only applicable to a MySQL database.
2940    
2941    =item partial
2942    
2943    If TRUE, then it is assumed that this is a partial load, and the table will not
2944    be analyzed and compacted at the end.
2945    
2946    =back
2947    
2948    =cut
2949    sub LoadTable {
2950        # Get the parameters.
2951        my ($self, $fileName, $relationName, %options) = @_;
2952        # 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.
2955      Trace("Loading table $relationName from $fileName") if T(2);      Trace("Loading table $relationName from $fileName") if T(2);
# Line 1797  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 1820  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 && ! $dbh->{_preIndex}) {          if ($options{truncate}) {
3003                # Indexes are created here for PostGres. For PostGres, indexes are
3004                # best built at the end. For MySQL, the reverse is true.
3005                if (! $dbh->{_preIndex}) {
3006              eval {              eval {
3007                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
3008              };              };
# Line 1840  Line 3010 
3010                  $retVal->AddMessage($@);                  $retVal->AddMessage($@);
3011              }              }
3012          }          }
3013                # 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
3015                # primary relations are allowed that privilege.
3016                Trace("Checking for full-text index on $relationName.") if T(2);
3017                if ($self->_IsPrimary($relationName)) {
3018                    $self->CreateSearchIndex($relationName);
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
3042    
3043  ID to assign to the new entity.  Name of the table to be analyzed and compacted.
3044    
3045  =item type  =back
3046    
3047  Type name for the new entity.  =cut
3048    
3049  =item values  sub Analyze {
3050        # Get the parameters.
3051        my ($self, $tableName) = @_;
3052        # Analyze the table.
3053        $self->{_dbh}->vacuum_it($tableName);
3054    }
3055    
3056    =head3 TruncateTable
3057    
3058        $erdb->TruncateTable($table);
3059    
3060    Delete all rows from a table quickly. This uses the built-in SQL
3061    C<TRUNCATE> statement, which effectively drops and re-creates a table
3062    with all its settings intact.
3063    
3064    =over 4
3065    
3066    =item table
3067    
3068  Hash containing additional values that might be needed by the data generation methods (optional).  Name of the table to be cleared.
3069    
3070  =back  =back
3071    
3072  =cut  =cut
3073    
3074  sub GenerateEntity {  sub TruncateTable {
3075      # Get the parameters.      # Get the parameters.
3076      my ($self, $id, $type, $values) = @_;      my ($self, $table) = @_;
3077      # Create the return hash.      # Get the database handle.
3078      my $this = { id => $id };      my $dbh = $self->{_dbh};
3079      # Get the metadata structure.      # Execute a truncation comment.
3080      my $metadata = $self->{_metaData};      $dbh->SQL("TRUNCATE TABLE $table");
     # 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);  
3081      }      }
3082      # Return the hash created.  
3083      return $this;  
3084    =head3 CreateSearchIndex
3085    
3086        $erdb->CreateSearchIndex($objectName);
3087    
3088    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
3092    
3093    =item objectName
3094    
3095    Name of the entity or relationship to be indexed.
3096    
3097    =back
3098    
3099    =cut
3100    
3101    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    =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
3135    
3136    =cut
3137    
3138    sub DropRelation {
3139        # Get the parameters.
3140        my ($self, $relationName) = @_;
3141        # Get the database handle.
3142        my $dbh = $self->{_dbh};
3143        # Drop the relation. The method used here has no effect if the relation
3144        # does not exist.
3145        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  =head3 GetEntity
3233    
3234  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $entityObject = $erdb->GetEntity($entityType, $ID);
3235    
3236  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
3237    
# Line 1925  Line 3247 
3247    
3248  =item RETURN  =item RETURN
3249    
3250  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
3251  instance is found with the specified key.  instance is found with the specified key.
3252    
3253  =back  =back
# Line 1945  Line 3267 
3267    
3268  =head3 GetChoices  =head3 GetChoices
3269    
3270  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>      my @values = $erdb->GetChoices($entityName, $fieldName);
3271    
3272  Return a list of all the values for the specified field that are represented in the  Return a list of all the values for the specified field that are represented in the
3273  specified entity.  specified entity.
# Line 2000  Line 3322 
3322    
3323  =head3 GetEntityValues  =head3 GetEntityValues
3324    
3325  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3326    
3327  Return a list of values from a specified entity instance. If the entity instance  Return a list of values from a specified entity instance. If the entity instance
3328  does not exist, an empty list is returned.  does not exist, an empty list is returned.
# Line 2044  Line 3366 
3366    
3367  =head3 GetAll  =head3 GetAll
3368    
3369  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>      my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3370    
3371  Return a list of values taken from the objects returned by a query. The first three  Return a list of values taken from the objects returned by a query. The first three
3372  parameters correspond to the parameters of the L</Get> method. The final parameter is  parameters correspond to the parameters of the L</Get> method. The final parameter is
# Line 2058  Line 3380 
3380  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
3381  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
3382  spreadsheet cell, and each feature will be represented by a list containing the  spreadsheet cell, and each feature will be represented by a list containing the
3383  feature ID followed by all of its aliases.  feature ID followed by all of its essentiality determinations.
3384    
3385  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)']);
3386    
3387  =over 4  =over 4
3388    
# Line 2138  Line 3460 
3460    
3461  =head3 Exists  =head3 Exists
3462    
3463  C<< my $found = $sprout->Exists($entityName, $entityID); >>      my $found = $sprout->Exists($entityName, $entityID);
3464    
3465  Return TRUE if an entity exists, else FALSE.  Return TRUE if an entity exists, else FALSE.
3466    
# Line 2173  Line 3495 
3495    
3496  =head3 EstimateRowSize  =head3 EstimateRowSize
3497    
3498  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>      my $rowSize = $erdb->EstimateRowSize($relName);
3499    
3500  Estimate the row size of the specified relation. The estimated row size is computed by adding  Estimate the row size of the specified relation. The estimated row size is computed by adding
3501  up the average length for each data type.  up the average length for each data type.
# Line 2211  Line 3533 
3533    
3534  =head3 GetFieldTable  =head3 GetFieldTable
3535    
3536  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>      my $fieldHash = $self->GetFieldTable($objectnName);
3537    
3538  Get the field structure for a specified entity or relationship.  Get the field structure for a specified entity or relationship.
3539    
# Line 2238  Line 3560 
3560      return $objectData->{Fields};      return $objectData->{Fields};
3561  }  }
3562    
3563    =head3 SplitKeywords
3564    
3565        my @keywords = ERDB::SplitKeywords($keywordString);
3566    
3567    This method returns a list of the positive keywords in the specified
3568    keyword string. All of the operators will have been stripped off,
3569    and if the keyword is preceded by a minus operator (C<->), it will
3570    not be in the list returned. The idea here is to get a list of the
3571    keywords the user wants to see. The list will be processed to remove
3572    duplicates.
3573    
3574    It is possible to create a string that confuses this method. For example
3575    
3576        frog toad -frog
3577    
3578    would return both C<frog> and C<toad>. If this is a problem we can deal
3579    with it later.
3580    
3581    =over 4
3582    
3583    =item keywordString
3584    
3585    The keyword string to be parsed.
3586    
3587    =item RETURN
3588    
3589    Returns a list of the words in the keyword string the user wants to
3590    see.
3591    
3592    =back
3593    
3594    =cut
3595    
3596    sub SplitKeywords {
3597        # Get the parameters.
3598        my ($keywordString) = @_;
3599        # Make a safety copy of the string. (This helps during debugging.)
3600        my $workString = $keywordString;
3601        # Convert operators we don't care about to spaces.
3602        $workString =~ tr/+"()<>/ /;
3603        # Split the rest of the string along space boundaries. Note that we
3604        # eliminate any words that are zero length or begin with a minus sign.
3605        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3606        # Use a hash to remove duplicates.
3607        my %words = map { $_ => 1 } @wordList;
3608        # Return the result.
3609        return sort keys %words;
3610    }
3611    
3612    =head3 ValidateFieldName
3613    
3614        my $okFlag = ERDB::ValidateFieldName($fieldName);
3615    
3616    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3617    be hyphenated words subject to certain restrictions.
3618    
3619    =over 4
3620    
3621    =item fieldName
3622    
3623    Field name to be validated.
3624    
3625    =item RETURN
3626    
3627    Returns TRUE if the field name is valid, else FALSE.
3628    
3629    =back
3630    
3631    =cut
3632    
3633    sub ValidateFieldName {
3634        # Get the parameters.
3635        my ($fieldName) = @_;
3636        # Declare the return variable. The field name is valid until we hear
3637        # differently.
3638        my $retVal = 1;
3639        # Compute the maximum name length.
3640        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3641        # Look for bad stuff in the name.
3642        if ($fieldName =~ /--/) {
3643            # Here we have a doubled minus sign.
3644            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3645            $retVal = 0;
3646        } elsif ($fieldName !~ /^[A-Za-z]/) {
3647            # Here the field name is missing the initial letter.
3648            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3649            $retVal = 0;
3650        } elsif (length($fieldName) > $maxLen) {
3651            # Here the field name is too long.
3652            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3653        } else {
3654            # Strip out the minus signs. Everything remaining must be a letter,
3655            # underscore, or digit.
3656            my $strippedName = $fieldName;
3657            $strippedName =~ s/-//g;
3658            if ($strippedName !~ /^(\w|\d)+$/) {
3659                Trace("Field name $fieldName contains illegal characters.") if T(1);
3660                $retVal = 0;
3661            }
3662        }
3663        # Return the result.
3664        return $retVal;
3665    }
3666    
3667    =head3 ReadMetaXML
3668    
3669        my $rawMetaData = ERDB::ReadDBD($fileName);
3670    
3671    This method reads a raw database definition XML file and returns it.
3672    Normally, the metadata used by the ERDB system has been processed and
3673    modified to make it easier to load and retrieve the data; however,
3674    this method can be used to get the data in its raw form.
3675    
3676    =over 4
3677    
3678    =item fileName
3679    
3680    Name of the XML file to read.
3681    
3682    =item RETURN
3683    
3684    Returns a hash reference containing the raw XML data from the specified file.
3685    
3686    =back
3687    
3688    =cut
3689    
3690    sub ReadMetaXML {
3691        # Get the parameters.
3692        my ($fileName) = @_;
3693        # Read the XML.
3694        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3695        Trace("XML metadata loaded from file $fileName.") if T(1);
3696        # Return the result.
3697        return $retVal;
3698    }
3699    
3700    =head3 GetEntityFieldHash
3701    
3702        my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3703    
3704    Get the field hash of the named entity in the specified raw XML structure.
3705    The field hash may not exist, in which case we need to create it.
3706    
3707    =over 4
3708    
3709    =item structure
3710    
3711    Raw XML structure defininng the database. This is not the run-time XML used by
3712    an ERDB object, since that has all sorts of optimizations built-in.
3713    
3714    =item entityName
3715    
3716    Name of the entity whose field structure is desired.
3717    
3718    =item RETURN
3719    
3720    Returns the field hash used to define the entity's fields.
3721    
3722    =back
3723    
3724    =cut
3725    
3726    sub GetEntityFieldHash {
3727        # Get the parameters.
3728        my ($structure, $entityName) = @_;
3729        # Get the entity structure.
3730        my $entityData = $structure->{Entities}->{$entityName};
3731        # Look for a field structure.
3732        my $retVal = $entityData->{Fields};
3733        # If it doesn't exist, create it.
3734        if (! defined($retVal)) {
3735            $entityData->{Fields} = {};
3736            $retVal = $entityData->{Fields};
3737        }
3738        # Return the result.
3739        return $retVal;
3740    }
3741    
3742    =head3 WriteMetaXML
3743    
3744        ERDB::WriteMetaXML($structure, $fileName);
3745    
3746    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3747    used to update the database definition. It must be used with care, however, since it
3748    will only work on a raw structure, not on the processed structure created by an ERDB
3749    constructor.
3750    
3751    =over 4
3752    
3753    =item structure
3754    
3755    XML structure to be written to the file.
3756    
3757    =item fileName
3758    
3759    Name of the output file to which the updated XML should be stored.
3760    
3761    =back
3762    
3763    =cut
3764    
3765    sub WriteMetaXML {
3766        # Get the parameters.
3767        my ($structure, $fileName) = @_;
3768        # Compute the output.
3769        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3770        # Write it to the file.
3771        my $xmlOut = Open(undef, ">$fileName");
3772        print $xmlOut $fileString;
3773    }
3774    
3775    
3776    =head3 HTMLNote
3777    
3778    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3779    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3780    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3781    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3782    
3783        my $realHtml = ERDB::HTMLNote($dataString);
3784    
3785    =over 4
3786    
3787    =item dataString
3788    
3789    String to convert to HTML.
3790    
3791    =item RETURN
3792    
3793    An HTML string derived from the input string.
3794    
3795    =back
3796    
3797    =cut
3798    
3799    sub HTMLNote {
3800        # Get the parameter.
3801        my ($dataString) = @_;
3802        # HTML-escape the text.
3803        my $retVal = CGI::escapeHTML($dataString);
3804        # Substitute the bulletin board codes.
3805        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3806        $retVal =~ s!\[p\]!</p><p>!g;
3807        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3808        $retVal =~ s!\[/link\]!</a>!g;
3809        # Return the result.
3810        return $retVal;
3811    }
3812    
3813    =head3 WikiNote
3814    
3815    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3816    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3817    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3818    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3819    
3820        my $wikiText = ERDB::WikiNote($dataString);
3821    
3822    =over 4
3823    
3824    =item dataString
3825    
3826    String to convert to Wiki text.
3827    
3828    =item RETURN
3829    
3830    An Wiki text string derived from the input string.
3831    
3832    =back
3833    
3834    =cut
3835    
3836    sub WikiNote {
3837        # Get the parameter.
3838        my ($dataString) = @_;
3839        # HTML-escape the text.
3840        my $retVal = CGI::escapeHTML($dataString);
3841        # Substitute the bulletin board codes.
3842        my $italic = WikiTools::ItalicCode();
3843        $retVal =~ s/\[\/?i\]/$italic/g;
3844        my $bold = WikiTools::BoldCode();
3845        $retVal =~ s/\[\/?b\]/$bold/g;
3846        # Paragraph breaks are the same no matter which Wiki you're using.
3847        $retVal =~ s!\[p\]!\n\n!g;
3848        # Now we do the links, which are complicated by the need to know two
3849        # things: the target URL and the text.
3850        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3851            # Replace the matched string with the Wiki markup for links. Note that
3852            # $-[0] is the starting position of the match for the entire expression,
3853            # and $+[0] is past the ending position.
3854            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3855        }
3856        # Return the result.
3857        return $retVal;
3858    }
3859    
3860    =head3 BeginTran
3861    
3862        $erdb->BeginTran();
3863    
3864    Start a database transaction.
3865    
3866    =cut
3867    
3868    sub BeginTran {
3869        my ($self) = @_;
3870        $self->{_dbh}->begin_tran();
3871    
3872    }
3873    
3874    =head3 CommitTran
3875    
3876        $erdb->CommitTran();
3877    
3878    Commit an active database transaction.
3879    
3880    =cut
3881    
3882    sub CommitTran {
3883        my ($self) = @_;
3884        $self->{_dbh}->commit_tran();
3885    }
3886    
3887    =head3 RollbackTran
3888    
3889        $erdb->RollbackTran();
3890    
3891    Roll back an active database transaction.
3892    
3893    =cut
3894    
3895    sub RollbackTran {
3896        my ($self) = @_;
3897        $self->{_dbh}->roll_tran();
3898    }
3899    
3900    =head3 UpdateField
3901    
3902        my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3903    
3904    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3905    returned.
3906    
3907    =over 4
3908    
3909    =item fieldName
3910    
3911    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3912    
3913    =item oldValue
3914    
3915    Value to be modified. All occurrences of this value in the named field will be replaced by the
3916    new value.
3917    
3918    =item newValue
3919    
3920    New value to be substituted for the old value when it's found.
3921    
3922    =item filter
3923    
3924    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3925    
3926    =item parms
3927    
3928    Reference to a list of parameter values in the filter.
3929    
3930    =item RETURN
3931    
3932    Returns the number of rows modified.
3933    
3934    =back
3935    
3936    =cut
3937    
3938    sub UpdateField {
3939        # Get the parameters.
3940        my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3941        # Get the object and field names from the field name parameter.
3942        $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3943        my $objectName = $1;
3944        my $realFieldName = _FixName($2);
3945        # Add the old value to the filter. Note we allow the possibility that no
3946        # filter was specified.
3947        my $realFilter = "$fieldName = ?";
3948        if ($filter) {
3949            $realFilter .= " AND $filter";
3950        }
3951        # Format the query filter.
3952        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3953            $self->_SetupSQL([$objectName], $realFilter);
3954        # Create the query. Since there is only one object name, the mapped-name data is not
3955        # necessary. Neither is the FROM clause.
3956        $suffix =~ s/^FROM.+WHERE\s+//;
3957        # Create the update statement.
3958        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3959        # Get the database handle.
3960        my $dbh = $self->{_dbh};
3961        # Add the old and new values to the parameter list. Note we allow the possibility that
3962        # there are no user-supplied parameters.
3963        my @params = ($newValue, $oldValue);
3964        if (defined $parms) {
3965            push @params, @{$parms};
3966        }
3967        # Execute the update.
3968        my $retVal = $dbh->SQL($command, 0, @params);
3969        # Make the funky zero a real zero.
3970        if ($retVal == 0) {
3971            $retVal = 0;
3972        }
3973        # Return the result.
3974        return $retVal;
3975    }
3976    
3977    
3978  =head2 Data Mining Methods  =head2 Data Mining Methods
3979    
3980  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
3981    
3982  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>      my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3983    
3984  Return a list of the useful attributes that would be returned by a B<Cross> call  Return a list of the useful attributes that would be returned by a B<Cross> call
3985  from an entity of the source entity type through the specified relationship. This  from an entity of the source entity type through the specified relationship. This
# Line 2298  Line 4035 
4035      # Push these onto the return list.      # Push these onto the return list.
4036      push @retVal, sort @fieldList2;      push @retVal, sort @fieldList2;
4037      # Return the result.      # Return the result.
4038      return @retVal;      return @retVal;
4039    }
4040    
4041    =head3 FindColumn
4042    
4043        my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
4044    
4045    Return the location a desired column in a data mining header line. The data
4046    mining header line is a tab-separated list of column names. The column
4047    identifier is either the numerical index of a column or the actual column
4048    name.
4049    
4050    =over 4
4051    
4052    =item headerLine
4053    
4054    The header line from a data mining command, which consists of a tab-separated
4055    list of column names.
4056    
4057    =item columnIdentifier
4058    
4059    Either the ordinal number of the desired column (1-based), or the name of the
4060    desired column.
4061    
4062    =item RETURN
4063    
4064    Returns the array index (0-based) of the desired column.
4065    
4066    =back
4067    
4068    =cut
4069    
4070    sub FindColumn {
4071        # Get the parameters.
4072        my ($headerLine, $columnIdentifier) = @_;
4073        # Declare the return variable.
4074        my $retVal;
4075        # Split the header line into column names.
4076        my @headers = ParseColumns($headerLine);
4077        # Determine whether we have a number or a name.
4078        if ($columnIdentifier =~ /^\d+$/) {
4079            # Here we have a number. Subtract 1 and validate the result.
4080            $retVal = $columnIdentifier - 1;
4081            if ($retVal < 0 || $retVal > $#headers) {
4082                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
4083            }
4084        } else {
4085            # Here we have a name. We need to find it in the list.
4086            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
4087                if ($headers[$i] eq $columnIdentifier) {
4088                    $retVal = $i;
4089                }
4090            }
4091            if (! defined($retVal)) {
4092                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
4093            }
4094        }
4095        # Return the result.
4096        return $retVal;
4097    }
4098    
4099    =head3 ParseColumns
4100    
4101        my @columns = ERDB::ParseColumns($line);
4102    
4103    Convert the specified data line to a list of columns.
4104    
4105    =over 4
4106    
4107    =item line
4108    
4109    A data mining input, consisting of a tab-separated list of columns terminated by a
4110    new-line.
4111    
4112    =item RETURN
4113    
4114    Returns a list consisting of the column values.
4115    
4116    =back
4117    
4118    =cut
4119    
4120    sub ParseColumns {
4121        # Get the parameters.
4122        my ($line) = @_;
4123        # Chop off the line-end.
4124        chomp $line;
4125        # Split it into a list.
4126        my @retVal = split(/\t/, $line);
4127        # Return the result.
4128        return @retVal;
4129    }
4130    
4131    =head2 Virtual Methods
4132    
4133    =head3 _CreatePPOIndex
4134    
4135        my $index = ERDB::_CreatePPOIndex($indexObject);
4136    
4137    Convert the XML for an ERDB index to the XML structure for a PPO
4138    index.
4139    
4140    =over 4
4141    
4142    =item indexObject
4143    
4144    ERDB XML structure for an index.
4145    
4146    =item RETURN
4147    
4148    PPO XML structure for the same index.
4149    
4150    =back
4151    
4152    =cut
4153    
4154    sub _CreatePPOIndex {
4155        # Get the parameters.
4156        my ($indexObject) = @_;
4157        # The incoming index contains a list of the index fields in the IndexFields
4158        # member. We loop through it to create the index tags.
4159        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
4160        # Wrap the fields in attribute tags.
4161        my $retVal = { attribute => \@fields };
4162        # Return the result.
4163        return $retVal;
4164    }
4165    
4166    =head3 _CreatePPOField
4167    
4168        my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject);
4169    
4170    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
4171    
4172    =over 4
4173    
4174    =item fieldName
4175    
4176    Name of the scalar field.
4177    
4178    =item fieldObject
4179    
4180    ERDB XML structure describing the field.
4181    
4182    =item RETURN
4183    
4184    Returns a PPO XML structure for the same field.
4185    
4186    =back
4187    
4188    =cut
4189    
4190    sub _CreatePPOField {
4191        # Get the parameters.
4192        my ($fieldName, $fieldObject) = @_;
4193        # Get the field type.
4194        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
4195        # Fix up the field name.
4196        $fieldName = _FixName($fieldName);
4197        # Build the scalar tag.
4198        my $retVal = { label => $fieldName, type => $type };
4199        # Return the result.
4200        return $retVal;
4201  }  }
4202    
4203  =head3 FindColumn  =head3 CleanKeywords
4204    
4205  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>      my $cleanedString = $erdb->CleanKeywords($searchExpression);
4206    
4207  Return the location a desired column in a data mining header line. The data  Clean up a search expression or keyword list. This is a virtual method that may
4208  mining header line is a tab-separated list of column names. The column  be overridden by the subclass. The base-class method removes extra spaces
4209  identifier is either the numerical index of a column or the actual column  and converts everything to lower case.
 name.  
4210    
4211  =over 4  =over 4
4212    
4213  =item headerLine  =item searchExpression
   
 The header line from a data mining command, which consists of a tab-separated  
 list of column names.  
   
 =item columnIdentifier  
4214    
4215  Either the ordinal number of the desired column (1-based), or the name of the  Search expression or keyword list to clean. Note that a search expression may
4216  desired column.  contain boolean operators which need to be preserved. This includes leading
4217    minus signs.
4218    
4219  =item RETURN  =item RETURN
4220    
4221  Returns the array index (0-based) of the desired column.  Cleaned expression or keyword list.
4222    
4223  =back  =back
4224    
4225  =cut  =cut
4226    
4227  sub FindColumn {  sub CleanKeywords {
4228      # Get the parameters.      # Get the parameters.
4229      my ($headerLine, $columnIdentifier) = @_;      my ($self, $searchExpression) = @_;
4230      # Declare the return variable.      # Lower-case the expression and copy it into the return variable. Note that we insure we
4231      my $retVal;      # don't accidentally end up with an undefined value.
4232      # Split the header line into column names.      my $retVal = lc($searchExpression || "");
4233      my @headers = ParseColumns($headerLine);      # Remove extra spaces.
4234      # Determine whether we have a number or a name.      $retVal =~ s/\s+/ /g;
4235      if ($columnIdentifier =~ /^\d+$/) {      $retVal =~ s/(^\s+)|(\s+$)//g;
         # Here we have a number. Subtract 1 and validate the result.  
         $retVal = $columnIdentifier - 1;  
         if ($retVal < 0 || $retVal > $#headers) {  
             Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");  
         }  
     } else {  
         # Here we have a name. We need to find it in the list.  
         for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {  
             if ($headers[$i] eq $columnIdentifier) {  
                 $retVal = $i;  
             }  
         }  
         if (! defined($retVal)) {  
             Confess("Invalid column identifier \"$columnIdentifier\": value not found.");  
         }  
     }  
4236      # Return the result.      # Return the result.
4237      return $retVal;      return $retVal;
4238  }  }
4239    
4240  =head3 ParseColumns  =head3 GetSourceObject
4241    
4242  C<< my @columns = ERDB::ParseColumns($line); >>      my $source = $erdb->GetSourceObject($entityName);
4243    
4244  Convert the specified data line to a list of columns.  Return the object to be used in loading special attributes of the specified entity. The
4245    algorithm for loading special attributes is stored in the C<DataGen> elements of the
4246    XML
4247    
4248    =head2 Internal Utility Methods
4249    
4250    =head3 _RelationMap
4251    
4252        my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
4253    
4254    Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
4255    to determine how to interpret the results of the query.
4256    
4257  =over 4  =over 4
4258    
4259  =item line  =item mappedNameHashRef
4260    
4261  A data mining input, consisting of a tab-separated list of columns terminated by a  Reference to a hash that maps modified object names to real object names.
4262  new-line.  
4263    =item mappedNameListRef
4264    
4265    Reference to a list of modified object names in the order they appear in the
4266    SELECT list.
4267    
4268  =item RETURN  =item RETURN
4269    
4270  Returns a list consisting of the column values.  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
4271    query followed by the actual name of that object. This enables the B<ERDBObject> to
4272    determine the order of the tables in the query and which object name belongs to each
4273    mapped object name. Most of the time these two values are the same; however, if a
4274    relation occurs twice in the query, the relation name in the field list and WHERE
4275    clause will use a mapped name (generally the actual relation name with a numeric
4276    suffix) that does not match the actual relation name.
4277    
4278  =back  =back
4279    
4280  =cut  =cut
4281    
4282  sub ParseColumns {  sub _RelationMap {
4283      # Get the parameters.      # Get the parameters.
4284      my ($line) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
4285      # Chop off the line-end.      # Declare the return variable.
4286      chomp $line;      my @retVal = ();
4287      # Split it into a list.      # Build the map.
4288      my @retVal = split(/\t/, $line);      for my $mappedName (@{$mappedNameListRef}) {
4289      # Return the result.          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
4290        }
4291        # Return it.
4292      return @retVal;      return @retVal;
4293  }  }
4294    
 =head2 Internal Utility Methods  
4295    
4296  =head3 SetupSQL  =head3 _SetupSQL
4297    
4298  Process a list of object names and a filter clause so that they can be used to  Process a list of object names and a filter clause so that they can be used to
4299  build an SQL statement. This method takes in a reference to a list of object names  build an SQL statement. This method takes in a reference to a list of object names
# Line 2413  Line 4313 
4313  A string containing the WHERE clause for the query (without the C<WHERE>) and also  A string containing the WHERE clause for the query (without the C<WHERE>) and also
4314  optionally the C<ORDER BY> and C<LIMIT> clauses.  optionally the C<ORDER BY> and C<LIMIT> clauses.
4315    
4316    =item matchClause
4317    
4318    An optional full-text search clause. If specified, it will be inserted at the
4319    front of the WHERE clause. It should already be SQL-formatted; that is, the
4320    field names should be in the form I<table>C<.>I<fieldName>.
4321    
4322  =item RETURN  =item RETURN
4323    
4324  Returns a three-element list. The first element is the SQL statement suffix, beginning  Returns a three-element list. The first element is the SQL statement suffix, beginning
# Line 2425  Line 4331 
4331  =cut  =cut
4332    
4333  sub _SetupSQL {  sub _SetupSQL {
4334      my ($self, $objectNames, $filterClause) = @_;      my ($self, $objectNames, $filterClause, $matchClause) = @_;
4335      # Adjust the list of object names to account for multiple occurrences of the      # Adjust the list of object names to account for multiple occurrences of the
4336      # same object. We start with a hash table keyed on object name that will      # same object. We start with a hash table keyed on object name that will
4337      # return the object suffix. The first time an object is encountered it will      # return the object suffix. The first time an object is encountered it will
# Line 2474  Line 4380 
4380      # FROM name1, name2, ... nameN      # FROM name1, name2, ... nameN
4381      #      #
4382      my $suffix = "FROM " . join(', ', @fromList);      my $suffix = "FROM " . join(', ', @fromList);
4383        # Now for the WHERE. First, we need a place for the filter string.
4384        my $filterString = "";
4385        # We will also keep a list of conditions to add to the WHERE clause in order to link
4386        # entities and relationships as well as primary relations to secondary ones.
4387        my @joinWhere = ();
4388      # Check for a filter clause.      # Check for a filter clause.
4389      if ($filterClause) {      if ($filterClause) {
4390          # Here we have one, so we convert its field names and add it to the query. First,          # Here we have one, so we convert its field names and add it to the query. First,
4391          # We create a copy of the filter string we can work with.          # We create a copy of the filter string we can work with.
4392          my $filterString = $filterClause;          $filterString = $filterClause;
4393          # Next, we sort the object names by length. This helps protect us from finding          # Next, we sort the object names by length. This helps protect us from finding
4394          # object names inside other object names when we're doing our search and replace.          # object names inside other object names when we're doing our search and replace.
4395          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
4396          # The final preparatory step is to create a hash table of relation names. The          # The final preparatory step is to create a hash table of relation names. The
4397          # table begins with the relation names already in the SELECT command. We may          # table begins with the relation names already in the SELECT command. We may
4398          # need to add relations later if there is filtering on a field in a secondary          # need to add relations later if there is filtering on a field in a secondary
# Line 2552  Line 4460 
4460                  }                  }
4461              }              }
4462          }          }
4463        }
4464          # The next step is to join the objects together. We only need to do this if there          # The next step is to join the objects together. We only need to do this if there
4465          # is more than one object in the object list. We start with the first object and          # is more than one object in the object list. We start with the first object and
4466          # run through the objects after it. Note also that we make a safety copy of the          # run through the objects after it. Note also that we make a safety copy of the
4467          # list before running through it.      # list before running through it, because we shift off the first object before
4468        # processing the rest.
4469          my @mappedObjectList = @mappedNameList;          my @mappedObjectList = @mappedNameList;
4470          my $lastMappedObject = shift @mappedObjectList;          my $lastMappedObject = shift @mappedObjectList;
4471          # Get the join table.          # Get the join table.
# Line 2584  Line 4494 
4494          # here is we want the filter clause to be empty if there's no WHERE filter.          # here is we want the filter clause to be empty if there's no WHERE filter.
4495          # We'll put the ORDER BY / LIMIT clauses in the following variable.          # We'll put the ORDER BY / LIMIT clauses in the following variable.
4496          my $orderClause = "";          my $orderClause = "";
4497        # This is only necessary if we have a filter string in which the ORDER BY
4498        # and LIMIT clauses can live.
4499        if ($filterString) {
4500          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
4501          # operator so that we find the first occurrence of either verb.          # operator so that we find the first occurrence of either verb.
4502          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
# Line 2592  Line 4505 
4505              $orderClause = $2 . substr($filterString, $pos);              $orderClause = $2 . substr($filterString, $pos);
4506              $filterString = $1;              $filterString = $1;
4507          }          }
4508          # Add the filter and the join clauses (if any) to the SELECT command.      }
4509        # All the things that are supposed to be in the WHERE clause of the
4510        # SELECT command need to be put into @joinWhere so we can string them
4511        # together. We begin with the match clause. This is important,
4512        # because the match clause's parameter mark must precede any parameter
4513        # marks in the filter string.
4514        if ($matchClause) {
4515            push @joinWhere, $matchClause;
4516        }
4517        # Add the filter string. We put it in parentheses to avoid operator
4518        # precedence problems with the match clause or the joins.
4519          if ($filterString) {          if ($filterString) {
4520              Trace("Filter string is \"$filterString\".") if T(4);              Trace("Filter string is \"$filterString\".") if T(4);
4521              push @joinWhere, "($filterString)";              push @joinWhere, "($filterString)";
4522          }          }
4523        # String it all together into a big filter clause.
4524          if (@joinWhere) {          if (@joinWhere) {
4525              $suffix .= " WHERE " . join(' AND ', @joinWhere);              $suffix .= " WHERE " . join(' AND ', @joinWhere);
4526          }          }
4527          # Add the sort or limit clause (if any) to the SELECT command.      # Add the sort or limit clause (if any).
4528          if ($orderClause) {          if ($orderClause) {
4529              $suffix .= " $orderClause";              $suffix .= " $orderClause";
4530          }          }
     }  
4531      # Return the suffix, the mapped name list, and the mapped name hash.      # Return the suffix, the mapped name list, and the mapped name hash.
4532      return ($suffix, \@mappedNameList, \%mappedNameHash);      return ($suffix, \@mappedNameList, \%mappedNameHash);
4533  }  }
4534    
4535  =head3 GetStatementHandle  =head3 _GetStatementHandle
4536    
4537  This method will prepare and execute an SQL query, returning the statement handle.  This method will prepare and execute an SQL query, returning the statement handle.
4538  The main reason for doing this here is so that everybody who does SQL queries gets  The main reason for doing this here is so that everybody who does SQL queries gets
# Line 2639  Line 4562 
4562  sub _GetStatementHandle {  sub _GetStatementHandle {
4563      # Get the parameters.      # Get the parameters.
4564      my ($self, $command, $params) = @_;      my ($self, $command, $params) = @_;
4565        Confess("Invalid parameter list.") if (! defined($params) || ref($params) ne 'ARRAY');
4566      # Trace the query.      # Trace the query.
4567      Trace("SQL query: $command") if T(SQL => 3);      Trace("SQL query: $command") if T(SQL => 3);
4568      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
# Line 2647  Line 4571 
4571      # Prepare the command.      # Prepare the command.
4572      my $sth = $dbh->prepare_command($command);      my $sth = $dbh->prepare_command($command);
4573      # Execute it with the parameters bound in.      # Execute it with the parameters bound in.
4574      $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
4575      # Return the statement handle.      # Return the statement handle.
4576      return $sth;      return $sth;
4577  }  }
4578    
4579  =head3 GetLoadStats  =head3 _GetLoadStats
4580    
4581  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
4582    
# Line 2664  Line 4588 
4588      return Stats->new();      return Stats->new();
4589  }  }
4590    
4591  =head3 GenerateFields  =head3 _DumpRelation
   
 Generate field values from a field structure and store in a specified table. The field names  
 are first sorted by pass count, certain pre-defined fields are removed from the list, and  
 then we rip through them evaluation the data generation string. Fields in the primary relation  
 are stored as scalars; fields in secondary relations are stored as value lists.  
   
 This is a static method.  
   
 =over 4  
   
 =item this  
   
 Hash table into which the field values should be placed.  
   
 =item fields  
   
 Field structure from which the field descriptors should be taken.  
   
 =item type  
   
 Type name of the object whose fields are being generated.  
   
 =item values (optional)  
   
 Reference to a value structure from which additional values can be taken.  
   
 =item from (optiona)  
   
 Reference to the source entity instance if relationship data is being generated.  
   
 =item to (optional)  
   
 Reference to the target entity instance if relationship data is being generated.  
   
 =back  
   
 =cut  
   
 sub _GenerateFields {  
     # Get the parameters.  
     my ($this, $fields, $type, $values, $from, $to) = @_;  
     # Sort the field names by pass number.  
     my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};  
     # Loop through the field names, generating data.  
     for my $name (@fieldNames) {  
         # Only proceed if this field needs to be generated.  
         if (!exists $this->{$name}) {  
             # Get this field's data generation descriptor.  
             my $fieldDescriptor = $fields->{$name};  
             my $data = $fieldDescriptor->{DataGen};  
             # Get the code to generate the field value.  
             my $codeString = $data->{content};  
             # Determine whether or not this field is in the primary relation.  
             if ($fieldDescriptor->{relation} eq $type) {  
                 # Here we have a primary relation field. Store the field value as  
                 # a scalar.  
                 $this->{$name} = eval($codeString);  
             } else {  
                 # Here we have a secondary relation field. Create a null list  
                 # and push the desired number of field values onto it.  
                 my @fieldValues = ();  
                 my $count = IntGen(0,$data->{testCount});  
                 for (my $i = 0; $i < $count; $i++) {  
                     my $newValue = eval($codeString);  
                     push @fieldValues, $newValue;  
                 }  
                 # Store the value list in the main hash.  
                 $this->{$name} = \@fieldValues;  
             }  
         }  
     }  
 }  
   
 =head3 DumpRelation  
4592    
4593  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.
4594    
4595  This is an instance method.  This is an instance method.
4596    
# Line 2788  Line 4638 
4638      close DTXOUT;      close DTXOUT;
4639  }  }
4640    
4641  =head3 GetStructure  =head3 _GetStructure
4642    
4643  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
4644    
# Line 2827  Line 4677 
4677      return $retVal;      return $retVal;
4678  }  }
4679    
4680  =head3 GetRelationTable  
4681    
4682    =head3 _GetRelationTable
4683    
4684  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
4685    
# Line 2856  Line 4708 
4708      return $objectData->{Relations};      return $objectData->{Relations};
4709  }  }
4710    
4711  =head3 ValidateFieldNames  =head3 _ValidateFieldNames
4712    
4713  Determine whether or not the field names are valid. A description of the problems with the names  Determine whether or not the field names are valid. A description of the problems with the names
4714  will be written to the standard error output. If there is an error, this method will abort. This is  will be written to the standard error output. If there is an error, this method will abort. This is
# Line 2883  Line 4735 
4735          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
4736              # Loop through the object's fields.              # Loop through the object's fields.
4737              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
4738                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
4739                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
4740                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($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";  
4741                          $retVal = 0;                          $retVal = 0;
4742                      }                      }
4743                  }                  }
4744              }              }
4745          }          }
     }  
4746      # If an error was found, fail.      # If an error was found, fail.
4747      if ($retVal  == 0) {      if ($retVal  == 0) {
4748          Confess("Errors found in field names.");          Confess("Errors found in field names.");
4749      }      }
4750  }  }
4751    
4752  =head3 LoadRelation  =head3 _LoadRelation
4753    
4754  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
4755  file with the same name as the relation exists in the specified directory.  file with the same name as the relation exists in the specified directory.
# Line 2962  Line 4800 
4800      # be a null string.      # be a null string.
4801      if ($fileName ne "") {      if ($fileName ne "") {
4802          # Load the relation from the file.          # Load the relation from the file.
4803          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4804      } elsif ($rebuild) {      } elsif ($rebuild) {
4805          # Here we are rebuilding, but no file exists, so we just re-create the table.          # Here we are rebuilding, but no file exists, so we just re-create the table.
4806          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 2971  Line 4809 
4809      return $retVal;      return $retVal;
4810  }  }
4811    
4812  =head3 LoadMetaData  
4813    =head3 _LoadMetaData
4814    
4815        my $metadata = ERDB::_LoadMetaData($filename);
4816    
4817  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4818  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 2996  Line 4837 
4837  sub _LoadMetaData {  sub _LoadMetaData {
4838      # Get the parameters.      # Get the parameters.
4839      my ($filename) = @_;      my ($filename) = @_;
4840      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4841      # 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
4842      # get the exact structure we want.      # get the exact structure we want.
4843      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 $filename.") if T(1);  
4844      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
4845      # the method below will fail.      # the method below will fail.
4846      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 3135  Line 4963 
4963              if ($found == 0) {              if ($found == 0) {
4964                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4965              }              }
4966              # Now we need to convert the relation's index list to an index table. We begin by creating              # Attach all the indexes to the relation.
4967              # an empty table in the relation structure.              _ProcessIndexes($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++;  
             }  
4968          }          }
4969          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4970          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 3159  Line 4978 
4978          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4979          # Format a description for the FROM field.          # Format a description for the FROM field.
4980          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4981          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].";
4982          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4983          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4984          # Add the FROM field.          # Add the FROM field.
# Line 3169  Line 4988 
4988                                                      PrettySort => 1});                                                      PrettySort => 1});
4989          # Format a description for the TO field.          # Format a description for the TO field.
4990          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4991          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].";
4992          # Get the TO entity's key type.          # Get the TO entity's key type.
4993          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4994          # Add the TO field.          # Add the TO field.
# Line 3181  Line 5000 
5000          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
5001                               Indexes => { } };                               Indexes => { } };
5002          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
5003    
5004            # Add the alternate indexes (if any). This MUST be done before the FROM and
5005            # TO indexes, because it erases the relation's index list.
5006            if (exists $relationshipStructure->{Indexes}) {
5007                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
5008            }
5009            # Add the relation to the master table.
5010          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
5011          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
5012          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
5013          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
5014      }      }
5015      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 3286  Line 5111 
5111          for my $relationshipName (@bothList) {          for my $relationshipName (@bothList) {
5112              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
5113              # Join to the entity from each direction.              # Join to the entity from each direction.
5114              $joinTable{"$entityName/$relationshipName"} =              $joinTable{"$entityName/$relationshipName"} =
5115                  "$entityName.id = $relationshipName.from_link";                  "$entityName.id = $relationshipName.from_link";
5116              $joinTable{"$relationshipName/$entityName"} =              $joinTable{"$relationshipName/$entityName"} =
5117                  "$relationshipName.to_link = $entityName.id";                  "$relationshipName.to_link = $entityName.id";
         }  
     }  
     # Add the join table to the structure.  
     $metadata->{Joins} = \%joinTable;  
     # Return the slurped and fixed-up structure.  
     return $metadata;  
 }  
   
 =head3 SortNeeded  
   
 C<< my $parms = $erdb->SortNeeded($relationName); >>  
   
 Return the pipe command for the sort that should be applied to the specified  
 relation when creating the load file.  
   
 For example, if the load file should be sorted ascending by the first  
 field, this method would return  
   
     sort -k1 -t"\t"  
   
 If the first field is numeric, the method would return  
   
     sort -k1n -t"\t"  
   
 Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate  
 keys using a sort.  
   
 =over 4  
   
 =item relationName  
   
 Name of the relation to be examined.  
   
 =item  
   
 Returns the sort command to use for sorting the relation, suitable for piping.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub SortNeeded {  
     # Get the parameters.  
     my ($self, $relationName) = @_;  
     # Declare a descriptor to hold the names of the key fields.  
     my @keyNames = ();  
     # Get the relation structure.  
     my $relationData = $self->_FindRelation($relationName);  
     # Find out if the relation is a primary entity relation,  
     # a relationship relation, or a secondary entity relation.  
     my $entityTable = $self->{_metaData}->{Entities};  
     my $relationshipTable = $self->{_metaData}->{Relationships};  
     if (exists $entityTable->{$relationName}) {  
         # Here we have a primary entity relation.  
         push @keyNames, "id";  
     } elsif (exists $relationshipTable->{$relationName}) {  
         # Here we have a relationship. We sort using the FROM index.  
         my $relationshipData = $relationshipTable->{$relationName};  
         my $index = $relationData->{Indexes}->{"idx${relationName}From"};  
         push @keyNames, @{$index->{IndexFields}};  
     } else {  
         # Here we have a secondary entity relation, so we have a sort on the ID field.  
         push @keyNames, "id";  
     }  
     # Now we parse the key names into sort parameters. First, we prime the return  
     # string.  
     my $retVal = "sort -t\"\t\" ";  
     # Get the relation's field list.  
     my @fields = @{$relationData->{Fields}};  
     # Loop through the keys.  
     for my $keyData (@keyNames) {  
         # Get the key and the ordering.  
         my ($keyName, $ordering);  
         if ($keyData =~ /^([^ ]+) DESC/) {  
             ($keyName, $ordering) = ($1, "descending");  
         } else {  
             ($keyName, $ordering) = ($keyData, "ascending");  
         }  
         # Find the key's position and type.  
         my $fieldSpec;  
         for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {  
             my $thisField = $fields[$i];  
             if ($thisField->{name} eq $keyName) {  
                 # Get the sort modifier for this field type. The modifier  
                 # decides whether we're using a character, numeric, or  
                 # floating-point sort.  
                 my $modifier = $TypeTable{$thisField->{type}}->{sort};  
                 # If the index is descending for this field, denote we want  
                 # to reverse the sort order on this field.  
                 if ($ordering eq 'descending') {  
                     $modifier .= "r";  
                 }  
                 # Store the position and modifier into the field spec, which  
                 # will stop the inner loop. Note that the field number is  
                 # 1-based in the sort command, so we have to increment the  
                 # index.  
                 $fieldSpec = ($i + 1) . $modifier;  
             }  
5118          }          }
         # Add this field to the sort command.  
         $retVal .= " -k$fieldSpec";  
5119      }      }
5120      # Return the result.      # Add the join table to the structure.
5121      return $retVal;      $metadata->{Joins} = \%joinTable;
5122        # Return the slurped and fixed-up structure.
5123        return $metadata;
5124  }  }
5125    
5126  =head3 CreateRelationshipIndex  =head3 _CreateRelationshipIndex
5127    
5128  Create an index for a relationship's relation.  Create an index for a relationship's relation.
5129    
# Line 3438  Line 5165 
5165          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
5166      }      }
5167      # Add the index to the relation.      # Add the index to the relation.
5168      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
5169    }
5170    
5171    =head3 _ProcessIndexes
5172    
5173        ERDB::_ProcessIndexes($indexList, $relation);
5174    
5175    Build the data structures for the specified indexes in the specified relation.
5176    
5177    =over 4
5178    
5179    =item indexList
5180    
5181    Reference to a list of indexes. Each index is a hash reference containing an optional
5182    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
5183    to a list of index field structures. An index field structure, in turn, is a reference
5184    to a hash that contains a C<name> attribute for the field name and an C<order>
5185    attribute that specifies either C<ascending> or C<descending>. In this sense the
5186    index list encapsulates the XML C<Indexes> structure in the database definition.
5187    
5188    =item relation
5189    
5190    The structure that describes the current relation. The new index descriptors will
5191    be stored in the structure's C<Indexes> member. Any previous data in the structure
5192    will be lost.
5193    
5194    =back
5195    
5196    =cut
5197    
5198    sub _ProcessIndexes {
5199        # Get the parameters.
5200        my ($indexList, $relation) = @_;
5201        # Now we need to convert the relation's index list to an index table. We begin by creating
5202        # an empty table in the relation structure.
5203        $relation->{Indexes} = { };
5204        # Loop through the indexes.
5205        my $count = 0;
5206        for my $index (@{$indexList}) {
5207            # Add this index to the index table.
5208            _AddIndex("idx$count", $relation, $index);
5209            # Increment the counter so that the next index has a different name.
5210            $count++;
5211        }
5212  }  }
5213    
5214  =head3 AddIndex  =head3 _AddIndex
5215    
5216  Add an index to a relation structure.  Add an index to a relation structure.
5217    
# Line 3487  Line 5257 
5257      $relationStructure->{Indexes}->{$indexName} = $newIndex;      $relationStructure->{Indexes}->{$indexName} = $newIndex;
5258  }  }
5259    
5260  =head3 FixupFields  =head3 _FixupFields
5261    
5262  This method fixes the field list for an entity or relationship. It will add the caller-specified  This method fixes the field list for an entity or relationship. It will add the caller-specified
5263  relation name to fields that do not have a name and set the C<PrettySort> value as specified.  relation name to fields that do not have a name and set the C<PrettySort> value as specified.
# Line 3525  Line 5295 
5295          # Here it doesn't, so we create a new one.          # Here it doesn't, so we create a new one.
5296          $structure->{Fields} = { };          $structure->{Fields} = { };
5297      } else {      } else {
5298          # Here we have a field list. Loop through its fields.          # Here we have a field list. We need to track the searchable fields, so we
5299            # create a list for stashing them.
5300            my @textFields = ();
5301            # Loop through the fields.
5302          my $fieldStructures = $structure->{Fields};          my $fieldStructures = $structure->{Fields};
5303          for my $fieldName (keys %{$fieldStructures}) {          for my $fieldName (keys %{$fieldStructures}) {
5304              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
# Line 3534  Line 5307 
5307              my $type = $fieldData->{type};              my $type = $fieldData->{type};
5308              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
5309              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
5310              # Plug in a data generator if we need one.              # Check for searchability.
5311              if (!exists $fieldData->{DataGen}) {              if ($fieldData->{searchable}) {
5312                  # The data generator will use the default for the field's type.                  # Only allow this for a primary relation.
5313                  $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };                  if ($fieldData->{relation} ne $defaultRelationName) {
5314                        Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
5315                    } else {
5316                        push @textFields, $fieldName;
5317                    }
5318              }              }
             # Plug in the defaults for the optional data generation parameters.  
             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
5319              # Add the PrettySortValue.              # Add the PrettySortValue.
5320              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
5321          }          }
5322            # If there are searchable fields, remember the fact.
5323            if (@textFields) {
5324                $structure->{searchFields} = \@textFields;
5325            }
5326      }      }
5327  }  }
5328    
5329  =head3 FixName  =head3 _FixName
5330    
5331  Fix the incoming field name so that it is a legal SQL column name.  Fix the incoming field name so that it is a legal SQL column name.
5332    
# Line 3576  Line 5355 
5355      return $fieldName;      return $fieldName;
5356  }  }
5357    
5358  =head3 FixNames  =head3 _FixNames
5359    
5360  Fix all the field names in a list.  Fix all the field names in a list.
5361    
# Line 3607  Line 5386 
5386      return @result;      return @result;
5387  }  }
5388    
5389  =head3 AddField  =head3 _AddField
5390    
5391  Add a field to a field list.  Add a field to a field list.
5392    
# Line 3642  Line 5421 
5421      $fieldList->{$fieldName} = $fieldStructure;      $fieldList->{$fieldName} = $fieldStructure;
5422  }  }
5423    
5424  =head3 ReOrderRelationTable  =head3 _ReOrderRelationTable
5425    
5426  This method will take a relation table and re-sort it according to the implicit ordering of the  This method will take a relation table and re-sort it according to the implicit ordering of the
5427  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
# Line 3703  Line 5482 
5482    
5483  }  }
5484    
5485  =head3 IsPrimary  =head3 _IsPrimary
5486    
5487  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
5488  if it has the same name as an entity or relationship.  if it has the same name as an entity or relationship.
# Line 3739  Line 5518 
5518      return $retVal;      return $retVal;
5519  }  }
5520    
5521  =head3 FindRelation  =head3 _FindRelation
5522    
5523  Return the descriptor for the specified relation.  Return the descriptor for the specified relation.
5524    
# Line 3768  Line 5547 
5547      return $retVal;      return $retVal;
5548  }  }
5549    
5550  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5551    
5552  =head3 ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5553    
5554  The relationship sentence consists of the relationship name between the names of the  The relationship sentence consists of the relationship name between the names of the
5555  two related entities and an arity indicator.  two related entities and an arity indicator.
# Line 3800  Line 5579 
5579      # Get the parameters.      # Get the parameters.
5580      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5581      # Format the relationship sentence.      # Format the relationship sentence.
5582      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5583      # Compute the arity.      # Compute the arity.
5584      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5585      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 3808  Line 5587 
5587      return $result;      return $result;
5588  }  }
5589    
5590  =head3 ComputeRelationshipHeading  =head3 _ComputeRelationshipHeading
5591    
5592  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
5593  names hyperlinked to the appropriate entity sections of the document.  names hyperlinked to the appropriate entity sections of the document.
# Line 3845  Line 5624 
5624      return $result;      return $result;
5625  }  }
5626    
5627  =head3 ShowRelationTable  =head3 _WikiRelationTable
5628    
5629    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5630    table with three columns-- the field name, the field type, and the field description.
5631    
5632    This is a static method.
5633    
5634    =over 4
5635    
5636    =item relationName
5637    
5638    Name of the relation being formatted.
5639    
5640    =item relationData
5641    
5642    Hash containing the relation's fields and indexes.
5643    
5644    =item RETURN
5645    
5646    Returns a Wiki string that can be used to display the relation name and all of its fields.
5647    
5648    =back
5649    
5650    =cut
5651    
5652    sub _WikiRelationTable {
5653        # Get the parameters.
5654        my ($relationName, $relationData) = @_;
5655        # We'll create a list of lists in here, then call WikiTools::Table to
5656        # convert it into a table.
5657        my @rows = ();
5658        # Push in the header row.
5659        push @rows, [qw(Field Type Description)];
5660        # Loop through the fields.
5661        for my $field (@{$relationData->{Fields}}) {
5662            # Create this field's row. We always have a name and type.
5663            my @row = ($field->{name}, $field->{type});
5664            # If we have a description, add it as the third column.
5665            if (exists $field->{Notes}) {
5666                push @row, WikiNote($field->{Notes}->{content});
5667            }
5668            # Push this row onto the table list.
5669            push @rows, \@row;
5670        }
5671        # Store the rows as a Wiki table with a level-4 heading.
5672        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5673                          WikiTools::Table(@rows));
5674        # Now we show the relation's indexes. These are formatted as another
5675        # table.
5676        @rows = ();
5677        # Push in the header row.
5678        push @rows, [qw(Index Unique Fields Notes)];
5679        # Get the index hash.
5680        my $indexTable = $relationData->{Indexes};
5681        # Loop through the indexes. For an entity, there is always at least one index.
5682        # For a relationship, there are at least two. The upshot is we don't need to
5683        # worry about accidentally generating a frivolous table here.
5684        for my $indexName (sort keys %$indexTable) {
5685