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revision 1.55, Sat Jun 24 23:49:10 2006 UTC revision 1.85, Fri Feb 9 22:59:53 2007 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 FIG;      use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 59  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
 To facilitate testing, the ERDB module supports automatic generation of test data. This process  
 is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
 fully implemented.  
   
76  =head2 XML Database Description  =head2 XML Database Description
77    
78  =head3 Data Types  =head3 Data Types
# Line 91  Line 92 
92    
93  32-bit signed integer  32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99  =item date  =item date
100    
101  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 186  Line 191 
191    
192  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
194  with the respect to field names, so a best practice is to use lower-case letters only.  with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198  =item type  =item type
199    
# Line 205  Line 212 
212  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
213  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227  =back  =back
228    
229  =head3 Indexes  =head3 Indexes
230    
231  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 must
232  be from the primary relation. The alternate indexes assist in ordering results  all be from the same relation. The alternate indexes assist in ordering results
233  from a query. A relationship can have up to two indexes-- a I<to-index> and a  from a query. A relationship can have up to two indexes-- a I<to-index> and a
234  I<from-index>. These order the results when crossing the relationship. For  I<from-index>. These order the results when crossing the relationship. For
235  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
# Line 238  Line 257 
257    
258  =back  =back
259    
260  The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.  The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
261    have a B<Unique> attribute. If specified, the index will be generated as a unique
262    index.
263    
264  =head3 Object and Field Names  =head3 Object and Field Names
265    
# Line 316  Line 337 
337    
338  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
339  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
340  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "avgLen" is the average byte length for estimating
341  # string is specified in the field definition. "avgLen" is the average byte length for estimating  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
342  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
343  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
344                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
345                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
346                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
347                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
348                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
349                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
350                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
351                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
352                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
353                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
355                                   indexMod =>   0, notes => "signed, 64-bit integer"},
356                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
357                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
358                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
359                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
360                   'hash-string' =>                   'hash-string' =>
361                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
362                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
363                   'id-string' =>                   'id-string' =>
364                               { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, dataGen => "SringGen(22)" },                               { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
365                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
366                   'key-string' =>                   'key-string' =>
367                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
368                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
369                   'name-string' =>                   'name-string' =>
370                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
371                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
372                   'medium-string' =>                   'medium-string' =>
373                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                  );                  );
376    
377  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 344  Line 380 
380                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
381                   );                   );
382    
383  # Table for interpreting string patterns.  # Options for XML input and output.
384    
385    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
386                                      Entities => 'Entity',
387                                      Fields => 'Field',
388                                      Indexes => 'Index',
389                                      IndexFields => 'IndexField'
390                                    },
391                      KeyAttr =>    { Relationship => 'name',
392                                      Entity => 'name',
393                                      Field => 'name'
394                                    },
395                      SuppressEmpty => 1,
396                     );
397    
398  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
399                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
400                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
401                       'V' => "aeiou",                    NormalizeSpace => 2,
402                       'K' => "bcdfghjklmnoprstvwxyz"                   );
403    my %XmlOutOpts = (
404                      RootName => 'Database',
405                      XMLDecl => 1,
406                     );                     );
407    
408    
409  =head2 Public Methods  =head2 Public Methods
410    
411  =head3 new  =head3 new
# Line 493  Line 546 
546          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
547          # If there's descriptive text, display it.          # If there's descriptive text, display it.
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 511  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 550  Line 607 
607          $retVal .= "</p>\n";          $retVal .= "</p>\n";
608          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
609          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
610              $retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
611          }          }
612          # Generate the relationship's relation table.          # Generate the relationship's relation table.
613          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
# Line 597  Line 654 
654      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
655  }  }
656    
657    =head3 FindIndexForEntity
658    
659    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
660    
661    This method locates the entry in an entity's index list that begins with the
662    specified attribute name. If the entity has no index list, one will be
663    created. This method works on raw XML, not a live ERDB object.
664    
665    =over 4
666    
667    =item xml
668    
669    The raw XML structure defining the database.
670    
671    =item entityName
672    
673    The name of the relevant entity.
674    
675    =item attributeName
676    
677    The name of the attribute relevant to the search.
678    
679    =item RETURN
680    
681    The numerical index in the index list of the index entry for the specified entity and
682    attribute, or C<undef> if no such index exists.
683    
684    =back
685    
686    =cut
687    
688    sub FindIndexForEntity {
689        # Get the parameters.
690        my ($xml, $entityName, $attributeName) = @_;
691        # Declare the return variable.
692        my $retVal;
693        # Get the named entity.
694        my $entityData = $xml->{Entities}->{$entityName};
695        if (! $entityData) {
696            Confess("Entity $entityName not found in DBD structure.");
697        } else {
698            # Insure it has an index list.
699            if (! exists $entityData->{Indexes}) {
700                $entityData->{Indexes} = [];
701            } else {
702                # Search for the desired index.
703                my $indexList = $entityData->{Indexes};
704                my $n = scalar @{$indexList};
705                Trace("Searching $n indexes in index list for $entityName.") if T(2);
706                # We use an indexed FOR here because we're returning an
707                # index number instead of an object. We do THAT so we can
708                # delete the index from the list if needed.
709                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
710                    my $index = $indexList->[$i];
711                    my $fields = $index->{IndexFields};
712                    # Technically this IF should be safe (that is, we are guaranteed
713                    # the existence of a "$fields->[0]"), because when we load the XML
714                    # we have SuppressEmpty specified.
715                    if ($fields->[0]->{name} eq $attributeName) {
716                        $retVal = $i;
717                    }
718                }
719            }
720        }
721        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
722        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
723        # Return the result.
724        return $retVal;
725    }
726    
727  =head3 CreateTables  =head3 CreateTables
728    
729  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 684  Line 811 
811      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
812      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
813      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
814      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
815        # index will not be built until the table has been loaded.
816      if ($indexFlag) {      if ($indexFlag) {
817          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
818      }      }
# Line 841  Line 969 
969      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
970          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
971          # Get the index's field list.          # Get the index's field list.
972          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
973            # Get a hash of the relation's field types.
974            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
975            # We need to check for text fields so we can append a length limitation for them. To do
976            # that, we need the relation's field list.
977            my $relFields = $relationData->{Fields};
978            for (my $i = 0; $i <= $#rawFields; $i++) {
979                # Get the field type.
980                my $field = $rawFields[$i];
981                my $type = $types{$field};
982                # Ask if it requires using prefix notation for the index.
983                my $mod = $TypeTable{$type}->{indexMod};
984                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
985                if ($mod) {
986                    # Append the prefix length to the field name,
987                    $rawFields[$i] .= "($mod)";
988                }
989            }
990            my @fieldList = _FixNames(@rawFields);
991          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
992          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
993          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
994          # Create the index.          # Create the index.
995          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
996                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
997          if ($rv) {          if ($rv) {
998              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
999          } else {          } else {
# Line 856  Line 1002 
1002      }      }
1003  }  }
1004    
1005    =head3 GetSecondaryFields
1006    
1007    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1008    
1009    This method will return a list of the name and type of each of the secondary
1010    fields for a specified entity. Secondary fields are stored in two-column tables
1011    in addition to the primary entity table. This enables the field to have no value
1012    or to have multiple values.
1013    
1014    =over 4
1015    
1016    =item entityName
1017    
1018    Name of the entity whose secondary fields are desired.
1019    
1020    =item RETURN
1021    
1022    Returns a hash mapping the field names to their field types.
1023    
1024    =back
1025    
1026    =cut
1027    
1028    sub GetSecondaryFields {
1029        # Get the parameters.
1030        my ($self, $entityName) = @_;
1031        # Declare the return variable.
1032        my %retVal = ();
1033        # Look for the entity.
1034        my $table = $self->GetFieldTable($entityName);
1035        # Loop through the fields, pulling out the secondaries.
1036        for my $field (sort keys %{$table}) {
1037            if ($table->{$field}->{relation} ne $entityName) {
1038                # Here we have a secondary field.
1039                $retVal{$field} = $table->{$field}->{type};
1040            }
1041        }
1042        # Return the result.
1043        return %retVal;
1044    }
1045    
1046    =head3 GetFieldRelationName
1047    
1048    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1049    
1050    Return the name of the relation containing a specified field.
1051    
1052    =over 4
1053    
1054    =item objectName
1055    
1056    Name of the entity or relationship containing the field.
1057    
1058    =item fieldName
1059    
1060    Name of the relevant field in that entity or relationship.
1061    
1062    =item RETURN
1063    
1064    Returns the name of the database relation containing the field, or C<undef> if
1065    the field does not exist.
1066    
1067    =back
1068    
1069    =cut
1070    
1071    sub GetFieldRelationName {
1072        # Get the parameters.
1073        my ($self, $objectName, $fieldName) = @_;
1074        # Declare the return variable.
1075        my $retVal;
1076        # Get the object field table.
1077        my $table = $self->GetFieldTable($objectName);
1078        # Only proceed if the field exists.
1079        if (exists $table->{$fieldName}) {
1080            # Determine the name of the relation that contains this field.
1081            $retVal = $table->{$fieldName}->{relation};
1082        }
1083        # Return the result.
1084        return $retVal;
1085    }
1086    
1087    =head3 DeleteValue
1088    
1089    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1090    
1091    Delete secondary field values from the database. This method can be used to delete all
1092    values of a specified field for a particular entity instance, or only a single value.
1093    
1094    Secondary fields are stored in two-column relations separate from an entity's primary
1095    table, and as a result a secondary field can legitimately have no value or multiple
1096    values. Therefore, it makes sense to talk about deleting secondary fields where it
1097    would not make sense for primary fields.
1098    
1099    =over 4
1100    
1101    =item entityName
1102    
1103    Name of the entity from which the fields are to be deleted.
1104    
1105    =item id
1106    
1107    ID of the entity instance to be processed. If the instance is not found, this
1108    method will have no effect. If C<undef> is specified, all values for all of
1109    the entity instances will be deleted.
1110    
1111    =item fieldName
1112    
1113    Name of the field whose values are to be deleted.
1114    
1115    =item fieldValue (optional)
1116    
1117    Value to be deleted. If not specified, then all values of the specified field
1118    will be deleted for the entity instance. If specified, then only the values which
1119    match this parameter will be deleted.
1120    
1121    =item RETURN
1122    
1123    Returns the number of rows deleted.
1124    
1125    =back
1126    
1127    =cut
1128    
1129    sub DeleteValue {
1130        # Get the parameters.
1131        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1132        # Declare the return value.
1133        my $retVal = 0;
1134        # We need to set up an SQL command to do the deletion. First, we
1135        # find the name of the field's relation.
1136        my $table = $self->GetFieldTable($entityName);
1137        my $field = $table->{$fieldName};
1138        my $relation = $field->{relation};
1139        # Make sure this is a secondary field.
1140        if ($relation eq $entityName) {
1141            Confess("Cannot delete values of $fieldName for $entityName.");
1142        } else {
1143            # Set up the SQL command to delete all values.
1144            my $sql = "DELETE FROM $relation";
1145            # Build the filter.
1146            my @filters = ();
1147            my @parms = ();
1148            # Check for a filter by ID.
1149            if (defined $id) {
1150                push @filters, "id = ?";
1151                push @parms, $id;
1152            }
1153            # Check for a filter by value.
1154            if (defined $fieldValue) {
1155                push @filters, "$fieldName = ?";
1156                push @parms, $fieldValue;
1157            }
1158            # Append the filters to the command.
1159            if (@filters) {
1160                $sql .= " WHERE " . join(" AND ", @filters);
1161            }
1162            # Execute the command.
1163            my $dbh = $self->{_dbh};
1164            $retVal = $dbh->SQL($sql, 0, @parms);
1165        }
1166        # Return the result.
1167        return $retVal;
1168    }
1169    
1170  =head3 LoadTables  =head3 LoadTables
1171    
1172  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
# Line 950  Line 1261 
1261      return sort keys %{$entityList};      return sort keys %{$entityList};
1262  }  }
1263    
1264    =head3 GetDataTypes
1265    
1266    C<< my %types = ERDB::GetDataTypes(); >>
1267    
1268    Return a table of ERDB data types. The table returned is a hash of hashes.
1269    The keys of the big hash are the datatypes. Each smaller hash has several
1270    values used to manage the data. The most interesting is the SQL type (key
1271    C<sqlType>) and the descriptive node (key C<notes>).
1272    
1273    Note that changing the values in the smaller hashes will seriously break
1274    things, so this data should be treated as read-only.
1275    
1276    =cut
1277    
1278    sub GetDataTypes {
1279        return %TypeTable;
1280    }
1281    
1282    
1283  =head3 IsEntity  =head3 IsEntity
1284    
1285  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
# Line 1094  Line 1424 
1424      return $retVal;      return $retVal;
1425  }  }
1426    
1427    
1428    
1429    =head3 Search
1430    
1431    C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1432    
1433    Perform a full text search with filtering. The search will be against a specified object
1434    in the object name list. That object will get an extra field containing the search
1435    relevance. Note that except for the search expression, the parameters of this method are
1436    the same as those for L</Get> and follow the same rules.
1437    
1438    =over 4
1439    
1440    =item searchExpression
1441    
1442    Boolean search expression for the text fields of the target object. The default mode for
1443    a Boolean search expression is OR, but we want the default to be AND, so we will
1444    add a C<+> operator to each word with no other operator before it.
1445    
1446    =item idx
1447    
1448    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1449    
1450    =item objectNames
1451    
1452    List containing the names of the entity and relationship objects to be retrieved.
1453    
1454    =item filterClause
1455    
1456    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1457    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1458    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1459    in the filter clause should be added to the parameter list as additional parameters. The
1460    fields in a filter clause can come from primary entity relations, relationship relations,
1461    or secondary entity relations; however, all of the entities and relationships involved must
1462    be included in the list of object names.
1463    
1464    =item params
1465    
1466    Reference to a list of parameter values to be substituted into the filter clause.
1467    
1468    =item RETURN
1469    
1470    Returns a query object for the specified search.
1471    
1472    =back
1473    
1474    =cut
1475    
1476    sub Search {
1477        # Get the parameters.
1478        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1479        # Declare the return variable.
1480        my $retVal;
1481        # Create a safety copy of the parameter list. Note we have to be careful to insure
1482        # a parameter list exists before we copy it.
1483        my @myParams = ();
1484        if (defined $params) {
1485            @myParams = @{$params};
1486        }
1487        # Get the first object's structure so we have access to the searchable fields.
1488        my $object1Name = $objectNames->[$idx];
1489        my $object1Structure = $self->_GetStructure($object1Name);
1490        # Get the field list.
1491        if (! exists $object1Structure->{searchFields}) {
1492            Confess("No searchable index for $object1Name.");
1493        } else {
1494            # Get the field list.
1495            my @fields = @{$object1Structure->{searchFields}};
1496            # Clean the search expression.
1497            my $actualKeywords = $self->CleanKeywords($searchExpression);
1498            # Prefix a "+" to each uncontrolled word. This converts the default
1499            # search mode from OR to AND.
1500            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1501            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1502            # We need two match expressions, one for the filter clause and one in the
1503            # query itself. Both will use a parameter mark, so we need to push the
1504            # search expression onto the front of the parameter list twice.
1505            unshift @myParams, $actualKeywords, $actualKeywords;
1506            # Build the match expression.
1507            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1508            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1509            # Process the SQL stuff.
1510            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1511                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1512            # Create the query. Note that the match clause is inserted at the front of
1513            # the select fields.
1514            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1515                ".* $suffix";
1516            my $sth = $self->_GetStatementHandle($command, \@myParams);
1517            # Now we create the relation map, which enables DBQuery to determine the order, name
1518            # and mapped name for each object in the query.
1519            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1520            # Return the statement object.
1521            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1522        }
1523        return $retVal;
1524    }
1525    
1526  =head3 GetFlat  =head3 GetFlat
1527    
1528  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>  C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
# Line 1147  Line 1576 
1576      return @retVal;      return @retVal;
1577  }  }
1578    
1579    =head3 SpecialFields
1580    
1581    C<< my %specials = $erdb->SpecialFields($entityName); >>
1582    
1583    Return a hash mapping special fields in the specified entity to the value of their
1584    C<special> attribute. This enables the subclass to get access to the special field
1585    attributes without needed to plumb the internal ERDB data structures.
1586    
1587    =over 4
1588    
1589    =item entityName
1590    
1591    Name of the entity whose special fields are desired.
1592    
1593    =item RETURN
1594    
1595    Returns a hash. The keys of the hash are the special field names, and the values
1596    are the values from each special field's C<special> attribute.
1597    
1598    =back
1599    
1600    =cut
1601    
1602    sub SpecialFields {
1603        # Get the parameters.
1604        my ($self, $entityName) = @_;
1605        # Declare the return variable.
1606        my %retVal = ();
1607        # Find the entity's data structure.
1608        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1609        # Loop through its fields, adding each special field to the return hash.
1610        my $fieldHash = $entityData->{Fields};
1611        for my $fieldName (keys %{$fieldHash}) {
1612            my $fieldData = $fieldHash->{$fieldName};
1613            if (exists $fieldData->{special}) {
1614                $retVal{$fieldName} = $fieldData->{special};
1615            }
1616        }
1617        # Return the result.
1618        return %retVal;
1619    }
1620    
1621  =head3 Delete  =head3 Delete
1622    
1623  C<< my $stats = $erdb->Delete($entityName, $objectID); >>  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1624    
1625  Delete an entity instance from the database. The instance is deleted along with all entity and  Delete an entity instance from the database. The instance is deleted along with all entity and
1626  relationship instances dependent on it. The idea of dependence here is recursive. An object is  relationship instances dependent on it. The definition of I<dependence> is recursive.
1627  always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  
1628  relationship connected to a dependent entity or the "to" entity connected to a 1-to-many  An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1629    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1630  dependent relationship.  dependent relationship.
1631    
1632  =over 4  =over 4
# Line 1168  Line 1640 
1640  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1641  then it is presumed to by a LIKE pattern.  then it is presumed to by a LIKE pattern.
1642    
1643  =item testFlag  =item options
1644    
1645  If TRUE, the delete statements will be traced without being executed.  A hash detailing the options for this delete operation.
1646    
1647  =item RETURN  =item RETURN
1648    
# Line 1179  Line 1651 
1651    
1652  =back  =back
1653    
1654    The permissible options for this method are as follows.
1655    
1656    =over 4
1657    
1658    =item testMode
1659    
1660    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1661    
1662    =item keepRoot
1663    
1664    If TRUE, then the entity instances will not be deleted, only the dependent records.
1665    
1666    =back
1667    
1668  =cut  =cut
1669  #: Return Type $%;  #: Return Type $%;
1670  sub Delete {  sub Delete {
1671      # Get the parameters.      # Get the parameters.
1672      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1673      # Declare the return variable.      # Declare the return variable.
1674      my $retVal = Stats->new();      my $retVal = Stats->new();
1675      # Get the DBKernel object.      # Get the DBKernel object.
# Line 1200  Line 1686 
1686      # FROM-relationships and entities.      # FROM-relationships and entities.
1687      my @fromPathList = ();      my @fromPathList = ();
1688      my @toPathList = ();      my @toPathList = ();
1689      # This final hash is used to remember what work still needs to be done. We push paths      # This final list is used to remember what work still needs to be done. We push paths
1690      # onto the list, then pop them off to extend the paths. We prime it with the starting      # onto the list, then pop them off to extend the paths. We prime it with the starting
1691      # point. Note that we will work hard to insure that the last item on a path in the      # point. Note that we will work hard to insure that the last item on a path in the
1692      # TODO list is always an entity.      # to-do list is always an entity.
1693      my @todoList = ([$entityName]);      my @todoList = ([$entityName]);
1694      while (@todoList) {      while (@todoList) {
1695          # Get the current path.          # Get the current path.
# Line 1211  Line 1697 
1697          # Copy it into a list.          # Copy it into a list.
1698          my @stackedPath = @{$current};          my @stackedPath = @{$current};
1699          # Pull off the last item on the path. It will always be an entity.          # Pull off the last item on the path. It will always be an entity.
1700          my $entityName = pop @stackedPath;          my $myEntityName = pop @stackedPath;
1701          # Add it to the alreadyFound list.          # Add it to the alreadyFound list.
1702          $alreadyFound{$entityName} = 1;          $alreadyFound{$myEntityName} = 1;
1703            # Figure out if we need to delete this entity.
1704            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1705          # Get the entity data.          # Get the entity data.
1706          my $entityData = $self->_GetStructure($entityName);              my $entityData = $self->_GetStructure($myEntityName);
1707          # The first task is to loop through the entity's relation. A DELETE command will              # Loop through the entity's relations. A DELETE command will be needed for each of them.
         # be needed for each of them.  
1708          my $relations = $entityData->{Relations};          my $relations = $entityData->{Relations};
1709          for my $relation (keys %{$relations}) {          for my $relation (keys %{$relations}) {
1710              my @augmentedList = (@stackedPath, $relation);              my @augmentedList = (@stackedPath, $relation);
1711              push @fromPathList, \@augmentedList;              push @fromPathList, \@augmentedList;
1712          }          }
1713            }
1714          # Now we need to look for relationships connected to this entity.          # Now we need to look for relationships connected to this entity.
1715          my $relationshipList = $self->{_metaData}->{Relationships};          my $relationshipList = $self->{_metaData}->{Relationships};
1716          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
1717              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
1718              # Check the FROM field. We're only interested if it's us.              # Check the FROM field. We're only interested if it's us.
1719              if ($relationship->{from} eq $entityName) {              if ($relationship->{from} eq $myEntityName) {
1720                  # Add the path to this relationship.                  # Add the path to this relationship.
1721                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1722                  push @fromPathList, \@augmentedList;                  push @fromPathList, \@augmentedList;
1723                  # Check the arity. If it's MM we're done. If it's 1M                  # Check the arity. If it's MM we're done. If it's 1M
1724                  # and the target hasn't been seen yet, we want to                  # and the target hasn't been seen yet, we want to
# Line 1249  Line 1737 
1737              }              }
1738              # Now check the TO field. In this case only the relationship needs              # Now check the TO field. In this case only the relationship needs
1739              # deletion.              # deletion.
1740              if ($relationship->{to} eq $entityName) {              if ($relationship->{to} eq $myEntityName) {
1741                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1742                  push @toPathList, \@augmentedList;                  push @toPathList, \@augmentedList;
1743              }              }
1744          }          }
1745      }      }
1746      # Create the first qualifier for the WHERE clause. This selects the      # Create the first qualifier for the WHERE clause. This selects the
1747      # keys of the primary entity records to be deleted. When we're deleting      # keys of the primary entity records to be deleted. When we're deleting
1748      # from a dependent table, we construct a join page from the first qualifier      # from a dependent table, we construct a join path from the first qualifier
1749      # to the table containing the dependent records to delete.      # to the table containing the dependent records to delete.
1750      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1751      # We need to make two passes. The first is through the to-list, and      # We need to make two passes. The first is through the to-list, and
# Line 1296  Line 1784 
1784                  }                  }
1785              }              }
1786              # Now we have our desired DELETE statement.              # Now we have our desired DELETE statement.
1787              if ($testFlag) {              if ($options{testMode}) {
1788                  # Here the user wants to trace without executing.                  # Here the user wants to trace without executing.
1789                  Trace($stmt) if T(0);                  Trace($stmt) if T(0);
1790              } else {              } else {
1791                  # Here we can delete. Note that the SQL method dies with a confessing                  # Here we can delete. Note that the SQL method dies with a confession
1792                  # if an error occurs, so we just go ahead and do it.                  # if an error occurs, so we just go ahead and do it.
1793                  Trace("Executing delete from $target using '$objectID'.") if T(3);                  Trace("Executing delete from $target using '$objectID'.") if T(3);
1794                  my $rv = $db->SQL($stmt, 0, $objectID);                  my $rv = $db->SQL($stmt, 0, $objectID);
# Line 1315  Line 1803 
1803      return $retVal;      return $retVal;
1804  }  }
1805    
1806  =head3 GetList  =head3 Disconnect
   
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>  
1807    
1808  Return a list of object descriptors for the specified objects as determined by the  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
 specified filter clause.  
1809    
1810  This method is essentially the same as L</Get> except it returns a list of objects rather  Disconnect an entity instance from all the objects to which it is related. This
1811  than a query object that can be used to get the results one record at a time.  will delete each relationship instance that connects to the specified entity.
1812    
1813  =over 4  =over 4
1814    
1815  =item objectNames  =item relationshipName
1816    
1817  List containing the names of the entity and relationship objects to be retrieved.  Name of the relationship whose instances are to be deleted.
1818    
1819  =item filterClause  =item originEntityName
1820    
1821  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  Name of the entity that is to be disconnected.
 be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  
 specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  
 in the filter clause should be added to the parameter list as additional parameters. The  
 fields in a filter clause can come from primary entity relations, relationship relations,  
 or secondary entity relations; however, all of the entities and relationships involved must  
 be included in the list of object names.  
1822    
1823  The filter clause can also specify a sort order. To do this, simply follow the filter string  =item originEntityID
1824  with an ORDER BY clause. For example, the following filter string gets all genomes for a  
1825  particular genus and sorts them by species name.  ID of the entity that is to be disconnected.
1826    
1827    =back
1828    
1829    =cut
1830    
1831    sub Disconnect {
1832        # Get the parameters.
1833        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1834        # Get the relationship descriptor.
1835        my $structure = $self->_GetStructure($relationshipName);
1836        # Insure we have a relationship.
1837        if (! exists $structure->{from}) {
1838            Confess("$relationshipName is not a relationship in the database.");
1839        } else {
1840            # Get the database handle.
1841            my $dbh = $self->{_dbh};
1842            # We'll set this value to 1 if we find our entity.
1843            my $found = 0;
1844            # Loop through the ends of the relationship.
1845            for my $dir ('from', 'to') {
1846                if ($structure->{$dir} eq $originEntityName) {
1847                    # Delete all relationship instances on this side of the entity instance.
1848                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
1849                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1850                    $found = 1;
1851                }
1852            }
1853            # Insure we found the entity on at least one end.
1854            if (! $found) {
1855                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1856            }
1857        }
1858    }
1859    
1860    =head3 DeleteRow
1861    
1862    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1863    
1864    Delete a row from a relationship. In most cases, only the from-link and to-link are
1865    needed; however, for relationships with intersection data values can be specified
1866    for the other fields using a hash.
1867    
1868    =over 4
1869    
1870    =item relationshipName
1871    
1872    Name of the relationship from which the row is to be deleted.
1873    
1874    =item fromLink
1875    
1876    ID of the entity instance in the From direction.
1877    
1878    =item toLink
1879    
1880    ID of the entity instance in the To direction.
1881    
1882    =item values
1883    
1884    Reference to a hash of other values to be used for filtering the delete.
1885    
1886    =back
1887    
1888    =cut
1889    
1890    sub DeleteRow {
1891        # Get the parameters.
1892        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1893        # Create a hash of all the filter information.
1894        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1895        if (defined $values) {
1896            for my $key (keys %{$values}) {
1897                $filter{$key} = $values->{$key};
1898            }
1899        }
1900        # Build an SQL statement out of the hash.
1901        my @filters = ();
1902        my @parms = ();
1903        for my $key (keys %filter) {
1904            push @filters, _FixName($key) . " = ?";
1905            push @parms, $filter{$key};
1906        }
1907        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1908        my $command = "DELETE FROM $relationshipName WHERE " .
1909                      join(" AND ", @filters);
1910        # Execute it.
1911        my $dbh = $self->{_dbh};
1912        $dbh->SQL($command, undef, @parms);
1913    }
1914    
1915    =head3 SortNeeded
1916    
1917    C<< my $parms = $erdb->SortNeeded($relationName); >>
1918    
1919    Return the pipe command for the sort that should be applied to the specified
1920    relation when creating the load file.
1921    
1922    For example, if the load file should be sorted ascending by the first
1923    field, this method would return
1924    
1925        sort -k1 -t"\t"
1926    
1927    If the first field is numeric, the method would return
1928    
1929        sort -k1n -t"\t"
1930    
1931    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1932    keys using a sort.
1933    
1934    =over 4
1935    
1936    =item relationName
1937    
1938    Name of the relation to be examined.
1939    
1940    =item
1941    
1942    Returns the sort command to use for sorting the relation, suitable for piping.
1943    
1944    =back
1945    
1946    =cut
1947    #: Return Type $;
1948    sub SortNeeded {
1949        # Get the parameters.
1950        my ($self, $relationName) = @_;
1951        # Declare a descriptor to hold the names of the key fields.
1952        my @keyNames = ();
1953        # Get the relation structure.
1954        my $relationData = $self->_FindRelation($relationName);
1955        # Find out if the relation is a primary entity relation,
1956        # a relationship relation, or a secondary entity relation.
1957        my $entityTable = $self->{_metaData}->{Entities};
1958        my $relationshipTable = $self->{_metaData}->{Relationships};
1959        if (exists $entityTable->{$relationName}) {
1960            # Here we have a primary entity relation.
1961            push @keyNames, "id";
1962        } elsif (exists $relationshipTable->{$relationName}) {
1963            # Here we have a relationship. We sort using the FROM index.
1964            my $relationshipData = $relationshipTable->{$relationName};
1965            my $index = $relationData->{Indexes}->{idxFrom};
1966            push @keyNames, @{$index->{IndexFields}};
1967        } else {
1968            # Here we have a secondary entity relation, so we have a sort on the ID field.
1969            push @keyNames, "id";
1970        }
1971        # Now we parse the key names into sort parameters. First, we prime the return
1972        # string.
1973        my $retVal = "sort -t\"\t\" ";
1974        # Get the relation's field list.
1975        my @fields = @{$relationData->{Fields}};
1976        # Loop through the keys.
1977        for my $keyData (@keyNames) {
1978            # Get the key and the ordering.
1979            my ($keyName, $ordering);
1980            if ($keyData =~ /^([^ ]+) DESC/) {
1981                ($keyName, $ordering) = ($1, "descending");
1982            } else {
1983                ($keyName, $ordering) = ($keyData, "ascending");
1984            }
1985            # Find the key's position and type.
1986            my $fieldSpec;
1987            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1988                my $thisField = $fields[$i];
1989                if ($thisField->{name} eq $keyName) {
1990                    # Get the sort modifier for this field type. The modifier
1991                    # decides whether we're using a character, numeric, or
1992                    # floating-point sort.
1993                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1994                    # If the index is descending for this field, denote we want
1995                    # to reverse the sort order on this field.
1996                    if ($ordering eq 'descending') {
1997                        $modifier .= "r";
1998                    }
1999                    # Store the position and modifier into the field spec, which
2000                    # will stop the inner loop. Note that the field number is
2001                    # 1-based in the sort command, so we have to increment the
2002                    # index.
2003                    $fieldSpec = ($i + 1) . $modifier;
2004                }
2005            }
2006            # Add this field to the sort command.
2007            $retVal .= " -k$fieldSpec";
2008        }
2009        # Return the result.
2010        return $retVal;
2011    }
2012    
2013    =head3 GetList
2014    
2015    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2016    
2017    Return a list of object descriptors for the specified objects as determined by the
2018    specified filter clause.
2019    
2020    This method is essentially the same as L</Get> except it returns a list of objects rather
2021    than a query object that can be used to get the results one record at a time.
2022    
2023    =over 4
2024    
2025    =item objectNames
2026    
2027    List containing the names of the entity and relationship objects to be retrieved.
2028    
2029    =item filterClause
2030    
2031    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2032    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2033    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2034    in the filter clause should be added to the parameter list as additional parameters. The
2035    fields in a filter clause can come from primary entity relations, relationship relations,
2036    or secondary entity relations; however, all of the entities and relationships involved must
2037    be included in the list of object names.
2038    
2039    The filter clause can also specify a sort order. To do this, simply follow the filter string
2040    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2041    particular genus and sorts them by species name.
2042    
2043  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2044    
# Line 1431  Line 2126 
2126  sub GetCount {  sub GetCount {
2127      # Get the parameters.      # Get the parameters.
2128      my ($self, $objectNames, $filter, $params) = @_;      my ($self, $objectNames, $filter, $params) = @_;
2129        # Insure the params argument is an array reference if the caller left it off.
2130        if (! defined($params)) {
2131            $params = [];
2132        }
2133      # Declare the return variable.      # Declare the return variable.
2134      my $retVal;      my $retVal;
2135      # Find out if we're counting an entity or a relationship.      # Find out if we're counting an entity or a relationship.
# Line 1609  Line 2308 
2308    
2309  =head3 InsertObject  =head3 InsertObject
2310    
2311  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2312    
2313  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2314  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 1623  Line 2322 
2322  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2323  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2324    
2325  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2326    
2327  =over 4  =over 4
2328    
# Line 1635  Line 2334 
2334    
2335  Hash of field names to values.  Hash of field names to values.
2336    
 =item RETURN  
   
 Returns 1 if successful, 0 if an error occurred.  
   
2337  =back  =back
2338    
2339  =cut  =cut
# Line 1737  Line 2432 
2432                  $retVal = $sth->execute(@parameterList);                  $retVal = $sth->execute(@parameterList);
2433                  if (!$retVal) {                  if (!$retVal) {
2434                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2435                      Trace("Insert error: $errorString.") if T(0);                      Confess("Error inserting into $relationName: $errorString");
2436                    } else {
2437                        Trace("Insert successful using $parameterList[0].") if T(3);
2438                  }                  }
2439              }              }
2440          }          }
2441      }      }
2442      # Return the success indicator.      # Return a 1 for backward compatability.
2443      return $retVal;      return 1;
2444    }
2445    
2446    =head3 UpdateEntity
2447    
2448    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2449    
2450    Update the values of an entity. This is an unprotected update, so it should only be
2451    done if the database resides on a database server.
2452    
2453    =over 4
2454    
2455    =item entityName
2456    
2457    Name of the entity to update. (This is the entity type.)
2458    
2459    =item id
2460    
2461    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2462    
2463    =item fields
2464    
2465    Reference to a hash mapping field names to their new values. All of the fields named
2466    must be in the entity's primary relation, and they cannot any of them be the ID field.
2467    
2468    =back
2469    
2470    =cut
2471    
2472    sub UpdateEntity {
2473        # Get the parameters.
2474        my ($self, $entityName, $id, $fields) = @_;
2475        # Get a list of the field names being updated.
2476        my @fieldList = keys %{$fields};
2477        # Verify that the fields exist.
2478        my $checker = $self->GetFieldTable($entityName);
2479        for my $field (@fieldList) {
2480            if ($field eq 'id') {
2481                Confess("Cannot update the ID field for entity $entityName.");
2482            } elsif ($checker->{$field}->{relation} ne $entityName) {
2483                Confess("Cannot find $field in primary relation of $entityName.");
2484            }
2485        }
2486        # Build the SQL statement.
2487        my @sets = ();
2488        my @valueList = ();
2489        for my $field (@fieldList) {
2490            push @sets, _FixName($field) . " = ?";
2491            push @valueList, $fields->{$field};
2492        }
2493        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2494        # Add the ID to the list of binding values.
2495        push @valueList, $id;
2496        # Call SQL to do the work.
2497        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2498        # Check for errors.
2499        if ($rows == 0) {
2500            Confess("Entity $id of type $entityName not found.");
2501        }
2502  }  }
2503    
2504  =head3 LoadTable  =head3 LoadTable
2505    
2506  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2507    
2508  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
2509  first.  first.
# Line 1815  Line 2570 
2570      };      };
2571      if (!defined $rv) {      if (!defined $rv) {
2572          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
2573          $retVal->AddMessage("Table load failed for $relationName using $fileName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2574          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
2575      } else {      } else {
2576          # Here we successfully loaded the table.          # Here we successfully loaded the table.
# Line 1823  Line 2578 
2578          my $size = -s $fileName;          my $size = -s $fileName;
2579          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
2580          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
2581          if ($truncateFlag && ! $dbh->{_preIndex}) {          if ($truncateFlag) {
2582                # Indexes are created here for PostGres. For PostGres, indexes are
2583                # best built at the end. For MySQL, the reverse is true.
2584                if (! $dbh->{_preIndex}) {
2585              eval {              eval {
2586                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
2587              };              };
# Line 1831  Line 2589 
2589                  $retVal->AddMessage($@);                  $retVal->AddMessage($@);
2590              }              }
2591          }          }
2592                # The full-text index (if any) is always built last, even for MySQL.
2593                # First we need to see if this table has a full-text index. Only
2594                # primary relations are allowed that privilege.
2595                Trace("Checking for full-text index on $relationName.") if T(2);
2596                if ($self->_IsPrimary($relationName)) {
2597                    $self->CreateSearchIndex($relationName);
2598                }
2599            }
2600      }      }
2601      # Analyze the table to improve performance.      # Analyze the table to improve performance.
2602        Trace("Analyzing and compacting $relationName.") if T(3);
2603      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
2604        Trace("$relationName load completed.") if T(3);
2605      # Return the statistics.      # Return the statistics.
2606      return $retVal;      return $retVal;
2607  }  }
2608    
2609  =head3 GenerateEntity  =head3 CreateSearchIndex
2610    
2611  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< $erdb->CreateSearchIndex($objectName); >>
2612    
2613  Generate the data for a new entity instance. This method creates a field hash suitable for  Check for a full-text search index on the specified entity or relationship object, and
2614  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  if one is required, rebuild it.
 of the fields are generated using information in the database schema.  
   
 Each data type has a default algorithm for generating random test data. This can be overridden  
 by including a B<DataGen> element in the field. If this happens, the content of the element is  
 executed as a PERL program in the context of this module. The element may make use of a C<$this>  
 variable which contains the field hash as it has been built up to the current point. If any  
 fields are dependent on other fields, the C<pass> attribute can be used to control the order  
 in which the fields are generated. A field with a high data pass number will be generated after  
 a field with a lower one. If any external values are needed, they should be passed in via the  
 optional third parameter, which will be available to the data generation script under the name  
 C<$value>. Several useful utility methods are provided for generating random values, including  
 L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated  
 in the form of a timestamp number rather than a string.  
2615    
2616  =over 4  =over 4
2617    
2618  =item id  =item objectName
2619    
2620  ID to assign to the new entity.  Name of the entity or relationship to be indexed.
2621    
2622  =item type  =back
2623    
2624  Type name for the new entity.  =cut
2625    
2626  =item values  sub CreateSearchIndex {
2627        # Get the parameters.
2628        my ($self, $objectName) = @_;
2629        # Get the relation's entity/relationship structure.
2630        my $structure = $self->_GetStructure($objectName);
2631        # Get the database handle.
2632        my $dbh = $self->{_dbh};
2633        Trace("Checking for search fields in $objectName.") if T(3);
2634        # Check for a searchable fields list.
2635        if (exists $structure->{searchFields}) {
2636            # Here we know that we need to create a full-text search index.
2637            # Get an SQL-formatted field name list.
2638            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2639            # Create the index. If it already exists, it will be dropped.
2640            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2641                               flds => $fields, kind => 'fulltext');
2642            Trace("Index created for $fields in $objectName.") if T(2);
2643        }
2644    }
2645    
2646    =head3 DropRelation
2647    
2648    C<< $erdb->DropRelation($relationName); >>
2649    
2650    Physically drop a relation from the database.
2651    
2652    =over 4
2653    
2654    =item relationName
2655    
2656  Hash containing additional values that might be needed by the data generation methods (optional).  Name of the relation to drop. If it does not exist, this method will have
2657    no effect.
2658    
2659  =back  =back
2660    
2661  =cut  =cut
2662    
2663  sub GenerateEntity {  sub DropRelation {
2664      # Get the parameters.      # Get the parameters.
2665      my ($self, $id, $type, $values) = @_;      my ($self, $relationName) = @_;
2666      # Create the return hash.      # Get the database handle.
2667      my $this = { id => $id };      my $dbh = $self->{_dbh};
2668      # Get the metadata structure.      # Drop the relation. The method used here has no effect if the relation
2669      my $metadata = $self->{_metaData};      # does not exist.
2670      # Get this entity's list of fields.      Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2671      if (!exists $metadata->{Entities}->{$type}) {      $dbh->drop_table(tbl => $relationName);
2672          Confess("Unrecognized entity type $type in GenerateEntity.");  }
2673    
2674    =head3 MatchSqlPattern
2675    
2676    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2677    
2678    Determine whether or not a specified value matches an SQL pattern. An SQL
2679    pattern has two wild card characters: C<%> that matches multiple characters,
2680    and C<_> that matches a single character. These can be escaped using a
2681    backslash (C<\>). We pull this off by converting the SQL pattern to a
2682    PERL regular expression. As per SQL rules, the match is case-insensitive.
2683    
2684    =over 4
2685    
2686    =item value
2687    
2688    Value to be matched against the pattern. Note that an undefined or empty
2689    value will not match anything.
2690    
2691    =item pattern
2692    
2693    SQL pattern against which to match the value. An undefined or empty pattern will
2694    match everything.
2695    
2696    =item RETURN
2697    
2698    Returns TRUE if the value and pattern match, else FALSE.
2699    
2700    =back
2701    
2702    =cut
2703    
2704    sub MatchSqlPattern {
2705        # Get the parameters.
2706        my ($value, $pattern) = @_;
2707        # Declare the return variable.
2708        my $retVal;
2709        # Insure we have a pattern.
2710        if (! defined($pattern) || $pattern eq "") {
2711            $retVal = 1;
2712        } else {
2713            # Break the pattern into pieces around the wildcard characters. Because we
2714            # use parentheses in the split function's delimiter expression, we'll get
2715            # list elements for the delimiters as well as the rest of the string.
2716            my @pieces = split /([_%]|\\[_%])/, $pattern;
2717            # Check some fast special cases.
2718            if ($pattern eq '%') {
2719                # A null pattern matches everything.
2720                $retVal = 1;
2721            } elsif (@pieces == 1) {
2722                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2723                $retVal = (lc($value) eq lc($pattern));
2724            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2725                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2726                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2727            } else {
2728                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2729                my $realPattern = "";
2730                for my $piece (@pieces) {
2731                    # Determine the type of piece.
2732                    if ($piece eq "") {
2733                        # Empty pieces are ignored.
2734                    } elsif ($piece eq "%") {
2735                        # Here we have a multi-character wildcard. Note that it can match
2736                        # zero or more characters.
2737                        $realPattern .= ".*"
2738                    } elsif ($piece eq "_") {
2739                        # Here we have a single-character wildcard.
2740                        $realPattern .= ".";
2741                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2742                        # This is an escape sequence (which is a rare thing, actually).
2743                        $realPattern .= substr($piece, 1, 1);
2744      } else {      } else {
2745          my $entity = $metadata->{Entities}->{$type};                      # Here we have raw text.
2746          my $fields = $entity->{Fields};                      $realPattern .= quotemeta($piece);
         # Generate data from the fields.  
         _GenerateFields($this, $fields, $type, $values);  
2747      }      }
2748      # Return the hash created.              }
2749      return $this;              # Do the match.
2750                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2751            }
2752        }
2753        # Return the result.
2754        return $retVal;
2755  }  }
2756    
2757  =head3 GetEntity  =head3 GetEntity
# Line 1932  Line 2790 
2790      return $retVal;      return $retVal;
2791  }  }
2792    
2793    =head3 GetChoices
2794    
2795    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2796    
2797    Return a list of all the values for the specified field that are represented in the
2798    specified entity.
2799    
2800    Note that if the field is not indexed, then this will be a very slow operation.
2801    
2802    =over 4
2803    
2804    =item entityName
2805    
2806    Name of an entity in the database.
2807    
2808    =item fieldName
2809    
2810    Name of a field belonging to the entity. This is a raw field name without
2811    the standard parenthesized notation used in most calls.
2812    
2813    =item RETURN
2814    
2815    Returns a list of the distinct values for the specified field in the database.
2816    
2817    =back
2818    
2819    =cut
2820    
2821    sub GetChoices {
2822        # Get the parameters.
2823        my ($self, $entityName, $fieldName) = @_;
2824        # Declare the return variable.
2825        my @retVal;
2826        # Get the entity data structure.
2827        my $entityData = $self->_GetStructure($entityName);
2828        # Get the field.
2829        my $fieldHash = $entityData->{Fields};
2830        if (! exists $fieldHash->{$fieldName}) {
2831            Confess("$fieldName not found in $entityName.");
2832        } else {
2833            # Get the name of the relation containing the field.
2834            my $relation = $fieldHash->{$fieldName}->{relation};
2835            # Fix up the field name.
2836            my $realName = _FixName($fieldName);
2837            # Get the database handle.
2838            my $dbh = $self->{_dbh};
2839            # Query the database.
2840            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2841            # Clean the results. They are stored as a list of lists, and we just want the one list.
2842            @retVal = sort map { $_->[0] } @{$results};
2843        }
2844        # Return the result.
2845        return @retVal;
2846    }
2847    
2848  =head3 GetEntityValues  =head3 GetEntityValues
2849    
2850  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2851    
2852  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance. If the entity instance
2853    does not exist, an empty list is returned.
2854    
2855  =over 4  =over 4
2856    
# Line 1993  Line 2907 
2907  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
2908  feature ID followed by all of its aliases.  feature ID followed by all of its aliases.
2909    
2910  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(alias)']); >>
2911    
2912  =over 4  =over 4
2913    
# Line 2171  Line 3085 
3085      return $objectData->{Fields};      return $objectData->{Fields};
3086  }  }
3087    
3088    =head3 SplitKeywords
3089    
3090    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3091    
3092    This method returns a list of the positive keywords in the specified
3093    keyword string. All of the operators will have been stripped off,
3094    and if the keyword is preceded by a minus operator (C<->), it will
3095    not be in the list returned. The idea here is to get a list of the
3096    keywords the user wants to see. The list will be processed to remove
3097    duplicates.
3098    
3099    It is possible to create a string that confuses this method. For example
3100    
3101        frog toad -frog
3102    
3103    would return both C<frog> and C<toad>. If this is a problem we can deal
3104    with it later.
3105    
3106    =over 4
3107    
3108    =item keywordString
3109    
3110    The keyword string to be parsed.
3111    
3112    =item RETURN
3113    
3114    Returns a list of the words in the keyword string the user wants to
3115    see.
3116    
3117    =back
3118    
3119    =cut
3120    
3121    sub SplitKeywords {
3122        # Get the parameters.
3123        my ($keywordString) = @_;
3124        # Make a safety copy of the string. (This helps during debugging.)
3125        my $workString = $keywordString;
3126        # Convert operators we don't care about to spaces.
3127        $workString =~ tr/+"()<>/ /;
3128        # Split the rest of the string along space boundaries. Note that we
3129        # eliminate any words that are zero length or begin with a minus sign.
3130        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3131        # Use a hash to remove duplicates.
3132        my %words = map { $_ => 1 } @wordList;
3133        # Return the result.
3134        return sort keys %words;
3135    }
3136    
3137    =head3 ValidateFieldName
3138    
3139    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3140    
3141    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3142    be hyphenated words subject to certain restrictions.
3143    
3144    =over 4
3145    
3146    =item fieldName
3147    
3148    Field name to be validated.
3149    
3150    =item RETURN
3151    
3152    Returns TRUE if the field name is valid, else FALSE.
3153    
3154    =back
3155    
3156    =cut
3157    
3158    sub ValidateFieldName {
3159        # Get the parameters.
3160        my ($fieldName) = @_;
3161        # Declare the return variable. The field name is valid until we hear
3162        # differently.
3163        my $retVal = 1;
3164        # Compute the maximum name length.
3165        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3166        # Look for bad stuff in the name.
3167        if ($fieldName =~ /--/) {
3168            # Here we have a doubled minus sign.
3169            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3170            $retVal = 0;
3171        } elsif ($fieldName !~ /^[A-Za-z]/) {
3172            # Here the field name is missing the initial letter.
3173            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3174            $retVal = 0;
3175        } elsif (length($fieldName) > $maxLen) {
3176            # Here the field name is too long.
3177            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3178        } else {
3179            # Strip out the minus signs. Everything remaining must be a letter,
3180            # underscore, or digit.
3181            my $strippedName = $fieldName;
3182            $strippedName =~ s/-//g;
3183            if ($strippedName !~ /^(\w|\d)+$/) {
3184                Trace("Field name $fieldName contains illegal characters.") if T(1);
3185                $retVal = 0;
3186            }
3187        }
3188        # Return the result.
3189        return $retVal;
3190    }
3191    
3192    =head3 ReadMetaXML
3193    
3194    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3195    
3196    This method reads a raw database definition XML file and returns it.
3197    Normally, the metadata used by the ERDB system has been processed and
3198    modified to make it easier to load and retrieve the data; however,
3199    this method can be used to get the data in its raw form.
3200    
3201    =over 4
3202    
3203    =item fileName
3204    
3205    Name of the XML file to read.
3206    
3207    =item RETURN
3208    
3209    Returns a hash reference containing the raw XML data from the specified file.
3210    
3211    =back
3212    
3213    =cut
3214    
3215    sub ReadMetaXML {
3216        # Get the parameters.
3217        my ($fileName) = @_;
3218        # Read the XML.
3219        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3220        Trace("XML metadata loaded from file $fileName.") if T(1);
3221        # Return the result.
3222        return $retVal;
3223    }
3224    
3225    =head3 GetEntityFieldHash
3226    
3227    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3228    
3229    Get the field hash of the named entity in the specified raw XML structure.
3230    The field hash may not exist, in which case we need to create it.
3231    
3232    =over 4
3233    
3234    =item structure
3235    
3236    Raw XML structure defininng the database. This is not the run-time XML used by
3237    an ERDB object, since that has all sorts of optimizations built-in.
3238    
3239    =item entityName
3240    
3241    Name of the entity whose field structure is desired.
3242    
3243    =item RETURN
3244    
3245    Returns the field hash used to define the entity's fields.
3246    
3247    =back
3248    
3249    =cut
3250    
3251    sub GetEntityFieldHash {
3252        # Get the parameters.
3253        my ($structure, $entityName) = @_;
3254        # Get the entity structure.
3255        my $entityData = $structure->{Entities}->{$entityName};
3256        # Look for a field structure.
3257        my $retVal = $entityData->{Fields};
3258        # If it doesn't exist, create it.
3259        if (! defined($retVal)) {
3260            $entityData->{Fields} = {};
3261            $retVal = $entityData->{Fields};
3262        }
3263        # Return the result.
3264        return $retVal;
3265    }
3266    
3267    =head3 WriteMetaXML
3268    
3269    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3270    
3271    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3272    used to update the database definition. It must be used with care, however, since it
3273    will only work on a raw structure, not on the processed structure created by an ERDB
3274    constructor.
3275    
3276    =over 4
3277    
3278    =item structure
3279    
3280    XML structure to be written to the file.
3281    
3282    =item fileName
3283    
3284    Name of the output file to which the updated XML should be stored.
3285    
3286    =back
3287    
3288    =cut
3289    
3290    sub WriteMetaXML {
3291        # Get the parameters.
3292        my ($structure, $fileName) = @_;
3293        # Compute the output.
3294        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3295        # Write it to the file.
3296        my $xmlOut = Open(undef, ">$fileName");
3297        print $xmlOut $fileString;
3298    }
3299    
3300    
3301    =head3 HTMLNote
3302    
3303    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3304    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3305    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3306    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3307    
3308    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3309    
3310    =over 4
3311    
3312    =item dataString
3313    
3314    String to convert to HTML.
3315    
3316    =item RETURN
3317    
3318    An HTML string derived from the input string.
3319    
3320    =back
3321    
3322    =cut
3323    
3324    sub HTMLNote {
3325        # Get the parameter.
3326        my ($dataString) = @_;
3327        # HTML-escape the text.
3328        my $retVal = CGI::escapeHTML($dataString);
3329        # Substitute the bulletin board codes.
3330        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3331        $retVal =~ s!\[p\]!</p><p>!g;
3332        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3333        $retVal =~ s!\[/link\]!</a>!g;
3334        # Return the result.
3335        return $retVal;
3336    }
3337    
3338    
3339  =head2 Data Mining Methods  =head2 Data Mining Methods
3340    
3341  =head3 GetUsefulCrossValues  =head3 GetUsefulCrossValues
# Line 2324  Line 3489 
3489      return @retVal;      return @retVal;
3490  }  }
3491    
3492    =head2 Virtual Methods
3493    
3494    =head3 CleanKeywords
3495    
3496    C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3497    
3498    Clean up a search expression or keyword list. This is a virtual method that may
3499    be overridden by the subclass. The base-class method removes extra spaces
3500    and converts everything to lower case.
3501    
3502    =over 4
3503    
3504    =item searchExpression
3505    
3506    Search expression or keyword list to clean. Note that a search expression may
3507    contain boolean operators which need to be preserved. This includes leading
3508    minus signs.
3509    
3510    =item RETURN
3511    
3512    Cleaned expression or keyword list.
3513    
3514    =back
3515    
3516    =cut
3517    
3518    sub CleanKeywords {
3519        # Get the parameters.
3520        my ($self, $searchExpression) = @_;
3521        # Lower-case the expression and copy it into the return variable. Note that we insure we
3522        # don't accidentally end up with an undefined value.
3523        my $retVal = lc($searchExpression || "");
3524        # Remove extra spaces.
3525        $retVal =~ s/\s+/ /g;
3526        $retVal =~ s/(^\s+)|(\s+$)//g;
3527        # Return the result.
3528        return $retVal;
3529    }
3530    
3531    =head3 GetSourceObject
3532    
3533    C<< my $source = $erdb->GetSourceObject($entityName); >>
3534    
3535    Return the object to be used in loading special attributes of the specified entity. The
3536    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3537    XML
3538    
3539  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3540    
3541  =head3 SetupSQL  =head3 _RelationMap
3542    
3543    C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3544    
3545    Create the relation map for an SQL query. The relation map is used by B<DBObject>
3546    to determine how to interpret the results of the query.
3547    
3548    =over 4
3549    
3550    =item mappedNameHashRef
3551    
3552    Reference to a hash that maps modified object names to real object names.
3553    
3554    =item mappedNameListRef
3555    
3556    Reference to a list of modified object names in the order they appear in the
3557    SELECT list.
3558    
3559    =item RETURN
3560    
3561    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3562    query followed by the actual name of that object. This enables the B<DBObject> to
3563    determine the order of the tables in the query and which object name belongs to each
3564    mapped object name. Most of the time these two values are the same; however, if a
3565    relation occurs twice in the query, the relation name in the field list and WHERE
3566    clause will use a mapped name (generally the actual relation name with a numeric
3567    suffix) that does not match the actual relation name.
3568    
3569    =back
3570    
3571    =cut
3572    
3573    sub _RelationMap {
3574        # Get the parameters.
3575        my ($mappedNameHashRef, $mappedNameListRef) = @_;
3576        # Declare the return variable.
3577        my @retVal = ();
3578        # Build the map.
3579        for my $mappedName (@{$mappedNameListRef}) {
3580            push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3581        }
3582        # Return it.
3583        return @retVal;
3584    }
3585    
3586    
3587    =head3 _SetupSQL
3588    
3589  Process a list of object names and a filter clause so that they can be used to  Process a list of object names and a filter clause so that they can be used to
3590  build an SQL statement. This method takes in a reference to a list of object names  build an SQL statement. This method takes in a reference to a list of object names
# Line 2346  Line 3604 
3604  A string containing the WHERE clause for the query (without the C<WHERE>) and also  A string containing the WHERE clause for the query (without the C<WHERE>) and also
3605  optionally the C<ORDER BY> and C<LIMIT> clauses.  optionally the C<ORDER BY> and C<LIMIT> clauses.
3606    
3607    =item matchClause
3608    
3609    An optional full-text search clause. If specified, it will be inserted at the
3610    front of the WHERE clause. It should already be SQL-formatted; that is, the
3611    field names should be in the form I<table>C<.>I<fieldName>.
3612    
3613  =item RETURN  =item RETURN
3614    
3615  Returns a three-element list. The first element is the SQL statement suffix, beginning  Returns a three-element list. The first element is the SQL statement suffix, beginning
# Line 2358  Line 3622 
3622  =cut  =cut
3623    
3624  sub _SetupSQL {  sub _SetupSQL {
3625      my ($self, $objectNames, $filterClause) = @_;      my ($self, $objectNames, $filterClause, $matchClause) = @_;
3626      # Adjust the list of object names to account for multiple occurrences of the      # Adjust the list of object names to account for multiple occurrences of the
3627      # same object. We start with a hash table keyed on object name that will      # same object. We start with a hash table keyed on object name that will
3628      # return the object suffix. The first time an object is encountered it will      # return the object suffix. The first time an object is encountered it will
# Line 2407  Line 3671 
3671      # FROM name1, name2, ... nameN      # FROM name1, name2, ... nameN
3672      #      #
3673      my $suffix = "FROM " . join(', ', @fromList);      my $suffix = "FROM " . join(', ', @fromList);
3674        # Now for the WHERE. First, we need a place for the filter string.
3675        my $filterString = "";
3676        # We will also keep a list of conditions to add to the WHERE clause in order to link
3677        # entities and relationships as well as primary relations to secondary ones.
3678        my @joinWhere = ();
3679      # Check for a filter clause.      # Check for a filter clause.
3680      if ($filterClause) {      if ($filterClause) {
3681          # Here we have one, so we convert its field names and add it to the query. First,          # Here we have one, so we convert its field names and add it to the query. First,
3682          # We create a copy of the filter string we can work with.          # We create a copy of the filter string we can work with.
3683          my $filterString = $filterClause;          $filterString = $filterClause;
3684          # Next, we sort the object names by length. This helps protect us from finding          # Next, we sort the object names by length. This helps protect us from finding
3685          # object names inside other object names when we're doing our search and replace.          # object names inside other object names when we're doing our search and replace.
3686          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
3687          # The final preparatory step is to create a hash table of relation names. The          # The final preparatory step is to create a hash table of relation names. The
3688          # table begins with the relation names already in the SELECT command. We may          # table begins with the relation names already in the SELECT command. We may
3689          # need to add relations later if there is filtering on a field in a secondary          # need to add relations later if there is filtering on a field in a secondary
# Line 2485  Line 3751 
3751                  }                  }
3752              }              }
3753          }          }
3754        }
3755          # The next step is to join the objects together. We only need to do this if there          # The next step is to join the objects together. We only need to do this if there
3756          # is more than one object in the object list. We start with the first object and          # is more than one object in the object list. We start with the first object and
3757          # run through the objects after it. Note also that we make a safety copy of the          # run through the objects after it. Note also that we make a safety copy of the
3758          # list before running through it.      # list before running through it, because we shift off the first object before
3759        # processing the rest.
3760          my @mappedObjectList = @mappedNameList;          my @mappedObjectList = @mappedNameList;
3761          my $lastMappedObject = shift @mappedObjectList;          my $lastMappedObject = shift @mappedObjectList;
3762          # Get the join table.          # Get the join table.
# Line 2517  Line 3785 
3785          # here is we want the filter clause to be empty if there's no WHERE filter.          # here is we want the filter clause to be empty if there's no WHERE filter.
3786          # We'll put the ORDER BY / LIMIT clauses in the following variable.          # We'll put the ORDER BY / LIMIT clauses in the following variable.
3787          my $orderClause = "";          my $orderClause = "";
3788        # This is only necessary if we have a filter string in which the ORDER BY
3789        # and LIMIT clauses can live.
3790        if ($filterString) {
3791          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy          # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3792          # operator so that we find the first occurrence of either verb.          # operator so that we find the first occurrence of either verb.
3793          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {          if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
# Line 2525  Line 3796 
3796              $orderClause = $2 . substr($filterString, $pos);              $orderClause = $2 . substr($filterString, $pos);
3797              $filterString = $1;              $filterString = $1;
3798          }          }
3799          # Add the filter and the join clauses (if any) to the SELECT command.      }
3800        # All the things that are supposed to be in the WHERE clause of the
3801        # SELECT command need to be put into @joinWhere so we can string them
3802        # together. We begin with the match clause. This is important,
3803        # because the match clause's parameter mark must precede any parameter
3804        # marks in the filter string.
3805        if ($matchClause) {
3806            push @joinWhere, $matchClause;
3807        }
3808        # Add the filter string. We put it in parentheses to avoid operator
3809        # precedence problems with the match clause or the joins.
3810          if ($filterString) {          if ($filterString) {
3811              Trace("Filter string is \"$filterString\".") if T(4);              Trace("Filter string is \"$filterString\".") if T(4);
3812              push @joinWhere, "($filterString)";              push @joinWhere, "($filterString)";
3813          }          }
3814        # String it all together into a big filter clause.
3815          if (@joinWhere) {          if (@joinWhere) {
3816              $suffix .= " WHERE " . join(' AND ', @joinWhere);              $suffix .= " WHERE " . join(' AND ', @joinWhere);
3817          }          }
3818          # Add the sort or limit clause (if any) to the SELECT command.      # Add the sort or limit clause (if any).
3819          if ($orderClause) {          if ($orderClause) {
3820              $suffix .= " $orderClause";              $suffix .= " $orderClause";
3821          }          }
     }  
3822      # Return the suffix, the mapped name list, and the mapped name hash.      # Return the suffix, the mapped name list, and the mapped name hash.
3823      return ($suffix, \@mappedNameList, \%mappedNameHash);      return ($suffix, \@mappedNameList, \%mappedNameHash);
3824  }  }
3825    
3826  =head3 GetStatementHandle  =head3 _GetStatementHandle
3827    
3828  This method will prepare and execute an SQL query, returning the statement handle.  This method will prepare and execute an SQL query, returning the statement handle.
3829  The main reason for doing this here is so that everybody who does SQL queries gets  The main reason for doing this here is so that everybody who does SQL queries gets
# Line 2580  Line 3861 
3861      # Prepare the command.      # Prepare the command.
3862      my $sth = $dbh->prepare_command($command);      my $sth = $dbh->prepare_command($command);
3863      # Execute it with the parameters bound in.      # Execute it with the parameters bound in.
3864      $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
3865      # Return the statement handle.      # Return the statement handle.
3866      return $sth;      return $sth;
3867  }  }
3868    
3869  =head3 GetLoadStats  =head3 _GetLoadStats
3870    
3871  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
3872    
# Line 2597  Line 3878 
3878      return Stats->new();      return Stats->new();
3879  }  }
3880    
3881  =head3 GenerateFields  =head3 _DumpRelation
   
 Generate field values from a field structure and store in a specified table. The field names  
 are first sorted by pass count, certain pre-defined fields are removed from the list, and  
 then we rip through them evaluation the data generation string. Fields in the primary relation  
 are stored as scalars; fields in secondary relations are stored as value lists.  
   
 This is a static method.  
   
 =over 4  
   
 =item this  
   
 Hash table into which the field values should be placed.  
   
 =item fields  
   
 Field structure from which the field descriptors should be taken.  
   
 =item type  
   
 Type name of the object whose fields are being generated.  
   
 =item values (optional)  
   
 Reference to a value structure from which additional values can be taken.  
   
 =item from (optiona)  
   
 Reference to the source entity instance if relationship data is being generated.  
   
 =item to (optional)  
   
 Reference to the target entity instance if relationship data is being generated.  
   
 =back  
   
 =cut  
   
 sub _GenerateFields {  
     # Get the parameters.  
     my ($this, $fields, $type, $values, $from, $to) = @_;  
     # Sort the field names by pass number.  
     my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};  
     # Loop through the field names, generating data.  
     for my $name (@fieldNames) {  
         # Only proceed if this field needs to be generated.  
         if (!exists $this->{$name}) {  
             # Get this field's data generation descriptor.  
             my $fieldDescriptor = $fields->{$name};  
             my $data = $fieldDescriptor->{DataGen};  
             # Get the code to generate the field value.  
             my $codeString = $data->{content};  
             # Determine whether or not this field is in the primary relation.  
             if ($fieldDescriptor->{relation} eq $type) {  
                 # Here we have a primary relation field. Store the field value as  
                 # a scalar.  
                 $this->{$name} = eval($codeString);  
             } else {  
                 # Here we have a secondary relation field. Create a null list  
                 # and push the desired number of field values onto it.  
                 my @fieldValues = ();  
                 my $count = IntGen(0,$data->{testCount});  
                 for (my $i = 0; $i < $count; $i++) {  
                     my $newValue = eval($codeString);  
                     push @fieldValues, $newValue;  
                 }  
                 # Store the value list in the main hash.  
                 $this->{$name} = \@fieldValues;  
             }  
         }  
     }  
 }  
   
 =head3 DumpRelation  
3882    
3883  Dump the specified relation's to the specified output file in tab-delimited format.  Dump the specified relation to the specified output file in tab-delimited format.
3884    
3885  This is an instance method.  This is an instance method.
3886    
# Line 2721  Line 3928 
3928      close DTXOUT;      close DTXOUT;
3929  }  }
3930    
3931  =head3 GetStructure  =head3 _GetStructure
3932    
3933  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
3934    
# Line 2760  Line 3967 
3967      return $retVal;      return $retVal;
3968  }  }
3969    
3970  =head3 GetRelationTable  
3971    
3972    =head3 _GetRelationTable
3973    
3974  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
3975    
# Line 2789  Line 3998 
3998      return $objectData->{Relations};      return $objectData->{Relations};
3999  }  }
4000    
4001  =head3 ValidateFieldNames  =head3 _ValidateFieldNames
4002    
4003  Determine whether or not the field names are valid. A description of the problems with the names  Determine whether or not the field names are valid. A description of the problems with the names
4004  will be written to the standard error output. If there is an error, this method will abort. This is  will be written to the standard error output. If there is an error, this method will abort. This is
# Line 2816  Line 4025 
4025          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
4026              # Loop through the object's fields.              # Loop through the object's fields.
4027              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
4028                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
4029                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
4030                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($fieldName)) {
                     print STDERR "Field name $fieldName has a doubled hyphen.\n";  
                     $retVal = 0;  
                 } elsif ($fieldName !~ /^[A-Za-z]/) {  
                     # Here the field name is missing the initial letter.  
                     print STDERR "Field name $fieldName does not begin with a letter.\n";  
                     $retVal = 0;  
                 } else {  
                     # Strip out the minus signs. Everything remaining must be a letter  
                     # or digit.  
                     my $strippedName = $fieldName;  
                     $strippedName =~ s/-//g;  
                     if ($strippedName !~ /^[A-Za-z0-9]+$/) {  
                         print STDERR "Field name $fieldName contains illegal characters.\n";  
4031                          $retVal = 0;                          $retVal = 0;
4032                      }                      }
4033                  }                  }
4034              }              }
4035          }          }
     }  
4036      # If an error was found, fail.      # If an error was found, fail.
4037      if ($retVal  == 0) {      if ($retVal  == 0) {
4038          Confess("Errors found in field names.");          Confess("Errors found in field names.");
4039      }      }
4040  }  }
4041    
4042  =head3 LoadRelation  =head3 _LoadRelation
4043    
4044  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk  Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
4045  file with the same name as the relation exists in the specified directory.  file with the same name as the relation exists in the specified directory.
# Line 2904  Line 4099 
4099      return $retVal;      return $retVal;
4100  }  }
4101    
4102  =head3 LoadMetaData  
4103    =head3 _LoadMetaData
4104    
4105  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4106  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 2929  Line 4125 
4125  sub _LoadMetaData {  sub _LoadMetaData {
4126      # Get the parameters.      # Get the parameters.
4127      my ($filename) = @_;      my ($filename) = @_;
4128      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4129      # Slurp the XML file into a variable. Extensive use of options is used to insure we      # Slurp the XML file into a variable. Extensive use of options is used to insure we
4130      # get the exact structure we want.      # get the exact structure we want.
4131      my $metadata = XML::Simple::XMLin($filename,      my $metadata = ReadMetaXML($filename);
                                       GroupTags => { Relationships => 'Relationship',  
                                                      Entities => 'Entity',  
                                                      Fields => 'Field',  
                                                      Indexes => 'Index',  
                                                      IndexFields => 'IndexField'},  
                                       KeyAttr => { Relationship => 'name',  
                                                    Entity => 'name',  
                                                    Field => 'name'},  
                                       ForceArray => ['Field', 'Index', 'IndexField'],  
                                       ForceContent => 1,  
                                       NormalizeSpace => 2  
                                       );  
     Trace("XML metadata loaded from file $filename.") if T(1);  
4132      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
4133      # the method below will fail.      # the method below will fail.
4134      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 3075  Line 4258 
4258              my $count = 0;              my $count = 0;
4259              for my $index (@{$indexList}) {              for my $index (@{$indexList}) {
4260                  # Add this index to the index table.                  # Add this index to the index table.
4261                  _AddIndex("idx$relationName$count", $relation, $index);                  _AddIndex("idx$count", $relation, $index);
4262                  # Increment the counter so that the next index has a different name.                  # Increment the counter so that the next index has a different name.
4263                  $count++;                  $count++;
4264              }              }
# Line 3092  Line 4275 
4275          _FixupFields($relationshipStructure, $relationshipName, 2, 3);          _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4276          # Format a description for the FROM field.          # Format a description for the FROM field.
4277          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
4278          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].";
4279          # Get the FROM entity's key type.          # Get the FROM entity's key type.
4280          my $fromType = $entityList->{$fromEntity}->{keyType};          my $fromType = $entityList->{$fromEntity}->{keyType};
4281          # Add the FROM field.          # Add the FROM field.
# Line 3102  Line 4285 
4285                                                      PrettySort => 1});                                                      PrettySort => 1});
4286          # Format a description for the TO field.          # Format a description for the TO field.
4287          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
4288          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].";
4289          # Get the TO entity's key type.          # Get the TO entity's key type.
4290          my $toType = $entityList->{$toEntity}->{keyType};          my $toType = $entityList->{$toEntity}->{keyType};
4291          # Add the TO field.          # Add the TO field.
# Line 3231  Line 4414 
4414      return $metadata;      return $metadata;
4415  }  }
4416    
4417  =head3 SortNeeded  =head3 _CreateRelationshipIndex
   
 C<< my $flag = $erdb->SortNeeded($relationName); >>  
   
 Return TRUE if the specified relation should be sorted during loading to remove duplicate keys,  
 else FALSE.  
   
 =over 4  
   
 =item relationName  
   
 Name of the relation to be examined.  
   
 =item RETURN  
   
 Returns TRUE if the relation needs a sort, else FALSE.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub SortNeeded {  
     # Get the parameters.  
     my ($self, $relationName) = @_;  
     # Declare the return variable.  
     my $retVal = 0;  
     # Find out if the relation is a primary entity relation.  
     my $entityTable = $self->{_metaData}->{Entities};  
     if (exists $entityTable->{$relationName}) {  
         my $keyType = $entityTable->{$relationName}->{keyType};  
         Trace("Relation $relationName found in entity table with key type $keyType.") if T(3);  
         # If the key is not a hash string, we must do the sort.  
         if ($keyType ne 'hash-string') {  
             $retVal = 1;  
         }  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 CreateRelationshipIndex  
4418    
4419  Create an index for a relationship's relation.  Create an index for a relationship's relation.
4420    
# Line 3313  Line 4456 
4456          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
4457      }      }
4458      # Add the index to the relation.      # Add the index to the relation.
4459      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4460  }  }
4461    
4462  =head3 AddIndex  =head3 _AddIndex
4463    
4464  Add an index to a relation structure.  Add an index to a relation structure.
4465    
# Line 3362  Line 4505 
4505      $relationStructure->{Indexes}->{$indexName} = $newIndex;      $relationStructure->{Indexes}->{$indexName} = $newIndex;
4506  }  }
4507    
4508  =head3 FixupFields  =head3 _FixupFields
4509    
4510  This method fixes the field list for an entity or relationship. It will add the caller-specified  This method fixes the field list for an entity or relationship. It will add the caller-specified
4511  relation name to fields that do not have a name and set the C<PrettySort> value as specified.  relation name to fields that do not have a name and set the C<PrettySort> value as specified.
# Line 3400  Line 4543 
4543          # Here it doesn't, so we create a new one.          # Here it doesn't, so we create a new one.
4544          $structure->{Fields} = { };          $structure->{Fields} = { };
4545      } else {      } else {
4546          # Here we have a field list. Loop through its fields.          # Here we have a field list. We need to track the searchable fields, so we
4547            # create a list for stashing them.
4548            my @textFields = ();
4549            # Loop through the fields.
4550          my $fieldStructures = $structure->{Fields};          my $fieldStructures = $structure->{Fields};
4551          for my $fieldName (keys %{$fieldStructures}) {          for my $fieldName (keys %{$fieldStructures}) {
4552              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
# Line 3409  Line 4555 
4555              my $type = $fieldData->{type};              my $type = $fieldData->{type};
4556              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
4557              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4558              # Plug in a data generator if we need one.              # Check for searchability.
4559              if (!exists $fieldData->{DataGen}) {              if ($fieldData->{searchable}) {
4560                  # The data generator will use the default for the field's type.                  # Only allow this for a primary relation.
4561                  $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };                  if ($fieldData->{relation} ne $defaultRelationName) {
4562                        Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4563                    } else {
4564                        push @textFields, $fieldName;
4565                    }
4566              }              }
             # Plug in the defaults for the optional data generation parameters.  
             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
4567              # Add the PrettySortValue.              # Add the PrettySortValue.
4568              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4569          }          }
4570            # If there are searchable fields, remember the fact.
4571            if (@textFields) {
4572                $structure->{searchFields} = \@textFields;
4573            }
4574      }      }
4575  }  }
4576    
4577  =head3 FixName  =head3 _FixName
4578    
4579  Fix the incoming field name so that it is a legal SQL column name.  Fix the incoming field name so that it is a legal SQL column name.
4580    
# Line 3451  Line 4603 
4603      return $fieldName;      return $fieldName;
4604  }  }
4605    
4606  =head3 FixNames  =head3 _FixNames
4607    
4608  Fix all the field names in a list.  Fix all the field names in a list.
4609    
# Line 3482  Line 4634 
4634      return @result;      return @result;
4635  }  }
4636    
4637  =head3 AddField  =head3 _AddField
4638    
4639  Add a field to a field list.  Add a field to a field list.
4640    
# Line 3517  Line 4669 
4669      $fieldList->{$fieldName} = $fieldStructure;      $fieldList->{$fieldName} = $fieldStructure;
4670  }  }
4671    
4672  =head3 ReOrderRelationTable  =head3 _ReOrderRelationTable
4673    
4674  This method will take a relation table and re-sort it according to the implicit ordering of the  This method will take a relation table and re-sort it according to the implicit ordering of the
4675  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.  C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
# Line 3578  Line 4730 
4730    
4731  }  }
4732    
4733  =head3 IsPrimary  =head3 _IsPrimary
4734    
4735  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary  Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
4736  if it has the same name as an entity or relationship.  if it has the same name as an entity or relationship.
# Line 3614  Line 4766 
4766      return $retVal;      return $retVal;
4767  }  }
4768    
4769  =head3 FindRelation  =head3 _FindRelation
4770    
4771  Return the descriptor for the specified relation.  Return the descriptor for the specified relation.
4772    
# Line 3645  Line 4797 
4797    
4798  =head2 HTML Documentation Utility Methods  =head2 HTML Documentation Utility Methods
4799    
4800  =head3 ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
4801    
4802  The relationship sentence consists of the relationship name between the names of the  The relationship sentence consists of the relationship name between the names of the
4803  two related entities and an arity indicator.  two related entities and an arity indicator.
# Line 3683  Line 4835 
4835      return $result;      return $result;
4836  }  }
4837    
4838  =head3 ComputeRelationshipHeading  =head3 _ComputeRelationshipHeading
4839    
4840  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
4841  names hyperlinked to the appropriate entity sections of the document.  names hyperlinked to the appropriate entity sections of the document.
# Line 3720  Line 4872 
4872      return $result;      return $result;
4873  }  }
4874    
4875  =head3 ShowRelationTable  =head3 _ShowRelationTable
4876    
4877  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
4878  table with three columns-- the field name, the field type, and the field description.  table with three columns-- the field name, the field type, and the field description.
# Line 3770  Line 4922 
4922          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
4923          # Add any note text.          # Add any note text.
4924          if (my $note = $indexData->{Notes}) {          if (my $note = $indexData->{Notes}) {
4925              $htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";              $htmlString .= "<li>" . HTMLNote($note->{content}) . "</li>\n";
4926          }          }
4927          # Add the fiield list.          # Add the fiield list.
4928          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
# Line 3781  Line 4933 
4933      $htmlString .= "</ul>\n";      $htmlString .= "</ul>\n";
4934  }  }
4935    
4936  =head3 OpenFieldTable  =head3 _OpenFieldTable
4937    
4938  This method creates the header string for the field table generated by L</ShowMetaData>.  This method creates the header string for the field table generated by L</ShowMetaData>.
4939    
# Line 3806  Line 4958 
4958      return _OpenTable($tablename, 'Field', 'Type', 'Description');      return _OpenTable($tablename, 'Field', 'Type', 'Description');
4959  }  }
4960    
4961  =head3 OpenTable  =head3 _OpenTable
4962    
4963  This method creates the header string for an HTML table.  This method creates the header string for an HTML table.
4964    
# Line 3836  Line 4988 
4988      # Compute the number of columns.      # Compute the number of columns.
4989      my $colCount = @colNames;      my $colCount = @colNames;
4990      # Generate the title row.      # Generate the title row.
4991      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";
4992      # Loop through the columns, adding the column header rows.      # Loop through the columns, adding the column header rows.
4993      $htmlString .= "<tr>";      $htmlString .= "<tr>";
4994      for my $colName (@colNames) {      for my $colName (@colNames) {
# Line 3846  Line 4998 
4998      return $htmlString;      return $htmlString;
4999  }  }
5000    
5001  =head3 CloseTable  =head3 _CloseTable
5002    
5003  This method returns the HTML for closing a table.  This method returns the HTML for closing a table.
5004    
# Line 3855  Line 5007 
5007  =cut  =cut
5008    
5009  sub _CloseTable {  sub _CloseTable {
5010      return "</table></p>\n";      return "</table>\n";
5011  }  }
5012    
5013  =head3 ShowField  =head3 _ShowField
5014    
5015  This method returns the HTML for displaying a row of field information in a field table.  This method returns the HTML for displaying a row of field information in a field table.
5016    
# Line 3885  Line 5037 
5037      my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";      my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";
5038      # If we have content, add it as a third column.      # If we have content, add it as a third column.
5039      if (exists $fieldData->{Notes}) {      if (exists $fieldData->{Notes}) {
5040          $htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";          $htmlString .= "<td>" . HTMLNote($fieldData->{Notes}->{content}) . "</td>";
5041      }      }
5042      # Close off the row.      # Close off the row.
5043      $htmlString .= "</tr>\n";      $htmlString .= "</tr>\n";
# Line 3893  Line 5045 
5045      return $htmlString;      return $htmlString;
5046  }  }
5047    
 =head3 HTMLNote  
   
 Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes  
 supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.  
 Except for C<[p]>, all the codes are closed by slash-codes. So, for  
 example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.  
   
 This is a static method.  
   
 =over 4  
   
 =item dataString  
   
 String to convert to HTML.  
   
 =item RETURN  
   
 An HTML string derived from the input string.  
   
 =back  
   
 =cut  
   
 sub _HTMLNote {  
     # Get the parameter.  
     my ($dataString) = @_;  
     # Substitute the codes.  
     $dataString =~ s!\[(/?[bi])\]!<$1>!g;  
     $dataString =~ s!\[p\]!</p><p>!g;  
     # Return the result.  
     return $dataString;  
 }  
   
 =head2 Data Generation Utilities  
   
 =head3 IntGen  
   
 C<< my $integer = IntGen($min, $max); >>  
   
 Returns a random number between the specified minimum and maximum (inclusive).  
   
 =over 4  
   
 =item min  
   
 Minimum permissible return value.  
   
 =item max  
   
 Maximum permissible return value.  
   
 =item RETURN  
   
 Returns a value no lower than the minimum and no greater than the maximum.  
   
 =back  
   
 =cut  
   
 sub IntGen {  
     # Get the parameters.  
     my ($min, $max) = @_;  
     # Determine the range of possible values. Note we put some space well above the  
     # maximum value to give it a fighting chance of apppearing in the list.  
     my $span = $max + 0.99 - $min;  
     # Create an integer in the range.  
     my $retVal = $min + int(rand($span));  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 RandChar  
   
 C<< my $char = RandChar($sourceString); >>  
   
 Select a random character from a string.  
   
 =over 4  
   
 =item sourceString  
   
 String from which the random character should be selected.  
   
 =item RETURN  
   
 Returns a single character from the incoming string.  
   
 =back  
   
 =cut  
   
 sub RandChar {  
     # Get the parameter.  
     my ($sourceString) = @_;  
     # Select a random character.  
     my $retVal = IntGen(0, (length $sourceString) - 1);  
     # Return it.  
     return substr($sourceString, $retVal, 1);  
 }  
   
 =head3 RandChars  
   
 C<< my $string = RandChars($sourceString, $length); >>  
   
 Create a string from characters taken from a source string.  
   
 =over 4  
   
 =item sourceString  
   
 String from which the random characters should be selected.  
   
 =item length  
   
 Number of characters to put in the output string.  
   
 =item RETURN  
   
 Returns a string of the specified length consisting of characters taken from the  
 source string.  
   
 =back  
   
 =cut  
   
 sub RandChars {  
     # Get the parameters.  
     my ($sourceString, $length) = @_;  
     # Call RandChar repeatedly to generate the string.  
     my $retVal = "";  
     for (my $i = 0; $i < $length; $i++) {  
         $retVal .= RandChar($sourceString);  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 RandParam  
   
 C<< my $value = RandParam($parm1, $parm2, ... $parmN); >>  
   
 Return a randomly-selected value from the parameter list.  
   
 =over 4  
   
 =item parm1, parm2, ... parmN  
   
 List of values of which one will be selected.  
   
 =item RETURN  
   
 Returns a randomly-chosen value from the specified list.  
   
 =back  
   
 =cut  
   
 sub RandParam {  
     # Get the parameter.  
     my @parms = @_;  
     # Choose a random parameter from the list.  
     my $chosenIndex = IntGen(0, $#parms);  
     return $parms[$chosenIndex];  
 }  
   
 =head3 StringGen  
   
 C<< my $string = StringGen($pattern1, $pattern2, ... $patternN); >>  
   
 Returns a random string derived from a randomly-chosen format pattern. The pattern  
 can either be a number (indicating the number of characters desired, or the letter  
 C<P> followed by a picture. The picture should contain C<A> when a letter is desired,  
 C<9> when a digit is desired, C<V> when a vowel is desired, C<K> when a consonant is  
 desired, and C<X> when a letter or a digit is desired. Any other character will be  
 translated as a literal.  
   
 =over 4  
   
 =item pattern1, pattern2, ... patternN  
   
 List of patterns to be used to generate string values.  
   
 =item RETURN  
   
 A single string generated from a pattern.  
   
 =back  
   
 =cut  
   
 sub StringGen {  
     # Get the parameters.  
     my @patterns = @_;  
     # Choose the appropriate pattern.  
     my $chosenPattern = RandParam(@patterns);  
     # Declare the return variable.  
     my $retVal = "";  
     # Determine whether this is a count or a picture pattern.  
     if ($chosenPattern =~ m/^\d+/) {  
         # Here we have a count. Get the string of source characters.  
         my $letterString = $PictureTable{'X'};  
         my $stringLen = length $letterString;  
         # Save the number of characters we have to generate.  
         my $charsLeft = $chosenPattern;  
         # Loop until the return variable is full.  
         while ($charsLeft > 0) {  
             # Generate a random position in the soruce string.  
             my $stringIndex = IntGen(0, $stringLen - 1);  
             # Compute the number of characters to pull out of the source string.  
             my $chunkSize = $stringLen - $stringIndex;  
             if ($chunkSize > $charsLeft) { $chunkSize = $charsLeft; }  
             # Stuff this chunk into the return value.  
             $retVal .= substr($letterString, $stringIndex, $chunkSize);  
             # Record the data moved.  
             $charsLeft -= $chunkSize;  
         }  
     } elsif ($chosenPattern =~ m/^P/) {  
         # Here we have a picture string. We will move through the picture one  
         # character at a time generating data.  
         for (my $i = 1; $i < length $chosenPattern; $i++) {  
             # Get this picture character.  
             my $chr = substr($chosenPattern, $i, 1);  
             # Check to see if the picture char is one we recognize.  
             if (exists $PictureTable{$chr}) {  
                 # Choose a random character from the available values for this  
                 # picture character.  
                 $retVal .= RandChar($PictureTable{$chr});  
             } else {  
                 # Copy in the picture character as a literal.  
                 $retVal .= $chr;  
             }  
         }  
     } else {  
         # Here we have neither a picture string or a letter count, so we treat  
         # the string as a literal.  
         $retVal = $chosenPattern;  
     }  
     # Return the string formed.  
     return $retVal;  
 }  
   
 =head3 DateGen  
   
 C<< my $date = DateGen($startDayOffset, $endDayOffset, $minutes); >>  
   
 Return a numeric timestamp within the specified range of days with the specified minute  
 value. The range of days is specified relevant to the current day. Thus, the call  
   
 C<< my $date = DateGen(-1, 5, 720); >>  
   
 will return a timestamp at noon (72 minutes past midnight) sometime during the week that  
 began on the preceding day. If you want a random minute of the day, simply combine with  
 a call to L</IntGen>, as follows.  
   
 C<< my $date = DateGen(-1, 5, IntGen(0, 1439)); >>  
   
 =over 4  
   
 =item startDayOffset  
   
 The earliest day that can be returned, relative to the current day.  
   
 =item endDayOffset  
   
 The latest day that can be returned, related to the current day.  
   
 =item minutes  
   
 Number of minutes into the selected day that should be used.  
   
 =back  
   
 =cut  
   
 sub DateGen {  
     # Get the parameters.  
     my ($startDayOffset, $endDayOffset, $minutes) = @_;  
     # Get midnight of the current day.  
     my $now = time();  
     my ($sec, $min, $hour) = localtime($now);  
     my $today = $now - (($hour * 60 + $min) * 60 + $sec);  
     # Compute the day we want.  
     my $newDay = IntGen($startDayOffset, $endDayOffset) * 86400 + $today;  
     # Add the minutes.  
     my $retVal = $newDay + $minutes * 60;  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 FloatGen  
   
 C<< my $number = FloatGen($min, $max); >>  
   
 Return a random floating-point number greater than or equal to the specified minimum and  
 less than the specified maximum.  
   
 =over 4  
   
 =item min  
   
 Minimum permissible value for the number returned.  
   
 =item max  
   
 Maximum permissible value for the number returned.  
   
 =item RETURN  
   
 Returns a floating-point number anywhere in the specified range.  
   
 =back  
   
 =cut  
   
 sub FloatGen {  
     # Get the parameters.  
     my ($min, $max) = @_;  
     # Generate the result.  
     my $retVal = rand($max - $min) + $min;  
     return $retVal;  
 }  
   
 =head3 ListGen  
   
 C<< my @list = ListGen($pattern, $count); >>  
   
 Return a list containing a fixed number of randomly-generated strings.  
   
 =over 4  
   
 =item pattern  
   
 A pattern (in the form expected by L</StringGen>) that should be used to generate the  
 strings in the list.  
   
 =item count  
   
 The number of list entries to generate.  
   
 =item RETURN  
   
 Returns a list consisting of the specified number of strings.  
   
 =back  
   
 =cut  
   
 sub ListGen {  
     # Get the parameters.  
     my ($pattern, $count) = @_;  
     # Generate the list.  
     my @retVal = ();  
     for (my $i = 0; $i < $count; $i++) {  
         push @retVal, StringGen($pattern);  
     }  
     # Return it.  
     return @retVal;  
 }  
   
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