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revision 1.82, Tue Jan 9 01:49:57 2007 UTC revision 1.92, Mon Jun 11 18:51:23 2007 UTC
# Line 6  Line 6 
6      use Data::Dumper;      use Data::Dumper;
7      use XML::Simple;      use XML::Simple;
8      use DBQuery;      use DBQuery;
9      use DBObject;      use ERDBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
     use FIG;  
13      use CGI;      use CGI;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
# Line 228  Line 227 
227    
228  =head3 Indexes  =head3 Indexes
229    
230  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
231  all be from the same relation. The alternate indexes assist in ordering results  index must all be from the same relation. The alternate indexes assist in searching
232  from a query. A relationship can have up to two indexes-- a I<to-index> and a  on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
233  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
234  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
235  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
236  the genomes of a contig. A relationship's index must specify only fields in  the genomes of a contig. In addition, it can have zero or more alternate
237    indexes. A relationship's index must specify only fields in
238  the relationship.  the relationship.
239    
240  The indexes for an entity must be listed inside the B<Indexes> tag. The from-index  The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
241  of a relationship is specified using the B<FromIndex> tag; the to-index is specified  The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
242  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
243    
244  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 303  Line 303 
303    
304  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
305  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306  fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing  fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
307  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
308    
309  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
310    
# Line 372  Line 372 
372                   'medium-string' =>                   'medium-string' =>
373                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                 indexMod =>   0, notes => "character string, 0 to 160 characters"},                                 indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                     'long-string' =>
376                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
377                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
378                  );                  );
379    
380  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 548  Line 551 
551          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
552              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
553          }          }
554          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
555            my $relCount = keys %{$relationshipList};
556            if ($relCount > 0) {
557                # First, we set up the relationship subsection.
558          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
559          # Loop through the relationships.          # Loop through the relationships.
560          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
# Line 564  Line 570 
570          }          }
571          # Close off the relationship list.          # Close off the relationship list.
572          $retVal .= "</ul>\n";          $retVal .= "</ul>\n";
573            }
574          # Get the entity's relations.          # Get the entity's relations.
575          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
576          # Create a header for the relation subsection.          # Create a header for the relation subsection.
# Line 650  Line 657 
657      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
658  }  }
659    
660    =head3 CreatePPO
661    
662    C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
663    
664    Create a PPO XML file from an ERDB data definition XML file. At the
665    current time, the PPO XML file can be used to create a database with
666    similar functionality. Eventually, the PPO will be able to use the
667    created XML to access the live ERDB database.
668    
669    =over 4
670    
671    =item erdbXMLFile
672    
673    Name of the XML data definition file for the ERDB database. This
674    file must exist.
675    
676    =item ppoXMLFile
677    
678    Output file for the PPO XML definition. If this file exists, it
679    will be overwritten.
680    
681    =back
682    
683    =cut
684    
685    sub CreatePPO {
686        # Get the parameters.
687        my ($erdbXMLFile, $ppoXMLFile) = @_;
688        # First, we want to slurp in the ERDB XML file in its raw form.
689        my $xml = ReadMetaXML($erdbXMLFile);
690        # Create a variable to hold all of the objects in the PPO project.
691        my @objects = ();
692        # Get the relationship hash.
693        my $relationships = $xml->{Relationships};
694        # Loop through the entities.
695        my $entities = $xml->{Entities};
696        for my $entityName (keys %{$entities}) {
697            # Get the entity's data structures.
698            my $entityObject = $entities->{$entityName};
699            # We put the object's fields in here, according to their type.
700            my (@object_refs, @scalars, @indexes, @arrays);
701            # Create the ID field for the entity. We get the key type from the
702            # entity object and compute the corresponding SQL type.
703            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
704            push @scalars, { label => 'id', type => $type };
705            # Loop through the entity fields.
706            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
707                # Get the field object.
708                my $fieldObject = $entityObject->{Fields}->{$fieldName};
709                # Convert it to a scalar tag.
710                my $scalar = _CreatePPOField($fieldName, $fieldObject);
711                # If we have a relation, this field is stored in an array.
712                # otherwise, it is a scalar. The array tag has scalars
713                # stored as an XML array. In ERDB, there is only ever one,
714                # but PPO can have more.
715                my $relation = $fieldObject->{relation};
716                if ($relation) {
717                    push @arrays, { scalar => [$scalar] };
718                } else {
719                    push @scalars, $scalar;
720                }
721            }
722            # Loop through the relationships. If this entity is the to-entity
723            # on a relationship of 1M arity, then it is implemented as a PPO
724            # object reference.
725            for my $relationshipName (keys %{$relationships}) {
726                # Get the relationship data.
727                my $relationshipData = $relationships->{$relationshipName};
728                # If we have a from for this entity and an arity of 1M, we
729                # have an object reference.
730                if ($relationshipData->{to} eq $entityName &&
731                    $relationshipData->{arity} eq '1M') {
732                    # Build the object reference tag.
733                    push @object_refs, { label => $relationshipName,
734                                         type => $relationshipData->{from} };
735                }
736            }
737            # Create the indexes.
738            my $indexList = $entityObject->{Indexes};
739            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
740            # Build the object XML tree.
741            my $object = { label => $entityName,
742                           object_ref => \@object_refs,
743                           scalar => \@scalars,
744                           index => \@indexes,
745                           array => \@arrays
746                          };
747            # Push the object onto the objects list.
748            push @objects, $object;
749        }
750        # Loop through the relationships, searching for MMs. The 1Ms were
751        # already handled by the entity search above.
752        for my $relationshipName (keys %{$relationships}) {
753            # Get this relationship's object.
754            my $relationshipObject = $relationships->{$relationshipName};
755            # Only proceed if it's many-to-many.
756            if ($relationshipObject->{arity} eq 'MM') {
757                # Create the tag lists for the relationship object.
758                my (@object_refs, @scalars, @indexes);
759                # The relationship will be created as an object with object
760                # references for its links to the participating entities.
761                my %links = ( from_link => $relationshipObject->{from},
762                              to_link => $relationshipObject->{to} );
763                for my $link (keys %links) {
764                    # Create an object_ref tag for this piece of the
765                    # relationship (from or to).
766                    my $object_ref = { label => $link,
767                                       type => $links{$link} };
768                    push @object_refs, $object_ref;
769                }
770                # Loop through the intersection data fields, creating scalar tags.
771                # There are no fancy array tags in a relationship.
772                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
773                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
774                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
775                }
776                # Finally, the indexes: currently we cannot support the to-index and
777                # from-index in PPO, so we just process the alternate indexes.
778                my $indexList = $relationshipObject->{Indexes};
779                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
780                # Wrap up all the stuff about this relationship.
781                my $object = { label => $relationshipName,
782                               scalar => \@scalars,
783                               object_ref => \@object_refs,
784                               index => \@indexes
785                             };
786                # Push it into the object list.
787                push @objects, $object;
788            }
789        }
790        # Compute a title.
791        my $title;
792        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
793            # Here we have a standard file name we can use for a title.
794            $title = $2;
795        } else {
796            # Here the file name is non-standard, so we carve up the
797            # database title.
798            $title = $xml->{Title}->{content};
799            $title =~ s/\s\.,//g;
800        }
801        # Wrap up the XML as a project.
802        my $ppoXML = { project => { label => $title,
803                                    object => \@objects }};
804        # Write out the results.
805        my $ppoString = XML::Simple::XMLout($ppoXML,
806                                            AttrIndent => 1,
807                                            KeepRoot => 1);
808        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
809    }
810    
811  =head3 FindIndexForEntity  =head3 FindIndexForEntity
812    
813  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
# Line 739  Line 897 
897      # Loop through the relations.      # Loop through the relations.
898      for my $relationName (@relNames) {      for my $relationName (@relNames) {
899          # Create a table for this relation.          # Create a table for this relation.
900          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
901          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
902      }      }
903  }  }
# Line 859  Line 1017 
1017              my $oldString = $fieldList->[$i];              my $oldString = $fieldList->[$i];
1018              if (length($oldString) > $maxLen) {              if (length($oldString) > $maxLen) {
1019                  # Here it's too big, so we truncate it.                  # Here it's too big, so we truncate it.
1020                  Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);                  Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1021                  $fieldList->[$i] = substr $oldString, 0, $maxLen;                  $fieldList->[$i] = substr $oldString, 0, $maxLen;
1022                  $retVal++;                  $retVal++;
1023              }              }
# Line 1841  Line 1999 
1999          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
2000              if ($structure->{$dir} eq $originEntityName) {              if ($structure->{$dir} eq $originEntityName) {
2001                  # Delete all relationship instances on this side of the entity instance.                  # Delete all relationship instances on this side of the entity instance.
2002                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2003                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2004                  $found = 1;                  $found = 1;
2005              }              }
# Line 1907  Line 2066 
2066      $dbh->SQL($command, undef, @parms);      $dbh->SQL($command, undef, @parms);
2067  }  }
2068    
2069    =head3 DeleteLike
2070    
2071    C<< my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms); >>
2072    
2073    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2074    filter, only fields from the relationship itself can be used.
2075    
2076    =over 4
2077    
2078    =item relName
2079    
2080    Name of the relationship whose records are to be deleted.
2081    
2082    =item filter
2083    
2084    A filter clause (L</Get>-style) for the delete query.
2085    
2086    =item parms
2087    
2088    Reference to a list of parameters for the filter clause.
2089    
2090    =item RETURN
2091    
2092    Returns a count of the number of rows deleted.
2093    
2094    =back
2095    
2096    =cut
2097    
2098    sub DeleteLike {
2099        # Get the parameters.
2100        my ($self, $objectName, $filter, $parms) = @_;
2101        # Declare the return variable.
2102        my $retVal;
2103        # Insure the parms argument is an array reference if the caller left it off.
2104        if (! defined($parms)) {
2105            $parms = [];
2106        }
2107        # Insure we have a relationship. The main reason for this is if we delete an entity
2108        # instance we have to yank out a bunch of other stuff with it.
2109        if ($self->IsEntity($objectName)) {
2110            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2111        } else {
2112            # Create the SQL command suffix to get the desierd records.
2113            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2114            # Convert it to a DELETE command.
2115            my $command = "DELETE $suffix";
2116            # Execute the command.
2117            my $dbh = $self->{_dbh};
2118            my $result = $dbh->SQL($command, 0, @{$parms});
2119            # Check the results. Note we convert the "0D0" result to a real zero.
2120            # A failure causes an abnormal termination, so the caller isn't going to
2121            # worry about it.
2122            if (! defined $result) {
2123                Confess("Error deleting from $objectName: " . $dbh->errstr());
2124            } elsif ($result == 0) {
2125                $retVal = 0;
2126            } else {
2127                $retVal = $result;
2128            }
2129        }
2130        # Return the result count.
2131        return $retVal;
2132    }
2133    
2134  =head3 SortNeeded  =head3 SortNeeded
2135    
2136  C<< my $parms = $erdb->SortNeeded($relationName); >>  C<< my $parms = $erdb->SortNeeded($relationName); >>
# Line 2047  Line 2271 
2271    
2272  =item RETURN  =item RETURN
2273    
2274  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2275    
2276  =back  =back
2277    
# Line 2428  Line 2652 
2652                  if (!$retVal) {                  if (!$retVal) {
2653                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2654                      Confess("Error inserting into $relationName: $errorString");                      Confess("Error inserting into $relationName: $errorString");
2655                    } else {
2656                        Trace("Insert successful using $parameterList[0].") if T(3);
2657                  }                  }
2658              }              }
2659          }          }
# Line 2543  Line 2769 
2769          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2770          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2771          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2772          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 1.5 / $rowSize;
2773            if ($estimate < 1000) {
2774                $estimate = 1000;
2775            }
2776          # Re-create the table without its index.          # Re-create the table without its index.
2777          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2778          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 2765  Line 2994 
2994    
2995  =item RETURN  =item RETURN
2996    
2997  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2998  instance is found with the specified key.  instance is found with the specified key.
2999    
3000  =back  =back
# Line 2898  Line 3127 
3127  fields specified returns multiple values, they are flattened in with the rest. For  fields specified returns multiple values, they are flattened in with the rest. For
3128  example, the following call will return a list of the features in a particular  example, the following call will return a list of the features in a particular
3129  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
3130  feature ID followed by all of its aliases.  feature ID followed by all of its essentiality determinations.
3131    
3132  C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']); >>
3133    
3134  =over 4  =over 4
3135    
# Line 3322  Line 3551 
3551      # Substitute the bulletin board codes.      # Substitute the bulletin board codes.
3552      $retVal =~ s!\[(/?[bi])\]!<$1>!g;      $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3553      $retVal =~ s!\[p\]!</p><p>!g;      $retVal =~ s!\[p\]!</p><p>!g;
3554        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3555        $retVal =~ s!\[/link\]!</a>!g;
3556        # Return the result.
3557        return $retVal;
3558    }
3559    
3560    =head3 BeginTran
3561    
3562    C<< $erdb->BeginTran(); >>
3563    
3564    Start a database transaction.
3565    
3566    =cut
3567    
3568    sub BeginTran {
3569        my ($self) = @_;
3570        $self->{_dbh}->begin_tran();
3571    
3572    }
3573    
3574    =head3 CommitTran
3575    
3576    C<< $erdb->CommitTran(); >>
3577    
3578    Commit an active database transaction.
3579    
3580    =cut
3581    
3582    sub CommitTran {
3583        my ($self) = @_;
3584        $self->{_dbh}->commit_tran();
3585    }
3586    
3587    =head3 RollbackTran
3588    
3589    C<< $erdb->RollbackTran(); >>
3590    
3591    Roll back an active database transaction.
3592    
3593    =cut
3594    
3595    sub RollbackTran {
3596        my ($self) = @_;
3597        $self->{_dbh}->roll_tran();
3598    }
3599    
3600    =head3 UpdateField
3601    
3602    C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>
3603    
3604    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3605    returned.
3606    
3607    =over 4
3608    
3609    =item fieldName
3610    
3611    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3612    
3613    =item oldValue
3614    
3615    Value to be modified. All occurrences of this value in the named field will be replaced by the
3616    new value.
3617    
3618    =item newValue
3619    
3620    New value to be substituted for the old value when it's found.
3621    
3622    =item filter
3623    
3624    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3625    
3626    =item parms
3627    
3628    Reference to a list of parameter values in the filter.
3629    
3630    =item RETURN
3631    
3632    Returns the number of rows modified.
3633    
3634    =back
3635    
3636    =cut
3637    
3638    sub UpdateField {
3639        # Get the parameters.
3640        my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3641        # Get the object and field names from the field name parameter.
3642        $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3643        my $objectName = $1;
3644        my $realFieldName = _FixName($2);
3645        # Add the old value to the filter. Note we allow the possibility that no
3646        # filter was specified.
3647        my $realFilter = "$fieldName = ?";
3648        if ($filter) {
3649            $realFilter .= " AND $filter";
3650        }
3651        # Format the query filter.
3652        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3653            $self->_SetupSQL([$objectName], $realFilter);
3654        # Create the query. Since there is only one object name, the mapped-name data is not
3655        # necessary. Neither is the FROM clause.
3656        $suffix =~ s/^FROM.+WHERE\s+//;
3657        # Create the update statement.
3658        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3659        # Get the database handle.
3660        my $dbh = $self->{_dbh};
3661        # Add the old and new values to the parameter list. Note we allow the possibility that
3662        # there are no user-supplied parameters.
3663        my @params = ($newValue, $oldValue);
3664        if (defined $parms) {
3665            push @params, @{$parms};
3666        }
3667        # Execute the update.
3668        my $retVal = $dbh->SQL($command, 0, @params);
3669        # Make the funky zero a real zero.
3670        if ($retVal == 0) {
3671            $retVal = 0;
3672        }
3673      # Return the result.      # Return the result.
3674      return $retVal;      return $retVal;
3675  }  }
# Line 3482  Line 3830 
3830    
3831  =head2 Virtual Methods  =head2 Virtual Methods
3832    
3833    =head3 _CreatePPOIndex
3834    
3835    C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3836    
3837    Convert the XML for an ERDB index to the XML structure for a PPO
3838    index.
3839    
3840    =over 4
3841    
3842    ERDB XML structure for an index.
3843    
3844    =item RETURN
3845    
3846    PPO XML structure for the same index.
3847    
3848    =back
3849    
3850    =cut
3851    
3852    sub _CreatePPOIndex {
3853        # Get the parameters.
3854        my ($indexObject) = @_;
3855        # The incoming index contains a list of the index fields in the IndexFields
3856        # member. We loop through it to create the index tags.
3857        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3858        # Wrap the fields in attribute tags.
3859        my $retVal = { attribute => \@fields };
3860        # Return the result.
3861        return $retVal;
3862    }
3863    
3864    =head3 _CreatePPOField
3865    
3866    C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3867    
3868    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3869    
3870    =over 4
3871    
3872    =item fieldName
3873    
3874    Name of the scalar field.
3875    
3876    =item fieldObject
3877    
3878    ERDB XML structure describing the field.
3879    
3880    =item RETURN
3881    
3882    Returns a PPO XML structure for the same field.
3883    
3884    =back
3885    
3886    =cut
3887    
3888    sub _CreatePPOField {
3889        # Get the parameters.
3890        my ($fieldName, $fieldObject) = @_;
3891        # Get the field type.
3892        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3893        # Fix up the field name.
3894        $fieldName = _FixName($fieldName);
3895        # Build the scalar tag.
3896        my $retVal = { label => $fieldName, type => $type };
3897        # Return the result.
3898        return $retVal;
3899    }
3900    
3901  =head3 CleanKeywords  =head3 CleanKeywords
3902    
3903  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
# Line 3533  Line 3949 
3949    
3950  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3951    
3952  Create the relation map for an SQL query. The relation map is used by B<DBObject>  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3953  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
3954    
3955  =over 4  =over 4
# Line 3550  Line 3966 
3966  =item RETURN  =item RETURN
3967    
3968  Returns a list of 2-tuples. Each tuple consists of an object name as used in the  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3969  query followed by the actual name of that object. This enables the B<DBObject> to  query followed by the actual name of that object. This enables the B<ERDBObject> to
3970  determine the order of the tables in the query and which object name belongs to each  determine the order of the tables in the query and which object name belongs to each
3971  mapped object name. Most of the time these two values are the same; however, if a  mapped object name. Most of the time these two values are the same; however, if a
3972  relation occurs twice in the query, the relation name in the field list and WHERE  relation occurs twice in the query, the relation name in the field list and WHERE
# Line 4093  Line 4509 
4509    
4510  =head3 _LoadMetaData  =head3 _LoadMetaData
4511    
4512    C<< my $metadata = ERDB::_LoadMetaData($filename); >>
4513    
4514  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4515  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
4516  load or use the database. The schema for the XML file is F<ERDatabase.xml>.  load or use the database. The schema for the XML file is F<ERDatabase.xml>.
# Line 4242  Line 4660 
4660              if ($found == 0) {              if ($found == 0) {
4661                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4662              }              }
4663              # Now we need to convert the relation's index list to an index table. We begin by creating              # Attach all the indexes to the relation.
4664              # an empty table in the relation structure.              _ProcessIndexes($indexList, $relation);
             $relation->{Indexes} = { };  
             # Loop through the indexes.  
             my $count = 0;  
             for my $index (@{$indexList}) {  
                 # Add this index to the index table.  
                 _AddIndex("idx$count", $relation, $index);  
                 # Increment the counter so that the next index has a different name.  
                 $count++;  
             }  
4665          }          }
4666          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4667          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 4266  Line 4675 
4675          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4676          # Format a description for the FROM field.          # Format a description for the FROM field.
4677          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4678          my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";          my $fromComment = "[b]id[/b] of the source [b][link #$fromEntity]$fromEntity\[/link][/b].";
4679          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4680          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4681          # Add the FROM field.          # Add the FROM field.
# Line 4276  Line 4685 
4685                                                      PrettySort => 1});                                                      PrettySort => 1});
4686          # Format a description for the TO field.          # Format a description for the TO field.
4687          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4688          my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";          my $toComment = "[b]id[/b] of the target [b][link #$toEntity]$toEntity\[/link][/b].";
4689          # Get the TO entity's key type.          # Get the TO entity's key type.
4690          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4691          # Add the TO field.          # Add the TO field.
# Line 4288  Line 4697 
4697          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
4698                               Indexes => { } };                               Indexes => { } };
4699          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
4700    
4701            # Add the alternate indexes (if any). This MUST be done before the FROM and
4702            # TO indexes, because it erases the relation's index list.
4703            if (exists $relationshipStructure->{Indexes}) {
4704                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
4705            }
4706            # Add the relation to the master table.
4707          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
4708          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
4709          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
4710          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
4711      }      }
4712      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 4450  Line 4865 
4865      _AddIndex("idx$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4866  }  }
4867    
4868    =head3 _ProcessIndexes
4869    
4870    C<< ERDB::_ProcessIndexes($indexList, $relation); >>
4871    
4872    Build the data structures for the specified indexes in the specified relation.
4873    
4874    =over 4
4875    
4876    =item indexList
4877    
4878    Reference to a list of indexes. Each index is a hash reference containing an optional
4879    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
4880    to a list of index field structures. An index field structure, in turn, is a reference
4881    to a hash that contains a C<name> attribute for the field name and an C<order>
4882    attribute that specifies either C<ascending> or C<descending>. In this sense the
4883    index list encapsulates the XML C<Indexes> structure in the database definition.
4884    
4885    =item relation
4886    
4887    The structure that describes the current relation. The new index descriptors will
4888    be stored in the structure's C<Indexes> member. Any previous data in the structure
4889    will be lost.
4890    
4891    =back
4892    
4893    =cut
4894    
4895    sub _ProcessIndexes {
4896        # Get the parameters.
4897        my ($indexList, $relation) = @_;
4898        # Now we need to convert the relation's index list to an index table. We begin by creating
4899        # an empty table in the relation structure.
4900        $relation->{Indexes} = { };
4901        # Loop through the indexes.
4902        my $count = 0;
4903        for my $index (@{$indexList}) {
4904            # Add this index to the index table.
4905            _AddIndex("idx$count", $relation, $index);
4906            # Increment the counter so that the next index has a different name.
4907            $count++;
4908        }
4909    }
4910    
4911  =head3 _AddIndex  =head3 _AddIndex
4912    
4913  Add an index to a relation structure.  Add an index to a relation structure.
# Line 4979  Line 5437 
5437      # Compute the number of columns.      # Compute the number of columns.
5438      my $colCount = @colNames;      my $colCount = @colNames;
5439      # Generate the title row.      # Generate the title row.
5440      my $htmlString = "<p><table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";      my $htmlString = "<table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";
5441      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
5442      $htmlString .= "<tr>";      $htmlString .= "<tr>";
5443      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 4998  Line 5456 
5456  =cut  =cut
5457    
5458  sub _CloseTable {  sub _CloseTable {
5459      return "</table></p>\n";      return "</table>\n";
5460  }  }
5461    
5462  =head3 _ShowField  =head3 _ShowField

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