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revision 1.16, Tue Jun 28 23:51:06 2005 UTC revision 1.44, Sat May 27 02:02:28 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;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
16    
# Line 108  Line 110 
110  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
111  0 and 1.  0 and 1.
112    
113    =item id-string
114    
115    variable-length string, maximum 25 characters
116    
117  =item key-string  =item key-string
118    
119  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 124  Line 130 
130    
131  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
132    
133    =item hash-string
134    
135    variable-length string, maximum 22 characters
136    
137  =back  =back
138    
139    The hash-string data type has a special meaning. The actual key passed into the loader will
140    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
141    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
142    digest. Therefore, it is presumed the keys will be unique. When the database is actually
143    in use, the hashed keys will be presented rather than the original values. For this reason,
144    they should not be used for entities where the key is meaningful.
145    
146  =head3 Global Tags  =head3 Global Tags
147    
148  The entire database definition must be inside a B<Database> tag. The display name of  The entire database definition must be inside a B<Database> tag. The display name of
# Line 300  Line 317 
317  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
318  # "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
319  # 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
320   #string is specified in the field definition.  # string is specified in the field definition. "avgLen" is the average byte length for estimating
321  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            dataGen => "StringGen('A')" },  # record sizes.
322                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },
323                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          dataGen => "StringGen(IntGen(10,250))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },
324                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },
325                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },
326                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           dataGen => "FloatGen(0.0, 100.0)" },                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
327                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            dataGen => "IntGen(0, 1)" },                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },
328                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },
329                     'hash-string' =>
330                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },
331                     'id-string' =>
332                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, dataGen => "SringGen(22)" },
333                   'key-string' =>                   'key-string' =>
334                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },
335                   'name-string' =>                   'name-string' =>
336                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },
337                   'medium-string' =>                   'medium-string' =>
338                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },
339                  );                  );
340    
341  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 369  Line 391 
391    
392  =head3 ShowMetaData  =head3 ShowMetaData
393    
394  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
395    
396  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
397  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 506  Line 528 
528          # Separate out the source, the target, and the join clause.          # Separate out the source, the target, and the join clause.
529          $joinKey =~ m!^([^/]+)/(.+)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
530          my ($sourceRelation, $targetRelation) = ($1, $2);          my ($sourceRelation, $targetRelation) = ($1, $2);
531          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);
532          my $source = $self->ComputeObjectSentence($sourceRelation);          my $source = $self->ComputeObjectSentence($sourceRelation);
533          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
534          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
# Line 524  Line 546 
546    
547  =head3 DumpMetaData  =head3 DumpMetaData
548    
549  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
550    
551  Return a dump of the metadata structure.  Return a dump of the metadata structure.
552    
# Line 539  Line 561 
561    
562  =head3 CreateTables  =head3 CreateTables
563    
564  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
565    
566  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
567  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 551  Line 573 
573  sub CreateTables {  sub CreateTables {
574      # Get the parameters.      # Get the parameters.
575      my ($self) = @_;      my ($self) = @_;
576      my $metadata = $self->{_metaData};      # Get the relation names.
577      my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
578      # Loop through the entities.      # Loop through the relations.
579      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}}) {  
580              # Create a table for this relation.              # Create a table for this relation.
581              $self->CreateTable($relationName);              $self->CreateTable($relationName);
582              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);  
583      }      }
584  }  }
585    
586  =head3 CreateTable  =head3 CreateTable
587    
588  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
589    
590  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
591    
# Line 587  Line 595 
595    
596  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
597    
598  =item $indexFlag  =item indexFlag
599    
600  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
601  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
602    
603    =item estimatedRows (optional)
604    
605    If specified, the estimated maximum number of rows for the relation. This
606    information allows the creation of tables using storage engines that are
607    faster but require size estimates, such as MyISAM.
608    
609  =back  =back
610    
611  =cut  =cut
612    
613  sub CreateTable {  sub CreateTable {
614      # Get the parameters.      # Get the parameters.
615      my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
616      # Get the database handle.      # Get the database handle.
617      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
618      # Get the relation data and determine whether or not the relation is primary.      # Get the relation data and determine whether or not the relation is primary.
# Line 622  Line 636 
636      # Insure the table is not already there.      # Insure the table is not already there.
637      $dbh->drop_table(tbl => $relationName);      $dbh->drop_table(tbl => $relationName);
638      Trace("Table $relationName dropped.") if T(2);      Trace("Table $relationName dropped.") if T(2);
639        # If there are estimated rows, create an estimate so we can take advantage of
640        # faster DB technologies.
641        my $estimation = undef;
642        if ($estimatedRows) {
643            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
644        }
645      # Create the table.      # Create the table.
646      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
647      $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
648      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
649      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here.
650      if ($indexFlag) {      if ($indexFlag) {
# Line 632  Line 652 
652      }      }
653  }  }
654    
655    =head3 VerifyFields
656    
657    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
658    
659    Run through the list of proposed field values, insuring that all the character fields are
660    below the maximum length. If any fields are too long, they will be truncated in place.
661    
662    =over 4
663    
664    =item relName
665    
666    Name of the relation for which the specified fields are destined.
667    
668    =item fieldList
669    
670    Reference to a list, in order, of the fields to be put into the relation.
671    
672    =item RETURN
673    
674    Returns the number of fields truncated.
675    
676    =back
677    
678    =cut
679    
680    sub VerifyFields {
681        # Get the parameters.
682        my ($self, $relName, $fieldList) = @_;
683        # Initialize the return value.
684        my $retVal = 0;
685        # Get the relation definition.
686        my $relData = $self->_FindRelation($relName);
687        # Get the list of field descriptors.
688        my $fieldTypes = $relData->{Fields};
689        my $fieldCount = scalar @{$fieldTypes};
690        # Loop through the two lists.
691        for (my $i = 0; $i < $fieldCount; $i++) {
692            # Get the type of the current field.
693            my $fieldType = $fieldTypes->[$i]->{type};
694            # If it's a character field, verify the length.
695            if ($fieldType =~ /string/) {
696                my $maxLen = $TypeTable{$fieldType}->{maxLen};
697                my $oldString = $fieldList->[$i];
698                if (length($oldString) > $maxLen) {
699                    # Here it's too big, so we truncate it.
700                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
701                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
702                    $retVal++;
703                }
704            }
705        }
706        # Return the truncation count.
707        return $retVal;
708    }
709    
710    =head3 DigestFields
711    
712    C<< $erdb->DigestFields($relName, $fieldList); >>
713    
714    Digest the strings in the field list that correspond to data type C<hash-string> in the
715    specified relation.
716    
717    =over 4
718    
719    =item relName
720    
721    Name of the relation to which the fields belong.
722    
723    =item fieldList
724    
725    List of field contents to be loaded into the relation.
726    
727    =back
728    
729    =cut
730    #: Return Type ;
731    sub DigestFields {
732        # Get the parameters.
733        my ($self, $relName, $fieldList) = @_;
734        # Get the relation definition.
735        my $relData = $self->_FindRelation($relName);
736        # Get the list of field descriptors.
737        my $fieldTypes = $relData->{Fields};
738        my $fieldCount = scalar @{$fieldTypes};
739        # Loop through the two lists.
740        for (my $i = 0; $i < $fieldCount; $i++) {
741            # Get the type of the current field.
742            my $fieldType = $fieldTypes->[$i]->{type};
743            # If it's a hash string, digest it in place.
744            if ($fieldType eq 'hash-string') {
745                $fieldList->[$i] = md5_base64($fieldList->[$i]);
746            }
747        }
748    }
749    
750  =head3 CreateIndex  =head3 CreateIndex
751    
752  C<< $database->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
753    
754  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
755  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
# Line 660  Line 775 
775          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
776          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
777          # Create the index.          # Create the index.
778          $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
779                                        flds => $flds, unique => $unique);
780            if ($rv) {
781          Trace("Index created: $indexName for $relationName ($flds)") if T(1);          Trace("Index created: $indexName for $relationName ($flds)") if T(1);
782            } else {
783                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
784            }
785      }      }
786  }  }
787    
788  =head3 LoadTables  =head3 LoadTables
789    
790  C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
791    
792  This method will load the database tables from a directory. The tables must already have been created  This method will load the database tables from a directory. The tables must already have been created
793  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
# Line 710  Line 830 
830      $directoryName =~ s!/\\$!!;      $directoryName =~ s!/\\$!!;
831      # Declare the return variable.      # Declare the return variable.
832      my $retVal = Stats->new();      my $retVal = Stats->new();
833      # Get the metadata structure.      # Get the relation names.
834      my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
835      # 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}}) {  
836              # Try to load this relation.              # Try to load this relation.
837              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
838              # Accumulate the statistics.              # Accumulate the statistics.
839              $retVal->Accumulate($result);              $retVal->Accumulate($result);
840          }          }
     }  
     # 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);  
     }  
841      # Add the duration of the load to the statistical object.      # Add the duration of the load to the statistical object.
842      $retVal->Add('duration', gettimeofday - $startTime);      $retVal->Add('duration', gettimeofday - $startTime);
843      # Return the accumulated statistics.      # Return the accumulated statistics.
844      return $retVal;      return $retVal;
845  }  }
846    
847    
848  =head3 GetTableNames  =head3 GetTableNames
849    
850  C<< my @names = $database->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
851    
852  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
853    
# Line 754  Line 864 
864    
865  =head3 GetEntityTypes  =head3 GetEntityTypes
866    
867  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
868    
869  Return a list of the entity type names.  Return a list of the entity type names.
870    
# Line 769  Line 879 
879      return sort keys %{$entityList};      return sort keys %{$entityList};
880  }  }
881    
882    =head3 IsEntity
883    
884    C<< my $flag = $erdb->IsEntity($entityName); >>
885    
886    Return TRUE if the parameter is an entity name, else FALSE.
887    
888    =over 4
889    
890    =item entityName
891    
892    Object name to be tested.
893    
894    =item RETURN
895    
896    Returns TRUE if the specified string is an entity name, else FALSE.
897    
898    =back
899    
900    =cut
901    
902    sub IsEntity {
903        # Get the parameters.
904        my ($self, $entityName) = @_;
905        # Test to see if it's an entity.
906        return exists $self->{_metaData}->{Entities}->{$entityName};
907    }
908    
909  =head3 Get  =head3 Get
910    
911  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
912    
913  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.
914  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 779  Line 916 
916  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
917  $genus.  $genus.
918    
919  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>
920    
921  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
922  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
923    
924  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
925    
926  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
927  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 796  Line 933 
933  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
934  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,
935    
936  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>
937    
938  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
939  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.
940  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
941  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
942  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  
943  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,
944  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.
945    
946    If an entity or relationship is mentioned twice, the name for the second occurrence will
947    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
948    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
949    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
950    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
951    
952  =over 4  =over 4
953    
954  =item objectNames  =item objectNames
# Line 829  Line 971 
971    
972  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
973    
974    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
975    be processed. The idea is to make it less likely to find the verb by accident.
976    
977  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
978  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
979  relation.  relation.
980    
981    Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
982    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
983    a positive number. So, for example
984    
985    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
986    
987    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
988    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
989    use
990    
991    C<< "LIMIT 10" >>
992    
993  =item param1, param2, ..., paramN  =item param1, param2, ..., paramN
994    
995  Parameter values to be substituted into the filter clause.  Parameter values to be substituted into the filter clause.
# Line 848  Line 1005 
1005  sub Get {  sub Get {
1006      # Get the parameters.      # Get the parameters.
1007      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, @params) = @_;
1008        # Adjust the list of object names to account for multiple occurrences of the
1009        # same object. We start with a hash table keyed on object name that will
1010        # return the object suffix. The first time an object is encountered it will
1011        # not be found in the hash. The next time the hash will map the object name
1012        # to 2, then 3, and so forth.
1013        my %objectHash = ();
1014        # This list will contain the object names as they are to appear in the
1015        # FROM list.
1016        my @fromList = ();
1017        # This list contains the suffixed object name for each object. It is exactly
1018        # parallel to the list in the $objectNames parameter.
1019        my @mappedNameList = ();
1020        # Finally, this hash translates from a mapped name to its original object name.
1021        my %mappedNameHash = ();
1022        # Now we create the lists. Note that for every single name we push something into
1023        # @fromList and @mappedNameList. This insures that those two arrays are exactly
1024        # parallel to $objectNames.
1025        for my $objectName (@{$objectNames}) {
1026            # Get the next suffix for this object.
1027            my $suffix = $objectHash{$objectName};
1028            if (! $suffix) {
1029                # Here we are seeing the object for the first time. The object name
1030                # is used as is.
1031                push @mappedNameList, $objectName;
1032                push @fromList, $objectName;
1033                $mappedNameHash{$objectName} = $objectName;
1034                # Denote the next suffix will be 2.
1035                $objectHash{$objectName} = 2;
1036            } else {
1037                # Here we've seen the object before. We construct a new name using
1038                # the suffix from the hash and update the hash.
1039                my $mappedName = "$objectName$suffix";
1040                $objectHash{$objectName} = $suffix + 1;
1041                # The FROM list has the object name followed by the mapped name. This
1042                # tells SQL it's still the same table, but we're using a different name
1043                # for it to avoid confusion.
1044                push @fromList, "$objectName $mappedName";
1045                # The mapped-name list contains the real mapped name.
1046                push @mappedNameList, $mappedName;
1047                # Finally, enable us to get back from the mapped name to the object name.
1048                $mappedNameHash{$mappedName} = $objectName;
1049            }
1050        }
1051      # Construct the SELECT statement. The general pattern is      # Construct the SELECT statement. The general pattern is
1052      #      #
1053      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN
1054      #      #
1055      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
1056      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .      my $command = "SELECT DISTINCT " . join('.*, ', @mappedNameList) . ".* FROM " .
1057                  join(', ', @{$objectNames});                  join(', ', @fromList);
1058      # Check for a filter clause.      # Check for a filter clause.
1059      if ($filterClause) {      if ($filterClause) {
1060          # Here we have one, so we convert its field names and add it to the query. First,          # Here we have one, so we convert its field names and add it to the query. First,
# Line 862  Line 1062 
1062          my $filterString = $filterClause;          my $filterString = $filterClause;
1063          # Next, we sort the object names by length. This helps protect us from finding          # Next, we sort the object names by length. This helps protect us from finding
1064          # object names inside other object names when we're doing our search and replace.          # object names inside other object names when we're doing our search and replace.
1065          my @sortedNames = sort { length($b) - length($a) } @{$objectNames};          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
1066          # We will also keep a list of conditions to add to the WHERE clause in order to link          # We will also keep a list of conditions to add to the WHERE clause in order to link
1067          # entities and relationships as well as primary relations to secondary ones.          # entities and relationships as well as primary relations to secondary ones.
1068          my @joinWhere = ();          my @joinWhere = ();
1069          # The final preparatory step is to create a hash table of relation names. The          # The final preparatory step is to create a hash table of relation names. The
1070          # table begins with the relation names already in the SELECT command.          # table begins with the relation names already in the SELECT command. We may
1071          my %fromNames = ();          # need to add relations later if there is filtering on a field in a secondary
1072          for my $objectName (@sortedNames) {          # relation. The secondary relations are the ones that contain multiply-
1073              $fromNames{$objectName} = 1;          # occurring or optional fields.
1074          }          my %fromNames = map { $_ => 1 } @sortedNames;
1075          # We are ready to begin. We loop through the object names, replacing each          # We are ready to begin. We loop through the object names, replacing each
1076          # object name's field references by the corresponding SQL field reference.          # object name's field references by the corresponding SQL field reference.
1077          # Along the way, if we find a secondary relation, we will need to add it          # Along the way, if we find a secondary relation, we will need to add it
1078          # to the FROM clause.          # to the FROM clause.
1079          for my $objectName (@sortedNames) {          for my $mappedName (@sortedNames) {
1080              # Get the length of the object name plus 2. This is the value we add to the              # Get the length of the object name plus 2. This is the value we add to the
1081              # size of the field name to determine the size of the field reference as a              # size of the field name to determine the size of the field reference as a
1082              # whole.              # whole.
1083              my $nameLength = 2 + length $objectName;              my $nameLength = 2 + length $mappedName;
1084                # Get the real object name for this mapped name.
1085                my $objectName = $mappedNameHash{$mappedName};
1086                Trace("Processing $mappedName for object $objectName.") if T(4);
1087              # Get the object's field list.              # Get the object's field list.
1088              my $fieldList = $self->_GetFieldTable($objectName);              my $fieldList = $self->GetFieldTable($objectName);
1089              # Find the field references for this object.              # Find the field references for this object.
1090              while ($filterString =~ m/$objectName\(([^)]*)\)/g) {              while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
1091                  # At this point, $1 contains the field name, and the current position                  # At this point, $1 contains the field name, and the current position
1092                  # is set immediately after the final parenthesis. We pull out the name of                  # is set immediately after the final parenthesis. We pull out the name of
1093                  # the field and the position and length of the field reference as a whole.                  # the field and the position and length of the field reference as a whole.
# Line 895  Line 1098 
1098                  if (!exists $fieldList->{$fieldName}) {                  if (!exists $fieldList->{$fieldName}) {
1099                      Confess("Field $fieldName not found for object $objectName.");                      Confess("Field $fieldName not found for object $objectName.");
1100                  } else {                  } else {
1101                        Trace("Processing $fieldName at position $pos.") if T(4);
1102                      # Get the field's relation.                      # Get the field's relation.
1103                      my $relationName = $fieldList->{$fieldName}->{relation};                      my $relationName = $fieldList->{$fieldName}->{relation};
1104                        # Now we have a secondary relation. We need to insure it matches the
1105                        # mapped name of the primary relation. First we peel off the suffix
1106                        # from the mapped name.
1107                        my $mappingSuffix = substr $mappedName, length($objectName);
1108                        # Put the mapping suffix onto the relation name to get the
1109                        # mapped relation name.
1110                        my $mappedRelationName = "$relationName$mappingSuffix";
1111                      # Insure the relation is in the FROM clause.                      # Insure the relation is in the FROM clause.
1112                      if (!exists $fromNames{$relationName}) {                      if (!exists $fromNames{$mappedRelationName}) {
1113                          # Add the relation to the FROM clause.                          # Add the relation to the FROM clause.
1114                            if ($mappedRelationName eq $relationName) {
1115                                # The name is un-mapped, so we add it without
1116                                # any frills.
1117                          $command .= ", $relationName";                          $command .= ", $relationName";
                         # Create its join sub-clause.  
1118                          push @joinWhere, "$objectName.id = $relationName.id";                          push @joinWhere, "$objectName.id = $relationName.id";
1119                          # Denote we have it available for future fields.                          } else {
1120                          $fromNames{$relationName} = 1;                              # Here we have a mapping situation.
1121                                $command .= ", $relationName $mappedRelationName";
1122                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
1123                            }
1124                            # Denote we have this relation available for future fields.
1125                            $fromNames{$mappedRelationName} = 1;
1126                      }                      }
1127                      # Form an SQL field reference from the relation name and the field name.                      # Form an SQL field reference from the relation name and the field name.
1128                      my $sqlReference = "$relationName." . _FixName($fieldName);                      my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
1129                      # Put it into the filter string in place of the old value.                      # Put it into the filter string in place of the old value.
1130                      substr($filterString, $pos, $len) = $sqlReference;                      substr($filterString, $pos, $len) = $sqlReference;
1131                      # Reposition the search.                      # Reposition the search.
# Line 919  Line 1137 
1137          # is more than one object in the object list. We start with the first object and          # is more than one object in the object list. We start with the first object and
1138          # run through the objects after it. Note also that we make a safety copy of the          # run through the objects after it. Note also that we make a safety copy of the
1139          # list before running through it.          # list before running through it.
1140          my @objectList = @{$objectNames};          my @mappedObjectList = @mappedNameList;
1141          my $lastObject = shift @objectList;          my $lastMappedObject = shift @mappedObjectList;
1142          # Get the join table.          # Get the join table.
1143          my $joinTable = $self->{_metaData}->{Joins};          my $joinTable = $self->{_metaData}->{Joins};
1144          # Loop through the object list.          # Loop through the object list.
1145          for my $thisObject (@objectList) {          for my $thisMappedObject (@mappedObjectList) {
1146              # Look for a join.              # Look for a join using the real object names.
1147                my $lastObject = $mappedNameHash{$lastMappedObject};
1148                my $thisObject = $mappedNameHash{$thisMappedObject};
1149              my $joinKey = "$lastObject/$thisObject";              my $joinKey = "$lastObject/$thisObject";
1150              if (!exists $joinTable->{$joinKey}) {              if (!exists $joinTable->{$joinKey}) {
1151                  # Here there's no join, so we throw an error.                  # Here there's no join, so we throw an error.
1152                  Confess("No join exists to connect from $lastObject to $thisObject.");                  Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
1153              } else {              } else {
1154                  # Get the join clause and add it to the WHERE list.                  # Get the join clause.
1155                  push @joinWhere, $joinTable->{$joinKey};                  my $unMappedJoin = $joinTable->{$joinKey};
1156                    # Fix the names.
1157                    $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
1158                    $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
1159                    push @joinWhere, $unMappedJoin;
1160                  # Save this object as the last object for the next iteration.                  # Save this object as the last object for the next iteration.
1161                  $lastObject = $thisObject;                  $lastMappedObject = $thisMappedObject;
1162              }              }
1163          }          }
1164          # Now we need to handle the whole ORDER BY thing. We'll put the order by clause          # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
1165          # in the following variable.          # here is we want the filter clause to be empty if there's no WHERE filter.
1166            # We'll put the ORDER BY / LIMIT clauses in the following variable.
1167          my $orderClause = "";          my $orderClause = "";
1168          # Locate the ORDER BY verb (if any).          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
1169          if ($filterString =~ m/^(.*)ORDER BY/g) {          # operator so that we find the first occurrence of either verb.
1170              # Here we have an ORDER BY verb. Split it off of the filter string.          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
1171                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
1172              my $pos = pos $filterString;              my $pos = pos $filterString;
1173              $orderClause = substr($filterString, $pos);              $orderClause = $2 . substr($filterString, $pos);
1174              $filterString = $1;              $filterString = $1;
1175          }          }
1176          # Add the filter and the join clauses (if any) to the SELECT command.          # Add the filter and the join clauses (if any) to the SELECT command.
1177          if ($filterString) {          if ($filterString) {
1178                Trace("Filter string is \"$filterString\".") if T(4);
1179              push @joinWhere, "($filterString)";              push @joinWhere, "($filterString)";
1180          }          }
1181          if (@joinWhere) {          if (@joinWhere) {
1182              $command .= " WHERE " . join(' AND ', @joinWhere);              $command .= " WHERE " . join(' AND ', @joinWhere);
1183          }          }
1184          # Add the sort clause (if any) to the SELECT command.          # Add the sort or limit clause (if any) to the SELECT command.
1185          if ($orderClause) {          if ($orderClause) {
1186              $command .= " ORDER BY $orderClause";              $command .= " $orderClause";
1187          }          }
1188      }      }
1189      Trace("SQL query: $command") if T(2);      Trace("SQL query: $command") if T(SQL => 3);
1190      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));
1191      my $sth = $dbh->prepare_command($command);      my $sth = $dbh->prepare_command($command);
1192      # Execute it with the parameters bound in.      # Execute it with the parameters bound in.
1193      $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());      $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());
1194        # Now we create the relation map, which enables DBQuery to determine the order, name
1195        # and mapped name for each object in the query.
1196        my @relationMap = ();
1197        for my $mappedName (@mappedNameList) {
1198            push @relationMap, [$mappedName, $mappedNameHash{$mappedName}];
1199        }
1200      # Return the statement object.      # Return the statement object.
1201      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1202        return $retVal;
1203    }
1204    
1205    =head3 Delete
1206    
1207    C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1208    
1209    Delete an entity instance from the database. The instance is deleted along with all entity and
1210    relationship instances dependent on it. The idea of dependence here is recursive. An object is
1211    always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1212    relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1213    dependent relationship.
1214    
1215    =over 4
1216    
1217    =item entityName
1218    
1219    Name of the entity type for the instance being deleted.
1220    
1221    =item objectID
1222    
1223    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1224    then it is presumed to by a LIKE pattern.
1225    
1226    =item testFlag
1227    
1228    If TRUE, the delete statements will be traced without being executed.
1229    
1230    =item RETURN
1231    
1232    Returns a statistics object indicating how many records of each particular table were
1233    deleted.
1234    
1235    =back
1236    
1237    =cut
1238    #: Return Type $%;
1239    sub Delete {
1240        # Get the parameters.
1241        my ($self, $entityName, $objectID, $testFlag) = @_;
1242        # Declare the return variable.
1243        my $retVal = Stats->new();
1244        # Get the DBKernel object.
1245        my $db = $self->{_dbh};
1246        # We're going to generate all the paths branching out from the starting entity. One of
1247        # the things we have to be careful about is preventing loops. We'll use a hash to
1248        # determine if we've hit a loop.
1249        my %alreadyFound = ();
1250        # These next lists will serve as our result stack. We start by pushing object lists onto
1251        # the stack, and then popping them off to do the deletes. This means the deletes will
1252        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1253        # sure we don't delete records that might be needed to forge relationships back to the
1254        # original item. We have two lists-- one for TO-relationships, and one for
1255        # FROM-relationships and entities.
1256        my @fromPathList = ();
1257        my @toPathList = ();
1258        # This final hash is used to remember what work still needs to be done. We push paths
1259        # onto the list, then pop them off to extend the paths. We prime it with the starting
1260        # point. Note that we will work hard to insure that the last item on a path in the
1261        # TODO list is always an entity.
1262        my @todoList = ([$entityName]);
1263        while (@todoList) {
1264            # Get the current path.
1265            my $current = pop @todoList;
1266            # Copy it into a list.
1267            my @stackedPath = @{$current};
1268            # Pull off the last item on the path. It will always be an entity.
1269            my $entityName = pop @stackedPath;
1270            # Add it to the alreadyFound list.
1271            $alreadyFound{$entityName} = 1;
1272            # Get the entity data.
1273            my $entityData = $self->_GetStructure($entityName);
1274            # The first task is to loop through the entity's relation. A DELETE command will
1275            # be needed for each of them.
1276            my $relations = $entityData->{Relations};
1277            for my $relation (keys %{$relations}) {
1278                my @augmentedList = (@stackedPath, $relation);
1279                push @fromPathList, \@augmentedList;
1280            }
1281            # Now we need to look for relationships connected to this entity.
1282            my $relationshipList = $self->{_metaData}->{Relationships};
1283            for my $relationshipName (keys %{$relationshipList}) {
1284                my $relationship = $relationshipList->{$relationshipName};
1285                # Check the FROM field. We're only interested if it's us.
1286                if ($relationship->{from} eq $entityName) {
1287                    # Add the path to this relationship.
1288                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1289                    push @fromPathList, \@augmentedList;
1290                    # Check the arity. If it's MM we're done. If it's 1M
1291                    # and the target hasn't been seen yet, we want to
1292                    # stack the entity for future processing.
1293                    if ($relationship->{arity} eq '1M') {
1294                        my $toEntity = $relationship->{to};
1295                        if (! exists $alreadyFound{$toEntity}) {
1296                            # Here we have a new entity that's dependent on
1297                            # the current entity, so we need to stack it.
1298                            my @stackList = (@augmentedList, $toEntity);
1299                            push @fromPathList, \@stackList;
1300                        } else {
1301                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1302                        }
1303                    }
1304                }
1305                # Now check the TO field. In this case only the relationship needs
1306                # deletion.
1307                if ($relationship->{to} eq $entityName) {
1308                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1309                    push @toPathList, \@augmentedList;
1310                }
1311            }
1312        }
1313        # Create the first qualifier for the WHERE clause. This selects the
1314        # keys of the primary entity records to be deleted. When we're deleting
1315        # from a dependent table, we construct a join page from the first qualifier
1316        # to the table containing the dependent records to delete.
1317        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1318        # We need to make two passes. The first is through the to-list, and
1319        # the second through the from-list. The from-list is second because
1320        # the to-list may need to pass through some of the entities the
1321        # from-list would delete.
1322        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1323        # Now it's time to do the deletes. We do it in two passes.
1324        for my $keyName ('to_link', 'from_link') {
1325            # Get the list for this key.
1326            my @pathList = @{$stackList{$keyName}};
1327            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1328            # Loop through this list.
1329            while (my $path = pop @pathList) {
1330                # Get the table whose rows are to be deleted.
1331                my @pathTables = @{$path};
1332                # Start the DELETE statement. We need to call DBKernel because the
1333                # syntax of a DELETE-USING varies among DBMSs.
1334                my $target = $pathTables[$#pathTables];
1335                my $stmt = $db->SetUsing(@pathTables);
1336                # Now start the WHERE. The first thing is the ID field from the starting table. That
1337                # starting table will either be the entity relation or one of the entity's
1338                # sub-relations.
1339                $stmt .= " WHERE $pathTables[0].id $qualifier";
1340                # Now we run through the remaining entities in the path, connecting them up.
1341                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1342                    # Connect the current relationship to the preceding entity.
1343                    my ($entity, $rel) = @pathTables[$i-1,$i];
1344                    # The style of connection depends on the direction of the relationship.
1345                    $stmt .= " AND $entity.id = $rel.$keyName";
1346                    if ($i + 1 <= $#pathTables) {
1347                        # Here there's a next entity, so connect that to the relationship's
1348                        # to-link.
1349                        my $entity2 = $pathTables[$i+1];
1350                        $stmt .= " AND $rel.to_link = $entity2.id";
1351                    }
1352                }
1353                # Now we have our desired DELETE statement.
1354                if ($testFlag) {
1355                    # Here the user wants to trace without executing.
1356                    Trace($stmt) if T(0);
1357                } else {
1358                    # Here we can delete. Note that the SQL method dies with a confessing
1359                    # if an error occurs, so we just go ahead and do it.
1360                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1361                    my $rv = $db->SQL($stmt, 0, $objectID);
1362                    # Accumulate the statistics for this delete. The only rows deleted
1363                    # are from the target table, so we use its name to record the
1364                    # statistic.
1365                    $retVal->Add($target, $rv);
1366                }
1367            }
1368        }
1369        # Return the result.
1370      return $retVal;      return $retVal;
1371  }  }
1372    
1373  =head3 GetList  =head3 GetList
1374    
1375  C<< my @dbObjects = $database->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>
1376    
1377  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
1378  specified filter clause.  specified filter clause.
# Line 1034  Line 1435 
1435    
1436  =head3 ComputeObjectSentence  =head3 ComputeObjectSentence
1437    
1438  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1439    
1440  Check an object name, and if it is a relationship convert it to a relationship sentence.  Check an object name, and if it is a relationship convert it to a relationship sentence.
1441    
# Line 1069  Line 1470 
1470    
1471  =head3 DumpRelations  =head3 DumpRelations
1472    
1473  C<< $database->DumpRelations($outputDirectory); >>  C<< $erdb->DumpRelations($outputDirectory); >>
1474    
1475  Write the contents of all the relations to tab-delimited files in the specified directory.  Write the contents of all the relations to tab-delimited files in the specified directory.
1476  Each file will have the same name as the relation dumped, with an extension of DTX.  Each file will have the same name as the relation dumped, with an extension of DTX.
# Line 1111  Line 1512 
1512    
1513  =head3 InsertObject  =head3 InsertObject
1514    
1515  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1516    
1517  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
1518  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 1120  Line 1521 
1521  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
1522  C<ZP_00210270.1> and C<gi|46206278>.  C<ZP_00210270.1> and C<gi|46206278>.
1523    
1524  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
1525    
1526  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
1527  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>.
1528    
1529  C<< $database->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'}); >>
1530    
1531  =over 4  =over 4
1532    
# Line 1250  Line 1651 
1651    
1652  =head3 LoadTable  =head3 LoadTable
1653    
1654  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
1655    
1656  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
1657  first.  first.
# Line 1271  Line 1672 
1672    
1673  =item RETURN  =item RETURN
1674    
1675  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.  
1676    
1677  =back  =back
1678    
# Line 1286  Line 1686 
1686      Trace("Loading table $relationName from $fileName") if T(2);      Trace("Loading table $relationName from $fileName") if T(2);
1687      # Get the database handle.      # Get the database handle.
1688      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
1689        # Get the input file size.
1690        my $fileSize = -s $fileName;
1691      # Get the relation data.      # Get the relation data.
1692      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
1693      # Check the truncation flag.      # Check the truncation flag.
1694      if ($truncateFlag) {      if ($truncateFlag) {
1695          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
1696            # Compute the row count estimate. We take the size of the load file,
1697            # divide it by the estimated row size, and then multiply by 1.5 to
1698            # leave extra room. We postulate a minimum row count of 1000 to
1699            # prevent problems with incoming empty load files.
1700            my $rowSize = $self->EstimateRowSize($relationName);
1701            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
1702          # Re-create the table without its index.          # Re-create the table without its index.
1703          $self->CreateTable($relationName, 0);          $self->CreateTable($relationName, 0, $estimate);
1704          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
1705          if ($dbh->{_preIndex}) {          if ($dbh->{_preIndex}) {
1706              eval {              eval {
# Line 1303  Line 1711 
1711              }              }
1712          }          }
1713      }      }
     # Determine whether or not this is a primary relation. Primary relations have an extra  
     # field indicating whether or not a given object is new or was loaded from the flat files.  
     my $primary = $self->_IsPrimary($relationName);  
     # Get the number of fields in this relation.  
     my @fieldList = @{$relation->{Fields}};  
     my $fieldCount = @fieldList;  
     # Start a database transaction.  
     $dbh->begin_tran;  
     # Open the relation file. We need to create a cleaned-up copy before loading.  
     open TABLEIN, '<', $fileName;  
     my $tempName = "$fileName.tbl";  
     open TABLEOUT, '>', $tempName;  
     my $inputCount = 0;  
     # Loop through the file.  
     while (<TABLEIN>) {  
         $inputCount++;  
         # Chop off the new-line character.  
         my $record = Tracer::Strip($_);  
         # Only proceed if the record is non-blank.  
         if ($record) {  
             # Escape all the backslashes found in the line.  
             $record =~ s/\\/\\\\/g;  
             # Insure the number of fields is correct.  
             my @fields = split /\t/, $record;  
             while (@fields > $fieldCount) {  
                 my $extraField = $fields[$#fields];  
                 delete $fields[$#fields];  
                 if ($extraField) {  
                     Trace("Nonblank extra field value \"$extraField\" deleted from record $inputCount of $fileName.") if T(1);  
                 }  
             }  
             while (@fields < $fieldCount) {  
                 push @fields, "";  
             }  
             # If this is a primary relation, add a 0 for the new-record flag (indicating that  
             # this record is not new, but part of the original load).  
             if ($primary) {  
                 push @fields, "0";  
             }  
             # Write the record.  
             $record = join "\t", @fields;  
             print TABLEOUT "$record\n";  
             # Count the record written.  
             my $count = $retVal->Add('records');  
             my $len = length $record;  
             Trace("Record $count written with $len characters.") if T(4);  
         } else {  
             # Here we have a blank record.  
             $retVal->Add('skipped');  
         }  
     }  
     # Close the files.  
     close TABLEIN;  
     close TABLEOUT;  
     Trace("Temporary file $tempName created.") if T(2);  
1714      # Load the table.      # Load the table.
1715      my $rv;      my $rv;
1716      eval {      eval {
1717          $rv = $dbh->load_table(file => $tempName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
1718      };      };
1719      if (!defined $rv) {      if (!defined $rv) {
1720          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
1721          $retVal->AddMessage("Table load failed for $relationName using $tempName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName.");
1722          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
1723      } else {      } else {
1724          # Here we successfully loaded the table. Trace the number of records loaded.          # Here we successfully loaded the table.
1725          Trace("$retVal->{records} records read for $relationName.") if T(2);          $retVal->Add("tables");
1726            my $size = -s $fileName;
1727            Trace("$size bytes loaded into $relationName.") if T(2);
1728          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
1729          if ($truncateFlag && ! $dbh->{_preIndex}) {          if ($truncateFlag && ! $dbh->{_preIndex}) {
1730              eval {              eval {
# Line 1379  Line 1734 
1734                  $retVal->AddMessage($@);                  $retVal->AddMessage($@);
1735              }              }
1736          }          }
         # Analyze the table to help optimize tables.  
1737      }      }
1738      # Commit the database changes.      # Analyze the table to improve performance.
     $dbh->commit_tran;  
1739      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
     # Delete the temporary file.  
     unlink $tempName;  
1740      # Return the statistics.      # Return the statistics.
1741      return $retVal;      return $retVal;
1742  }  }
1743    
1744  =head3 GenerateEntity  =head3 GenerateEntity
1745    
1746  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
1747    
1748  Generate the data for a new entity instance. This method creates a field hash suitable for  Generate the data for a new entity instance. This method creates a field hash suitable for
1749  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest
# Line 1450  Line 1801 
1801    
1802  =head3 GetEntity  =head3 GetEntity
1803    
1804  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
1805    
1806  Return an object describing the entity instance with a specified ID.  Return an object describing the entity instance with a specified ID.
1807    
# Line 1486  Line 1837 
1837    
1838  =head3 GetEntityValues  =head3 GetEntityValues
1839    
1840  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1841    
1842  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance.
1843    
# Line 1529  Line 1880 
1880    
1881  =head3 GetAll  =head3 GetAll
1882    
1883  C<< my @list = $sprout->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
1884    
1885  Return a list of values taken from the objects returned by a query. The first three  Return a list of values taken from the objects returned by a query. The first three
1886  parameters correspond to the parameters of the L</Get> method. The final parameter is  parameters correspond to the parameters of the L</Get> method. The final parameter is
# Line 1545  Line 1896 
1896  spreadsheet cell, and each feature will be represented by a list containing the  spreadsheet cell, and each feature will be represented by a list containing the
1897  feature ID followed by all of its aliases.  feature ID followed by all of its aliases.
1898    
1899  C<< $query = $sprout->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
1900    
1901  =over 4  =over 4
1902    
# Line 1594  Line 1945 
1945      } else {      } else {
1946          push @parmList, $parameterList;          push @parmList, $parameterList;
1947      }      }
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, @parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
1948      # Insure the counter has a value.      # Insure the counter has a value.
1949      if (!defined $count) {      if (!defined $count) {
1950          $count = 0;          $count = 0;
1951      }      }
1952        # Add the row limit to the filter clause.
1953        if ($count > 0) {
1954            $filterClause .= " LIMIT $count";
1955        }
1956        # Create the query.
1957        my $query = $self->Get($objectNames, $filterClause, @parmList);
1958        # Set up a counter of the number of records read.
1959        my $fetched = 0;
1960      # Loop through the records returned, extracting the fields. Note that if the      # Loop through the records returned, extracting the fields. Note that if the
1961      # 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.
1962      my @retVal = ();      my @retVal = ();
# Line 1614  Line 1969 
1969      return @retVal;      return @retVal;
1970  }  }
1971    
1972    =head3 EstimateRowSize
1973    
1974    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
1975    
1976    Estimate the row size of the specified relation. The estimated row size is computed by adding
1977    up the average length for each data type.
1978    
1979    =over 4
1980    
1981    =item relName
1982    
1983    Name of the relation whose estimated row size is desired.
1984    
1985    =item RETURN
1986    
1987    Returns an estimate of the row size for the specified relation.
1988    
1989    =back
1990    
1991    =cut
1992    #: Return Type $;
1993    sub EstimateRowSize {
1994        # Get the parameters.
1995        my ($self, $relName) = @_;
1996        # Declare the return variable.
1997        my $retVal = 0;
1998        # Find the relation descriptor.
1999        my $relation = $self->_FindRelation($relName);
2000        # Get the list of fields.
2001        for my $fieldData (@{$relation->{Fields}}) {
2002            # Get the field type and add its length.
2003            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2004            $retVal += $fieldLen;
2005        }
2006        # Return the result.
2007        return $retVal;
2008    }
2009    
2010    =head3 GetFieldTable
2011    
2012    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2013    
2014    Get the field structure for a specified entity or relationship.
2015    
2016    =over 4
2017    
2018    =item objectName
2019    
2020    Name of the desired entity or relationship.
2021    
2022    =item RETURN
2023    
2024    The table containing the field descriptors for the specified object.
2025    
2026    =back
2027    
2028    =cut
2029    
2030    sub GetFieldTable {
2031        # Get the parameters.
2032        my ($self, $objectName) = @_;
2033        # Get the descriptor from the metadata.
2034        my $objectData = $self->_GetStructure($objectName);
2035        # Return the object's field table.
2036        return $objectData->{Fields};
2037    }
2038    
2039    =head3 GetUsefulCrossValues
2040    
2041    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
2042    
2043    Return a list of the useful attributes that would be returned by a B<Cross> call
2044    from an entity of the source entity type through the specified relationship. This
2045    means it will return the fields of the target entity type and the intersection data
2046    fields in the relationship. Only primary table fields are returned. In other words,
2047    the field names returned will be for fields where there is always one and only one
2048    value.
2049    
2050    =over 4
2051    
2052    =item sourceEntity
2053    
2054    Name of the entity from which the relationship crossing will start.
2055    
2056    =item relationship
2057    
2058    Name of the relationship being crossed.
2059    
2060    =item RETURN
2061    
2062    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
2063    
2064    =back
2065    
2066    =cut
2067    #: Return Type @;
2068    sub GetUsefulCrossValues {
2069        # Get the parameters.
2070        my ($self, $sourceEntity, $relationship) = @_;
2071        # Declare the return variable.
2072        my @retVal = ();
2073        # Determine the target entity for the relationship. This is whichever entity is not
2074        # the source entity. So, if the source entity is the FROM, we'll get the name of
2075        # the TO, and vice versa.
2076        my $relStructure = $self->_GetStructure($relationship);
2077        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
2078        my $targetEntity = $relStructure->{$targetEntityType};
2079        # Get the field table for the entity.
2080        my $entityFields = $self->GetFieldTable($targetEntity);
2081        # The field table is a hash. The hash key is the field name. The hash value is a structure.
2082        # For the entity fields, the key aspect of the target structure is that the {relation} value
2083        # must match the entity name.
2084        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
2085                            keys %{$entityFields};
2086        # Push the fields found onto the return variable.
2087        push @retVal, sort @fieldList;
2088        # Get the field table for the relationship.
2089        my $relationshipFields = $self->GetFieldTable($relationship);
2090        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
2091        # This may end up being an empty set.
2092        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
2093                            keys %{$relationshipFields};
2094        # Push these onto the return list.
2095        push @retVal, sort @fieldList2;
2096        # Return the result.
2097        return @retVal;
2098    }
2099    
2100  =head2 Internal Utility Methods  =head2 Internal Utility Methods
2101    
2102  =head3 GetLoadStats  =head3 GetLoadStats
# Line 1625  Line 2108 
2108  =cut  =cut
2109    
2110  sub _GetLoadStats {  sub _GetLoadStats {
2111      return Stats->new('records');      return Stats->new();
2112  }  }
2113    
2114  =head3 GenerateFields  =head3 GenerateFields
# Line 1820  Line 2303 
2303      return $objectData->{Relations};      return $objectData->{Relations};
2304  }  }
2305    
 =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};  
 }  
   
2306  =head3 ValidateFieldNames  =head3 ValidateFieldNames
2307    
2308  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 2196  Line 2650 
2650          my @fromList = ();          my @fromList = ();
2651          my @toList = ();          my @toList = ();
2652          my @bothList = ();          my @bothList = ();
2653          Trace("Join table build for $entityName.") if T(3);          Trace("Join table build for $entityName.") if T(metadata => 4);
2654          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
2655              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
2656              # 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.
2657              my $fromEntity = $relationship->{from};              my $fromEntity = $relationship->{from};
2658              my $toEntity = $relationship->{to};              my $toEntity = $relationship->{to};
2659              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(3);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
2660              if ($fromEntity eq $entityName) {              if ($fromEntity eq $entityName) {
2661                  if ($toEntity eq $entityName) {                  if ($toEntity eq $entityName) {
2662                      # Here the relationship is recursive.                      # Here the relationship is recursive.
2663                      push @bothList, $relationshipName;                      push @bothList, $relationshipName;
2664                      Trace("Relationship $relationshipName put in both-list.") if T(3);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
2665                  } else {                  } else {
2666                      # Here the relationship comes from the entity.                      # Here the relationship comes from the entity.
2667                      push @fromList, $relationshipName;                      push @fromList, $relationshipName;
2668                      Trace("Relationship $relationshipName put in from-list.") if T(3);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
2669                  }                  }
2670              } elsif ($toEntity eq $entityName) {              } elsif ($toEntity eq $entityName) {
2671                  # Here the relationship goes to the entity.                  # Here the relationship goes to the entity.
2672                  push @toList, $relationshipName;                  push @toList, $relationshipName;
2673                  Trace("Relationship $relationshipName put in to-list.") if T(3);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
2674              }              }
2675          }          }
2676          # 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 2232  Line 2686 
2686                  # Create joins between the entity and this relationship.                  # Create joins between the entity and this relationship.
2687                  my $linkField = "$relationshipName.${linkType}_link";                  my $linkField = "$relationshipName.${linkType}_link";
2688                  my $joinClause = "$entityName.id = $linkField";                  my $joinClause = "$entityName.id = $linkField";
2689                  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);
2690                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
2691                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
2692                  # Create joins between this relationship and the other relationships.                  # Create joins between this relationship and the other relationships.
# Line 2253  Line 2707 
2707                              # relationship and itself are prohibited.                              # relationship and itself are prohibited.
2708                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";
2709                              $joinTable{$joinKey} = $relJoinClause;                              $joinTable{$joinKey} = $relJoinClause;
2710                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
2711                          }                          }
2712                      }                      }
2713                  }                  }
# Line 2262  Line 2716 
2716                  # relationship can only be ambiguous with another recursive relationship,                  # relationship can only be ambiguous with another recursive relationship,
2717                  # and the incoming relationship from the outer loop is never recursive.                  # and the incoming relationship from the outer loop is never recursive.
2718                  for my $otherName (@bothList) {                  for my $otherName (@bothList) {
2719                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(3);                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
2720                      # Join from the left.                      # Join from the left.
2721                      $joinTable{"$relationshipName/$otherName"} =                      $joinTable{"$relationshipName/$otherName"} =
2722                          "$linkField = $otherName.from_link";                          "$linkField = $otherName.from_link";
# Line 2277  Line 2731 
2731          # 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
2732          # possible to get the same effect using multiple queries.          # possible to get the same effect using multiple queries.
2733          for my $relationshipName (@bothList) {          for my $relationshipName (@bothList) {
2734              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(3);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
2735              # Join to the entity from each direction.              # Join to the entity from each direction.
2736              $joinTable{"$entityName/$relationshipName"} =              $joinTable{"$entityName/$relationshipName"} =
2737                  "$entityName.id = $relationshipName.from_link";                  "$entityName.id = $relationshipName.from_link";
# Line 2291  Line 2745 
2745      return $metadata;      return $metadata;
2746  }  }
2747    
2748    =head3 SortNeeded
2749    
2750    C<< my $flag = $erdb->SortNeeded($relationName); >>
2751    
2752    Return TRUE if the specified relation should be sorted during loading to remove duplicate keys,
2753    else FALSE.
2754    
2755    =over 4
2756    
2757    =item relationName
2758    
2759    Name of the relation to be examined.
2760    
2761    =item RETURN
2762    
2763    Returns TRUE if the relation needs a sort, else FALSE.
2764    
2765    =back
2766    
2767    =cut
2768    #: Return Type $;
2769    sub SortNeeded {
2770        # Get the parameters.
2771        my ($self, $relationName) = @_;
2772        # Declare the return variable.
2773        my $retVal = 0;
2774        # Find out if the relation is a primary entity relation.
2775        my $entityTable = $self->{_metaData}->{Entities};
2776        if (exists $entityTable->{$relationName}) {
2777            my $keyType = $entityTable->{$relationName}->{keyType};
2778            Trace("Relation $relationName found in entity table with key type $keyType.") if T(3);
2779            # If the key is not a hash string, we must do the sort.
2780            if ($keyType ne 'hash-string') {
2781                $retVal = 1;
2782            }
2783        }
2784        # Return the result.
2785        return $retVal;
2786    }
2787    
2788  =head3 CreateRelationshipIndex  =head3 CreateRelationshipIndex
2789    
2790  Create an index for a relationship's relation.  Create an index for a relationship's relation.
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