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revision 1.78, Tue Nov 28 01:02:42 2006 UTC revision 1.90, Fri Apr 27 22:19:49 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 548  Line 548 
548          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
549              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
550          }          }
551          # 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.
552            my $relCount = keys %{$relationshipList};
553            if ($relCount > 0) {
554                # First, we set up the relationship subsection.
555          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
556          # Loop through the relationships.          # Loop through the relationships.
557          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
# Line 564  Line 567 
567          }          }
568          # Close off the relationship list.          # Close off the relationship list.
569          $retVal .= "</ul>\n";          $retVal .= "</ul>\n";
570            }
571          # Get the entity's relations.          # Get the entity's relations.
572          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
573          # Create a header for the relation subsection.          # Create a header for the relation subsection.
# Line 650  Line 654 
654      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
655  }  }
656    
657    =head3 CreatePPO
658    
659    C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
660    
661    Create a PPO XML file from an ERDB data definition XML file. At the
662    current time, the PPO XML file can be used to create a database with
663    similar functionality. Eventually, the PPO will be able to use the
664    created XML to access the live ERDB database.
665    
666    =over 4
667    
668    =item erdbXMLFile
669    
670    Name of the XML data definition file for the ERDB database. This
671    file must exist.
672    
673    =item ppoXMLFile
674    
675    Output file for the PPO XML definition. If this file exists, it
676    will be overwritten.
677    
678    =back
679    
680    =cut
681    
682    sub CreatePPO {
683        # Get the parameters.
684        my ($erdbXMLFile, $ppoXMLFile) = @_;
685        # First, we want to slurp in the ERDB XML file in its raw form.
686        my $xml = ReadMetaXML($erdbXMLFile);
687        # Create a variable to hold all of the objects in the PPO project.
688        my @objects = ();
689        # Get the relationship hash.
690        my $relationships = $xml->{Relationships};
691        # Loop through the entities.
692        my $entities = $xml->{Entities};
693        for my $entityName (keys %{$entities}) {
694            # Get the entity's data structures.
695            my $entityObject = $entities->{$entityName};
696            # We put the object's fields in here, according to their type.
697            my (@object_refs, @scalars, @indexes, @arrays);
698            # Create the ID field for the entity. We get the key type from the
699            # entity object and compute the corresponding SQL type.
700            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
701            push @scalars, { label => 'id', type => $type };
702            # Loop through the entity fields.
703            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
704                # Get the field object.
705                my $fieldObject = $entityObject->{Fields}->{$fieldName};
706                # Convert it to a scalar tag.
707                my $scalar = _CreatePPOField($fieldName, $fieldObject);
708                # If we have a relation, this field is stored in an array.
709                # otherwise, it is a scalar. The array tag has scalars
710                # stored as an XML array. In ERDB, there is only ever one,
711                # but PPO can have more.
712                my $relation = $fieldObject->{relation};
713                if ($relation) {
714                    push @arrays, { scalar => [$scalar] };
715                } else {
716                    push @scalars, $scalar;
717                }
718            }
719            # Loop through the relationships. If this entity is the to-entity
720            # on a relationship of 1M arity, then it is implemented as a PPO
721            # object reference.
722            for my $relationshipName (keys %{$relationships}) {
723                # Get the relationship data.
724                my $relationshipData = $relationships->{$relationshipName};
725                # If we have a from for this entity and an arity of 1M, we
726                # have an object reference.
727                if ($relationshipData->{to} eq $entityName &&
728                    $relationshipData->{arity} eq '1M') {
729                    # Build the object reference tag.
730                    push @object_refs, { label => $relationshipName,
731                                         type => $relationshipData->{from} };
732                }
733            }
734            # Create the indexes.
735            my $indexList = $entityObject->{Indexes};
736            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
737            # Build the object XML tree.
738            my $object = { label => $entityName,
739                           object_ref => \@object_refs,
740                           scalar => \@scalars,
741                           index => \@indexes,
742                           array => \@arrays
743                          };
744            # Push the object onto the objects list.
745            push @objects, $object;
746        }
747        # Loop through the relationships, searching for MMs. The 1Ms were
748        # already handled by the entity search above.
749        for my $relationshipName (keys %{$relationships}) {
750            # Get this relationship's object.
751            my $relationshipObject = $relationships->{$relationshipName};
752            # Only proceed if it's many-to-many.
753            if ($relationshipObject->{arity} eq 'MM') {
754                # Create the tag lists for the relationship object.
755                my (@object_refs, @scalars, @indexes);
756                # The relationship will be created as an object with object
757                # references for its links to the participating entities.
758                my %links = ( from_link => $relationshipObject->{from},
759                              to_link => $relationshipObject->{to} );
760                for my $link (keys %links) {
761                    # Create an object_ref tag for this piece of the
762                    # relationship (from or to).
763                    my $object_ref = { label => $link,
764                                       type => $links{$link} };
765                    push @object_refs, $object_ref;
766                }
767                # Loop through the intersection data fields, creating scalar tags.
768                # There are no fancy array tags in a relationship.
769                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
770                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
771                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
772                }
773                # Finally, the indexes: currently we cannot support the to-index and
774                # from-index in PPO, so we just process the alternate indexes.
775                my $indexList = $relationshipObject->{Indexes};
776                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
777                # Wrap up all the stuff about this relationship.
778                my $object = { label => $relationshipName,
779                               scalar => \@scalars,
780                               object_ref => \@object_refs,
781                               index => \@indexes
782                             };
783                # Push it into the object list.
784                push @objects, $object;
785            }
786        }
787        # Compute a title.
788        my $title;
789        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
790            # Here we have a standard file name we can use for a title.
791            $title = $2;
792        } else {
793            # Here the file name is non-standard, so we carve up the
794            # database title.
795            $title = $xml->{Title}->{content};
796            $title =~ s/\s\.,//g;
797        }
798        # Wrap up the XML as a project.
799        my $ppoXML = { project => { label => $title,
800                                    object => \@objects }};
801        # Write out the results.
802        my $ppoString = XML::Simple::XMLout($ppoXML,
803                                            AttrIndent => 1,
804                                            KeepRoot => 1);
805        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
806    }
807    
808  =head3 FindIndexForEntity  =head3 FindIndexForEntity
809    
810  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>  C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
# Line 739  Line 894 
894      # Loop through the relations.      # Loop through the relations.
895      for my $relationName (@relNames) {      for my $relationName (@relNames) {
896          # Create a table for this relation.          # Create a table for this relation.
897          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
898          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
899      }      }
900  }  }
# Line 1493  Line 1648 
1648          my $actualKeywords = $self->CleanKeywords($searchExpression);          my $actualKeywords = $self->CleanKeywords($searchExpression);
1649          # Prefix a "+" to each uncontrolled word. This converts the default          # Prefix a "+" to each uncontrolled word. This converts the default
1650          # search mode from OR to AND.          # search mode from OR to AND.
1651          $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;          $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1652          Trace("Actual keywords for search are\n$actualKeywords") if T(3);          Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1653          # We need two match expressions, one for the filter clause and one in the          # We need two match expressions, one for the filter clause and one in the
1654          # query itself. Both will use a parameter mark, so we need to push the          # query itself. Both will use a parameter mark, so we need to push the
# Line 1841  Line 1996 
1996          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
1997              if ($structure->{$dir} eq $originEntityName) {              if ($structure->{$dir} eq $originEntityName) {
1998                  # Delete all relationship instances on this side of the entity instance.                  # Delete all relationship instances on this side of the entity instance.
1999                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2000                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2001                  $found = 1;                  $found = 1;
2002              }              }
# Line 1852  Line 2008 
2008      }      }
2009  }  }
2010    
2011    =head3 DeleteRow
2012    
2013    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
2014    
2015    Delete a row from a relationship. In most cases, only the from-link and to-link are
2016    needed; however, for relationships with intersection data values can be specified
2017    for the other fields using a hash.
2018    
2019    =over 4
2020    
2021    =item relationshipName
2022    
2023    Name of the relationship from which the row is to be deleted.
2024    
2025    =item fromLink
2026    
2027    ID of the entity instance in the From direction.
2028    
2029    =item toLink
2030    
2031    ID of the entity instance in the To direction.
2032    
2033    =item values
2034    
2035    Reference to a hash of other values to be used for filtering the delete.
2036    
2037    =back
2038    
2039    =cut
2040    
2041    sub DeleteRow {
2042        # Get the parameters.
2043        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2044        # Create a hash of all the filter information.
2045        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2046        if (defined $values) {
2047            for my $key (keys %{$values}) {
2048                $filter{$key} = $values->{$key};
2049            }
2050        }
2051        # Build an SQL statement out of the hash.
2052        my @filters = ();
2053        my @parms = ();
2054        for my $key (keys %filter) {
2055            push @filters, _FixName($key) . " = ?";
2056            push @parms, $filter{$key};
2057        }
2058        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2059        my $command = "DELETE FROM $relationshipName WHERE " .
2060                      join(" AND ", @filters);
2061        # Execute it.
2062        my $dbh = $self->{_dbh};
2063        $dbh->SQL($command, undef, @parms);
2064    }
2065    
2066  =head3 SortNeeded  =head3 SortNeeded
2067    
2068  C<< my $parms = $erdb->SortNeeded($relationName); >>  C<< my $parms = $erdb->SortNeeded($relationName); >>
# Line 1992  Line 2203 
2203    
2204  =item RETURN  =item RETURN
2205    
2206  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2207    
2208  =back  =back
2209    
# Line 2373  Line 2584 
2584                  if (!$retVal) {                  if (!$retVal) {
2585                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2586                      Confess("Error inserting into $relationName: $errorString");                      Confess("Error inserting into $relationName: $errorString");
2587                    } else {
2588                        Trace("Insert successful using $parameterList[0].") if T(3);
2589                  }                  }
2590              }              }
2591          }          }
# Line 2488  Line 2701 
2701          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2702          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2703          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2704          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 1.5 / $rowSize;
2705            if ($estimate < 1000) {
2706                $estimate = 1000;
2707            }
2708          # Re-create the table without its index.          # Re-create the table without its index.
2709          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2710          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 2530  Line 2746 
2746              # The full-text index (if any) is always built last, even for MySQL.              # The full-text index (if any) is always built last, even for MySQL.
2747              # First we need to see if this table has a full-text index. Only              # First we need to see if this table has a full-text index. Only
2748              # primary relations are allowed that privilege.              # primary relations are allowed that privilege.
2749                Trace("Checking for full-text index on $relationName.") if T(2);
2750              if ($self->_IsPrimary($relationName)) {              if ($self->_IsPrimary($relationName)) {
2751                  # Get the relation's entity/relationship structure.                  $self->CreateSearchIndex($relationName);
                 my $structure = $self->_GetStructure($relationName);  
                 # Check for a searchable fields list.  
                 if (exists $structure->{searchFields}) {  
                     # Here we know that we need to create a full-text search index.  
                     # Get an SQL-formatted field name list.  
                     my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));  
                     # Create the index.  
                     $dbh->create_index(tbl => $relationName, idx => "search_idx",  
                                        flds => $fields, kind => 'fulltext');  
                 }  
2752              }              }
2753          }          }
2754      }      }
# Line 2553  Line 2760 
2760      return $retVal;      return $retVal;
2761  }  }
2762    
2763    =head3 CreateSearchIndex
2764    
2765    C<< $erdb->CreateSearchIndex($objectName); >>
2766    
2767    Check for a full-text search index on the specified entity or relationship object, and
2768    if one is required, rebuild it.
2769    
2770    =over 4
2771    
2772    =item objectName
2773    
2774    Name of the entity or relationship to be indexed.
2775    
2776    =back
2777    
2778    =cut
2779    
2780    sub CreateSearchIndex {
2781        # Get the parameters.
2782        my ($self, $objectName) = @_;
2783        # Get the relation's entity/relationship structure.
2784        my $structure = $self->_GetStructure($objectName);
2785        # Get the database handle.
2786        my $dbh = $self->{_dbh};
2787        Trace("Checking for search fields in $objectName.") if T(3);
2788        # Check for a searchable fields list.
2789        if (exists $structure->{searchFields}) {
2790            # Here we know that we need to create a full-text search index.
2791            # Get an SQL-formatted field name list.
2792            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2793            # Create the index. If it already exists, it will be dropped.
2794            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2795                               flds => $fields, kind => 'fulltext');
2796            Trace("Index created for $fields in $objectName.") if T(2);
2797        }
2798    }
2799    
2800  =head3 DropRelation  =head3 DropRelation
2801    
2802  C<< $erdb->DropRelation($relationName); >>  C<< $erdb->DropRelation($relationName); >>
# Line 2682  Line 2926 
2926    
2927  =item RETURN  =item RETURN
2928    
2929  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
2930  instance is found with the specified key.  instance is found with the specified key.
2931    
2932  =back  =back
# Line 3239  Line 3483 
3483      # Substitute the bulletin board codes.      # Substitute the bulletin board codes.
3484      $retVal =~ s!\[(/?[bi])\]!<$1>!g;      $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3485      $retVal =~ s!\[p\]!</p><p>!g;      $retVal =~ s!\[p\]!</p><p>!g;
3486        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3487        $retVal =~ s!\[/link\]!</a>!g;
3488        # Return the result.
3489        return $retVal;
3490    }
3491    
3492    =head3 BeginTran
3493    
3494    C<< $erdb->BeginTran(); >>
3495    
3496    Start a database transaction.
3497    
3498    =cut
3499    
3500    sub BeginTran {
3501        my ($self) = @_;
3502        $self->{_dbh}->begin_tran();
3503    
3504    }
3505    
3506    =head3 CommitTran
3507    
3508    C<< $erdb->CommitTran(); >>
3509    
3510    Commit an active database transaction.
3511    
3512    =cut
3513    
3514    sub CommitTran {
3515        my ($self) = @_;
3516        $self->{_dbh}->commit_tran();
3517    }
3518    
3519    =head3 RollbackTran
3520    
3521    C<< $erdb->RollbackTran(); >>
3522    
3523    Roll back an active database transaction.
3524    
3525    =cut
3526    
3527    sub RollbackTran {
3528        my ($self) = @_;
3529        $self->{_dbh}->roll_tran();
3530    }
3531    
3532    =head3 UpdateField
3533    
3534    C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>
3535    
3536    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3537    returned.
3538    
3539    =over 4
3540    
3541    =item fieldName
3542    
3543    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3544    
3545    =item oldValue
3546    
3547    Value to be modified. All occurrences of this value in the named field will be replaced by the
3548    new value.
3549    
3550    =item newValue
3551    
3552    New value to be substituted for the old value when it's found.
3553    
3554    =item filter
3555    
3556    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3557    
3558    =item parms
3559    
3560    Reference to a list of parameter values in the filter.
3561    
3562    =item RETURN
3563    
3564    Returns the number of rows modified.
3565    
3566    =back
3567    
3568    =cut
3569    
3570    sub UpdateField {
3571        # Get the parameters.
3572        my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3573        # Get the object and field names from the field name parameter.
3574        $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3575        my $objectName = $1;
3576        my $realFieldName = _FixName($2);
3577        # Add the old value to the filter. Note we allow the possibility that no
3578        # filter was specified.
3579        my $realFilter = "$fieldName = ?";
3580        if ($filter) {
3581            $realFilter .= " AND $filter";
3582        }
3583        # Format the query filter.
3584        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3585            $self->_SetupSQL([$objectName], $realFilter);
3586        # Create the query. Since there is only one object name, the mapped-name data is not
3587        # necessary. Neither is the FROM clause.
3588        $suffix =~ s/^FROM.+WHERE\s+//;
3589        # Create the update statement.
3590        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3591        # Get the database handle.
3592        my $dbh = $self->{_dbh};
3593        # Add the old and new values to the parameter list. Note we allow the possibility that
3594        # there are no user-supplied parameters.
3595        my @params = ($newValue, $oldValue);
3596        if (defined $parms) {
3597            push @params, @{$parms};
3598        }
3599        # Execute the update.
3600        my $retVal = $dbh->SQL($command, 0, @params);
3601        # Make the funky zero a real zero.
3602        if ($retVal == 0) {
3603            $retVal = 0;
3604        }
3605      # Return the result.      # Return the result.
3606      return $retVal;      return $retVal;
3607  }  }
# Line 3399  Line 3762 
3762    
3763  =head2 Virtual Methods  =head2 Virtual Methods
3764    
3765    =head3 _CreatePPOIndex
3766    
3767    C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3768    
3769    Convert the XML for an ERDB index to the XML structure for a PPO
3770    index.
3771    
3772    =over 4
3773    
3774    ERDB XML structure for an index.
3775    
3776    =item RETURN
3777    
3778    PPO XML structure for the same index.
3779    
3780    =back
3781    
3782    =cut
3783    
3784    sub _CreatePPOIndex {
3785        # Get the parameters.
3786        my ($indexObject) = @_;
3787        # The incoming index contains a list of the index fields in the IndexFields
3788        # member. We loop through it to create the index tags.
3789        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3790        # Wrap the fields in attribute tags.
3791        my $retVal = { attribute => \@fields };
3792        # Return the result.
3793        return $retVal;
3794    }
3795    
3796    =head3 _CreatePPOField
3797    
3798    C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3799    
3800    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3801    
3802    =over 4
3803    
3804    =item fieldName
3805    
3806    Name of the scalar field.
3807    
3808    =item fieldObject
3809    
3810    ERDB XML structure describing the field.
3811    
3812    =item RETURN
3813    
3814    Returns a PPO XML structure for the same field.
3815    
3816    =back
3817    
3818    =cut
3819    
3820    sub _CreatePPOField {
3821        # Get the parameters.
3822        my ($fieldName, $fieldObject) = @_;
3823        # Get the field type.
3824        my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3825        # Fix up the field name.
3826        $fieldName = _FixName($fieldName);
3827        # Build the scalar tag.
3828        my $retVal = { label => $fieldName, type => $type };
3829        # Return the result.
3830        return $retVal;
3831    }
3832    
3833  =head3 CleanKeywords  =head3 CleanKeywords
3834    
3835  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
# Line 3450  Line 3881 
3881    
3882  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3883    
3884  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>
3885  to determine how to interpret the results of the query.  to determine how to interpret the results of the query.
3886    
3887  =over 4  =over 4
# Line 3467  Line 3898 
3898  =item RETURN  =item RETURN
3899    
3900  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
3901  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
3902  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
3903  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
3904  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 4010  Line 4441 
4441    
4442  =head3 _LoadMetaData  =head3 _LoadMetaData
4443    
4444    C<< my $metadata = ERDB::_LoadMetaData($filename); >>
4445    
4446  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.
4447  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
4448  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 4159  Line 4592 
4592              if ($found == 0) {              if ($found == 0) {
4593                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };                  push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4594              }              }
4595              # 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.
4596              # 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++;  
             }  
4597          }          }
4598          # Finally, we add the relation structure to the entity.          # Finally, we add the relation structure to the entity.
4599          $entityStructure->{Relations} = $relationTable;          $entityStructure->{Relations} = $relationTable;
# Line 4183  Line 4607 
4607          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4608          # Format a description for the FROM field.          # Format a description for the FROM field.
4609          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4610          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].";
4611          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4612          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4613          # Add the FROM field.          # Add the FROM field.
# Line 4193  Line 4617 
4617                                                      PrettySort => 1});                                                      PrettySort => 1});
4618          # Format a description for the TO field.          # Format a description for the TO field.
4619          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4620          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].";
4621          # Get the TO entity's key type.          # Get the TO entity's key type.
4622          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4623          # Add the TO field.          # Add the TO field.
# Line 4205  Line 4629 
4629          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),          my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
4630                               Indexes => { } };                               Indexes => { } };
4631          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };          $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
4632    
4633            # Add the alternate indexes (if any). This MUST be done before the FROM and
4634            # TO indexes, because it erases the relation's index list.
4635            if (exists $relationshipStructure->{Indexes}) {
4636                _ProcessIndexes($relationshipStructure->{Indexes}, $thisRelation);
4637            }
4638            # Add the relation to the master table.
4639          # Create the FROM and TO indexes.          # Create the FROM and TO indexes.
4640          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
4641          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);          _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
         # Add the relation to the master table.  
4642          $masterRelationTable{$relationshipName} = $thisRelation;          $masterRelationTable{$relationshipName} = $thisRelation;
4643      }      }
4644      # Now store the master relation table in the metadata structure.      # Now store the master relation table in the metadata structure.
# Line 4367  Line 4797 
4797      _AddIndex("idx$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4798  }  }
4799    
4800    =head3 _ProcessIndexes
4801    
4802    C<< ERDB::_ProcessIndexes($indexList, $relation); >>
4803    
4804    Build the data structures for the specified indexes in the specified relation.
4805    
4806    =over 4
4807    
4808    =item indexList
4809    
4810    Reference to a list of indexes. Each index is a hash reference containing an optional
4811    C<Notes> value that describes the index and an C<IndexFields> value that is a reference
4812    to a list of index field structures. An index field structure, in turn, is a reference
4813    to a hash that contains a C<name> attribute for the field name and an C<order>
4814    attribute that specifies either C<ascending> or C<descending>. In this sense the
4815    index list encapsulates the XML C<Indexes> structure in the database definition.
4816    
4817    =item relation
4818    
4819    The structure that describes the current relation. The new index descriptors will
4820    be stored in the structure's C<Indexes> member. Any previous data in the structure
4821    will be lost.
4822    
4823    =back
4824    
4825    =cut
4826    
4827    sub _ProcessIndexes {
4828        # Get the parameters.
4829        my ($indexList, $relation) = @_;
4830        # Now we need to convert the relation's index list to an index table. We begin by creating
4831        # an empty table in the relation structure.
4832        $relation->{Indexes} = { };
4833        # Loop through the indexes.
4834        my $count = 0;
4835        for my $index (@{$indexList}) {
4836            # Add this index to the index table.
4837            _AddIndex("idx$count", $relation, $index);
4838            # Increment the counter so that the next index has a different name.
4839            $count++;
4840        }
4841    }
4842    
4843  =head3 _AddIndex  =head3 _AddIndex
4844    
4845  Add an index to a relation structure.  Add an index to a relation structure.
# Line 4896  Line 5369 
5369      # Compute the number of columns.      # Compute the number of columns.
5370      my $colCount = @colNames;      my $colCount = @colNames;
5371      # Generate the title row.      # Generate the title row.
5372      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";
5373      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
5374      $htmlString .= "<tr>";      $htmlString .= "<tr>";
5375      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 4915  Line 5388 
5388  =cut  =cut
5389    
5390  sub _CloseTable {  sub _CloseTable {
5391      return "</table></p>\n";      return "</table>\n";
5392  }  }
5393    
5394  =head3 _ShowField  =head3 _ShowField

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