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revision 1.20, Sun Sep 11 17:02:33 2005 UTC revision 1.68, Tue Sep 19 00:12:21 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 90  Line 91 
91    
92  32-bit signed integer  32-bit signed integer
93    
94    =item counter
95    
96    32-bit unsigned integer
97    
98  =item date  =item date
99    
100  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 109  Line 114 
114  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
115  0 and 1.  0 and 1.
116    
117    =item id-string
118    
119    variable-length string, maximum 25 characters
120    
121  =item key-string  =item key-string
122    
123  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 134 
134    
135  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
136    
137    =item hash-string
138    
139    variable-length string, maximum 22 characters
140    
141  =back  =back
142    
143    The hash-string data type has a special meaning. The actual key passed into the loader will
144    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
145    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
146    digest. Therefore, it is presumed the keys will be unique. When the database is actually
147    in use, the hashed keys will be presented rather than the original values. For this reason,
148    they should not be used for entities where the key is meaningful.
149    
150  =head3 Global Tags  =head3 Global Tags
151    
152  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 302  Line 322 
322  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
323  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation
324  # string is specified in the field definition. "avgLen" is the average byte length for estimating  # string is specified in the field definition. "avgLen" is the average byte length for estimating
325  # record sizes.  # record sizes. "sort" is the key modifier for the sort command.
326  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",  dataGen => "StringGen('A')" },
327                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n", dataGen => "IntGen(0, 99999999)" },
328                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n", dataGen => "IntGen(0, 99999999)" },
329                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",  dataGen => "StringGen(IntGen(10,250))" },
330                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",  dataGen => "StringGen(IntGen(80,1000))" },
331                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n", dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
332                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   2, dataGen => "IntGen(0, 1)" },                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g", dataGen => "FloatGen(0.0, 100.0)" },
333                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n", dataGen => "IntGen(0, 1)" },
334                     'hash-string' =>
335                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",  dataGen => "SringGen(22)" },
336                     'id-string' =>
337                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",  dataGen => "SringGen(22)" },
338                   'key-string' =>                   'key-string' =>
339                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",  dataGen => "StringGen(IntGen(10,40))" },
340                   'name-string' =>                   'name-string' =>
341                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",  dataGen => "StringGen(IntGen(10,80))" },
342                   'medium-string' =>                   'medium-string' =>
343                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",  dataGen => "StringGen(IntGen(10,160))" },
344                  );                  );
345    
346  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 402  Line 427 
427      # Write the HTML heading stuff.      # Write the HTML heading stuff.
428      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
429      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
430        # Write the documentation.
431        print HTMLOUT $self->DisplayMetaData();
432        # Close the document.
433        print HTMLOUT "</body>\n</html>\n";
434        # Close the file.
435        close HTMLOUT;
436    }
437    
438    =head3 DisplayMetaData
439    
440    C<< my $html = $erdb->DisplayMetaData(); >>
441    
442    Return an HTML description of the database. This description can be used to help users create
443    the data to be loaded into the relations and form queries. The output is raw includable HTML
444    without any HEAD or BODY tags.
445    
446    =over 4
447    
448    =item filename
449    
450    The name of the output file.
451    
452    =back
453    
454    =cut
455    
456    sub DisplayMetaData {
457        # Get the parameters.
458        my ($self) = @_;
459        # Get the metadata and the title string.
460        my $metadata = $self->{_metaData};
461        # Get the title string.
462        my $title = $metadata->{Title};
463        # Get the entity and relationship lists.
464        my $entityList = $metadata->{Entities};
465        my $relationshipList = $metadata->{Relationships};
466        # Declare the return variable.
467        my $retVal = "";
468        # Open the output file.
469        Trace("Building MetaData table of contents.") if T(4);
470      # 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
471      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
472      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";
473      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
474      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
475          # Display this item.          # Display this item.
476          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
477      }      }
478      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
479      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";
480      # Loop through the Relationships.      # Loop through the Relationships.
481      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
482          # Display this item.          # Display this item.
483          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
484          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
485      }      }
486      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
487      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";
488      # Close off the table of contents itself.      # Close off the table of contents itself.
489      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
490      # 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.
491      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
492      # Loop through the entities.      # Loop through the entities.
493      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
494          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
495          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
496          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
497          # Get the entity data.          # Get the entity data.
498          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
499          # If there's descriptive text, display it.          # If there's descriptive text, display it.
500          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
501              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
502          }          }
503          # 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.
504          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
505          # Loop through the relationships.          # Loop through the relationships.
506          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
507              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 511 
511                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
512                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
513                  # Display the relationship data.                  # Display the relationship data.
514                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
515              }              }
516          }          }
517          # Close off the relationship list.          # Close off the relationship list.
518          print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
519          # Get the entity's relations.          # Get the entity's relations.
520          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
521          # Create a header for the relation subsection.          # Create a header for the relation subsection.
522          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
523          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
524          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
525              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
526              print HTMLOUT $htmlString;              $retVal .= $htmlString;
527          }          }
528      }      }
529      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
530      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
531      # Loop through the relationships.      # Loop through the relationships.
532      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
533          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 535 
535          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
536          # Create the relationship header.          # Create the relationship header.
537          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
538          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
539          # Get the entity names.          # Get the entity names.
540          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
541          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 545 
545          # since both sentences will say the same thing.          # since both sentences will say the same thing.
546          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
547          if ($arity eq "11") {          if ($arity eq "11") {
548              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
549          } else {          } else {
550              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
551              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
552                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
553              }              }
554          }          }
555          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
556          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
557          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
558              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
559          }          }
560          # Generate the relationship's relation table.          # Generate the relationship's relation table.
561          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
562          print HTMLOUT $htmlString;          $retVal .= $htmlString;
563      }      }
564      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
565      # Denote we're starting the join table.      # Denote we're starting the join table.
566      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
567      # Create a table header.      # Create a table header.
568      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
569      # Loop through the joins.      # Loop through the joins.
570      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
571      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 508  Line 573 
573          # Separate out the source, the target, and the join clause.          # Separate out the source, the target, and the join clause.
574          $joinKey =~ m!^([^/]+)/(.+)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
575          my ($sourceRelation, $targetRelation) = ($1, $2);          my ($sourceRelation, $targetRelation) = ($1, $2);
576          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
577          my $source = $self->ComputeObjectSentence($sourceRelation);          my $source = $self->ComputeObjectSentence($sourceRelation);
578          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
579          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
580          # Display them in a table row.          # Display them in a table row.
581          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";
582      }      }
583      # Close the table.      # Close the table.
584      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
585      # Close the document.      Trace("Built MetaData HTML.") if T(3);
586      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
587      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
588  }  }
589    
590  =head3 DumpMetaData  =head3 DumpMetaData
# Line 553  Line 616 
616  sub CreateTables {  sub CreateTables {
617      # Get the parameters.      # Get the parameters.
618      my ($self) = @_;      my ($self) = @_;
619      my $metadata = $self->{_metaData};      # Get the relation names.
620      my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
621      # Loop through the entities.      # Loop through the relations.
622      my $entityHash = $metadata->{Entities};      for my $relationName (@relNames) {
     for my $entityName (keys %{$entityHash}) {  
         my $entityData = $entityHash->{$entityName};  
         # Tell the user what we're doing.  
         Trace("Creating relations for entity $entityName.") if T(1);  
         # Loop through the entity's relations.  
         for my $relationName (keys %{$entityData->{Relations}}) {  
623              # Create a table for this relation.              # Create a table for this relation.
624              $self->CreateTable($relationName);              $self->CreateTable($relationName);
625              Trace("Relation $relationName created.") if T(1);          Trace("Relation $relationName created.") if T(2);
         }  
     }  
     # Loop through the relationships.  
     my $relationshipTable = $metadata->{Relationships};  
     for my $relationshipName (keys %{$metadata->{Relationships}}) {  
         # Create a table for this relationship.  
         Trace("Creating relationship $relationshipName.") if T(1);  
         $self->CreateTable($relationshipName);  
626      }      }
627  }  }
628    
# Line 646  Line 695 
695      }      }
696  }  }
697    
698    =head3 VerifyFields
699    
700    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
701    
702    Run through the list of proposed field values, insuring that all the character fields are
703    below the maximum length. If any fields are too long, they will be truncated in place.
704    
705    =over 4
706    
707    =item relName
708    
709    Name of the relation for which the specified fields are destined.
710    
711    =item fieldList
712    
713    Reference to a list, in order, of the fields to be put into the relation.
714    
715    =item RETURN
716    
717    Returns the number of fields truncated.
718    
719    =back
720    
721    =cut
722    
723    sub VerifyFields {
724        # Get the parameters.
725        my ($self, $relName, $fieldList) = @_;
726        # Initialize the return value.
727        my $retVal = 0;
728        # Get the relation definition.
729        my $relData = $self->_FindRelation($relName);
730        # Get the list of field descriptors.
731        my $fieldTypes = $relData->{Fields};
732        my $fieldCount = scalar @{$fieldTypes};
733        # Loop through the two lists.
734        for (my $i = 0; $i < $fieldCount; $i++) {
735            # Get the type of the current field.
736            my $fieldType = $fieldTypes->[$i]->{type};
737            # If it's a character field, verify the length.
738            if ($fieldType =~ /string/) {
739                my $maxLen = $TypeTable{$fieldType}->{maxLen};
740                my $oldString = $fieldList->[$i];
741                if (length($oldString) > $maxLen) {
742                    # Here it's too big, so we truncate it.
743                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
744                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
745                    $retVal++;
746                }
747            }
748        }
749        # Return the truncation count.
750        return $retVal;
751    }
752    
753    =head3 DigestFields
754    
755    C<< $erdb->DigestFields($relName, $fieldList); >>
756    
757    Digest the strings in the field list that correspond to data type C<hash-string> in the
758    specified relation.
759    
760    =over 4
761    
762    =item relName
763    
764    Name of the relation to which the fields belong.
765    
766    =item fieldList
767    
768    List of field contents to be loaded into the relation.
769    
770    =back
771    
772    =cut
773    #: Return Type ;
774    sub DigestFields {
775        # Get the parameters.
776        my ($self, $relName, $fieldList) = @_;
777        # Get the relation definition.
778        my $relData = $self->_FindRelation($relName);
779        # Get the list of field descriptors.
780        my $fieldTypes = $relData->{Fields};
781        my $fieldCount = scalar @{$fieldTypes};
782        # Loop through the two lists.
783        for (my $i = 0; $i < $fieldCount; $i++) {
784            # Get the type of the current field.
785            my $fieldType = $fieldTypes->[$i]->{type};
786            # If it's a hash string, digest it in place.
787            if ($fieldType eq 'hash-string') {
788                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
789            }
790        }
791    }
792    
793    =head3 DigestKey
794    
795    C<< my $digested = $erdb->DigestKey($keyValue); >>
796    
797    Return the digested value of a symbolic key. The digested value can then be plugged into a
798    key-based search into a table with key-type hash-string.
799    
800    Currently the digesting process is independent of the database structure, but that may not
801    always be the case, so this is an instance method instead of a static method.
802    
803    =over 4
804    
805    =item keyValue
806    
807    Key value to digest.
808    
809    =item RETURN
810    
811    Digested value of the key.
812    
813    =back
814    
815    =cut
816    
817    sub DigestKey {
818        # Get the parameters.
819        my ($self, $keyValue) = @_;
820        # Compute the digest.
821        my $retVal = md5_base64($keyValue);
822        # Return the result.
823        return $retVal;
824    }
825    
826  =head3 CreateIndex  =head3 CreateIndex
827    
828  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 674  Line 851 
851          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
852          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
853          # Create the index.          # Create the index.
854          $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
855                                        flds => $flds, unique => $unique);
856            if ($rv) {
857          Trace("Index created: $indexName for $relationName ($flds)") if T(1);          Trace("Index created: $indexName for $relationName ($flds)") if T(1);
858            } else {
859                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
860            }
861      }      }
862  }  }
863    
# Line 724  Line 906 
906      $directoryName =~ s!/\\$!!;      $directoryName =~ s!/\\$!!;
907      # Declare the return variable.      # Declare the return variable.
908      my $retVal = Stats->new();      my $retVal = Stats->new();
909      # Get the metadata structure.      # Get the relation names.
910      my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
911      # Loop through the entities.      for my $relationName (@relNames) {
     for my $entity (values %{$metaData->{Entities}}) {  
         # Loop through the entity's relations.  
         for my $relationName (keys %{$entity->{Relations}}) {  
912              # Try to load this relation.              # Try to load this relation.
913              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
914              # Accumulate the statistics.              # Accumulate the statistics.
915              $retVal->Accumulate($result);              $retVal->Accumulate($result);
916          }          }
     }  
     # Loop through the relationships.  
     for my $relationshipName (keys %{$metaData->{Relationships}}) {  
         # Try to load this relationship's relation.  
         my $result = $self->_LoadRelation($directoryName, $relationshipName, $rebuild);  
         # Accumulate the statistics.  
         $retVal->Accumulate($result);  
     }  
917      # Add the duration of the load to the statistical object.      # Add the duration of the load to the statistical object.
918      $retVal->Add('duration', gettimeofday - $startTime);      $retVal->Add('duration', gettimeofday - $startTime);
919      # Return the accumulated statistics.      # Return the accumulated statistics.
920      return $retVal;      return $retVal;
921  }  }
922    
923    
924  =head3 GetTableNames  =head3 GetTableNames
925    
926  C<< my @names = $erdb->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
# Line 812  Line 984 
984    
985  =head3 Get  =head3 Get
986    
987  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
988    
989  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.
990  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 820  Line 992 
992  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
993  $genus.  $genus.
994    
995  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
996    
997  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
998  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 837  Line 1009 
1009  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
1010  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,
1011    
1012  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1013    
1014  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
1015  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.
1016  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
1017  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
1018  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  
1019  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,
1020  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.
1021    
1022    If an entity or relationship is mentioned twice, the name for the second occurrence will
1023    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1024    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1025    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1026    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1027    
1028  =over 4  =over 4
1029    
1030  =item objectNames  =item objectNames
# Line 870  Line 1047 
1047    
1048  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1049    
1050    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1051    be processed. The idea is to make it less likely to find the verb by accident.
1052    
1053  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
1054  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
1055  relation.  relation.
1056    
1057  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1058    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1059    a positive number. So, for example
1060    
1061    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1062    
1063  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
1064    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1065    use
1066    
1067    C<< "LIMIT 10" >>
1068    
1069    =item params
1070    
1071    Reference to a list of parameter values to be substituted into the filter clause.
1072    
1073  =item RETURN  =item RETURN
1074    
# Line 888  Line 1080 
1080    
1081  sub Get {  sub Get {
1082      # Get the parameters.      # Get the parameters.
1083      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1084      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1085      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1086      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1087      #      # Create the query.
1088      my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1089      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1090                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1091      # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1092      if ($filterClause) {      # and mapped name for each object in the query.
1093          # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1094          # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1095          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 thing. We'll put the order by clause  
         # in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY verb (if any).  
         if ($filterString =~ m/^(.*)ORDER BY/g) {  
             # Here we have an ORDER BY verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " ORDER BY $orderClause";  
         }  
1096      }      }
     Trace("SQL query: $command") if T(3);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1097      # Return the statement object.      # Return the statement object.
1098      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1099      return $retVal;      return $retVal;
1100  }  }
1101    
1102  =head3 GetList  =head3 GetFlat
   
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1103    
1104  Return a list of object descriptors for the specified objects as determined by the  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
 specified filter clause.  
1105    
1106  This method is essentially the same as L</Get> except it returns a list of objects rather  This is a variation of L</GetAll> that asks for only a single field per record and
1107  than a query object that can be used to get the results one record at a time.  returns a single flattened list.
1108    
1109  =over 4  =over 4
1110    
# Line 1028  Line 1114 
1114    
1115  =item filterClause  =item filterClause
1116    
1117  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1118  be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1119  specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1120  in the filter clause should be added to the parameter list as additional parameters. The  parameter list as additional parameters. The fields in a filter clause can come from primary
1121  fields in a filter clause can come from primary entity relations, relationship relations,  entity relations, relationship relations, or secondary entity relations; however, all of the
1122  or secondary entity relations; however, all of the entities and relationships involved must  entities and relationships involved must be included in the list of object names.
 be included in the list of object names.  
   
 The filter clause can also specify a sort order. To do this, simply follow the filter string  
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
1123    
1124  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  =item parameterList
1125    
1126  The rules for field references in a sort order are the same as those for field references in the  List of the parameters to be substituted in for the parameters marks in the filter clause.
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
1127    
1128  =item param1, param2, ..., paramN  =item field
1129    
1130  Parameter values to be substituted into the filter clause.  Name of the field to be used to get the elements of the list returned.
1131    
1132  =item RETURN  =item RETURN
1133    
1134  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of values.
1135    
1136  =back  =back
1137    
1138  =cut  =cut
1139  #: Return Type @%  #: Return Type @;
1140  sub GetList {  sub GetFlat {
1141      # Get the parameters.      # Get the parameters.
1142      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1143      # Declare the return variable.      # Construct the query.
1144        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1145        # Create the result list.
1146      my @retVal = ();      my @retVal = ();
1147      # Perform the query.      # Loop through the records, adding the field values found to the result list.
1148      my $query = $self->Get($objectNames, $filterClause, @params);      while (my $row = $query->Fetch()) {
1149      # Loop through the results.          push @retVal, $row->Value($field);
     while (my $object = $query->Fetch) {  
         push @retVal, $object;  
1150      }      }
1151      # Return the result.      # Return the list created.
1152      return @retVal;      return @retVal;
1153  }  }
1154    
1155  =head3 ComputeObjectSentence  =head3 Delete
1156    
1157  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1158    
1159  Check an object name, and if it is a relationship convert it to a relationship sentence.  Delete an entity instance from the database. The instance is deleted along with all entity and
1160    relationship instances dependent on it. The idea of dependence here is recursive. An object is
1161    always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1162    relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1163    dependent relationship.
1164    
1165  =over 4  =over 4
1166    
1167  =item objectName  =item entityName
1168    
1169  Name of the entity or relationship.  Name of the entity type for the instance being deleted.
1170    
1171  =item RETURN  =item objectID
1172    
1173  Returns a string containing the entity name or a relationship sentence.  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1174    then it is presumed to by a LIKE pattern.
1175    
1176  =back  =item testFlag
1177    
1178    If TRUE, the delete statements will be traced without being executed.
1179    
1180    =item RETURN
1181    
1182    Returns a statistics object indicating how many records of each particular table were
1183    deleted.
1184    
1185    =back
1186    
1187    =cut
1188    #: Return Type $%;
1189    sub Delete {
1190        # Get the parameters.
1191        my ($self, $entityName, $objectID, $testFlag) = @_;
1192        # Declare the return variable.
1193        my $retVal = Stats->new();
1194        # Get the DBKernel object.
1195        my $db = $self->{_dbh};
1196        # We're going to generate all the paths branching out from the starting entity. One of
1197        # the things we have to be careful about is preventing loops. We'll use a hash to
1198        # determine if we've hit a loop.
1199        my %alreadyFound = ();
1200        # These next lists will serve as our result stack. We start by pushing object lists onto
1201        # the stack, and then popping them off to do the deletes. This means the deletes will
1202        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1203        # sure we don't delete records that might be needed to forge relationships back to the
1204        # original item. We have two lists-- one for TO-relationships, and one for
1205        # FROM-relationships and entities.
1206        my @fromPathList = ();
1207        my @toPathList = ();
1208        # This final hash is used to remember what work still needs to be done. We push paths
1209        # onto the list, then pop them off to extend the paths. We prime it with the starting
1210        # point. Note that we will work hard to insure that the last item on a path in the
1211        # TODO list is always an entity.
1212        my @todoList = ([$entityName]);
1213        while (@todoList) {
1214            # Get the current path.
1215            my $current = pop @todoList;
1216            # Copy it into a list.
1217            my @stackedPath = @{$current};
1218            # Pull off the last item on the path. It will always be an entity.
1219            my $entityName = pop @stackedPath;
1220            # Add it to the alreadyFound list.
1221            $alreadyFound{$entityName} = 1;
1222            # Get the entity data.
1223            my $entityData = $self->_GetStructure($entityName);
1224            # The first task is to loop through the entity's relation. A DELETE command will
1225            # be needed for each of them.
1226            my $relations = $entityData->{Relations};
1227            for my $relation (keys %{$relations}) {
1228                my @augmentedList = (@stackedPath, $relation);
1229                push @fromPathList, \@augmentedList;
1230            }
1231            # Now we need to look for relationships connected to this entity.
1232            my $relationshipList = $self->{_metaData}->{Relationships};
1233            for my $relationshipName (keys %{$relationshipList}) {
1234                my $relationship = $relationshipList->{$relationshipName};
1235                # Check the FROM field. We're only interested if it's us.
1236                if ($relationship->{from} eq $entityName) {
1237                    # Add the path to this relationship.
1238                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1239                    push @fromPathList, \@augmentedList;
1240                    # Check the arity. If it's MM we're done. If it's 1M
1241                    # and the target hasn't been seen yet, we want to
1242                    # stack the entity for future processing.
1243                    if ($relationship->{arity} eq '1M') {
1244                        my $toEntity = $relationship->{to};
1245                        if (! exists $alreadyFound{$toEntity}) {
1246                            # Here we have a new entity that's dependent on
1247                            # the current entity, so we need to stack it.
1248                            my @stackList = (@augmentedList, $toEntity);
1249                            push @fromPathList, \@stackList;
1250                        } else {
1251                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1252                        }
1253                    }
1254                }
1255                # Now check the TO field. In this case only the relationship needs
1256                # deletion.
1257                if ($relationship->{to} eq $entityName) {
1258                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1259                    push @toPathList, \@augmentedList;
1260                }
1261            }
1262        }
1263        # Create the first qualifier for the WHERE clause. This selects the
1264        # keys of the primary entity records to be deleted. When we're deleting
1265        # from a dependent table, we construct a join page from the first qualifier
1266        # to the table containing the dependent records to delete.
1267        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1268        # We need to make two passes. The first is through the to-list, and
1269        # the second through the from-list. The from-list is second because
1270        # the to-list may need to pass through some of the entities the
1271        # from-list would delete.
1272        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1273        # Now it's time to do the deletes. We do it in two passes.
1274        for my $keyName ('to_link', 'from_link') {
1275            # Get the list for this key.
1276            my @pathList = @{$stackList{$keyName}};
1277            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1278            # Loop through this list.
1279            while (my $path = pop @pathList) {
1280                # Get the table whose rows are to be deleted.
1281                my @pathTables = @{$path};
1282                # Start the DELETE statement. We need to call DBKernel because the
1283                # syntax of a DELETE-USING varies among DBMSs.
1284                my $target = $pathTables[$#pathTables];
1285                my $stmt = $db->SetUsing(@pathTables);
1286                # Now start the WHERE. The first thing is the ID field from the starting table. That
1287                # starting table will either be the entity relation or one of the entity's
1288                # sub-relations.
1289                $stmt .= " WHERE $pathTables[0].id $qualifier";
1290                # Now we run through the remaining entities in the path, connecting them up.
1291                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1292                    # Connect the current relationship to the preceding entity.
1293                    my ($entity, $rel) = @pathTables[$i-1,$i];
1294                    # The style of connection depends on the direction of the relationship.
1295                    $stmt .= " AND $entity.id = $rel.$keyName";
1296                    if ($i + 1 <= $#pathTables) {
1297                        # Here there's a next entity, so connect that to the relationship's
1298                        # to-link.
1299                        my $entity2 = $pathTables[$i+1];
1300                        $stmt .= " AND $rel.to_link = $entity2.id";
1301                    }
1302                }
1303                # Now we have our desired DELETE statement.
1304                if ($testFlag) {
1305                    # Here the user wants to trace without executing.
1306                    Trace($stmt) if T(0);
1307                } else {
1308                    # Here we can delete. Note that the SQL method dies with a confessing
1309                    # if an error occurs, so we just go ahead and do it.
1310                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1311                    my $rv = $db->SQL($stmt, 0, $objectID);
1312                    # Accumulate the statistics for this delete. The only rows deleted
1313                    # are from the target table, so we use its name to record the
1314                    # statistic.
1315                    $retVal->Add($target, $rv);
1316                }
1317            }
1318        }
1319        # Return the result.
1320        return $retVal;
1321    }
1322    
1323    =head3 GetList
1324    
1325    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1326    
1327    Return a list of object descriptors for the specified objects as determined by the
1328    specified filter clause.
1329    
1330    This method is essentially the same as L</Get> except it returns a list of objects rather
1331    than a query object that can be used to get the results one record at a time.
1332    
1333    =over 4
1334    
1335    =item objectNames
1336    
1337    List containing the names of the entity and relationship objects to be retrieved.
1338    
1339    =item filterClause
1340    
1341    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1342    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1343    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1344    in the filter clause should be added to the parameter list as additional parameters. The
1345    fields in a filter clause can come from primary entity relations, relationship relations,
1346    or secondary entity relations; however, all of the entities and relationships involved must
1347    be included in the list of object names.
1348    
1349    The filter clause can also specify a sort order. To do this, simply follow the filter string
1350    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1351    particular genus and sorts them by species name.
1352    
1353    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1354    
1355    The rules for field references in a sort order are the same as those for field references in the
1356    filter clause in general; however, odd things may happen if a sort field is from a secondary
1357    relation.
1358    
1359    =item params
1360    
1361    Reference to a list of parameter values to be substituted into the filter clause.
1362    
1363    =item RETURN
1364    
1365    Returns a list of B<DBObject>s that satisfy the query conditions.
1366    
1367    =back
1368    
1369    =cut
1370    #: Return Type @%
1371    sub GetList {
1372        # Get the parameters.
1373        my ($self, $objectNames, $filterClause, $params) = @_;
1374        # Declare the return variable.
1375        my @retVal = ();
1376        # Perform the query.
1377        my $query = $self->Get($objectNames, $filterClause, $params);
1378        # Loop through the results.
1379        while (my $object = $query->Fetch) {
1380            push @retVal, $object;
1381        }
1382        # Return the result.
1383        return @retVal;
1384    }
1385    
1386    =head3 GetCount
1387    
1388    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1389    
1390    Return the number of rows found by a specified query. This method would
1391    normally be used to count the records in a single table. For example, in a
1392    genetics database
1393    
1394        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1395    
1396    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1397    to use it to return records based on a join. For example,
1398    
1399        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1400                                    ['homo %']);
1401    
1402    would return the number of features for genomes in the genus I<homo>. Note that
1403    only the rows from the first table are counted. If the above command were
1404    
1405        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1406                                    ['homo %']);
1407    
1408    it would return the number of genomes, not the number of genome/feature pairs.
1409    
1410    =over 4
1411    
1412    =item objectNames
1413    
1414    Reference to a list of the objects (entities and relationships) included in the
1415    query.
1416    
1417    =item filter
1418    
1419    A filter clause for restricting the query. The rules are the same as for the L</Get>
1420    method.
1421    
1422    =item params
1423    
1424    Reference to a list of the parameter values to be substituted for the parameter marks
1425    in the filter.
1426    
1427    =item RETURN
1428    
1429    Returns a count of the number of records in the first table that would satisfy
1430    the query.
1431    
1432    =back
1433    
1434    =cut
1435    
1436    sub GetCount {
1437        # Get the parameters.
1438        my ($self, $objectNames, $filter, $params) = @_;
1439        # Insure the params argument is an array reference if the caller left it off.
1440        if (! defined($params)) {
1441            $params = [];
1442        }
1443        # Declare the return variable.
1444        my $retVal;
1445        # Find out if we're counting an entity or a relationship.
1446        my $countedField;
1447        if ($self->IsEntity($objectNames->[0])) {
1448            $countedField = "id";
1449        } else {
1450            # For a relationship we count the to-link because it's usually more
1451            # numerous. Note we're automatically converting to the SQL form
1452            # of the field name (to_link vs. to-link).
1453            $countedField = "to_link";
1454        }
1455        # Create the SQL command suffix to get the desired records.
1456        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1457                                                                                $filter);
1458        # Prefix it with text telling it we want a record count.
1459        my $firstObject = $mappedNameListRef->[0];
1460        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
1461        # Prepare and execute the command.
1462        my $sth = $self->_GetStatementHandle($command, $params);
1463        # Get the count value.
1464        ($retVal) = $sth->fetchrow_array();
1465        # Check for a problem.
1466        if (! defined($retVal)) {
1467            if ($sth->err) {
1468                # Here we had an SQL error.
1469                Confess("Error retrieving row count: " . $sth->errstr());
1470            } else {
1471                # Here we have no result.
1472                Confess("No result attempting to retrieve row count.");
1473            }
1474        }
1475        # Return the result.
1476        return $retVal;
1477    }
1478    
1479    =head3 ComputeObjectSentence
1480    
1481    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1482    
1483    Check an object name, and if it is a relationship convert it to a relationship sentence.
1484    
1485    =over 4
1486    
1487    =item objectName
1488    
1489    Name of the entity or relationship.
1490    
1491    =item RETURN
1492    
1493    Returns a string containing the entity name or a relationship sentence.
1494    
1495    =back
1496    
1497  =cut  =cut
1498    
# Line 1150  Line 1553 
1553      }      }
1554  }  }
1555    
1556    =head3 InsertValue
1557    
1558    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
1559    
1560    This method will insert a new value into the database. The value must be one
1561    associated with a secondary relation, since primary values cannot be inserted:
1562    they occur exactly once. Secondary values, on the other hand, can be missing
1563    or multiply-occurring.
1564    
1565    =over 4
1566    
1567    =item entityID
1568    
1569    ID of the object that is to receive the new value.
1570    
1571    =item fieldName
1572    
1573    Field name for the new value-- this includes the entity name, since
1574    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
1575    
1576    =item value
1577    
1578    New value to be put in the field.
1579    
1580    =back
1581    
1582    =cut
1583    
1584    sub InsertValue {
1585        # Get the parameters.
1586        my ($self, $entityID, $fieldName, $value) = @_;
1587        # Parse the entity name and the real field name.
1588        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
1589            my $entityName = $1;
1590            my $fieldTitle = $2;
1591            # Get its descriptor.
1592            if (!$self->IsEntity($entityName)) {
1593                Confess("$entityName is not a valid entity.");
1594            } else {
1595                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1596                # Find the relation containing this field.
1597                my $fieldHash = $entityData->{Fields};
1598                if (! exists $fieldHash->{$fieldTitle}) {
1599                    Confess("$fieldTitle not found in $entityName.");
1600                } else {
1601                    my $relation = $fieldHash->{$fieldTitle}->{relation};
1602                    if ($relation eq $entityName) {
1603                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
1604                    } else {
1605                        # Now we can create an INSERT statement.
1606                        my $dbh = $self->{_dbh};
1607                        my $fixedName = _FixName($fieldTitle);
1608                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
1609                        # Execute the command.
1610                        $dbh->SQL($statement, 0, $entityID, $value);
1611                    }
1612                }
1613            }
1614        } else {
1615            Confess("$fieldName is not a valid field name.");
1616        }
1617    }
1618    
1619  =head3 InsertObject  =head3 InsertObject
1620    
1621  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
# Line 1166  Line 1632 
1632  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
1633  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
1634    
1635  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1636    
1637  =over 4  =over 4
1638    
# Line 1312  Line 1778 
1778    
1779  =item RETURN  =item RETURN
1780    
1781  Returns a statistical object containing the number of records read and a list of  Returns a statistical object containing a list of the error messages.
 the error messages.  
1782    
1783  =back  =back
1784    
# Line 1327  Line 1792 
1792      Trace("Loading table $relationName from $fileName") if T(2);      Trace("Loading table $relationName from $fileName") if T(2);
1793      # Get the database handle.      # Get the database handle.
1794      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
1795        # Get the input file size.
1796        my $fileSize = -s $fileName;
1797      # Get the relation data.      # Get the relation data.
1798      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
1799      # Check the truncation flag.      # Check the truncation flag.
# Line 1337  Line 1804 
1804          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
1805          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
1806          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
         my $fileSize = -s $fileName;  
1807          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
1808          # Re-create the table without its index.          # Re-create the table without its index.
1809          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
# Line 1361  Line 1827 
1827          $retVal->AddMessage("Table load failed for $relationName using $fileName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName.");
1828          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
1829      } else {      } else {
1830          # Here we successfully loaded the table. Trace the number of records loaded.          # Here we successfully loaded the table.
1831          Trace("$retVal->{records} records read for $relationName.") if T(2);          $retVal->Add("tables");
1832            my $size = -s $fileName;
1833            Trace("$size bytes loaded into $relationName.") if T(2);
1834          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
1835          if ($truncateFlag && ! $dbh->{_preIndex}) {          if ($truncateFlag && ! $dbh->{_preIndex}) {
1836              eval {              eval {
# Line 1373  Line 1841 
1841              }              }
1842          }          }
1843      }      }
     # Commit the database changes.  
     $dbh->commit_tran;  
1844      # Analyze the table to improve performance.      # Analyze the table to improve performance.
1845        Trace("Analyzing and compacting $relationName.") if T(3);
1846      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
1847        Trace("$relationName load completed.") if T(3);
1848      # Return the statistics.      # Return the statistics.
1849      return $retVal;      return $retVal;
1850  }  }
# Line 1468  Line 1936 
1936      # Get the parameters.      # Get the parameters.
1937      my ($self, $entityType, $ID) = @_;      my ($self, $entityType, $ID) = @_;
1938      # Create a query.      # Create a query.
1939      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
1940      # Get the first (and only) object.      # Get the first (and only) object.
1941      my $retVal = $query->Fetch();      my $retVal = $query->Fetch();
1942      # Return the result.      # Return the result.
# Line 1479  Line 1947 
1947    
1948  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1949    
1950  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance. If the entity instance
1951    does not exist, an empty list is returned.
1952    
1953  =over 4  =over 4
1954    
# Line 1581  Line 2050 
2050      # list is a scalar we convert it into a singleton list.      # list is a scalar we convert it into a singleton list.
2051      my @parmList = ();      my @parmList = ();
2052      if (ref $parameterList eq "ARRAY") {      if (ref $parameterList eq "ARRAY") {
2053            Trace("GetAll parm list is an array.") if T(4);
2054          @parmList = @{$parameterList};          @parmList = @{$parameterList};
2055      } else {      } else {
2056            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2057          push @parmList, $parameterList;          push @parmList, $parameterList;
2058      }      }
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, @parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
2059      # Insure the counter has a value.      # Insure the counter has a value.
2060      if (!defined $count) {      if (!defined $count) {
2061          $count = 0;          $count = 0;
2062      }      }
2063        # Add the row limit to the filter clause.
2064        if ($count > 0) {
2065            $filterClause .= " LIMIT $count";
2066        }
2067        # Create the query.
2068        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2069        # Set up a counter of the number of records read.
2070        my $fetched = 0;
2071      # Loop through the records returned, extracting the fields. Note that if the      # Loop through the records returned, extracting the fields. Note that if the
2072      # counter is non-zero, we stop when the number of records read hits the count.      # counter is non-zero, we stop when the number of records read hits the count.
2073      my @retVal = ();      my @retVal = ();
# Line 1601  Line 2076 
2076          push @retVal, \@rowData;          push @retVal, \@rowData;
2077          $fetched++;          $fetched++;
2078      }      }
2079        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2080      # Return the resulting list.      # Return the resulting list.
2081      return @retVal;      return @retVal;
2082  }  }
2083    
2084    =head3 Exists
2085    
2086    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2087    
2088    Return TRUE if an entity exists, else FALSE.
2089    
2090    =over 4
2091    
2092    =item entityName
2093    
2094    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2095    
2096    =item entityID
2097    
2098    ID of the entity instance whose existence is to be checked.
2099    
2100    =item RETURN
2101    
2102    Returns TRUE if the entity instance exists, else FALSE.
2103    
2104    =back
2105    
2106    =cut
2107    #: Return Type $;
2108    sub Exists {
2109        # Get the parameters.
2110        my ($self, $entityName, $entityID) = @_;
2111        # Check for the entity instance.
2112        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2113        my $testInstance = $self->GetEntity($entityName, $entityID);
2114        # Return an existence indicator.
2115        my $retVal = ($testInstance ? 1 : 0);
2116        return $retVal;
2117    }
2118    
2119  =head3 EstimateRowSize  =head3 EstimateRowSize
2120    
2121  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
# Line 1643  Line 2154 
2154      return $retVal;      return $retVal;
2155  }  }
2156    
2157    =head3 GetFieldTable
2158    
2159    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2160    
2161    Get the field structure for a specified entity or relationship.
2162    
2163    =over 4
2164    
2165    =item objectName
2166    
2167    Name of the desired entity or relationship.
2168    
2169    =item RETURN
2170    
2171    The table containing the field descriptors for the specified object.
2172    
2173    =back
2174    
2175    =cut
2176    
2177    sub GetFieldTable {
2178        # Get the parameters.
2179        my ($self, $objectName) = @_;
2180        # Get the descriptor from the metadata.
2181        my $objectData = $self->_GetStructure($objectName);
2182        # Return the object's field table.
2183        return $objectData->{Fields};
2184    }
2185    
2186    =head2 Data Mining Methods
2187    
2188    =head3 GetUsefulCrossValues
2189    
2190    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
2191    
2192    Return a list of the useful attributes that would be returned by a B<Cross> call
2193    from an entity of the source entity type through the specified relationship. This
2194    means it will return the fields of the target entity type and the intersection data
2195    fields in the relationship. Only primary table fields are returned. In other words,
2196    the field names returned will be for fields where there is always one and only one
2197    value.
2198    
2199    =over 4
2200    
2201    =item sourceEntity
2202    
2203    Name of the entity from which the relationship crossing will start.
2204    
2205    =item relationship
2206    
2207    Name of the relationship being crossed.
2208    
2209    =item RETURN
2210    
2211    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
2212    
2213    =back
2214    
2215    =cut
2216    #: Return Type @;
2217    sub GetUsefulCrossValues {
2218        # Get the parameters.
2219        my ($self, $sourceEntity, $relationship) = @_;
2220        # Declare the return variable.
2221        my @retVal = ();
2222        # Determine the target entity for the relationship. This is whichever entity is not
2223        # the source entity. So, if the source entity is the FROM, we'll get the name of
2224        # the TO, and vice versa.
2225        my $relStructure = $self->_GetStructure($relationship);
2226        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
2227        my $targetEntity = $relStructure->{$targetEntityType};
2228        # Get the field table for the entity.
2229        my $entityFields = $self->GetFieldTable($targetEntity);
2230        # The field table is a hash. The hash key is the field name. The hash value is a structure.
2231        # For the entity fields, the key aspect of the target structure is that the {relation} value
2232        # must match the entity name.
2233        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
2234                            keys %{$entityFields};
2235        # Push the fields found onto the return variable.
2236        push @retVal, sort @fieldList;
2237        # Get the field table for the relationship.
2238        my $relationshipFields = $self->GetFieldTable($relationship);
2239        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
2240        # This may end up being an empty set.
2241        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
2242                            keys %{$relationshipFields};
2243        # Push these onto the return list.
2244        push @retVal, sort @fieldList2;
2245        # Return the result.
2246        return @retVal;
2247    }
2248    
2249    =head3 FindColumn
2250    
2251    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2252    
2253    Return the location a desired column in a data mining header line. The data
2254    mining header line is a tab-separated list of column names. The column
2255    identifier is either the numerical index of a column or the actual column
2256    name.
2257    
2258    =over 4
2259    
2260    =item headerLine
2261    
2262    The header line from a data mining command, which consists of a tab-separated
2263    list of column names.
2264    
2265    =item columnIdentifier
2266    
2267    Either the ordinal number of the desired column (1-based), or the name of the
2268    desired column.
2269    
2270    =item RETURN
2271    
2272    Returns the array index (0-based) of the desired column.
2273    
2274    =back
2275    
2276    =cut
2277    
2278    sub FindColumn {
2279        # Get the parameters.
2280        my ($headerLine, $columnIdentifier) = @_;
2281        # Declare the return variable.
2282        my $retVal;
2283        # Split the header line into column names.
2284        my @headers = ParseColumns($headerLine);
2285        # Determine whether we have a number or a name.
2286        if ($columnIdentifier =~ /^\d+$/) {
2287            # Here we have a number. Subtract 1 and validate the result.
2288            $retVal = $columnIdentifier - 1;
2289            if ($retVal < 0 || $retVal > $#headers) {
2290                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2291            }
2292        } else {
2293            # Here we have a name. We need to find it in the list.
2294            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2295                if ($headers[$i] eq $columnIdentifier) {
2296                    $retVal = $i;
2297                }
2298            }
2299            if (! defined($retVal)) {
2300                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2301            }
2302        }
2303        # Return the result.
2304        return $retVal;
2305    }
2306    
2307    =head3 ParseColumns
2308    
2309    C<< my @columns = ERDB::ParseColumns($line); >>
2310    
2311    Convert the specified data line to a list of columns.
2312    
2313    =over 4
2314    
2315    =item line
2316    
2317    A data mining input, consisting of a tab-separated list of columns terminated by a
2318    new-line.
2319    
2320    =item RETURN
2321    
2322    Returns a list consisting of the column values.
2323    
2324    =back
2325    
2326    =cut
2327    
2328    sub ParseColumns {
2329        # Get the parameters.
2330        my ($line) = @_;
2331        # Chop off the line-end.
2332        chomp $line;
2333        # Split it into a list.
2334        my @retVal = split(/\t/, $line);
2335        # Return the result.
2336        return @retVal;
2337    }
2338    
2339  =head2 Internal Utility Methods  =head2 Internal Utility Methods
2340    
2341    =head3 SetupSQL
2342    
2343    Process a list of object names and a filter clause so that they can be used to
2344    build an SQL statement. This method takes in a reference to a list of object names
2345    and a filter clause. It will return a corrected filter clause, a list of mapped
2346    names and the mapped name hash.
2347    
2348    This is an instance method.
2349    
2350    =over 4
2351    
2352    =item objectNames
2353    
2354    Reference to a list of the object names to be included in the query.
2355    
2356    =item filterClause
2357    
2358    A string containing the WHERE clause for the query (without the C<WHERE>) and also
2359    optionally the C<ORDER BY> and C<LIMIT> clauses.
2360    
2361    =item RETURN
2362    
2363    Returns a three-element list. The first element is the SQL statement suffix, beginning
2364    with the FROM clause. The second element is a reference to a list of the names to be
2365    used in retrieving the fields. The third element is a hash mapping the names to the
2366    objects they represent.
2367    
2368    =back
2369    
2370    =cut
2371    
2372    sub _SetupSQL {
2373        my ($self, $objectNames, $filterClause) = @_;
2374        # Adjust the list of object names to account for multiple occurrences of the
2375        # same object. We start with a hash table keyed on object name that will
2376        # return the object suffix. The first time an object is encountered it will
2377        # not be found in the hash. The next time the hash will map the object name
2378        # to 2, then 3, and so forth.
2379        my %objectHash = ();
2380        # This list will contain the object names as they are to appear in the
2381        # FROM list.
2382        my @fromList = ();
2383        # This list contains the suffixed object name for each object. It is exactly
2384        # parallel to the list in the $objectNames parameter.
2385        my @mappedNameList = ();
2386        # Finally, this hash translates from a mapped name to its original object name.
2387        my %mappedNameHash = ();
2388        # Now we create the lists. Note that for every single name we push something into
2389        # @fromList and @mappedNameList. This insures that those two arrays are exactly
2390        # parallel to $objectNames.
2391        for my $objectName (@{$objectNames}) {
2392            # Get the next suffix for this object.
2393            my $suffix = $objectHash{$objectName};
2394            if (! $suffix) {
2395                # Here we are seeing the object for the first time. The object name
2396                # is used as is.
2397                push @mappedNameList, $objectName;
2398                push @fromList, $objectName;
2399                $mappedNameHash{$objectName} = $objectName;
2400                # Denote the next suffix will be 2.
2401                $objectHash{$objectName} = 2;
2402            } else {
2403                # Here we've seen the object before. We construct a new name using
2404                # the suffix from the hash and update the hash.
2405                my $mappedName = "$objectName$suffix";
2406                $objectHash{$objectName} = $suffix + 1;
2407                # The FROM list has the object name followed by the mapped name. This
2408                # tells SQL it's still the same table, but we're using a different name
2409                # for it to avoid confusion.
2410                push @fromList, "$objectName $mappedName";
2411                # The mapped-name list contains the real mapped name.
2412                push @mappedNameList, $mappedName;
2413                # Finally, enable us to get back from the mapped name to the object name.
2414                $mappedNameHash{$mappedName} = $objectName;
2415            }
2416        }
2417        # Begin the SELECT suffix. It starts with
2418        #
2419        # FROM name1, name2, ... nameN
2420        #
2421        my $suffix = "FROM " . join(', ', @fromList);
2422        # Check for a filter clause.
2423        if ($filterClause) {
2424            # Here we have one, so we convert its field names and add it to the query. First,
2425            # We create a copy of the filter string we can work with.
2426            my $filterString = $filterClause;
2427            # Next, we sort the object names by length. This helps protect us from finding
2428            # object names inside other object names when we're doing our search and replace.
2429            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
2430            # We will also keep a list of conditions to add to the WHERE clause in order to link
2431            # entities and relationships as well as primary relations to secondary ones.
2432            my @joinWhere = ();
2433            # The final preparatory step is to create a hash table of relation names. The
2434            # table begins with the relation names already in the SELECT command. We may
2435            # need to add relations later if there is filtering on a field in a secondary
2436            # relation. The secondary relations are the ones that contain multiply-
2437            # occurring or optional fields.
2438            my %fromNames = map { $_ => 1 } @sortedNames;
2439            # We are ready to begin. We loop through the object names, replacing each
2440            # object name's field references by the corresponding SQL field reference.
2441            # Along the way, if we find a secondary relation, we will need to add it
2442            # to the FROM clause.
2443            for my $mappedName (@sortedNames) {
2444                # Get the length of the object name plus 2. This is the value we add to the
2445                # size of the field name to determine the size of the field reference as a
2446                # whole.
2447                my $nameLength = 2 + length $mappedName;
2448                # Get the real object name for this mapped name.
2449                my $objectName = $mappedNameHash{$mappedName};
2450                Trace("Processing $mappedName for object $objectName.") if T(4);
2451                # Get the object's field list.
2452                my $fieldList = $self->GetFieldTable($objectName);
2453                # Find the field references for this object.
2454                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
2455                    # At this point, $1 contains the field name, and the current position
2456                    # is set immediately after the final parenthesis. We pull out the name of
2457                    # the field and the position and length of the field reference as a whole.
2458                    my $fieldName = $1;
2459                    my $len = $nameLength + length $fieldName;
2460                    my $pos = pos($filterString) - $len;
2461                    # Insure the field exists.
2462                    if (!exists $fieldList->{$fieldName}) {
2463                        Confess("Field $fieldName not found for object $objectName.");
2464                    } else {
2465                        Trace("Processing $fieldName at position $pos.") if T(4);
2466                        # Get the field's relation.
2467                        my $relationName = $fieldList->{$fieldName}->{relation};
2468                        # Now we have a secondary relation. We need to insure it matches the
2469                        # mapped name of the primary relation. First we peel off the suffix
2470                        # from the mapped name.
2471                        my $mappingSuffix = substr $mappedName, length($objectName);
2472                        # Put the mapping suffix onto the relation name to get the
2473                        # mapped relation name.
2474                        my $mappedRelationName = "$relationName$mappingSuffix";
2475                        # Insure the relation is in the FROM clause.
2476                        if (!exists $fromNames{$mappedRelationName}) {
2477                            # Add the relation to the FROM clause.
2478                            if ($mappedRelationName eq $relationName) {
2479                                # The name is un-mapped, so we add it without
2480                                # any frills.
2481                                $suffix .= ", $relationName";
2482                                push @joinWhere, "$objectName.id = $relationName.id";
2483                            } else {
2484                                # Here we have a mapping situation.
2485                                $suffix .= ", $relationName $mappedRelationName";
2486                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
2487                            }
2488                            # Denote we have this relation available for future fields.
2489                            $fromNames{$mappedRelationName} = 1;
2490                        }
2491                        # Form an SQL field reference from the relation name and the field name.
2492                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
2493                        # Put it into the filter string in place of the old value.
2494                        substr($filterString, $pos, $len) = $sqlReference;
2495                        # Reposition the search.
2496                        pos $filterString = $pos + length $sqlReference;
2497                    }
2498                }
2499            }
2500            # The next step is to join the objects together. We only need to do this if there
2501            # is more than one object in the object list. We start with the first object and
2502            # run through the objects after it. Note also that we make a safety copy of the
2503            # list before running through it.
2504            my @mappedObjectList = @mappedNameList;
2505            my $lastMappedObject = shift @mappedObjectList;
2506            # Get the join table.
2507            my $joinTable = $self->{_metaData}->{Joins};
2508            # Loop through the object list.
2509            for my $thisMappedObject (@mappedObjectList) {
2510                # Look for a join using the real object names.
2511                my $lastObject = $mappedNameHash{$lastMappedObject};
2512                my $thisObject = $mappedNameHash{$thisMappedObject};
2513                my $joinKey = "$lastObject/$thisObject";
2514                if (!exists $joinTable->{$joinKey}) {
2515                    # Here there's no join, so we throw an error.
2516                    Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
2517                } else {
2518                    # Get the join clause.
2519                    my $unMappedJoin = $joinTable->{$joinKey};
2520                    # Fix the names.
2521                    $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
2522                    $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
2523                    push @joinWhere, $unMappedJoin;
2524                    # Save this object as the last object for the next iteration.
2525                    $lastMappedObject = $thisMappedObject;
2526                }
2527            }
2528            # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
2529            # here is we want the filter clause to be empty if there's no WHERE filter.
2530            # We'll put the ORDER BY / LIMIT clauses in the following variable.
2531            my $orderClause = "";
2532            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
2533            # operator so that we find the first occurrence of either verb.
2534            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
2535                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
2536                my $pos = pos $filterString;
2537                $orderClause = $2 . substr($filterString, $pos);
2538                $filterString = $1;
2539            }
2540            # Add the filter and the join clauses (if any) to the SELECT command.
2541            if ($filterString) {
2542                Trace("Filter string is \"$filterString\".") if T(4);
2543                push @joinWhere, "($filterString)";
2544            }
2545            if (@joinWhere) {
2546                $suffix .= " WHERE " . join(' AND ', @joinWhere);
2547            }
2548            # Add the sort or limit clause (if any) to the SELECT command.
2549            if ($orderClause) {
2550                $suffix .= " $orderClause";
2551            }
2552        }
2553        # Return the suffix, the mapped name list, and the mapped name hash.
2554        return ($suffix, \@mappedNameList, \%mappedNameHash);
2555    }
2556    
2557    =head3 GetStatementHandle
2558    
2559    This method will prepare and execute an SQL query, returning the statement handle.
2560    The main reason for doing this here is so that everybody who does SQL queries gets
2561    the benefit of tracing.
2562    
2563    This is an instance method.
2564    
2565    =over 4
2566    
2567    =item command
2568    
2569    Command to prepare and execute.
2570    
2571    =item params
2572    
2573    Reference to a list of the values to be substituted in for the parameter marks.
2574    
2575    =item RETURN
2576    
2577    Returns a prepared and executed statement handle from which the caller can extract
2578    results.
2579    
2580    =back
2581    
2582    =cut
2583    
2584    sub _GetStatementHandle {
2585        # Get the parameters.
2586        my ($self, $command, $params) = @_;
2587        # Trace the query.
2588        Trace("SQL query: $command") if T(SQL => 3);
2589        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
2590        # Get the database handle.
2591        my $dbh = $self->{_dbh};
2592        # Prepare the command.
2593        my $sth = $dbh->prepare_command($command);
2594        # Execute it with the parameters bound in.
2595        $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
2596        # Return the statement handle.
2597        return $sth;
2598    }
2599    
2600  =head3 GetLoadStats  =head3 GetLoadStats
2601    
2602  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
# Line 1654  Line 2606 
2606  =cut  =cut
2607    
2608  sub _GetLoadStats {  sub _GetLoadStats {
2609      return Stats->new('records');      return Stats->new();
2610  }  }
2611    
2612  =head3 GenerateFields  =head3 GenerateFields
# Line 1849  Line 2801 
2801      return $objectData->{Relations};      return $objectData->{Relations};
2802  }  }
2803    
 =head3 GetFieldTable  
   
 Get the field structure for a specified entity or relationship.  
   
 This is an instance method.  
   
 =over 4  
   
 =item objectName  
   
 Name of the desired entity or relationship.  
   
 =item RETURN  
   
 The table containing the field descriptors for the specified object.  
   
 =back  
   
 =cut  
   
 sub _GetFieldTable {  
     # Get the parameters.  
     my ($self, $objectName) = @_;  
     # Get the descriptor from the metadata.  
     my $objectData = $self->_GetStructure($objectName);  
     # Return the object's field table.  
     return $objectData->{Fields};  
 }  
   
2804  =head3 ValidateFieldNames  =head3 ValidateFieldNames
2805    
2806  Determine whether or not the field names are valid. A description of the problems with the names  Determine whether or not the field names are valid. A description of the problems with the names
# Line 2225  Line 3148 
3148          my @fromList = ();          my @fromList = ();
3149          my @toList = ();          my @toList = ();
3150          my @bothList = ();          my @bothList = ();
3151          Trace("Join table build for $entityName.") if T(4);          Trace("Join table build for $entityName.") if T(metadata => 4);
3152          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
3153              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
3154              # 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.
3155              my $fromEntity = $relationship->{from};              my $fromEntity = $relationship->{from};
3156              my $toEntity = $relationship->{to};              my $toEntity = $relationship->{to};
3157              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
3158              if ($fromEntity eq $entityName) {              if ($fromEntity eq $entityName) {
3159                  if ($toEntity eq $entityName) {                  if ($toEntity eq $entityName) {
3160                      # Here the relationship is recursive.                      # Here the relationship is recursive.
3161                      push @bothList, $relationshipName;                      push @bothList, $relationshipName;
3162                      Trace("Relationship $relationshipName put in both-list.") if T(4);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
3163                  } else {                  } else {
3164                      # Here the relationship comes from the entity.                      # Here the relationship comes from the entity.
3165                      push @fromList, $relationshipName;                      push @fromList, $relationshipName;
3166                      Trace("Relationship $relationshipName put in from-list.") if T(4);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
3167                  }                  }
3168              } elsif ($toEntity eq $entityName) {              } elsif ($toEntity eq $entityName) {
3169                  # Here the relationship goes to the entity.                  # Here the relationship goes to the entity.
3170                  push @toList, $relationshipName;                  push @toList, $relationshipName;
3171                  Trace("Relationship $relationshipName put in to-list.") if T(4);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
3172              }              }
3173          }          }
3174          # Create the nonrecursive joins. Note that we build two hashes for running          # Create the nonrecursive joins. Note that we build two hashes for running
# Line 2261  Line 3184 
3184                  # Create joins between the entity and this relationship.                  # Create joins between the entity and this relationship.
3185                  my $linkField = "$relationshipName.${linkType}_link";                  my $linkField = "$relationshipName.${linkType}_link";
3186                  my $joinClause = "$entityName.id = $linkField";                  my $joinClause = "$entityName.id = $linkField";
3187                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(4);                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
3188                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
3189                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
3190                  # Create joins between this relationship and the other relationships.                  # Create joins between this relationship and the other relationships.
# Line 2282  Line 3205 
3205                              # relationship and itself are prohibited.                              # relationship and itself are prohibited.
3206                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";
3207                              $joinTable{$joinKey} = $relJoinClause;                              $joinTable{$joinKey} = $relJoinClause;
3208                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
3209                          }                          }
3210                      }                      }
3211                  }                  }
# Line 2291  Line 3214 
3214                  # relationship can only be ambiguous with another recursive relationship,                  # relationship can only be ambiguous with another recursive relationship,
3215                  # and the incoming relationship from the outer loop is never recursive.                  # and the incoming relationship from the outer loop is never recursive.
3216                  for my $otherName (@bothList) {                  for my $otherName (@bothList) {
3217                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(4);                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
3218                      # Join from the left.                      # Join from the left.
3219                      $joinTable{"$relationshipName/$otherName"} =                      $joinTable{"$relationshipName/$otherName"} =
3220                          "$linkField = $otherName.from_link";                          "$linkField = $otherName.from_link";
# Line 2306  Line 3229 
3229          # rise to situations where we can't create the path we want; however, it is always          # rise to situations where we can't create the path we want; however, it is always
3230          # possible to get the same effect using multiple queries.          # possible to get the same effect using multiple queries.
3231          for my $relationshipName (@bothList) {          for my $relationshipName (@bothList) {
3232              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(4);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
3233              # Join to the entity from each direction.              # Join to the entity from each direction.
3234              $joinTable{"$entityName/$relationshipName"} =              $joinTable{"$entityName/$relationshipName"} =
3235                  "$entityName.id = $relationshipName.from_link";                  "$entityName.id = $relationshipName.from_link";
# Line 2320  Line 3243 
3243      return $metadata;      return $metadata;
3244  }  }
3245    
3246    =head3 SortNeeded
3247    
3248    C<< my $parms = $erdb->SortNeeded($relationName); >>
3249    
3250    Return the pipe command for the sort that should be applied to the specified
3251    relation when creating the load file.
3252    
3253    For example, if the load file should be sorted ascending by the first
3254    field, this method would return
3255    
3256        sort -k1 -t"\t"
3257    
3258    If the first field is numeric, the method would return
3259    
3260        sort -k1n -t"\t"
3261    
3262    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
3263    keys using a sort.
3264    
3265    =over 4
3266    
3267    =item relationName
3268    
3269    Name of the relation to be examined.
3270    
3271    =item
3272    
3273    Returns the sort command to use for sorting the relation, suitable for piping.
3274    
3275    =back
3276    
3277    =cut
3278    #: Return Type $;
3279    sub SortNeeded {
3280        # Get the parameters.
3281        my ($self, $relationName) = @_;
3282        # Declare a descriptor to hold the names of the key fields.
3283        my @keyNames = ();
3284        # Get the relation structure.
3285        my $relationData = $self->_FindRelation($relationName);
3286        # Find out if the relation is a primary entity relation,
3287        # a relationship relation, or a secondary entity relation.
3288        my $entityTable = $self->{_metaData}->{Entities};
3289        my $relationshipTable = $self->{_metaData}->{Relationships};
3290        if (exists $entityTable->{$relationName}) {
3291            # Here we have a primary entity relation.
3292            push @keyNames, "id";
3293        } elsif (exists $relationshipTable->{$relationName}) {
3294            # Here we have a relationship. We sort using the FROM index.
3295            my $relationshipData = $relationshipTable->{$relationName};
3296            my $index = $relationData->{Indexes}->{"idx${relationName}From"};
3297            push @keyNames, @{$index->{IndexFields}};
3298        } else {
3299            # Here we have a secondary entity relation, so we have a sort on the ID field.
3300            push @keyNames, "id";
3301        }
3302        # Now we parse the key names into sort parameters. First, we prime the return
3303        # string.
3304        my $retVal = "sort -t\"\t\" ";
3305        # Get the relation's field list.
3306        my @fields = @{$relationData->{Fields}};
3307        # Loop through the keys.
3308        for my $keyData (@keyNames) {
3309            # Get the key and the ordering.
3310            my ($keyName, $ordering);
3311            if ($keyData =~ /^([^ ]+) DESC/) {
3312                ($keyName, $ordering) = ($1, "descending");
3313            } else {
3314                ($keyName, $ordering) = ($keyData, "ascending");
3315            }
3316            # Find the key's position and type.
3317            my $fieldSpec;
3318            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
3319                my $thisField = $fields[$i];
3320                if ($thisField->{name} eq $keyName) {
3321                    # Get the sort modifier for this field type. The modifier
3322                    # decides whether we're using a character, numeric, or
3323                    # floating-point sort.
3324                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
3325                    # If the index is descending for this field, denote we want
3326                    # to reverse the sort order on this field.
3327                    if ($ordering eq 'descending') {
3328                        $modifier .= "r";
3329                    }
3330                    # Store the position and modifier into the field spec, which
3331                    # will stop the inner loop. Note that the field number is
3332                    # 1-based in the sort command, so we have to increment the
3333                    # index.
3334                    $fieldSpec = ($i + 1) . $modifier;
3335                }
3336            }
3337            # Add this field to the sort command.
3338            $retVal .= " -k$fieldSpec";
3339        }
3340        # Return the result.
3341        return $retVal;
3342    }
3343    
3344  =head3 CreateRelationshipIndex  =head3 CreateRelationshipIndex
3345    
3346  Create an index for a relationship's relation.  Create an index for a relationship's relation.

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