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revision 1.38, Fri Mar 17 22:02:03 2006 UTC revision 1.51, Fri Jun 23 22:53:08 2006 UTC
# Line 9  Line 9 
9      use DBObject;      use DBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13      use FIG;      use FIG;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
# Line 109  Line 110 
110  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
111  0 and 1.  0 and 1.
112    
113    =item id-string
114    
115    variable-length string, maximum 25 characters
116    
117  =item key-string  =item key-string
118    
119  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 130 
130    
131  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
132    
133    =item hash-string
134    
135    variable-length string, maximum 22 characters
136    
137  =back  =back
138    
139    The hash-string data type has a special meaning. The actual key passed into the loader will
140    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
141    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
142    digest. Therefore, it is presumed the keys will be unique. When the database is actually
143    in use, the hashed keys will be presented rather than the original values. For this reason,
144    they should not be used for entities where the key is meaningful.
145    
146  =head3 Global Tags  =head3 Global Tags
147    
148  The entire database definition must be inside a B<Database> tag. The display name of  The entire database definition must be inside a B<Database> tag. The display name of
# Line 310  Line 326 
326                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
327                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },
328                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },
329                     'hash-string' =>
330                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },
331                     'id-string' =>
332                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, dataGen => "SringGen(22)" },
333                   'key-string' =>                   'key-string' =>
334                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },
335                   'name-string' =>                   'name-string' =>
# Line 402  Line 422 
422      # Write the HTML heading stuff.      # Write the HTML heading stuff.
423      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
424      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
425        # Write the documentation.
426        print HTMLOUT $self->DisplayMetaData();
427        # Close the document.
428        print HTMLOUT "</body>\n</html>\n";
429        # Close the file.
430        close HTMLOUT;
431    }
432    
433    =head3 DisplayMetaData
434    
435    C<< my $html = $erdb->DisplayMetaData(); >>
436    
437    Return an HTML description of the database. This description can be used to help users create
438    the data to be loaded into the relations and form queries. The output is raw includable HTML
439    without any HEAD or BODY tags.
440    
441    =over 4
442    
443    =item filename
444    
445    The name of the output file.
446    
447    =back
448    
449    =cut
450    
451    sub DisplayMetaData {
452        # Get the parameters.
453        my ($self) = @_;
454        # Get the metadata and the title string.
455        my $metadata = $self->{_metaData};
456        # Get the title string.
457        my $title = $metadata->{Title};
458        # Get the entity and relationship lists.
459        my $entityList = $metadata->{Entities};
460        my $relationshipList = $metadata->{Relationships};
461        # Declare the return variable.
462        my $retVal = "";
463        # Open the output file.
464        Trace("Building MetaData table of contents.") if T(4);
465      # Here we do the table of contents. It starts as an unordered list of section names. Each      # Here we do the table of contents. It starts as an unordered list of section names. Each
466      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
467      print HTMLOUT "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";      $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
468      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
469      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
470          # Display this item.          # Display this item.
471          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
472      }      }
473      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
474      print HTMLOUT "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";      $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
475      # Loop through the Relationships.      # Loop through the Relationships.
476      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
477          # Display this item.          # Display this item.
478          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
479          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
480      }      }
481      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
482      print HTMLOUT "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";      $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
483      # Close off the table of contents itself.      # Close off the table of contents itself.
484      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
485      # Now we start with the actual data. Denote we're starting the entity section.      # Now we start with the actual data. Denote we're starting the entity section.
486      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
487      # Loop through the entities.      # Loop through the entities.
488      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
489          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
490          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
491          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
492          # Get the entity data.          # Get the entity data.
493          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
494          # If there's descriptive text, display it.          # If there's descriptive text, display it.
495          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
496              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
497          }          }
498          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
499          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
500          # Loop through the relationships.          # Loop through the relationships.
501          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
502              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 506 
506                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
507                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
508                  # Display the relationship data.                  # Display the relationship data.
509                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
510              }              }
511          }          }
512          # Close off the relationship list.          # Close off the relationship list.
513          print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
514          # Get the entity's relations.          # Get the entity's relations.
515          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
516          # Create a header for the relation subsection.          # Create a header for the relation subsection.
517          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
518          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
519          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
520              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
521              print HTMLOUT $htmlString;              $retVal .= $htmlString;
522          }          }
523      }      }
524      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
525      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
526      # Loop through the relationships.      # Loop through the relationships.
527      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
528          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 530 
530          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
531          # Create the relationship header.          # Create the relationship header.
532          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
533          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
534          # Get the entity names.          # Get the entity names.
535          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
536          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 540 
540          # since both sentences will say the same thing.          # since both sentences will say the same thing.
541          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
542          if ($arity eq "11") {          if ($arity eq "11") {
543              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
544          } else {          } else {
545              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
546              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
547                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
548              }              }
549          }          }
550          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
551          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
552          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
553              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
554          }          }
555          # Generate the relationship's relation table.          # Generate the relationship's relation table.
556          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
557          print HTMLOUT $htmlString;          $retVal .= $htmlString;
558      }      }
559      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
560      # Denote we're starting the join table.      # Denote we're starting the join table.
561      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
562      # Create a table header.      # Create a table header.
563      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
564      # Loop through the joins.      # Loop through the joins.
565      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
566      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 513  Line 573 
573          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
574          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
575          # Display them in a table row.          # Display them in a table row.
576          print HTMLOUT "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";          $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
577      }      }
578      # Close the table.      # Close the table.
579      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
580      # Close the document.      Trace("Built MetaData HTML.") if T(3);
581      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
582      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
583  }  }
584    
585  =head3 DumpMetaData  =head3 DumpMetaData
# Line 687  Line 745 
745      return $retVal;      return $retVal;
746  }  }
747    
748    =head3 DigestFields
749    
750    C<< $erdb->DigestFields($relName, $fieldList); >>
751    
752    Digest the strings in the field list that correspond to data type C<hash-string> in the
753    specified relation.
754    
755    =over 4
756    
757    =item relName
758    
759    Name of the relation to which the fields belong.
760    
761    =item fieldList
762    
763    List of field contents to be loaded into the relation.
764    
765    =back
766    
767    =cut
768    #: Return Type ;
769    sub DigestFields {
770        # Get the parameters.
771        my ($self, $relName, $fieldList) = @_;
772        # Get the relation definition.
773        my $relData = $self->_FindRelation($relName);
774        # Get the list of field descriptors.
775        my $fieldTypes = $relData->{Fields};
776        my $fieldCount = scalar @{$fieldTypes};
777        # Loop through the two lists.
778        for (my $i = 0; $i < $fieldCount; $i++) {
779            # Get the type of the current field.
780            my $fieldType = $fieldTypes->[$i]->{type};
781            # If it's a hash string, digest it in place.
782            if ($fieldType eq 'hash-string') {
783                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
784            }
785        }
786    }
787    
788    =head3 DigestKey
789    
790    C<< my $digested = $erdb->DigestKey($keyValue); >>
791    
792    Return the digested value of a symbolic key. The digested value can then be plugged into a
793    key-based search into a table with key-type hash-string.
794    
795    Currently the digesting process is independent of the database structure, but that may not
796    always be the case, so this is an instance method instead of a static method.
797    
798    =over 4
799    
800    =item keyValue
801    
802    Key value to digest.
803    
804    =item RETURN
805    
806    Digested value ofthe key.
807    
808    =back
809    
810    =cut
811    
812    sub DigestKey {
813        # Get the parameters.
814        my ($self, $keyValue) = @_;
815        # Compute the digest.
816        my $retVal = md5_base64($keyValue);
817        # Return the result.
818        return $retVal;
819    }
820    
821  =head3 CreateIndex  =head3 CreateIndex
822    
823  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 848  Line 979 
979    
980  =head3 Get  =head3 Get
981    
982  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
983    
984  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.
985  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 856  Line 987 
987  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
988  $genus.  $genus.
989    
990  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
991    
992  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
993  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
# Line 873  Line 1004 
1004  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
1005  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,
1006    
1007  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1008    
1009  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
1010  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.
1011  In particular, you can't specify any entity or relationship more than once, and if a  In particular, if a relationship is recursive, the path is determined by the order in which
1012  relationship is recursive, the path is determined by the order in which the entity  the entity and the relationship appear. For example, consider a recursive relationship
1013  and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
 which relates B<People> objects to other B<People> objects. If the join path is  
1014  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1015  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1016    
1017    If an entity or relationship is mentioned twice, the name for the second occurrence will
1018    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1019    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1020    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1021    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1022    
1023  =over 4  =over 4
1024    
1025  =item objectNames  =item objectNames
# Line 913  Line 1049 
1049  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1050  relation.  relation.
1051    
1052  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1053    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1054    a positive number. So, for example
1055    
1056    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1057    
1058  Parameter values to be substituted into the filter clause.  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1059    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1060    use
1061    
1062    C<< "LIMIT 10" >>
1063    
1064    =item params
1065    
1066    Reference to a list of parameter values to be substituted into the filter clause.
1067    
1068  =item RETURN  =item RETURN
1069    
# Line 927  Line 1075 
1075    
1076  sub Get {  sub Get {
1077      # Get the parameters.      # Get the parameters.
1078      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1079      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1080      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1081      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1082      #      # Create the query.
1083      my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1084      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1085                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1086      # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1087      if ($filterClause) {      # and mapped name for each object in the query.
1088          # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1089          # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1090          my $filterString = $filterClause;          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command.  
         my %fromNames = ();  
         for my $objectName (@sortedNames) {  
             $fromNames{$objectName} = 1;  
         }  
         # We are ready to begin. We loop through the object names, replacing each  
         # object name's field references by the corresponding SQL field reference.  
         # Along the way, if we find a secondary relation, we will need to add it  
         # to the FROM clause.  
         for my $objectName (@sortedNames) {  
             # Get the length of the object name plus 2. This is the value we add to the  
             # size of the field name to determine the size of the field reference as a  
             # whole.  
             my $nameLength = 2 + length $objectName;  
             # Get the object's field list.  
             my $fieldList = $self->GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                 # At this point, $1 contains the field name, and the current position  
                 # is set immediately after the final parenthesis. We pull out the name of  
                 # the field and the position and length of the field reference as a whole.  
                 my $fieldName = $1;  
                 my $len = $nameLength + length $fieldName;  
                 my $pos = pos($filterString) - $len;  
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
                 } else {  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$relationName}) {  
                         # Add the relation to the FROM clause.  
                         $command .= ", $relationName";  
                         # Create its join sub-clause.  
                         push @joinWhere, "$objectName.id = $relationName.id";  
                         # Denote we have it available for future fields.  
                         $fromNames{$relationName} = 1;  
                     }  
                     # Form an SQL field reference from the relation name and the field name.  
                     my $sqlReference = "$relationName." . _FixName($fieldName);  
                     # Put it into the filter string in place of the old value.  
                     substr($filterString, $pos, $len) = $sqlReference;  
                     # Reposition the search.  
                     pos $filterString = $pos + length $sqlReference;  
                 }  
             }  
         }  
         # The next step is to join the objects together. We only need to do this if there  
         # is more than one object in the object list. We start with the first object and  
         # run through the objects after it. Note also that we make a safety copy of the  
         # list before running through it.  
         my @objectList = @{$objectNames};  
         my $lastObject = shift @objectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisObject (@objectList) {  
             # Look for a join.  
             my $joinKey = "$lastObject/$thisObject";  
             if (!exists $joinTable->{$joinKey}) {  
                 # Here there's no join, so we throw an error.  
                 Confess("No join exists to connect from $lastObject to $thisObject.");  
             } else {  
                 # Get the join clause and add it to the WHERE list.  
                 push @joinWhere, $joinTable->{$joinKey};  
                 # Save this object as the last object for the next iteration.  
                 $lastObject = $thisObject;  
             }  
         }  
         # Now we need to handle the whole ORDER BY / LIMIT thing. The important part  
         # here is we want the filter clause to be empty if there's no WHERE filter.  
         # We'll put the ORDER BY / LIMIT clauses in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy  
         # operator so that we find the first occurrence of either verb.  
         if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {  
             # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = $2 . substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort or limit clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " $orderClause";  
         }  
1091      }      }
     Trace("SQL query: $command") if T(SQL => 4);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1092      # Return the statement object.      # Return the statement object.
1093      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1094      return $retVal;      return $retVal;
1095  }  }
1096    
1097    =head3 GetFlat
1098    
1099    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1100    
1101    This is a variation of L</GetAll> that asks for only a single field per record and
1102    returns a single flattened list.
1103    
1104    =over 4
1105    
1106    =item objectNames
1107    
1108    List containing the names of the entity and relationship objects to be retrieved.
1109    
1110    =item filterClause
1111    
1112    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1113    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1114    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1115    parameter list as additional parameters. The fields in a filter clause can come from primary
1116    entity relations, relationship relations, or secondary entity relations; however, all of the
1117    entities and relationships involved must be included in the list of object names.
1118    
1119    =item parameterList
1120    
1121    List of the parameters to be substituted in for the parameters marks in the filter clause.
1122    
1123    =item field
1124    
1125    Name of the field to be used to get the elements of the list returned.
1126    
1127    =item RETURN
1128    
1129    Returns a list of values.
1130    
1131    =back
1132    
1133    =cut
1134    #: Return Type @;
1135    sub GetFlat {
1136        # Get the parameters.
1137        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1138        # Construct the query.
1139        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1140        # Create the result list.
1141        my @retVal = ();
1142        # Loop through the records, adding the field values found to the result list.
1143        while (my $row = $query->Fetch()) {
1144            push @retVal, $row->Value($field);
1145        }
1146        # Return the list created.
1147        return @retVal;
1148    }
1149    
1150  =head3 Delete  =head3 Delete
1151    
1152  C<< my $stats = $erdb->Delete($entityName, $objectID); >>  C<< my $stats = $erdb->Delete($entityName, $objectID); >>
# Line 1221  Line 1317 
1317    
1318  =head3 GetList  =head3 GetList
1319    
1320  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1321    
1322  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
1323  specified filter clause.  specified filter clause.
# Line 1255  Line 1351 
1351  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1352  relation.  relation.
1353    
1354  =item param1, param2, ..., paramN  =item params
1355    
1356  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1357    
1358  =item RETURN  =item RETURN
1359    
# Line 1269  Line 1365 
1365  #: Return Type @%  #: Return Type @%
1366  sub GetList {  sub GetList {
1367      # Get the parameters.      # Get the parameters.
1368      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1369      # Declare the return variable.      # Declare the return variable.
1370      my @retVal = ();      my @retVal = ();
1371      # Perform the query.      # Perform the query.
1372      my $query = $self->Get($objectNames, $filterClause, @params);      my $query = $self->Get($objectNames, $filterClause, $params);
1373      # Loop through the results.      # Loop through the results.
1374      while (my $object = $query->Fetch) {      while (my $object = $query->Fetch) {
1375          push @retVal, $object;          push @retVal, $object;
# Line 1282  Line 1378 
1378      return @retVal;      return @retVal;
1379  }  }
1380    
1381    =head3 GetCount
1382    
1383    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1384    
1385    Return the number of rows found by a specified query. This method would
1386    normally be used to count the records in a single table. For example, in a
1387    genetics database
1388    
1389        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1390    
1391    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1392    to use it to return records based on a join. For example,
1393    
1394        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1395                                    ['homo %']);
1396    
1397    would return the number of features for genomes in the genus I<homo>. Note that
1398    only the rows from the first table are counted. If the above command were
1399    
1400        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1401                                    ['homo %']);
1402    
1403    it would return the number of genomes, not the number of genome/feature pairs.
1404    
1405    =over 4
1406    
1407    =item objectNames
1408    
1409    Reference to a list of the objects (entities and relationships) included in the
1410    query.
1411    
1412    =item filter
1413    
1414    A filter clause for restricting the query. The rules are the same as for the L</Get>
1415    method.
1416    
1417    =item params
1418    
1419    Reference to a list of the parameter values to be substituted for the parameter marks
1420    in the filter.
1421    
1422    =item RETURN
1423    
1424    Returns a count of the number of records in the first table that would satisfy
1425    the query.
1426    
1427    =back
1428    
1429    =cut
1430    
1431    sub GetCount {
1432        # Get the parameters.
1433        my ($self, $objectNames, $filter, $params) = @_;
1434        # Declare the return variable.
1435        my $retVal;
1436        # Find out if we're counting an entity or a relationship.
1437        my $countedField;
1438        if ($self->IsEntity($objectNames->[0])) {
1439            $countedField = "id";
1440        } else {
1441            # For a relationship we count the to-link because it's usually more
1442            # numerous. Note we're automatically converting to the SQL form
1443            # of the field name (to_link vs. to-link).
1444            $countedField = "to_link";
1445        }
1446        # Create the SQL command suffix to get the desired records.
1447        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1448                                                                                $filter);
1449        # Prefix it with text telling it we want a record count.
1450        my $firstObject = $mappedNameListRef->[0];
1451        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
1452        # Prepare and execute the command.
1453        my $sth = $self->_GetStatementHandle($command, $params);
1454        # Get the count value.
1455        ($retVal) = $sth->fetchrow_array();
1456        # Check for a problem.
1457        if (! defined($retVal)) {
1458            if ($sth->err) {
1459                # Here we had an SQL error.
1460                Confess("Error retrieving row count: " . $sth->errstr());
1461            } else {
1462                # Here we have no result.
1463                Confess("No result attempting to retrieve row count.");
1464            }
1465        }
1466        # Return the result.
1467        return $retVal;
1468    }
1469    
1470  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1471    
1472  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
# Line 1359  Line 1544 
1544      }      }
1545  }  }
1546    
1547    =head3 InsertValue
1548    
1549    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
1550    
1551    This method will insert a new value into the database. The value must be one
1552    associated with a secondary relation, since primary values cannot be inserted:
1553    they occur exactly once. Secondary values, on the other hand, can be missing
1554    or multiply-occurring.
1555    
1556    =over 4
1557    
1558    =item entityID
1559    
1560    ID of the object that is to receive the new value.
1561    
1562    =item fieldName
1563    
1564    Field name for the new value-- this includes the entity name, since
1565    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
1566    
1567    =item value
1568    
1569    New value to be put in the field.
1570    
1571    =back
1572    
1573    =cut
1574    
1575    sub InsertValue {
1576        # Get the parameters.
1577        my ($self, $entityID, $fieldName, $value) = @_;
1578        # Parse the entity name and the real field name.
1579        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
1580            my $entityName = $1;
1581            my $fieldTitle = $2;
1582            # Get its descriptor.
1583            if (!$self->IsEntity($entityName)) {
1584                Confess("$entityName is not a valid entity.");
1585            } else {
1586                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1587                # Find the relation containing this field.
1588                my $fieldHash = $entityData->{Fields};
1589                if (! exist $fieldHash->{$fieldTitle}) {
1590                    Confess("$fieldTitle not found in $entityName.");
1591                } else {
1592                    my $relation = $fieldHash->{$fieldTitle}->{relation};
1593                    if ($relation eq $entityName) {
1594                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
1595                    } else {
1596                        # Now we can create an INSERT statement.
1597                        my $dbh = $self->{_dbh};
1598                        my $fixedName = _FixName($fieldTitle);
1599                        my $statement = "INSERT INTO $relation ($fixedName) VALUES(?, ?)";
1600                        # Execute the command.
1601                        $dbh->SQL($statement, 0, $entityID, $value);
1602                    }
1603                }
1604            }
1605        } else {
1606            Confess("$fieldName is not a valid field name.");
1607        }
1608    }
1609    
1610  =head3 InsertObject  =head3 InsertObject
1611    
1612  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
# Line 1677  Line 1925 
1925      # Get the parameters.      # Get the parameters.
1926      my ($self, $entityType, $ID) = @_;      my ($self, $entityType, $ID) = @_;
1927      # Create a query.      # Create a query.
1928      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
1929      # Get the first (and only) object.      # Get the first (and only) object.
1930      my $retVal = $query->Fetch();      my $retVal = $query->Fetch();
1931      # Return the result.      # Return the result.
# Line 1790  Line 2038 
2038      # list is a scalar we convert it into a singleton list.      # list is a scalar we convert it into a singleton list.
2039      my @parmList = ();      my @parmList = ();
2040      if (ref $parameterList eq "ARRAY") {      if (ref $parameterList eq "ARRAY") {
2041            Trace("GetAll parm list is an array.") if T(4);
2042          @parmList = @{$parameterList};          @parmList = @{$parameterList};
2043      } else {      } else {
2044            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2045          push @parmList, $parameterList;          push @parmList, $parameterList;
2046      }      }
2047      # Insure the counter has a value.      # Insure the counter has a value.
# Line 1803  Line 2053 
2053          $filterClause .= " LIMIT $count";          $filterClause .= " LIMIT $count";
2054      }      }
2055      # Create the query.      # Create the query.
2056      my $query = $self->Get($objectNames, $filterClause, @parmList);      my $query = $self->Get($objectNames, $filterClause, \@parmList);
2057      # Set up a counter of the number of records read.      # Set up a counter of the number of records read.
2058      my $fetched = 0;      my $fetched = 0;
2059      # Loop through the records returned, extracting the fields. Note that if the      # Loop through the records returned, extracting the fields. Note that if the
# Line 1885  Line 2135 
2135      return $objectData->{Fields};      return $objectData->{Fields};
2136  }  }
2137    
2138    =head2 Data Mining Methods
2139    
2140  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
2141    
2142  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
# Line 1946  Line 2198 
2198      return @retVal;      return @retVal;
2199  }  }
2200    
2201    =head3 FindColumn
2202    
2203    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2204    
2205    Return the location a desired column in a data mining header line. The data
2206    mining header line is a tab-separated list of column names. The column
2207    identifier is either the numerical index of a column or the actual column
2208    name.
2209    
2210    =over 4
2211    
2212    =item headerLine
2213    
2214    The header line from a data mining command, which consists of a tab-separated
2215    list of column names.
2216    
2217    =item columnIdentifier
2218    
2219    Either the ordinal number of the desired column (1-based), or the name of the
2220    desired column.
2221    
2222    =item RETURN
2223    
2224    Returns the array index (0-based) of the desired column.
2225    
2226    =back
2227    
2228    =cut
2229    
2230    sub FindColumn {
2231        # Get the parameters.
2232        my ($headerLine, $columnIdentifier) = @_;
2233        # Declare the return variable.
2234        my $retVal;
2235        # Split the header line into column names.
2236        my @headers = ParseColumns($headerLine);
2237        # Determine whether we have a number or a name.
2238        if ($columnIdentifier =~ /^\d+$/) {
2239            # Here we have a number. Subtract 1 and validate the result.
2240            $retVal = $columnIdentifier - 1;
2241            if ($retVal < 0 || $retVal > $#headers) {
2242                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2243            }
2244        } else {
2245            # Here we have a name. We need to find it in the list.
2246            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2247                if ($headers[$i] eq $columnIdentifier) {
2248                    $retVal = $i;
2249                }
2250            }
2251            if (! defined($retVal)) {
2252                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2253            }
2254        }
2255        # Return the result.
2256        return $retVal;
2257    }
2258    
2259    =head3 ParseColumns
2260    
2261    C<< my @columns = ERDB::ParseColumns($line); >>
2262    
2263    Convert the specified data line to a list of columns.
2264    
2265    =over 4
2266    
2267    =item line
2268    
2269    A data mining input, consisting of a tab-separated list of columns terminated by a
2270    new-line.
2271    
2272    =item RETURN
2273    
2274    Returns a list consisting of the column values.
2275    
2276    =back
2277    
2278    =cut
2279    
2280    sub ParseColumns {
2281        # Get the parameters.
2282        my ($line) = @_;
2283        # Chop off the line-end.
2284        chomp $line;
2285        # Split it into a list.
2286        my @retVal = split(/\t/, $line);
2287        # Return the result.
2288        return @retVal;
2289    }
2290    
2291  =head2 Internal Utility Methods  =head2 Internal Utility Methods
2292    
2293    =head3 SetupSQL
2294    
2295    Process a list of object names and a filter clause so that they can be used to
2296    build an SQL statement. This method takes in a reference to a list of object names
2297    and a filter clause. It will return a corrected filter clause, a list of mapped
2298    names and the mapped name hash.
2299    
2300    This is an instance method.
2301    
2302    =over 4
2303    
2304    =item objectNames
2305    
2306    Reference to a list of the object names to be included in the query.
2307    
2308    =item filterClause
2309    
2310    A string containing the WHERE clause for the query (without the C<WHERE>) and also
2311    optionally the C<ORDER BY> and C<LIMIT> clauses.
2312    
2313    =item RETURN
2314    
2315    Returns a three-element list. The first element is the SQL statement suffix, beginning
2316    with the FROM clause. The second element is a reference to a list of the names to be
2317    used in retrieving the fields. The third element is a hash mapping the names to the
2318    objects they represent.
2319    
2320    =back
2321    
2322    =cut
2323    
2324    sub _SetupSQL {
2325        my ($self, $objectNames, $filterClause) = @_;
2326        # Adjust the list of object names to account for multiple occurrences of the
2327        # same object. We start with a hash table keyed on object name that will
2328        # return the object suffix. The first time an object is encountered it will
2329        # not be found in the hash. The next time the hash will map the object name
2330        # to 2, then 3, and so forth.
2331        my %objectHash = ();
2332        # This list will contain the object names as they are to appear in the
2333        # FROM list.
2334        my @fromList = ();
2335        # This list contains the suffixed object name for each object. It is exactly
2336        # parallel to the list in the $objectNames parameter.
2337        my @mappedNameList = ();
2338        # Finally, this hash translates from a mapped name to its original object name.
2339        my %mappedNameHash = ();
2340        # Now we create the lists. Note that for every single name we push something into
2341        # @fromList and @mappedNameList. This insures that those two arrays are exactly
2342        # parallel to $objectNames.
2343        for my $objectName (@{$objectNames}) {
2344            # Get the next suffix for this object.
2345            my $suffix = $objectHash{$objectName};
2346            if (! $suffix) {
2347                # Here we are seeing the object for the first time. The object name
2348                # is used as is.
2349                push @mappedNameList, $objectName;
2350                push @fromList, $objectName;
2351                $mappedNameHash{$objectName} = $objectName;
2352                # Denote the next suffix will be 2.
2353                $objectHash{$objectName} = 2;
2354            } else {
2355                # Here we've seen the object before. We construct a new name using
2356                # the suffix from the hash and update the hash.
2357                my $mappedName = "$objectName$suffix";
2358                $objectHash{$objectName} = $suffix + 1;
2359                # The FROM list has the object name followed by the mapped name. This
2360                # tells SQL it's still the same table, but we're using a different name
2361                # for it to avoid confusion.
2362                push @fromList, "$objectName $mappedName";
2363                # The mapped-name list contains the real mapped name.
2364                push @mappedNameList, $mappedName;
2365                # Finally, enable us to get back from the mapped name to the object name.
2366                $mappedNameHash{$mappedName} = $objectName;
2367            }
2368        }
2369        # Begin the SELECT suffix. It starts with
2370        #
2371        # FROM name1, name2, ... nameN
2372        #
2373        my $suffix = "FROM " . join(', ', @fromList);
2374        # Check for a filter clause.
2375        if ($filterClause) {
2376            # Here we have one, so we convert its field names and add it to the query. First,
2377            # We create a copy of the filter string we can work with.
2378            my $filterString = $filterClause;
2379            # Next, we sort the object names by length. This helps protect us from finding
2380            # object names inside other object names when we're doing our search and replace.
2381            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
2382            # We will also keep a list of conditions to add to the WHERE clause in order to link
2383            # entities and relationships as well as primary relations to secondary ones.
2384            my @joinWhere = ();
2385            # The final preparatory step is to create a hash table of relation names. The
2386            # table begins with the relation names already in the SELECT command. We may
2387            # need to add relations later if there is filtering on a field in a secondary
2388            # relation. The secondary relations are the ones that contain multiply-
2389            # occurring or optional fields.
2390            my %fromNames = map { $_ => 1 } @sortedNames;
2391            # We are ready to begin. We loop through the object names, replacing each
2392            # object name's field references by the corresponding SQL field reference.
2393            # Along the way, if we find a secondary relation, we will need to add it
2394            # to the FROM clause.
2395            for my $mappedName (@sortedNames) {
2396                # Get the length of the object name plus 2. This is the value we add to the
2397                # size of the field name to determine the size of the field reference as a
2398                # whole.
2399                my $nameLength = 2 + length $mappedName;
2400                # Get the real object name for this mapped name.
2401                my $objectName = $mappedNameHash{$mappedName};
2402                Trace("Processing $mappedName for object $objectName.") if T(4);
2403                # Get the object's field list.
2404                my $fieldList = $self->GetFieldTable($objectName);
2405                # Find the field references for this object.
2406                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
2407                    # At this point, $1 contains the field name, and the current position
2408                    # is set immediately after the final parenthesis. We pull out the name of
2409                    # the field and the position and length of the field reference as a whole.
2410                    my $fieldName = $1;
2411                    my $len = $nameLength + length $fieldName;
2412                    my $pos = pos($filterString) - $len;
2413                    # Insure the field exists.
2414                    if (!exists $fieldList->{$fieldName}) {
2415                        Confess("Field $fieldName not found for object $objectName.");
2416                    } else {
2417                        Trace("Processing $fieldName at position $pos.") if T(4);
2418                        # Get the field's relation.
2419                        my $relationName = $fieldList->{$fieldName}->{relation};
2420                        # Now we have a secondary relation. We need to insure it matches the
2421                        # mapped name of the primary relation. First we peel off the suffix
2422                        # from the mapped name.
2423                        my $mappingSuffix = substr $mappedName, length($objectName);
2424                        # Put the mapping suffix onto the relation name to get the
2425                        # mapped relation name.
2426                        my $mappedRelationName = "$relationName$mappingSuffix";
2427                        # Insure the relation is in the FROM clause.
2428                        if (!exists $fromNames{$mappedRelationName}) {
2429                            # Add the relation to the FROM clause.
2430                            if ($mappedRelationName eq $relationName) {
2431                                # The name is un-mapped, so we add it without
2432                                # any frills.
2433                                $suffix .= ", $relationName";
2434                                push @joinWhere, "$objectName.id = $relationName.id";
2435                            } else {
2436                                # Here we have a mapping situation.
2437                                $suffix .= ", $relationName $mappedRelationName";
2438                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
2439                            }
2440                            # Denote we have this relation available for future fields.
2441                            $fromNames{$mappedRelationName} = 1;
2442                        }
2443                        # Form an SQL field reference from the relation name and the field name.
2444                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
2445                        # Put it into the filter string in place of the old value.
2446                        substr($filterString, $pos, $len) = $sqlReference;
2447                        # Reposition the search.
2448                        pos $filterString = $pos + length $sqlReference;
2449                    }
2450                }
2451            }
2452            # The next step is to join the objects together. We only need to do this if there
2453            # is more than one object in the object list. We start with the first object and
2454            # run through the objects after it. Note also that we make a safety copy of the
2455            # list before running through it.
2456            my @mappedObjectList = @mappedNameList;
2457            my $lastMappedObject = shift @mappedObjectList;
2458            # Get the join table.
2459            my $joinTable = $self->{_metaData}->{Joins};
2460            # Loop through the object list.
2461            for my $thisMappedObject (@mappedObjectList) {
2462                # Look for a join using the real object names.
2463                my $lastObject = $mappedNameHash{$lastMappedObject};
2464                my $thisObject = $mappedNameHash{$thisMappedObject};
2465                my $joinKey = "$lastObject/$thisObject";
2466                if (!exists $joinTable->{$joinKey}) {
2467                    # Here there's no join, so we throw an error.
2468                    Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
2469                } else {
2470                    # Get the join clause.
2471                    my $unMappedJoin = $joinTable->{$joinKey};
2472                    # Fix the names.
2473                    $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
2474                    $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
2475                    push @joinWhere, $unMappedJoin;
2476                    # Save this object as the last object for the next iteration.
2477                    $lastMappedObject = $thisMappedObject;
2478                }
2479            }
2480            # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
2481            # here is we want the filter clause to be empty if there's no WHERE filter.
2482            # We'll put the ORDER BY / LIMIT clauses in the following variable.
2483            my $orderClause = "";
2484            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
2485            # operator so that we find the first occurrence of either verb.
2486            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
2487                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
2488                my $pos = pos $filterString;
2489                $orderClause = $2 . substr($filterString, $pos);
2490                $filterString = $1;
2491            }
2492            # Add the filter and the join clauses (if any) to the SELECT command.
2493            if ($filterString) {
2494                Trace("Filter string is \"$filterString\".") if T(4);
2495                push @joinWhere, "($filterString)";
2496            }
2497            if (@joinWhere) {
2498                $suffix .= " WHERE " . join(' AND ', @joinWhere);
2499            }
2500            # Add the sort or limit clause (if any) to the SELECT command.
2501            if ($orderClause) {
2502                $suffix .= " $orderClause";
2503            }
2504        }
2505        # Return the suffix, the mapped name list, and the mapped name hash.
2506        return ($suffix, \@mappedNameList, \%mappedNameHash);
2507    }
2508    
2509    =head3 GetStatementHandle
2510    
2511    This method will prepare and execute an SQL query, returning the statement handle.
2512    The main reason for doing this here is so that everybody who does SQL queries gets
2513    the benefit of tracing.
2514    
2515    This is an instance method.
2516    
2517    =over 4
2518    
2519    =item command
2520    
2521    Command to prepare and execute.
2522    
2523    =item params
2524    
2525    Reference to a list of the values to be substituted in for the parameter marks.
2526    
2527    =item RETURN
2528    
2529    Returns a prepared and executed statement handle from which the caller can extract
2530    results.
2531    
2532    =back
2533    
2534    =cut
2535    
2536    sub _GetStatementHandle {
2537        # Get the parameters.
2538        my ($self, $command, $params) = @_;
2539        # Trace the query.
2540        Trace("SQL query: $command") if T(SQL => 3);
2541        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
2542        # Get the database handle.
2543        my $dbh = $self->{_dbh};
2544        # Prepare the command.
2545        my $sth = $dbh->prepare_command($command);
2546        # Execute it with the parameters bound in.
2547        $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
2548        # Return the statement handle.
2549        return $sth;
2550    }
2551    
2552  =head3 GetLoadStats  =head3 GetLoadStats
2553    
2554  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
# Line 2505  Line 3106 
3106              # Determine if this relationship has our entity in one of its link fields.              # Determine if this relationship has our entity in one of its link fields.
3107              my $fromEntity = $relationship->{from};              my $fromEntity = $relationship->{from};
3108              my $toEntity = $relationship->{to};              my $toEntity = $relationship->{to};
3109              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
3110              if ($fromEntity eq $entityName) {              if ($fromEntity eq $entityName) {
3111                  if ($toEntity eq $entityName) {                  if ($toEntity eq $entityName) {
3112                      # Here the relationship is recursive.                      # Here the relationship is recursive.
# Line 2594  Line 3195 
3195      return $metadata;      return $metadata;
3196  }  }
3197    
3198    =head3 SortNeeded
3199    
3200    C<< my $flag = $erdb->SortNeeded($relationName); >>
3201    
3202    Return TRUE if the specified relation should be sorted during loading to remove duplicate keys,
3203    else FALSE.
3204    
3205    =over 4
3206    
3207    =item relationName
3208    
3209    Name of the relation to be examined.
3210    
3211    =item RETURN
3212    
3213    Returns TRUE if the relation needs a sort, else FALSE.
3214    
3215    =back
3216    
3217    =cut
3218    #: Return Type $;
3219    sub SortNeeded {
3220        # Get the parameters.
3221        my ($self, $relationName) = @_;
3222        # Declare the return variable.
3223        my $retVal = 0;
3224        # Find out if the relation is a primary entity relation.
3225        my $entityTable = $self->{_metaData}->{Entities};
3226        if (exists $entityTable->{$relationName}) {
3227            my $keyType = $entityTable->{$relationName}->{keyType};
3228            Trace("Relation $relationName found in entity table with key type $keyType.") if T(3);
3229            # If the key is not a hash string, we must do the sort.
3230            if ($keyType ne 'hash-string') {
3231                $retVal = 1;
3232            }
3233        }
3234        # Return the result.
3235        return $retVal;
3236    }
3237    
3238  =head3 CreateRelationshipIndex  =head3 CreateRelationshipIndex
3239    
3240  Create an index for a relationship's relation.  Create an index for a relationship's relation.
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