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revision 1.44, Sat May 27 02:02:28 2006 UTC revision 1.45, Tue Jun 6 05:05:15 2006 UTC
# Line 422  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 466  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 490  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 500  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 533  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 908  Line 946 
946    
947  =head3 Get  =head3 Get
948    
949  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
950    
951  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.
952  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 916  Line 954 
954  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
955  $genus.  $genus.
956    
957  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
958    
959  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
960  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 933  Line 971 
971  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
972  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,
973    
974  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
975    
976  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
977  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 990  Line 1028 
1028    
1029  C<< "LIMIT 10" >>  C<< "LIMIT 10" >>
1030    
1031  =item param1, param2, ..., paramN  =item params
1032    
1033  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1034    
1035  =item RETURN  =item RETURN
1036    
# Line 1004  Line 1042 
1042    
1043  sub Get {  sub Get {
1044      # Get the parameters.      # Get the parameters.
1045      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1046      # Adjust the list of object names to account for multiple occurrences of the      # Process the SQL stuff.
1047      # same object. We start with a hash table keyed on object name that will      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1048      # return the object suffix. The first time an object is encountered it will          $self->_SetupSQL($objectNames, $filterClause);
1049      # not be found in the hash. The next time the hash will map the object name      # Create the query.
1050      # to 2, then 3, and so forth.      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1051      my %objectHash = ();          ".* $suffix";
1052      # This list will contain the object names as they are to appear in the      my $sth = $self->_GetStatementHandle($command, $params);
     # FROM list.  
     my @fromList = ();  
     # This list contains the suffixed object name for each object. It is exactly  
     # parallel to the list in the $objectNames parameter.  
     my @mappedNameList = ();  
     # Finally, this hash translates from a mapped name to its original object name.  
     my %mappedNameHash = ();  
     # Now we create the lists. Note that for every single name we push something into  
     # @fromList and @mappedNameList. This insures that those two arrays are exactly  
     # parallel to $objectNames.  
     for my $objectName (@{$objectNames}) {  
         # Get the next suffix for this object.  
         my $suffix = $objectHash{$objectName};  
         if (! $suffix) {  
             # Here we are seeing the object for the first time. The object name  
             # is used as is.  
             push @mappedNameList, $objectName;  
             push @fromList, $objectName;  
             $mappedNameHash{$objectName} = $objectName;  
             # Denote the next suffix will be 2.  
             $objectHash{$objectName} = 2;  
         } else {  
             # Here we've seen the object before. We construct a new name using  
             # the suffix from the hash and update the hash.  
             my $mappedName = "$objectName$suffix";  
             $objectHash{$objectName} = $suffix + 1;  
             # The FROM list has the object name followed by the mapped name. This  
             # tells SQL it's still the same table, but we're using a different name  
             # for it to avoid confusion.  
             push @fromList, "$objectName $mappedName";  
             # The mapped-name list contains the real mapped name.  
             push @mappedNameList, $mappedName;  
             # Finally, enable us to get back from the mapped name to the object name.  
             $mappedNameHash{$mappedName} = $objectName;  
         }  
     }  
     # Construct the SELECT statement. The general pattern is  
     #  
     # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN  
     #  
     my $dbh = $self->{_dbh};  
     my $command = "SELECT DISTINCT " . join('.*, ', @mappedNameList) . ".* FROM " .  
                 join(', ', @fromList);  
     # Check for a filter clause.  
     if ($filterClause) {  
         # Here we have one, so we convert its field names and add it to the query. First,  
         # We create a copy of the filter string we can work with.  
         my $filterString = $filterClause;  
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @mappedNameList;  
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command. We may  
         # need to add relations later if there is filtering on a field in a secondary  
         # relation. The secondary relations are the ones that contain multiply-  
         # occurring or optional fields.  
         my %fromNames = map { $_ => 1 } @sortedNames;  
         # 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 $mappedName (@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 $mappedName;  
             # Get the real object name for this mapped name.  
             my $objectName = $mappedNameHash{$mappedName};  
             Trace("Processing $mappedName for object $objectName.") if T(4);  
             # Get the object's field list.  
             my $fieldList = $self->GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$mappedName\(([^)]*)\)/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 {  
                     Trace("Processing $fieldName at position $pos.") if T(4);  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Now we have a secondary relation. We need to insure it matches the  
                     # mapped name of the primary relation. First we peel off the suffix  
                     # from the mapped name.  
                     my $mappingSuffix = substr $mappedName, length($objectName);  
                     # Put the mapping suffix onto the relation name to get the  
                     # mapped relation name.  
                     my $mappedRelationName = "$relationName$mappingSuffix";  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$mappedRelationName}) {  
                         # Add the relation to the FROM clause.  
                         if ($mappedRelationName eq $relationName) {  
                             # The name is un-mapped, so we add it without  
                             # any frills.  
                             $command .= ", $relationName";  
                             push @joinWhere, "$objectName.id = $relationName.id";  
                         } else {  
                             # Here we have a mapping situation.  
                             $command .= ", $relationName $mappedRelationName";  
                             push @joinWhere, "$mappedRelationName.id = $mappedName.id";  
                         }  
                         # Denote we have this relation available for future fields.  
                         $fromNames{$mappedRelationName} = 1;  
                     }  
                     # Form an SQL field reference from the relation name and the field name.  
                     my $sqlReference = "$mappedRelationName." . _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 @mappedObjectList = @mappedNameList;  
         my $lastMappedObject = shift @mappedObjectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisMappedObject (@mappedObjectList) {  
             # Look for a join using the real object names.  
             my $lastObject = $mappedNameHash{$lastMappedObject};  
             my $thisObject = $mappedNameHash{$thisMappedObject};  
             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 $lastMappedObject to $thisMappedObject.");  
             } else {  
                 # Get the join clause.  
                 my $unMappedJoin = $joinTable->{$joinKey};  
                 # Fix the names.  
                 $unMappedJoin =~ s/$lastObject/$lastMappedObject/;  
                 $unMappedJoin =~ s/$thisObject/$thisMappedObject/;  
                 push @joinWhere, $unMappedJoin;  
                 # Save this object as the last object for the next iteration.  
                 $lastMappedObject = $thisMappedObject;  
             }  
         }  
         # 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) {  
             Trace("Filter string is \"$filterString\".") if T(4);  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort or limit clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " $orderClause";  
         }  
     }  
     Trace("SQL query: $command") if T(SQL => 3);  
     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());  
1053      # 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
1054      # and mapped name for each object in the query.      # and mapped name for each object in the query.
1055      my @relationMap = ();      my @relationMap = ();
1056      for my $mappedName (@mappedNameList) {      for my $mappedName (@{$mappedNameListRef}) {
1057          push @relationMap, [$mappedName, $mappedNameHash{$mappedName}];          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1058      }      }
1059      # Return the statement object.      # Return the statement object.
1060      my $retVal = DBQuery::_new($self, $sth, \@relationMap);      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1061      return $retVal;      return $retVal;
1062  }  }
1063    
1064    =head3 GetFlat
1065    
1066    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1067    
1068    This is a variation of L</GetAll> that asks for only a single field per record and
1069    returns a single flattened list.
1070    
1071    =over 4
1072    
1073    =item objectNames
1074    
1075    List containing the names of the entity and relationship objects to be retrieved.
1076    
1077    =item filterClause
1078    
1079    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1080    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1081    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1082    parameter list as additional parameters. The fields in a filter clause can come from primary
1083    entity relations, relationship relations, or secondary entity relations; however, all of the
1084    entities and relationships involved must be included in the list of object names.
1085    
1086    =item parameterList
1087    
1088    List of the parameters to be substituted in for the parameters marks in the filter clause.
1089    
1090    =item field
1091    
1092    Name of the field to be used to get the elements of the list returned.
1093    
1094    =item RETURN
1095    
1096    Returns a list of values.
1097    
1098    =back
1099    
1100    =cut
1101    #: Return Type @;
1102    sub GetFlat {
1103        # Get the parameters.
1104        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1105        # Construct the query.
1106        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1107        # Create the result list.
1108        my @retVal = ();
1109        # Loop through the records, adding the field values found to the result list.
1110        while (my $row = $query->Fetch()) {
1111            push @retVal, $row->Value($field);
1112        }
1113        # Return the list created.
1114        return @retVal;
1115    }
1116    
1117  =head3 Delete  =head3 Delete
1118    
1119  C<< my $stats = $erdb->Delete($entityName, $objectID); >>  C<< my $stats = $erdb->Delete($entityName, $objectID); >>
# Line 1372  Line 1284 
1284    
1285  =head3 GetList  =head3 GetList
1286    
1287  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1288    
1289  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
1290  specified filter clause.  specified filter clause.
# Line 1406  Line 1318 
1318  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1319  relation.  relation.
1320    
1321  =item param1, param2, ..., paramN  =item params
1322    
1323  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1324    
1325  =item RETURN  =item RETURN
1326    
# Line 1420  Line 1332 
1332  #: Return Type @%  #: Return Type @%
1333  sub GetList {  sub GetList {
1334      # Get the parameters.      # Get the parameters.
1335      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1336      # Declare the return variable.      # Declare the return variable.
1337      my @retVal = ();      my @retVal = ();
1338      # Perform the query.      # Perform the query.
1339      my $query = $self->Get($objectNames, $filterClause, @params);      my $query = $self->Get($objectNames, $filterClause, $params);
1340      # Loop through the results.      # Loop through the results.
1341      while (my $object = $query->Fetch) {      while (my $object = $query->Fetch) {
1342          push @retVal, $object;          push @retVal, $object;
# Line 1433  Line 1345 
1345      return @retVal;      return @retVal;
1346  }  }
1347    
1348    =head3 GetCount
1349    
1350    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1351    
1352    Return the number of rows found by a specified query. This method would
1353    normally be used to count the records in a single table. For example, in a
1354    genetics database
1355    
1356        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1357    
1358    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1359    to use it to return records based on a join. For example,
1360    
1361        my $count = $erdb->GetCount(['Feature', 'Genome'], 'Genome(genus-species) LIKE ?',
1362                                    ['homo %']);
1363    
1364    would return the number of features for genomes in the genus I<homo>. Note that
1365    only the rows from the first table are counted. If the above command were
1366    
1367        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1368                                    ['homo %']);
1369    
1370    it would return the number of genomes, not the number of genome/feature pairs.
1371    
1372    =over 4
1373    
1374    =item objectNames
1375    
1376    Reference to a list of the objects (entities and relationships) included in the
1377    query.
1378    
1379    =item filter
1380    
1381    A filter clause for restricting the query. The rules are the same as for the L</Get>
1382    method.
1383    
1384    =item params
1385    
1386    Reference to a list of the parameter values to be substituted for the parameter marks
1387    in the filter.
1388    
1389    =item RETURN
1390    
1391    Returns a count of the number of records in the first table that would satisfy
1392    the query.
1393    
1394    =back
1395    
1396    =cut
1397    
1398    sub GetCount {
1399        # Get the parameters.
1400        my ($self, $objectNames, $filter, $params) = @_;
1401        # Declare the return variable.
1402        my $retVal;
1403        # Create the SQL command suffix to get the desired records.
1404        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1405                                                                                $filter);
1406        # Prefix it with text telling it we want a record count.
1407        my $firstObject = $mappedNameListRef->[0];
1408        my $command = "SELECT COUNT($firstObject.id) $suffix";
1409        # Prepare and execute the command.
1410        my $sth = $self->_GetStatementHandle($command, $params);
1411        # Get the count value.
1412        ($retVal) = $sth->fetchrow_array();
1413        # Check for a problem.
1414        if (! defined($retVal)) {
1415            if ($sth->err) {
1416                # Here we had an SQL error.
1417                Confess("Error retrieving row count: " . $sth->errstr());
1418            } else {
1419                # Here we have no result.
1420                Confess("No result attempting to retrieve row count.");
1421            }
1422        }
1423        # Return the result.
1424        return $retVal;
1425    }
1426    
1427  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1428    
1429  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
# Line 1828  Line 1819 
1819      # Get the parameters.      # Get the parameters.
1820      my ($self, $entityType, $ID) = @_;      my ($self, $entityType, $ID) = @_;
1821      # Create a query.      # Create a query.
1822      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
1823      # Get the first (and only) object.      # Get the first (and only) object.
1824      my $retVal = $query->Fetch();      my $retVal = $query->Fetch();
1825      # Return the result.      # Return the result.
# Line 1941  Line 1932 
1932      # list is a scalar we convert it into a singleton list.      # list is a scalar we convert it into a singleton list.
1933      my @parmList = ();      my @parmList = ();
1934      if (ref $parameterList eq "ARRAY") {      if (ref $parameterList eq "ARRAY") {
1935            Trace("GetAll parm list is an array.") if T(4);
1936          @parmList = @{$parameterList};          @parmList = @{$parameterList};
1937      } else {      } else {
1938            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
1939          push @parmList, $parameterList;          push @parmList, $parameterList;
1940      }      }
1941      # Insure the counter has a value.      # Insure the counter has a value.
# Line 1954  Line 1947 
1947          $filterClause .= " LIMIT $count";          $filterClause .= " LIMIT $count";
1948      }      }
1949      # Create the query.      # Create the query.
1950      my $query = $self->Get($objectNames, $filterClause, @parmList);      my $query = $self->Get($objectNames, $filterClause, \@parmList);
1951      # Set up a counter of the number of records read.      # Set up a counter of the number of records read.
1952      my $fetched = 0;      my $fetched = 0;
1953      # Loop through the records returned, extracting the fields. Note that if the      # Loop through the records returned, extracting the fields. Note that if the
# Line 2099  Line 2092 
2092    
2093  =head2 Internal Utility Methods  =head2 Internal Utility Methods
2094    
2095    =head3 SetupSQL
2096    
2097    Process a list of object names and a filter clause so that they can be used to
2098    build an SQL statement. This method takes in a reference to a list of object names
2099    and a filter clause. It will return a corrected filter clause, a list of mapped
2100    names and the mapped name hash.
2101    
2102    This is an instance method.
2103    
2104    =over 4
2105    
2106    =item objectNames
2107    
2108    Reference to a list of the object names to be included in the query.
2109    
2110    =item filterClause
2111    
2112    A string containing the WHERE clause for the query (without the C<WHERE>) and also
2113    optionally the C<ORDER BY> and C<LIMIT> clauses.
2114    
2115    =item RETURN
2116    
2117    Returns a three-element list. The first element is the SQL statement suffix, beginning
2118    with the FROM clause. The second element is a reference to a list of the names to be
2119    used in retrieving the fields. The third element is a hash mapping the names to the
2120    objects they represent.
2121    
2122    =back
2123    
2124    =cut
2125    
2126    sub _SetupSQL {
2127        my ($self, $objectNames, $filterClause) = @_;
2128        # Adjust the list of object names to account for multiple occurrences of the
2129        # same object. We start with a hash table keyed on object name that will
2130        # return the object suffix. The first time an object is encountered it will
2131        # not be found in the hash. The next time the hash will map the object name
2132        # to 2, then 3, and so forth.
2133        my %objectHash = ();
2134        # This list will contain the object names as they are to appear in the
2135        # FROM list.
2136        my @fromList = ();
2137        # This list contains the suffixed object name for each object. It is exactly
2138        # parallel to the list in the $objectNames parameter.
2139        my @mappedNameList = ();
2140        # Finally, this hash translates from a mapped name to its original object name.
2141        my %mappedNameHash = ();
2142        # Now we create the lists. Note that for every single name we push something into
2143        # @fromList and @mappedNameList. This insures that those two arrays are exactly
2144        # parallel to $objectNames.
2145        for my $objectName (@{$objectNames}) {
2146            # Get the next suffix for this object.
2147            my $suffix = $objectHash{$objectName};
2148            if (! $suffix) {
2149                # Here we are seeing the object for the first time. The object name
2150                # is used as is.
2151                push @mappedNameList, $objectName;
2152                push @fromList, $objectName;
2153                $mappedNameHash{$objectName} = $objectName;
2154                # Denote the next suffix will be 2.
2155                $objectHash{$objectName} = 2;
2156            } else {
2157                # Here we've seen the object before. We construct a new name using
2158                # the suffix from the hash and update the hash.
2159                my $mappedName = "$objectName$suffix";
2160                $objectHash{$objectName} = $suffix + 1;
2161                # The FROM list has the object name followed by the mapped name. This
2162                # tells SQL it's still the same table, but we're using a different name
2163                # for it to avoid confusion.
2164                push @fromList, "$objectName $mappedName";
2165                # The mapped-name list contains the real mapped name.
2166                push @mappedNameList, $mappedName;
2167                # Finally, enable us to get back from the mapped name to the object name.
2168                $mappedNameHash{$mappedName} = $objectName;
2169            }
2170        }
2171        # Begin the SELECT suffix. It starts with
2172        #
2173        # FROM name1, name2, ... nameN
2174        #
2175        my $suffix = "FROM " . join(', ', @fromList);
2176        # Check for a filter clause.
2177        if ($filterClause) {
2178            # Here we have one, so we convert its field names and add it to the query. First,
2179            # We create a copy of the filter string we can work with.
2180            my $filterString = $filterClause;
2181            # Next, we sort the object names by length. This helps protect us from finding
2182            # object names inside other object names when we're doing our search and replace.
2183            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
2184            # We will also keep a list of conditions to add to the WHERE clause in order to link
2185            # entities and relationships as well as primary relations to secondary ones.
2186            my @joinWhere = ();
2187            # The final preparatory step is to create a hash table of relation names. The
2188            # table begins with the relation names already in the SELECT command. We may
2189            # need to add relations later if there is filtering on a field in a secondary
2190            # relation. The secondary relations are the ones that contain multiply-
2191            # occurring or optional fields.
2192            my %fromNames = map { $_ => 1 } @sortedNames;
2193            # We are ready to begin. We loop through the object names, replacing each
2194            # object name's field references by the corresponding SQL field reference.
2195            # Along the way, if we find a secondary relation, we will need to add it
2196            # to the FROM clause.
2197            for my $mappedName (@sortedNames) {
2198                # Get the length of the object name plus 2. This is the value we add to the
2199                # size of the field name to determine the size of the field reference as a
2200                # whole.
2201                my $nameLength = 2 + length $mappedName;
2202                # Get the real object name for this mapped name.
2203                my $objectName = $mappedNameHash{$mappedName};
2204                Trace("Processing $mappedName for object $objectName.") if T(4);
2205                # Get the object's field list.
2206                my $fieldList = $self->GetFieldTable($objectName);
2207                # Find the field references for this object.
2208                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
2209                    # At this point, $1 contains the field name, and the current position
2210                    # is set immediately after the final parenthesis. We pull out the name of
2211                    # the field and the position and length of the field reference as a whole.
2212                    my $fieldName = $1;
2213                    my $len = $nameLength + length $fieldName;
2214                    my $pos = pos($filterString) - $len;
2215                    # Insure the field exists.
2216                    if (!exists $fieldList->{$fieldName}) {
2217                        Confess("Field $fieldName not found for object $objectName.");
2218                    } else {
2219                        Trace("Processing $fieldName at position $pos.") if T(4);
2220                        # Get the field's relation.
2221                        my $relationName = $fieldList->{$fieldName}->{relation};
2222                        # Now we have a secondary relation. We need to insure it matches the
2223                        # mapped name of the primary relation. First we peel off the suffix
2224                        # from the mapped name.
2225                        my $mappingSuffix = substr $mappedName, length($objectName);
2226                        # Put the mapping suffix onto the relation name to get the
2227                        # mapped relation name.
2228                        my $mappedRelationName = "$relationName$mappingSuffix";
2229                        # Insure the relation is in the FROM clause.
2230                        if (!exists $fromNames{$mappedRelationName}) {
2231                            # Add the relation to the FROM clause.
2232                            if ($mappedRelationName eq $relationName) {
2233                                # The name is un-mapped, so we add it without
2234                                # any frills.
2235                                $suffix .= ", $relationName";
2236                                push @joinWhere, "$objectName.id = $relationName.id";
2237                            } else {
2238                                # Here we have a mapping situation.
2239                                $suffix .= ", $relationName $mappedRelationName";
2240                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
2241                            }
2242                            # Denote we have this relation available for future fields.
2243                            $fromNames{$mappedRelationName} = 1;
2244                        }
2245                        # Form an SQL field reference from the relation name and the field name.
2246                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
2247                        # Put it into the filter string in place of the old value.
2248                        substr($filterString, $pos, $len) = $sqlReference;
2249                        # Reposition the search.
2250                        pos $filterString = $pos + length $sqlReference;
2251                    }
2252                }
2253            }
2254            # The next step is to join the objects together. We only need to do this if there
2255            # is more than one object in the object list. We start with the first object and
2256            # run through the objects after it. Note also that we make a safety copy of the
2257            # list before running through it.
2258            my @mappedObjectList = @mappedNameList;
2259            my $lastMappedObject = shift @mappedObjectList;
2260            # Get the join table.
2261            my $joinTable = $self->{_metaData}->{Joins};
2262            # Loop through the object list.
2263            for my $thisMappedObject (@mappedObjectList) {
2264                # Look for a join using the real object names.
2265                my $lastObject = $mappedNameHash{$lastMappedObject};
2266                my $thisObject = $mappedNameHash{$thisMappedObject};
2267                my $joinKey = "$lastObject/$thisObject";
2268                if (!exists $joinTable->{$joinKey}) {
2269                    # Here there's no join, so we throw an error.
2270                    Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
2271                } else {
2272                    # Get the join clause.
2273                    my $unMappedJoin = $joinTable->{$joinKey};
2274                    # Fix the names.
2275                    $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
2276                    $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
2277                    push @joinWhere, $unMappedJoin;
2278                    # Save this object as the last object for the next iteration.
2279                    $lastMappedObject = $thisMappedObject;
2280                }
2281            }
2282            # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
2283            # here is we want the filter clause to be empty if there's no WHERE filter.
2284            # We'll put the ORDER BY / LIMIT clauses in the following variable.
2285            my $orderClause = "";
2286            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
2287            # operator so that we find the first occurrence of either verb.
2288            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
2289                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
2290                my $pos = pos $filterString;
2291                $orderClause = $2 . substr($filterString, $pos);
2292                $filterString = $1;
2293            }
2294            # Add the filter and the join clauses (if any) to the SELECT command.
2295            if ($filterString) {
2296                Trace("Filter string is \"$filterString\".") if T(4);
2297                push @joinWhere, "($filterString)";
2298            }
2299            if (@joinWhere) {
2300                $suffix .= " WHERE " . join(' AND ', @joinWhere);
2301            }
2302            # Add the sort or limit clause (if any) to the SELECT command.
2303            if ($orderClause) {
2304                $suffix .= " $orderClause";
2305            }
2306        }
2307        # Return the suffix, the mapped name list, and the mapped name hash.
2308        return ($suffix, \@mappedNameList, \%mappedNameHash);
2309    }
2310    
2311    =head3 GetStatementHandle
2312    
2313    This method will prepare and execute an SQL query, returning the statement handle.
2314    The main reason for doing this here is so that everybody who does SQL queries gets
2315    the benefit of tracing.
2316    
2317    This is an instance method.
2318    
2319    =over 4
2320    
2321    =item command
2322    
2323    Command to prepare and execute.
2324    
2325    =item params
2326    
2327    Reference to a list of the values to be substituted in for the parameter marks.
2328    
2329    =item RETURN
2330    
2331    Returns a prepared and executed statement handle from which the caller can extract
2332    results.
2333    
2334    =back
2335    
2336    =cut
2337    
2338    sub _GetStatementHandle {
2339        # Get the parameters.
2340        my ($self, $command, $params) = @_;
2341        # Trace the query.
2342        Trace("SQL query: $command") if T(SQL => 3);
2343        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
2344        # Get the database handle.
2345        my $dbh = $self->{_dbh};
2346        # Prepare the command.
2347        my $sth = $dbh->prepare_command($command);
2348        # Execute it with the parameters bound in.
2349        $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
2350        # Return the statement handle.
2351        return $sth;
2352    }
2353    
2354  =head3 GetLoadStats  =head3 GetLoadStats
2355    
2356  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
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