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revision 1.41, Wed Mar 29 20:51:37 2006 UTC revision 1.69, Fri Sep 29 15:06:17 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 =>   1, 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 513  Line 578 
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 687  Line 750 
750      return $retVal;      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 848  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 856  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 873  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.
# Line 930  Line 1066 
1066    
1067  C<< "LIMIT 10" >>  C<< "LIMIT 10" >>
1068    
1069  =item param1, param2, ..., paramN  =item params
1070    
1071  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1072    
1073  =item RETURN  =item RETURN
1074    
# Line 944  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, $params) = @_;
1084      # Adjust the list of object names to account for multiple occurrences of the      # Process the SQL stuff.
1085      # same object. We start with a hash table keyed on object name that will      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1086      # return the object suffix. The first time an object is encountered it will          $self->_SetupSQL($objectNames, $filterClause);
1087      # not be found in the hash. The next time the hash will map the object name      # Create the query.
1088      # to 2, then 3, and so forth.      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1089      my %objectHash = ();          ".* $suffix";
1090      # This list will contain the object names as they are to appear in the      my $sth = $self->_GetStatementHandle($command, $params);
1091      # FROM list.      # Now we create the relation map, which enables DBQuery to determine the order, name
1092      my @fromList = ();      # and mapped name for each object in the query.
1093      # This list contains the suffixed object name for each object. It is exactly      my @relationMap = ();
1094      # parallel to the list in the $objectNames parameter.      for my $mappedName (@{$mappedNameListRef}) {
1095      my @mappedNameList = ();          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
     # Finally, this hash translates from a mapped name to its original object name.  
     my %mappedNameHash = ();  
     # Now we create the lists. Note that for every single name we push something into  
     # @fromList and @mappedNameList. This insures that those two arrays are exactly  
     # parallel to $objectNames.  
     for my $objectName (@{$objectNames}) {  
         # Get the next suffix for this object.  
         my $suffix = $objectHash{$objectName};  
         if (! $suffix) {  
             # Here we are seeing the object for the first time. The object name  
             # is used as is.  
             push @mappedNameList, $objectName;  
             push @fromList, $objectName;  
             $mappedNameHash{$objectName} = $objectName;  
             # Denote the next suffix will be 2.  
             $objectHash{$objectName} = 2;  
         } else {  
             # Here we've seen the object before. We construct a new name using  
             # the suffix from the hash and update the hash.  
             my $mappedName = "$objectName$suffix";  
             $objectHash{$objectName} = $suffix + 1;  
             # The FROM list has the object name followed by the mapped name. This  
             # tells SQL it's still the same table, but we're using a different name  
             # for it to avoid confusion.  
             push @fromList, "$objectName $mappedName";  
             # The mapped-name list contains the real mapped name.  
             push @mappedNameList, $mappedName;  
             # Finally, enable us to get back from the mapped name to the object name.  
             $mappedNameHash{$mappedName} = $objectName;  
         }  
     }  
     # Construct the SELECT statement. The general pattern is  
     #  
     # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN  
     #  
     my $dbh = $self->{_dbh};  
     my $command = "SELECT DISTINCT " . join('.*, ', @mappedNameList) . ".* FROM " .  
                 join(', ', @fromList);  
     # Check for a filter clause.  
     if ($filterClause) {  
         # Here we have one, so we convert its field names and add it to the query. First,  
         # We create a copy of the filter string we can work with.  
         my $filterString = $filterClause;  
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @mappedNameList;  
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command. We may  
         # need to add relations later if there is filtering on a field in a secondary  
         # relation. The secondary relations are the ones that contain multiply-  
         # occurring or optional fields.  
         my %fromNames = map { $_ => 1 } @sortedNames;  
         # We are ready to begin. We loop through the object names, replacing each  
         # object name's field references by the corresponding SQL field reference.  
         # Along the way, if we find a secondary relation, we will need to add it  
         # to the FROM clause.  
         for my $mappedName (@sortedNames) {  
             # Get the length of the object name plus 2. This is the value we add to the  
             # size of the field name to determine the size of the field reference as a  
             # whole.  
             my $nameLength = 2 + length $mappedName;  
             # Get the real object name for this mapped name.  
             my $objectName = $mappedNameHash{$mappedName};  
             Trace("Processing $mappedName for object $objectName.") if T(4);  
             # Get the object's field list.  
             my $fieldList = $self->GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {  
                 # At this point, $1 contains the field name, and the current position  
                 # is set immediately after the final parenthesis. We pull out the name of  
                 # the field and the position and length of the field reference as a whole.  
                 my $fieldName = $1;  
                 my $len = $nameLength + length $fieldName;  
                 my $pos = pos($filterString) - $len;  
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
                 } else {  
                     Trace("Processing $fieldName at position $pos.") if T(4);  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Now we have a secondary relation. We need to insure it matches the  
                     # mapped name of the primary relation. First we peel off the suffix  
                     # from the mapped name.  
                     my $mappingSuffix = substr $mappedName, length($objectName);  
                     # Put the mapping suffix onto the relation name to get the  
                     # mapped relation name.  
                     my $mappedRelationName = "$relationName$mappingSuffix";  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$mappedRelationName}) {  
                         # Add the relation to the FROM clause.  
                         if ($mappedRelationName eq $relationName) {  
                             # The name is un-mapped, so we add it without  
                             # any frills.  
                             $command .= ", $relationName";  
                             push @joinWhere, "$objectName.id = $relationName.id";  
                         } else {  
                             # Here we have a mapping situation.  
                             $command .= ", $relationName $mappedRelationName";  
                             push @joinWhere, "$mappedRelationName.id = $mappedName.id";  
                         }  
                         # Denote we have this relation available for future fields.  
                         $fromNames{$mappedRelationName} = 1;  
1096                      }                      }
1097                      # Form an SQL field reference from the relation name and the field name.      # Return the statement object.
1098                      my $sqlReference = "$mappedRelationName." . _FixName($fieldName);      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1099                      # Put it into the filter string in place of the old value.      return $retVal;
                     substr($filterString, $pos, $len) = $sqlReference;  
                     # Reposition the search.  
                     pos $filterString = $pos + length $sqlReference;  
1100                  }                  }
1101    
1102    =head3 GetFlat
1103    
1104    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1105    
1106    This is a variation of L</GetAll> that asks for only a single field per record and
1107    returns a single flattened list.
1108    
1109    =over 4
1110    
1111    =item objectNames
1112    
1113    List containing the names of the entity and relationship objects to be retrieved.
1114    
1115    =item filterClause
1116    
1117    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1118    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1119    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1120    parameter list as additional parameters. The fields in a filter clause can come from primary
1121    entity relations, relationship relations, or secondary entity relations; however, all of the
1122    entities and relationships involved must be included in the list of object names.
1123    
1124    =item parameterList
1125    
1126    List of the parameters to be substituted in for the parameters marks in the filter clause.
1127    
1128    =item field
1129    
1130    Name of the field to be used to get the elements of the list returned.
1131    
1132    =item RETURN
1133    
1134    Returns a list of values.
1135    
1136    =back
1137    
1138    =cut
1139    #: Return Type @;
1140    sub GetFlat {
1141        # Get the parameters.
1142        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1143        # Construct the query.
1144        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1145        # Create the result list.
1146        my @retVal = ();
1147        # Loop through the records, adding the field values found to the result list.
1148        while (my $row = $query->Fetch()) {
1149            push @retVal, $row->Value($field);
1150              }              }
1151          }      # Return the list created.
1152          # The next step is to join the objects together. We only need to do this if there      return @retVal;
         # is more than one object in the object list. We start with the first object and  
         # run through the objects after it. Note also that we make a safety copy of the  
         # list before running through it.  
         my @mappedObjectList = @mappedNameList;  
         my $lastMappedObject = shift @mappedObjectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisMappedObject (@mappedObjectList) {  
             # Look for a join using the real object names.  
             my $lastObject = $mappedNameHash{$lastMappedObject};  
             my $thisObject = $mappedNameHash{$thisMappedObject};  
             my $joinKey = "$lastObject/$thisObject";  
             if (!exists $joinTable->{$joinKey}) {  
                 # Here there's no join, so we throw an error.  
                 Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");  
             } else {  
                 # Get the join clause.  
                 my $unMappedJoin = $joinTable->{$joinKey};  
                 # Fix the names.  
                 $unMappedJoin =~ s/$lastObject/$lastMappedObject/;  
                 $unMappedJoin =~ s/$thisObject/$thisMappedObject/;  
                 push @joinWhere, $unMappedJoin;  
                 # Save this object as the last object for the next iteration.  
                 $lastMappedObject = $thisMappedObject;  
             }  
         }  
         # Now we need to handle the whole ORDER BY / LIMIT thing. The important part  
         # here is we want the filter clause to be empty if there's no WHERE filter.  
         # We'll put the ORDER BY / LIMIT clauses in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy  
         # operator so that we find the first occurrence of either verb.  
         if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {  
             # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = $2 . substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             Trace("Filter string is \"$filterString\".") if T(4);  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort or limit clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " $orderClause";  
         }  
     }  
     Trace("SQL query: $command") if T(SQL => 3);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
     # Now we create the relation map, which enables DBQuery to determine the order, name  
     # and mapped name for each object in the query.  
     my @relationMap = ();  
     for my $mappedName (@mappedNameList) {  
         push @relationMap, [$mappedName, $mappedNameHash{$mappedName}];  
     }  
     # Return the statement object.  
     my $retVal = DBQuery::_new($self, $sth, \@relationMap);  
     return $retVal;  
1153  }  }
1154    
1155  =head3 Delete  =head3 Delete
# Line 1312  Line 1322 
1322    
1323  =head3 GetList  =head3 GetList
1324    
1325  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1326    
1327  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
1328  specified filter clause.  specified filter clause.
# Line 1346  Line 1356 
1356  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1357  relation.  relation.
1358    
1359  =item param1, param2, ..., paramN  =item params
1360    
1361  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1362    
1363  =item RETURN  =item RETURN
1364    
# Line 1360  Line 1370 
1370  #: Return Type @%  #: Return Type @%
1371  sub GetList {  sub GetList {
1372      # Get the parameters.      # Get the parameters.
1373      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1374      # Declare the return variable.      # Declare the return variable.
1375      my @retVal = ();      my @retVal = ();
1376      # Perform the query.      # Perform the query.
1377      my $query = $self->Get($objectNames, $filterClause, @params);      my $query = $self->Get($objectNames, $filterClause, $params);
1378      # Loop through the results.      # Loop through the results.
1379      while (my $object = $query->Fetch) {      while (my $object = $query->Fetch) {
1380          push @retVal, $object;          push @retVal, $object;
# Line 1373  Line 1383 
1383      return @retVal;      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  =head3 ComputeObjectSentence
1480    
1481  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
# Line 1450  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 1466  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 1676  Line 1842 
1842          }          }
1843      }      }
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 $retVal;
1850  }  }
# Line 1768  Line 1936 
1936      # Get the parameters.      # Get the parameters.
1937      my ($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.
1943      return $retVal;      return $retVal;
1944  }  }
1945    
1946    =head3 GetChoices
1947    
1948    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
1949    
1950    Return a list of all the values for the specified field that are represented in the
1951    specified entity.
1952    
1953    Note that if the field is not indexed, then this will be a very slow operation.
1954    
1955    =over 4
1956    
1957    =item entityName
1958    
1959    Name of an entity in the database.
1960    
1961    =item fieldName
1962    
1963    Name of a field belonging to the entity. This is a raw field name without
1964    the standard parenthesized notation used in most calls.
1965    
1966    =item RETURN
1967    
1968    Returns a list of the distinct values for the specified field in the database.
1969    
1970    =back
1971    
1972    =cut
1973    
1974    sub GetChoices {
1975        # Get the parameters.
1976        my ($self, $entityName, $fieldName) = @_;
1977        # Declare the return variable.
1978        my @retVal;
1979        # Get the entity data structure.
1980        my $entityData = $self->_GetStructure($entityName);
1981        # Get the field.
1982        my $fieldHash = $entityData->{Fields};
1983        if (! exists $fieldHash->{$fieldName}) {
1984            Confess("$fieldName not found in $entityName.");
1985        } else {
1986            # Get the name of the relation containing the field.
1987            my $relation = $fieldHash->{$fieldName}->{relation};
1988            # Fix up the field name.
1989            my $realName = _FixName($fieldName);
1990            # Get the database handle.
1991            my $dbh = $self->{_dbh};
1992            # Query the database.
1993            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
1994            # Clean the results. They are stored as a list of lists, and we just want the one list.
1995            @retVal = sort map { $_->[0] } @{$results};
1996        }
1997        # Return the result.
1998        return @retVal;
1999    }
2000    
2001  =head3 GetEntityValues  =head3 GetEntityValues
2002    
2003  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2004    
2005  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance. If the entity instance
2006    does not exist, an empty list is returned.
2007    
2008  =over 4  =over 4
2009    
# Line 1881  Line 2105 
2105      # list is a scalar we convert it into a singleton list.      # list is a scalar we convert it into a singleton list.
2106      my @parmList = ();      my @parmList = ();
2107      if (ref $parameterList eq "ARRAY") {      if (ref $parameterList eq "ARRAY") {
2108            Trace("GetAll parm list is an array.") if T(4);
2109          @parmList = @{$parameterList};          @parmList = @{$parameterList};
2110      } else {      } else {
2111            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2112          push @parmList, $parameterList;          push @parmList, $parameterList;
2113      }      }
2114      # Insure the counter has a value.      # Insure the counter has a value.
# Line 1894  Line 2120 
2120          $filterClause .= " LIMIT $count";          $filterClause .= " LIMIT $count";
2121      }      }
2122      # Create the query.      # Create the query.
2123      my $query = $self->Get($objectNames, $filterClause, @parmList);      my $query = $self->Get($objectNames, $filterClause, \@parmList);
2124      # Set up a counter of the number of records read.      # Set up a counter of the number of records read.
2125      my $fetched = 0;      my $fetched = 0;
2126      # Loop through the records returned, extracting the fields. Note that if the      # Loop through the records returned, extracting the fields. Note that if the
# Line 1905  Line 2131 
2131          push @retVal, \@rowData;          push @retVal, \@rowData;
2132          $fetched++;          $fetched++;
2133      }      }
2134        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2135      # Return the resulting list.      # Return the resulting list.
2136      return @retVal;      return @retVal;
2137  }  }
2138    
2139    =head3 Exists
2140    
2141    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2142    
2143    Return TRUE if an entity exists, else FALSE.
2144    
2145    =over 4
2146    
2147    =item entityName
2148    
2149    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2150    
2151    =item entityID
2152    
2153    ID of the entity instance whose existence is to be checked.
2154    
2155    =item RETURN
2156    
2157    Returns TRUE if the entity instance exists, else FALSE.
2158    
2159    =back
2160    
2161    =cut
2162    #: Return Type $;
2163    sub Exists {
2164        # Get the parameters.
2165        my ($self, $entityName, $entityID) = @_;
2166        # Check for the entity instance.
2167        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2168        my $testInstance = $self->GetEntity($entityName, $entityID);
2169        # Return an existence indicator.
2170        my $retVal = ($testInstance ? 1 : 0);
2171        return $retVal;
2172    }
2173    
2174  =head3 EstimateRowSize  =head3 EstimateRowSize
2175    
2176  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
# Line 1976  Line 2238 
2238      return $objectData->{Fields};      return $objectData->{Fields};
2239  }  }
2240    
2241    =head2 Data Mining Methods
2242    
2243  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
2244    
2245  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
# Line 2037  Line 2301 
2301      return @retVal;      return @retVal;
2302  }  }
2303    
2304    =head3 FindColumn
2305    
2306    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2307    
2308    Return the location a desired column in a data mining header line. The data
2309    mining header line is a tab-separated list of column names. The column
2310    identifier is either the numerical index of a column or the actual column
2311    name.
2312    
2313    =over 4
2314    
2315    =item headerLine
2316    
2317    The header line from a data mining command, which consists of a tab-separated
2318    list of column names.
2319    
2320    =item columnIdentifier
2321    
2322    Either the ordinal number of the desired column (1-based), or the name of the
2323    desired column.
2324    
2325    =item RETURN
2326    
2327    Returns the array index (0-based) of the desired column.
2328    
2329    =back
2330    
2331    =cut
2332    
2333    sub FindColumn {
2334        # Get the parameters.
2335        my ($headerLine, $columnIdentifier) = @_;
2336        # Declare the return variable.
2337        my $retVal;
2338        # Split the header line into column names.
2339        my @headers = ParseColumns($headerLine);
2340        # Determine whether we have a number or a name.
2341        if ($columnIdentifier =~ /^\d+$/) {
2342            # Here we have a number. Subtract 1 and validate the result.
2343            $retVal = $columnIdentifier - 1;
2344            if ($retVal < 0 || $retVal > $#headers) {
2345                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2346            }
2347        } else {
2348            # Here we have a name. We need to find it in the list.
2349            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2350                if ($headers[$i] eq $columnIdentifier) {
2351                    $retVal = $i;
2352                }
2353            }
2354            if (! defined($retVal)) {
2355                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2356            }
2357        }
2358        # Return the result.
2359        return $retVal;
2360    }
2361    
2362    =head3 ParseColumns
2363    
2364    C<< my @columns = ERDB::ParseColumns($line); >>
2365    
2366    Convert the specified data line to a list of columns.
2367    
2368    =over 4
2369    
2370    =item line
2371    
2372    A data mining input, consisting of a tab-separated list of columns terminated by a
2373    new-line.
2374    
2375    =item RETURN
2376    
2377    Returns a list consisting of the column values.
2378    
2379    =back
2380    
2381    =cut
2382    
2383    sub ParseColumns {
2384        # Get the parameters.
2385        my ($line) = @_;
2386        # Chop off the line-end.
2387        chomp $line;
2388        # Split it into a list.
2389        my @retVal = split(/\t/, $line);
2390        # Return the result.
2391        return @retVal;
2392    }
2393    
2394  =head2 Internal Utility Methods  =head2 Internal Utility Methods
2395    
2396    =head3 SetupSQL
2397    
2398    Process a list of object names and a filter clause so that they can be used to
2399    build an SQL statement. This method takes in a reference to a list of object names
2400    and a filter clause. It will return a corrected filter clause, a list of mapped
2401    names and the mapped name hash.
2402    
2403    This is an instance method.
2404    
2405    =over 4
2406    
2407    =item objectNames
2408    
2409    Reference to a list of the object names to be included in the query.
2410    
2411    =item filterClause
2412    
2413    A string containing the WHERE clause for the query (without the C<WHERE>) and also
2414    optionally the C<ORDER BY> and C<LIMIT> clauses.
2415    
2416    =item RETURN
2417    
2418    Returns a three-element list. The first element is the SQL statement suffix, beginning
2419    with the FROM clause. The second element is a reference to a list of the names to be
2420    used in retrieving the fields. The third element is a hash mapping the names to the
2421    objects they represent.
2422    
2423    =back
2424    
2425    =cut
2426    
2427    sub _SetupSQL {
2428        my ($self, $objectNames, $filterClause) = @_;
2429        # Adjust the list of object names to account for multiple occurrences of the
2430        # same object. We start with a hash table keyed on object name that will
2431        # return the object suffix. The first time an object is encountered it will
2432        # not be found in the hash. The next time the hash will map the object name
2433        # to 2, then 3, and so forth.
2434        my %objectHash = ();
2435        # This list will contain the object names as they are to appear in the
2436        # FROM list.
2437        my @fromList = ();
2438        # This list contains the suffixed object name for each object. It is exactly
2439        # parallel to the list in the $objectNames parameter.
2440        my @mappedNameList = ();
2441        # Finally, this hash translates from a mapped name to its original object name.
2442        my %mappedNameHash = ();
2443        # Now we create the lists. Note that for every single name we push something into
2444        # @fromList and @mappedNameList. This insures that those two arrays are exactly
2445        # parallel to $objectNames.
2446        for my $objectName (@{$objectNames}) {
2447            # Get the next suffix for this object.
2448            my $suffix = $objectHash{$objectName};
2449            if (! $suffix) {
2450                # Here we are seeing the object for the first time. The object name
2451                # is used as is.
2452                push @mappedNameList, $objectName;
2453                push @fromList, $objectName;
2454                $mappedNameHash{$objectName} = $objectName;
2455                # Denote the next suffix will be 2.
2456                $objectHash{$objectName} = 2;
2457            } else {
2458                # Here we've seen the object before. We construct a new name using
2459                # the suffix from the hash and update the hash.
2460                my $mappedName = "$objectName$suffix";
2461                $objectHash{$objectName} = $suffix + 1;
2462                # The FROM list has the object name followed by the mapped name. This
2463                # tells SQL it's still the same table, but we're using a different name
2464                # for it to avoid confusion.
2465                push @fromList, "$objectName $mappedName";
2466                # The mapped-name list contains the real mapped name.
2467                push @mappedNameList, $mappedName;
2468                # Finally, enable us to get back from the mapped name to the object name.
2469                $mappedNameHash{$mappedName} = $objectName;
2470            }
2471        }
2472        # Begin the SELECT suffix. It starts with
2473        #
2474        # FROM name1, name2, ... nameN
2475        #
2476        my $suffix = "FROM " . join(', ', @fromList);
2477        # Check for a filter clause.
2478        if ($filterClause) {
2479            # Here we have one, so we convert its field names and add it to the query. First,
2480            # We create a copy of the filter string we can work with.
2481            my $filterString = $filterClause;
2482            # Next, we sort the object names by length. This helps protect us from finding
2483            # object names inside other object names when we're doing our search and replace.
2484            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
2485            # We will also keep a list of conditions to add to the WHERE clause in order to link
2486            # entities and relationships as well as primary relations to secondary ones.
2487            my @joinWhere = ();
2488            # The final preparatory step is to create a hash table of relation names. The
2489            # table begins with the relation names already in the SELECT command. We may
2490            # need to add relations later if there is filtering on a field in a secondary
2491            # relation. The secondary relations are the ones that contain multiply-
2492            # occurring or optional fields.
2493            my %fromNames = map { $_ => 1 } @sortedNames;
2494            # We are ready to begin. We loop through the object names, replacing each
2495            # object name's field references by the corresponding SQL field reference.
2496            # Along the way, if we find a secondary relation, we will need to add it
2497            # to the FROM clause.
2498            for my $mappedName (@sortedNames) {
2499                # Get the length of the object name plus 2. This is the value we add to the
2500                # size of the field name to determine the size of the field reference as a
2501                # whole.
2502                my $nameLength = 2 + length $mappedName;
2503                # Get the real object name for this mapped name.
2504                my $objectName = $mappedNameHash{$mappedName};
2505                Trace("Processing $mappedName for object $objectName.") if T(4);
2506                # Get the object's field list.
2507                my $fieldList = $self->GetFieldTable($objectName);
2508                # Find the field references for this object.
2509                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
2510                    # At this point, $1 contains the field name, and the current position
2511                    # is set immediately after the final parenthesis. We pull out the name of
2512                    # the field and the position and length of the field reference as a whole.
2513                    my $fieldName = $1;
2514                    my $len = $nameLength + length $fieldName;
2515                    my $pos = pos($filterString) - $len;
2516                    # Insure the field exists.
2517                    if (!exists $fieldList->{$fieldName}) {
2518                        Confess("Field $fieldName not found for object $objectName.");
2519                    } else {
2520                        Trace("Processing $fieldName at position $pos.") if T(4);
2521                        # Get the field's relation.
2522                        my $relationName = $fieldList->{$fieldName}->{relation};
2523                        # Now we have a secondary relation. We need to insure it matches the
2524                        # mapped name of the primary relation. First we peel off the suffix
2525                        # from the mapped name.
2526                        my $mappingSuffix = substr $mappedName, length($objectName);
2527                        # Put the mapping suffix onto the relation name to get the
2528                        # mapped relation name.
2529                        my $mappedRelationName = "$relationName$mappingSuffix";
2530                        # Insure the relation is in the FROM clause.
2531                        if (!exists $fromNames{$mappedRelationName}) {
2532                            # Add the relation to the FROM clause.
2533                            if ($mappedRelationName eq $relationName) {
2534                                # The name is un-mapped, so we add it without
2535                                # any frills.
2536                                $suffix .= ", $relationName";
2537                                push @joinWhere, "$objectName.id = $relationName.id";
2538                            } else {
2539                                # Here we have a mapping situation.
2540                                $suffix .= ", $relationName $mappedRelationName";
2541                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
2542                            }
2543                            # Denote we have this relation available for future fields.
2544                            $fromNames{$mappedRelationName} = 1;
2545                        }
2546                        # Form an SQL field reference from the relation name and the field name.
2547                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
2548                        # Put it into the filter string in place of the old value.
2549                        substr($filterString, $pos, $len) = $sqlReference;
2550                        # Reposition the search.
2551                        pos $filterString = $pos + length $sqlReference;
2552                    }
2553                }
2554            }
2555            # The next step is to join the objects together. We only need to do this if there
2556            # is more than one object in the object list. We start with the first object and
2557            # run through the objects after it. Note also that we make a safety copy of the
2558            # list before running through it.
2559            my @mappedObjectList = @mappedNameList;
2560            my $lastMappedObject = shift @mappedObjectList;
2561            # Get the join table.
2562            my $joinTable = $self->{_metaData}->{Joins};
2563            # Loop through the object list.
2564            for my $thisMappedObject (@mappedObjectList) {
2565                # Look for a join using the real object names.
2566                my $lastObject = $mappedNameHash{$lastMappedObject};
2567                my $thisObject = $mappedNameHash{$thisMappedObject};
2568                my $joinKey = "$lastObject/$thisObject";
2569                if (!exists $joinTable->{$joinKey}) {
2570                    # Here there's no join, so we throw an error.
2571                    Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
2572                } else {
2573                    # Get the join clause.
2574                    my $unMappedJoin = $joinTable->{$joinKey};
2575                    # Fix the names.
2576                    $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
2577                    $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
2578                    push @joinWhere, $unMappedJoin;
2579                    # Save this object as the last object for the next iteration.
2580                    $lastMappedObject = $thisMappedObject;
2581                }
2582            }
2583            # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
2584            # here is we want the filter clause to be empty if there's no WHERE filter.
2585            # We'll put the ORDER BY / LIMIT clauses in the following variable.
2586            my $orderClause = "";
2587            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
2588            # operator so that we find the first occurrence of either verb.
2589            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
2590                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
2591                my $pos = pos $filterString;
2592                $orderClause = $2 . substr($filterString, $pos);
2593                $filterString = $1;
2594            }
2595            # Add the filter and the join clauses (if any) to the SELECT command.
2596            if ($filterString) {
2597                Trace("Filter string is \"$filterString\".") if T(4);
2598                push @joinWhere, "($filterString)";
2599            }
2600            if (@joinWhere) {
2601                $suffix .= " WHERE " . join(' AND ', @joinWhere);
2602            }
2603            # Add the sort or limit clause (if any) to the SELECT command.
2604            if ($orderClause) {
2605                $suffix .= " $orderClause";
2606            }
2607        }
2608        # Return the suffix, the mapped name list, and the mapped name hash.
2609        return ($suffix, \@mappedNameList, \%mappedNameHash);
2610    }
2611    
2612    =head3 GetStatementHandle
2613    
2614    This method will prepare and execute an SQL query, returning the statement handle.
2615    The main reason for doing this here is so that everybody who does SQL queries gets
2616    the benefit of tracing.
2617    
2618    This is an instance method.
2619    
2620    =over 4
2621    
2622    =item command
2623    
2624    Command to prepare and execute.
2625    
2626    =item params
2627    
2628    Reference to a list of the values to be substituted in for the parameter marks.
2629    
2630    =item RETURN
2631    
2632    Returns a prepared and executed statement handle from which the caller can extract
2633    results.
2634    
2635    =back
2636    
2637    =cut
2638    
2639    sub _GetStatementHandle {
2640        # Get the parameters.
2641        my ($self, $command, $params) = @_;
2642        # Trace the query.
2643        Trace("SQL query: $command") if T(SQL => 3);
2644        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
2645        # Get the database handle.
2646        my $dbh = $self->{_dbh};
2647        # Prepare the command.
2648        my $sth = $dbh->prepare_command($command);
2649        # Execute it with the parameters bound in.
2650        $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
2651        # Return the statement handle.
2652        return $sth;
2653    }
2654    
2655  =head3 GetLoadStats  =head3 GetLoadStats
2656    
2657  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
# Line 2685  Line 3298 
3298      return $metadata;      return $metadata;
3299  }  }
3300    
3301    =head3 SortNeeded
3302    
3303    C<< my $parms = $erdb->SortNeeded($relationName); >>
3304    
3305    Return the pipe command for the sort that should be applied to the specified
3306    relation when creating the load file.
3307    
3308    For example, if the load file should be sorted ascending by the first
3309    field, this method would return
3310    
3311        sort -k1 -t"\t"
3312    
3313    If the first field is numeric, the method would return
3314    
3315        sort -k1n -t"\t"
3316    
3317    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
3318    keys using a sort.
3319    
3320    =over 4
3321    
3322    =item relationName
3323    
3324    Name of the relation to be examined.
3325    
3326    =item
3327    
3328    Returns the sort command to use for sorting the relation, suitable for piping.
3329    
3330    =back
3331    
3332    =cut
3333    #: Return Type $;
3334    sub SortNeeded {
3335        # Get the parameters.
3336        my ($self, $relationName) = @_;
3337        # Declare a descriptor to hold the names of the key fields.
3338        my @keyNames = ();
3339        # Get the relation structure.
3340        my $relationData = $self->_FindRelation($relationName);
3341        # Find out if the relation is a primary entity relation,
3342        # a relationship relation, or a secondary entity relation.
3343        my $entityTable = $self->{_metaData}->{Entities};
3344        my $relationshipTable = $self->{_metaData}->{Relationships};
3345        if (exists $entityTable->{$relationName}) {
3346            # Here we have a primary entity relation.
3347            push @keyNames, "id";
3348        } elsif (exists $relationshipTable->{$relationName}) {
3349            # Here we have a relationship. We sort using the FROM index.
3350            my $relationshipData = $relationshipTable->{$relationName};
3351            my $index = $relationData->{Indexes}->{"idx${relationName}From"};
3352            push @keyNames, @{$index->{IndexFields}};
3353        } else {
3354            # Here we have a secondary entity relation, so we have a sort on the ID field.
3355            push @keyNames, "id";
3356        }
3357        # Now we parse the key names into sort parameters. First, we prime the return
3358        # string.
3359        my $retVal = "sort -t\"\t\" ";
3360        # Get the relation's field list.
3361        my @fields = @{$relationData->{Fields}};
3362        # Loop through the keys.
3363        for my $keyData (@keyNames) {
3364            # Get the key and the ordering.
3365            my ($keyName, $ordering);
3366            if ($keyData =~ /^([^ ]+) DESC/) {
3367                ($keyName, $ordering) = ($1, "descending");
3368            } else {
3369                ($keyName, $ordering) = ($keyData, "ascending");
3370            }
3371            # Find the key's position and type.
3372            my $fieldSpec;
3373            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
3374                my $thisField = $fields[$i];
3375                if ($thisField->{name} eq $keyName) {
3376                    # Get the sort modifier for this field type. The modifier
3377                    # decides whether we're using a character, numeric, or
3378                    # floating-point sort.
3379                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
3380                    # If the index is descending for this field, denote we want
3381                    # to reverse the sort order on this field.
3382                    if ($ordering eq 'descending') {
3383                        $modifier .= "r";
3384                    }
3385                    # Store the position and modifier into the field spec, which
3386                    # will stop the inner loop. Note that the field number is
3387                    # 1-based in the sort command, so we have to increment the
3388                    # index.
3389                    $fieldSpec = ($i + 1) . $modifier;
3390                }
3391            }
3392            # Add this field to the sort command.
3393            $retVal .= " -k$fieldSpec";
3394        }
3395        # Return the result.
3396        return $retVal;
3397    }
3398    
3399  =head3 CreateRelationshipIndex  =head3 CreateRelationshipIndex
3400    
3401  Create an index for a relationship's relation.  Create an index for a relationship's relation.

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