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revision 1.94, Thu Dec 6 14:58:03 2007 UTC revision 1.105, Tue Sep 23 20:43:42 2008 UTC
# Line 11  Line 11 
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
13      use CGI;      use CGI;
14        use WikiTools;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 101  Line 102 
102    
103  =item text  =item text
104    
105  long string; Text fields cannot be used in indexes or sorting and do not support the  long string; Text fields do not support the normal syntax of filter clauses,
106  normal syntax of filter clauses, but can be up to a billion character in length  but can be up to a billion character in length
107    
108    =item dna
109    
110    long string, used to store DNA and protein sequences
111    
112    =item image
113    
114    long string, used to store encoded image data
115    
116  =item float  =item float
117    
# Line 347  Line 356 
356                                 indexMod =>   0, notes => "signed 32-bit integer"},                                 indexMod =>   0, notes => "signed 32-bit integer"},
357                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
358                                 indexMod =>   0, notes => "unsigned 32-bit integer"},                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
359                      image =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 100000, sort => "",
360                                   indexMod => 255, notes => "UUencoded image, suitable for import into GD, should never be indexed"},
361                      dna =>      { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 100000, sort => "",
362                                   indexMod => 255, notes => "DNA or protein sequence, should never be indexed"},
363                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
364                                 indexMod =>   0, notes => "character string, 0 to 255 characters"},                                 indexMod =>   0, notes => "character string, 0 to 255 characters"},
365                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
# Line 389  Line 402 
402                                    Entities => 'Entity',                                    Entities => 'Entity',
403                                    Fields => 'Field',                                    Fields => 'Field',
404                                    Indexes => 'Index',                                    Indexes => 'Index',
405                                    IndexFields => 'IndexField'                                    IndexFields => 'IndexField',
406                                      Issues => 'Issue',
407                                      Shapes => 'Shape'
408                                  },                                  },
409                    KeyAttr =>    { Relationship => 'name',                    KeyAttr =>    { Relationship => 'name',
410                                    Entity => 'name',                                    Entity => 'name',
411                                    Field => 'name'                                    Field => 'name',
412                                      Shape => 'name'
413                                  },                                  },
414                    SuppressEmpty => 1,                    SuppressEmpty => 1,
415                   );                   );
416    
417  my %XmlInOpts  = (  my %XmlInOpts  = (
418                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],                    ForceArray => [qw(Field Index IndexField Relationship Entity Shape)],
419                    ForceContent => 1,                    ForceContent => 1,
420                    NormalizeSpace => 2,                    NormalizeSpace => 2,
421                   );                   );
# Line 408  Line 424 
424                    XMLDecl => 1,                    XMLDecl => 1,
425                   );                   );
426    
   
427  =head2 Public Methods  =head2 Public Methods
428    
429  =head3 new  =head3 new
# Line 433  Line 448 
448    
449  sub new {  sub new {
450      # Get the parameters.      # Get the parameters.
451      my ($class, $dbh, $metaFileName, $options) = @_;      my ($class, $dbh, $metaFileName, %options) = @_;
452      # Load the meta-data.      # Load the meta-data.
453      my $metaData = _LoadMetaData($metaFileName);      my $metaData = _LoadMetaData($metaFileName);
454      # Create the object.      # Create the object.
# Line 657  Line 672 
672      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
673  }  }
674    
675    =head3 GenerateWikiData
676    
677        my @wikiLines = $erdb->GenerateWikiData();
678    
679    Build a description of the database for the wiki. The database will be
680    organized into a single page, with sections for each entity and relationship.
681    The return value is a list of text lines.
682    
683    =cut
684    
685    sub GenerateWikiData {
686        # Get the parameters.
687        my ($self) = @_;
688        # We'll build the wiki text in here.
689        my @retVal = ();
690        # Get the metadata object.
691        my $metadata = $self->{_metaData};
692        # Get the title string. This will become the page name.
693        my $title = $metadata->{Title}->{content};
694        # Get the entity and relationship lists.
695        my $entityList = $metadata->{Entities};
696        my $relationshipList = $metadata->{Relationships};
697        my $shapeList = $metadata->{Shapes};
698        # Start with the introductory text.
699        push @retVal, WikiTools::Heading(2, "Introduction");
700        if (my $notes = $metadata->{Notes}) {
701            push @retVal, WikiNote($notes->{content});
702        }
703        # Generate issue list.
704        if (my $issues = $metadata->{Issues}) {
705            push @retVal, WikiTools::Heading(3, 'Issues');
706            push @retVal, WikiTools::List(map { $_->{content} } @{$issues});
707        }
708        # Start the entity section.
709        push @retVal, WikiTools::Heading(2, "Entities");
710        # Loop through the entities. Note that unlike the situation with HTML, we
711        # don't need to generate the table of contents manually, just the data
712        # itself.
713        for my $key (sort keys %$entityList) {
714            # Create a header for this entity.
715            push @retVal, "", WikiTools::Heading(3, $key);
716            # Get the entity data.
717            my $entityData = $entityList->{$key};
718            # Plant the notes here, if there are any.
719            push @retVal, _ObjectNotes($entityData);
720            # Now we list the entity's relationships (if any). First, we build a list
721            # of the relationships relevant to this entity.
722            my @rels = ();
723            for my $rel (sort keys %$relationshipList) {
724                my $relStructure = $relationshipList->{$rel};
725                if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
726                    # Get the relationship sentence.
727                    my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
728                    # Linkify it.
729                    my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
730                    $relSentence =~ s/$rel/$linkedRel/;
731                    push @rels, $relSentence;
732                }
733            }
734            # Add the relationships as a Wiki list.
735            push @retVal, WikiTools::List(@rels);
736            # Get the entity's relations.
737            my $relationList = $entityData->{Relations};
738            # Loop through the relations, displaying them.
739            for my $relation (sort keys %{$relationList}) {
740                my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
741                push @retVal, $wikiString;
742            }
743        }
744        # Now the entities are documented. Next we do the relationships.
745        push @retVal, WikiTools::Heading(2, "Relationships");
746        for my $key (sort keys %$relationshipList) {
747            my $relationshipData = $relationshipList->{$key};
748            # Create the relationship heading.
749            push @retVal, WikiTools::Heading(3, $key);
750            # Describe the relationship arity. Note there's a bit of trickiness involving recursive
751            # many-to-many relationships. In a normal many-to-many we use two sentences to describe
752            # the arity (one for each direction). This is a bad idea for a recursive relationship,
753            # since both sentences will say the same thing.
754            my $arity = $relationshipData->{arity};
755            my $fromEntity = $relationshipData->{from};
756            my $toEntity = $relationshipData->{to};
757            my @listElements = ();
758            my $boldCode = WikiTools::BoldCode();
759            if ($arity eq "11") {
760                push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
761            } else {
762                push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.";
763                if ($arity eq "MM" && $fromEntity ne $toEntity) {
764                    push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.";
765                }
766            }
767            push @retVal, WikiTools::List(@listElements);
768            # Plant the notes here, if there are any.
769            push @retVal, _ObjectNotes($relationshipData);
770            # Finally, the relationship table.
771            my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
772            push @retVal, $wikiString;
773        }
774        # Now loop through the miscellaneous shapes.
775        if ($shapeList) {
776            push @retVal, WikiTools::Heading(2, "Miscellaneous");
777            for my $shape (sort keys %$shapeList) {
778                push @retVal, WikiTools::Heading(3, $shape);
779                my $shapeData = $shapeList->{$shape};
780                push @retVal, _ObjectNotes($shapeData);
781            }
782        }
783        # All done. Return the lines.
784        return @retVal;
785    }
786    
787    
788  =head3 CreatePPO  =head3 CreatePPO
789    
790      ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);      ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
# Line 946  Line 1074 
1074          # Push the result into the field list.          # Push the result into the field list.
1075          push @fieldList, $fieldString;          push @fieldList, $fieldString;
1076      }      }
     # If this is a root table, add the "new_record" flag. It defaults to 0, so  
     if ($rootFlag) {  
         push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";  
     }  
1077      # Convert the field list into a comma-delimited string.      # Convert the field list into a comma-delimited string.
1078      my $fieldThing = join(', ', @fieldList);      my $fieldThing = join(', ', @fieldList);
1079      # Insure the table is not already there.      # Insure the table is not already there.
# Line 1416  Line 1540 
1540      return sort keys %{$entityList};      return sort keys %{$entityList};
1541  }  }
1542    
1543    
1544    =head3 GetConnectingRelationships
1545    
1546        my @list = $erdb->GetConnectingRelationships($entityName);
1547    
1548    Return a list of the relationships connected to the specified entity.
1549    
1550    =over 4
1551    
1552    =item entityName
1553    
1554    Entity whose connected relationships are desired.
1555    
1556    =item RETURN
1557    
1558    Returns a list of the relationships that originate from the entity.
1559    If the entity is on the from end, it will return the relationship
1560    name. If the entity is on the to end it will return the converse of
1561    the relationship name.
1562    
1563    =back
1564    
1565    =cut
1566    
1567    sub GetConnectingRelationships {
1568        # Get the parameters.
1569        my ($self, $entityName) = @_;
1570        # Declare the return variable.
1571        my @retVal;
1572        # Get the relationship list.
1573        my $relationships = $self->{_metaData}->{Relationships};
1574        # Find the entity.
1575        my $entity = $self->{_metaData}->{Entities}->{$entityName};
1576        # Only proceed if the entity exists.
1577        if (! defined $entity) {
1578            Trace("Entity $entityName not found.") if T(3);
1579        } else {
1580            # Loop through the relationships.
1581            my @rels = keys %$relationships;
1582            Trace(scalar(@rels) . " relationships found in connection search.") if T(3);
1583            for my $relationshipName (@rels) {
1584                my $relationship = $relationships->{$relationshipName};
1585                if ($relationship->{from} eq $entityName) {
1586                    # Here we have a forward relationship.
1587                    push @retVal, $relationshipName;
1588                } elsif ($relationship->{to} eq $entityName) {
1589                    # Here we have a backward relationship. In this case, the
1590                    # converse relationship name is preferred if it exists.
1591                    my $converse = $relationship->{converse} || $relationshipName;
1592                    push @retVal, $converse;
1593                }
1594            }
1595        }
1596        # Return the result.
1597        return @retVal;
1598    }
1599    
1600    
1601  =head3 GetDataTypes  =head3 GetDataTypes
1602    
1603      my %types = ERDB::GetDataTypes();      my %types = ERDB::GetDataTypes();
# Line 1999  Line 2181 
2181          # Loop through the ends of the relationship.          # Loop through the ends of the relationship.
2182          for my $dir ('from', 'to') {          for my $dir ('from', 'to') {
2183              if ($structure->{$dir} eq $originEntityName) {              if ($structure->{$dir} eq $originEntityName) {
                 # Delete all relationship instances on this side of the entity instance.  
                 Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");  
                 $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);  
2184                  $found = 1;                  $found = 1;
2185                    # Here we want to delete all relationship instances on this side of the
2186                    # entity instance.
2187                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2188                    # We do this delete in batches to keep it from dragging down the
2189                    # server.
2190                    my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2191                    my $done = 0;
2192                    while (! $done) {
2193                        # Do the delete.
2194                        my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2195                        # See if we're done. We're done if no rows were found or the delete is unlimited.
2196                        $done = ($rows == 0 || ! $limitClause);
2197                    }
2198              }              }
2199          }          }
2200          # Insure we found the entity on at least one end.          # Insure we found the entity on at least one end.
# Line 2190  Line 2382 
2382      }      }
2383      # Now we parse the key names into sort parameters. First, we prime the return      # Now we parse the key names into sort parameters. First, we prime the return
2384      # string.      # string.
2385      my $retVal = "sort -t\"\t\" ";      my $retVal = "sort -S 1G -T\"$FIG_Config::temp\" -t\"\t\" ";
2386      # Get the relation's field list.      # Get the relation's field list.
2387      my @fields = @{$relationData->{Fields}};      my @fields = @{$relationData->{Fields}};
2388      # Loop through the keys.      # Loop through the keys.
# Line 2220  Line 2412 
2412                  # will stop the inner loop. Note that the field number is                  # will stop the inner loop. Note that the field number is
2413                  # 1-based in the sort command, so we have to increment the                  # 1-based in the sort command, so we have to increment the
2414                  # index.                  # index.
2415                  $fieldSpec = ($i + 1) . $modifier;                  my $realI = $i + 1;
2416                    $fieldSpec = "$realI,$realI$modifier";
2417              }              }
2418          }          }
2419          # Add this field to the sort command.          # Add this field to the sort command.
# Line 2312  Line 2505 
2505  would return the number of features for genomes in the genus I<homo>. Note that  would return the number of features for genomes in the genus I<homo>. Note that
2506  only the rows from the first table are counted. If the above command were  only the rows from the first table are counted. If the above command were
2507    
2508      my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',      my $count = $erdb->GetCount(['Genome', 'HasFeature'], 'Genome(genus-species) LIKE ?',
2509                                  ['homo %']);                                  ['homo %']);
2510    
2511  it would return the number of genomes, not the number of genome/feature pairs.  it would return the number of genomes, not the number of genome/feature pairs.
# Line 2611  Line 2804 
2804                  push @missing, $fieldName;                  push @missing, $fieldName;
2805              }              }
2806          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
         }  
2807          # Only proceed if there are no missing fields.          # Only proceed if there are no missing fields.
2808          if (@missing > 0) {          if (@missing > 0) {
2809              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
# Line 2723  Line 2911 
2911    
2912  =head3 LoadTable  =head3 LoadTable
2913    
2914      my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag);      my $results = $erdb->LoadTable($fileName, $relationName, %options);
2915    
2916  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2917  first.  first.
# Line 2738  Line 2926 
2926    
2927  Name of the relation to be loaded. This is the same as the table name.  Name of the relation to be loaded. This is the same as the table name.
2928    
2929  =item truncateFlag  =item options
2930    
2931  TRUE if the table should be dropped and re-created, else FALSE  A hash of load options.
2932    
2933  =item RETURN  =item RETURN
2934    
# Line 2748  Line 2936 
2936    
2937  =back  =back
2938    
2939    The permissible options are as follows.
2940    
2941    =over 4
2942    
2943    =item truncate
2944    
2945    If TRUE, then the table will be erased before loading.
2946    
2947    =item mode
2948    
2949    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2950    This option is only applicable to a MySQL database.
2951    
2952    =item partial
2953    
2954    If TRUE, then it is assumed that this is a partial load, and the table will not
2955    be analyzed and compacted at the end.
2956    
2957    =back
2958    
2959  =cut  =cut
2960  sub LoadTable {  sub LoadTable {
2961      # Get the parameters.      # Get the parameters.
2962      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $fileName, $relationName, %options) = @_;
2963      # Create the statistical return object.      # Create the statistical return object.
2964      my $retVal = _GetLoadStats();      my $retVal = _GetLoadStats();
2965      # Trace the fact of the load.      # Trace the fact of the load.
# Line 2763  Line 2971 
2971      # Get the relation data.      # Get the relation data.
2972      my $relation = $self->_FindRelation($relationName);      my $relation = $self->_FindRelation($relationName);
2973      # Check the truncation flag.      # Check the truncation flag.
2974      if ($truncateFlag) {      if ($options{truncate}) {
2975          Trace("Creating table $relationName") if T(2);          Trace("Creating table $relationName") if T(2);
2976          # Compute the row count estimate. We take the size of the load file,          # Compute the row count estimate. We take the size of the load file,
2977          # divide it by the estimated row size, and then multiply by 2 to          # divide it by the estimated row size, and then multiply by 2 to
# Line 2789  Line 2997 
2997      # Load the table.      # Load the table.
2998      my $rv;      my $rv;
2999      eval {      eval {
3000          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);          $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
3001      };      };
3002      if (!defined $rv) {      if (!defined $rv) {
3003          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
# Line 2800  Line 3008 
3008          $retVal->Add("tables");          $retVal->Add("tables");
3009          my $size = -s $fileName;          my $size = -s $fileName;
3010          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
3011            $retVal->Add("bytes", $size);
3012          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
3013          if ($truncateFlag) {          if ($options{truncate}) {
3014              # Indexes are created here for PostGres. For PostGres, indexes are              # Indexes are created here for PostGres. For PostGres, indexes are
3015              # best built at the end. For MySQL, the reverse is true.              # best built at the end. For MySQL, the reverse is true.
3016              if (! $dbh->{_preIndex}) {              if (! $dbh->{_preIndex}) {
# Line 2822  Line 3031 
3031          }          }
3032      }      }
3033      # Analyze the table to improve performance.      # Analyze the table to improve performance.
3034        if (! $options{partial}) {
3035      Trace("Analyzing and compacting $relationName.") if T(3);      Trace("Analyzing and compacting $relationName.") if T(3);
3036      $dbh->vacuum_it($relationName);          $self->Analyze($relationName);
3037        }
3038      Trace("$relationName load completed.") if T(3);      Trace("$relationName load completed.") if T(3);
3039      # Return the statistics.      # Return the statistics.
3040      return $retVal;      return $retVal;
3041  }  }
3042    
3043    =head3 Analyze
3044    
3045        $erdb->Analyze($tableName);
3046    
3047    Analyze and compact a table in the database. This is useful after a load
3048    to improve the performance of the indexes.
3049    
3050    =over 4
3051    
3052    =item tableName
3053    
3054    Name of the table to be analyzed and compacted.
3055    
3056    =back
3057    
3058    =cut
3059    
3060    sub Analyze {
3061        # Get the parameters.
3062        my ($self, $tableName) = @_;
3063        # Analyze the table.
3064        $self->{_dbh}->vacuum_it($tableName);
3065    }
3066    
3067    =head3 TruncateTable
3068    
3069        $erdb->TruncateTable($table);
3070    
3071    Delete all rows from a table quickly. This uses the built-in SQL
3072    C<TRUNCATE> statement, which effectively drops and re-creates a table
3073    with all its settings intact.
3074    
3075    =over 4
3076    
3077    =item table
3078    
3079    Name of the table to be cleared.
3080    
3081    =back
3082    
3083    =cut
3084    
3085    sub TruncateTable {
3086        # Get the parameters.
3087        my ($self, $table) = @_;
3088        # Get the database handle.
3089        my $dbh = $self->{_dbh};
3090        # Execute a truncation comment.
3091        $dbh->SQL("TRUNCATE TABLE $table");
3092    }
3093    
3094    
3095  =head3 CreateSearchIndex  =head3 CreateSearchIndex
3096    
3097      $erdb->CreateSearchIndex($objectName);      $erdb->CreateSearchIndex($objectName);
# Line 3009  Line 3272 
3272      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3273      # Get the first (and only) object.      # Get the first (and only) object.
3274      my $retVal = $query->Fetch();      my $retVal = $query->Fetch();
3275        if (T(3)) {
3276            if ($retVal) {
3277                Trace("Entity $entityType \"$ID\" found.");
3278            } else {
3279                Trace("Entity $entityType \"$ID\" not found.");
3280            }
3281        }
3282      # Return the result.      # Return the result.
3283      return $retVal;      return $retVal;
3284  }  }
# Line 3201  Line 3471 
3471          push @retVal, \@rowData;          push @retVal, \@rowData;
3472          $fetched++;          $fetched++;
3473      }      }
     Trace("$fetched rows returned in GetAll.") if T(SQL => 4);  
3474      # Return the resulting list.      # Return the resulting list.
3475      return @retVal;      return @retVal;
3476  }  }
# Line 3558  Line 3827 
3827      return $retVal;      return $retVal;
3828  }  }
3829    
3830    =head3 WikiNote
3831    
3832    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3833    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3834    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3835    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3836    
3837        my $wikiText = ERDB::WikiNote($dataString);
3838    
3839    =over 4
3840    
3841    =item dataString
3842    
3843    String to convert to Wiki text.
3844    
3845    =item RETURN
3846    
3847    An Wiki text string derived from the input string.
3848    
3849    =back
3850    
3851    =cut
3852    
3853    sub WikiNote {
3854        # Get the parameter.
3855        my ($dataString) = @_;
3856        # HTML-escape the text.
3857        my $retVal = CGI::escapeHTML($dataString);
3858        # Substitute the bulletin board codes.
3859        my $italic = WikiTools::ItalicCode();
3860        $retVal =~ s/\[\/?i\]/$italic/g;
3861        my $bold = WikiTools::BoldCode();
3862        $retVal =~ s/\[\/?b\]/$bold/g;
3863        # Paragraph breaks are the same no matter which Wiki you're using.
3864        $retVal =~ s!\[p\]!\n\n!g;
3865        # Now we do the links, which are complicated by the need to know two
3866        # things: the target URL and the text.
3867        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3868            # Replace the matched string with the Wiki markup for links. Note that
3869            # $-[0] is the starting position of the match for the entire expression,
3870            # and $+[0] is past the ending position.
3871            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3872        }
3873        # Return the result.
3874        return $retVal;
3875    }
3876    
3877  =head3 BeginTran  =head3 BeginTran
3878    
3879      $erdb->BeginTran();      $erdb->BeginTran();
# Line 3840  Line 4156 
4156    
4157  =over 4  =over 4
4158    
4159    =item indexObject
4160    
4161  ERDB XML structure for an index.  ERDB XML structure for an index.
4162    
4163  =item RETURN  =item RETURN
# Line 4499  Line 4817 
4817      # be a null string.      # be a null string.
4818      if ($fileName ne "") {      if ($fileName ne "") {
4819          # Load the relation from the file.          # Load the relation from the file.
4820          $retVal = $self->LoadTable($fileName, $relationName, $rebuild);          $retVal = $self->LoadTable($fileName, $relationName, truncate => $rebuild);
4821      } elsif ($rebuild) {      } elsif ($rebuild) {
4822          # Here we are rebuilding, but no file exists, so we just re-create the table.          # Here we are rebuilding, but no file exists, so we just re-create the table.
4823          $self->CreateTable($relationName, 1);          $self->CreateTable($relationName, 1);
# Line 5246  Line 5564 
5564      return $retVal;      return $retVal;
5565  }  }
5566    
5567  =head2 HTML Documentation Utility Methods  =head2 Documentation Utility Methods
5568    
5569  =head3 _ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
5570    
# Line 5278  Line 5596 
5596      # Get the parameters.      # Get the parameters.
5597      my ($relationshipName, $relationshipStructure) = @_;      my ($relationshipName, $relationshipStructure) = @_;
5598      # Format the relationship sentence.      # Format the relationship sentence.
5599      my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";      my $result = "$relationshipStructure->{from} $relationshipName $relationshipStructure->{to}";
5600      # Compute the arity.      # Compute the arity.
5601      my $arityCode = $relationshipStructure->{arity};      my $arityCode = $relationshipStructure->{arity};
5602      my $arity = $ArityTable{$arityCode};      my $arity = $ArityTable{$arityCode};
# Line 5323  Line 5641 
5641      return $result;      return $result;
5642  }  }
5643    
5644    =head3 _WikiRelationTable
5645    
5646    Generate the Wiki text for a particular relation. The relation's data will be formatted as a
5647    table with three columns-- the field name, the field type, and the field description.
5648    
5649    This is a static method.
5650    
5651    =over 4
5652    
5653    =item relationName
5654    
5655    Name of the relation being formatted.
5656    
5657    =item relationData
5658    
5659    Hash containing the relation's fields and indexes.
5660    
5661    =item RETURN
5662    
5663    Returns a Wiki string that can be used to display the relation name and all of its fields.
5664    
5665    =back
5666    
5667    =cut
5668    
5669    sub _WikiRelationTable {
5670        # Get the parameters.
5671        my ($relationName, $relationData) = @_;
5672        # We'll create a list of lists in here, then call WikiTools::Table to
5673        # convert it into a table.
5674        my @rows = ();
5675        # Push in the header row.
5676        push @rows, [qw(Field Type Description)];
5677        # Loop through the fields.
5678        for my $field (@{$relationData->{Fields}}) {
5679            # Create this field's row. We always have a name and type.
5680            my @row = ($field->{name}, $field->{type});
5681            # If we have a description, add it as the third column.
5682            if (exists $field->{Notes}) {
5683                push @row, WikiNote($field->{Notes}->{content});
5684            }
5685            # Push this row onto the table list.
5686            push @rows, \@row;
5687        }
5688        # Store the rows as a Wiki table with a level-4 heading.
5689        my $retVal = join("\n\n", WikiTools::Heading(4, "$relationName Table"),
5690                          WikiTools::Table(@rows));
5691        # Now we show the relation's indexes. These are formatted as another
5692        # table.
5693        @rows = ();
5694        # Push in the header row.
5695        push @rows, [qw(Index Unique Fields Notes)];
5696        # Get the index hash.
5697        my $indexTable = $relationData->{Indexes};
5698        # Loop through the indexes. For an entity, there is always at least one index.
5699        # For a relationship, there are at least two. The upshot is we don't need to
5700        # worry about accidentally generating a frivolous table here.
5701        for my $indexName (sort keys %$indexTable) {
5702            my $indexData = $indexTable->{$indexName};
5703            # Determine whether or not the index is unique.
5704            my $unique = ((exists $indexData->{Unique} && $indexData->{Unique} eq "true") ?
5705                          "yes" : "");
5706            # Get the field list.
5707            my $fields = join(', ', @{$indexData->{IndexFields}});
5708            # Get the note text.
5709            my $description = "";
5710            if (my $note = $indexData->{Notes}) {
5711                $description = WikiNote($note->{content});
5712            }
5713            # Format this row.
5714            my @row = ($indexName, $unique, $fields, $description);
5715            push @rows, \@row;
5716        }
5717        # Add the index list to the result.
5718        $retVal .= "\n\n" . WikiTools::Table(@rows);
5719    }
5720    
5721  =head3 _ShowRelationTable  =head3 _ShowRelationTable
5722    
5723  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML  Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
# Line 5496  Line 5891 
5891      return $htmlString;      return $htmlString;
5892  }  }
5893    
5894    =head3 _ObjectNotes
5895    
5896        my @noteParagraphs = _ObjectNotes($objectData);
5897    
5898    Return a list of the notes and asides for an entity or relationship in
5899    Wiki format.
5900    
5901    =over 4
5902    
5903    =item objectData
5904    
5905    The metadata for the desired entity or relationship.
5906    
5907    =item RETURN
5908    
5909    Returns a list of text paragraphs in Wiki markup form.
5910    
5911    =back
5912    
5913    =cut
5914    
5915    sub _ObjectNotes {
5916        # Get the parameters.
5917        my ($objectData) = @_;
5918        # Declare the return variable.
5919        my @retVal;
5920        # Loop through the types of notes.
5921        for my $noteType (qw(Notes Asides)) {
5922            my $text = $objectData->{$noteType};
5923            if ($text) {
5924                push @retVal, "", WikiNote($text->{content});
5925            }
5926        }
5927        # Return the result.
5928        return @retVal;
5929    }
5930    
5931  1;  1;

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