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revision 1.20, Sun Sep 11 17:02:33 2005 UTC revision 1.77, Mon Nov 20 05:53:02 2006 UTC
# Line 9  Line 9 
9      use DBObject;      use DBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13      use FIG;      use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 58  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 90  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 109  Line 115 
115  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
116  0 and 1.  0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122  =item key-string  =item key-string
123    
124  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 135 
135    
136  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142  =back  =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151  =head3 Global Tags  =head3 Global Tags
152    
153  The entire database definition must be inside a B<Database> tag. The display name of  The entire database definition must be inside a B<Database> tag. The display name of
# Line 170  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 189  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 300  Line 335 
335    
336  # 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.
337  # "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
338  # 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
339  # 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,
340  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
341  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
342                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
343                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
344                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
345                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
346                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
347                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   2, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
348                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
349                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
350                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
351                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
352                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
353                                   indexMod =>   0, notes => "signed, 64-bit integer"},
354                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
355                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
356                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
357                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
358                     'hash-string' =>
359                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
360                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
361                     'id-string' =>
362                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
363                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
364                   'key-string' =>                   'key-string' =>
365                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
367                   'name-string' =>                   'name-string' =>
368                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
370                   'medium-string' =>                   'medium-string' =>
371                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
373                  );                  );
374    
375  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 324  Line 378 
378                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
379                   );                   );
380    
381  # Table for interpreting string patterns.  # Options for XML input and output.
382    
383    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
384                                      Entities => 'Entity',
385                                      Fields => 'Field',
386                                      Indexes => 'Index',
387                                      IndexFields => 'IndexField'
388                                    },
389                      KeyAttr =>    { Relationship => 'name',
390                                      Entity => 'name',
391                                      Field => 'name'
392                                    },
393                      SuppressEmpty => 1,
394                     );
395    
396  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
397                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField'],
398                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
399                       'V' => "aeiou",                    NormalizeSpace => 2,
400                       'K' => "bcdfghjklmnoprstvwxyz"                   );
401    my %XmlOutOpts = (
402                      RootName => 'Database',
403                      XMLDecl => 1,
404                     );                     );
405    
406    
407  =head2 Public Methods  =head2 Public Methods
408    
409  =head3 new  =head3 new
# Line 402  Line 473 
473      # Write the HTML heading stuff.      # Write the HTML heading stuff.
474      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
475      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
476        # Write the documentation.
477        print HTMLOUT $self->DisplayMetaData();
478        # Close the document.
479        print HTMLOUT "</body>\n</html>\n";
480        # Close the file.
481        close HTMLOUT;
482    }
483    
484    =head3 DisplayMetaData
485    
486    C<< my $html = $erdb->DisplayMetaData(); >>
487    
488    Return an HTML description of the database. This description can be used to help users create
489    the data to be loaded into the relations and form queries. The output is raw includable HTML
490    without any HEAD or BODY tags.
491    
492    =over 4
493    
494    =item filename
495    
496    The name of the output file.
497    
498    =back
499    
500    =cut
501    
502    sub DisplayMetaData {
503        # Get the parameters.
504        my ($self) = @_;
505        # Get the metadata and the title string.
506        my $metadata = $self->{_metaData};
507        # Get the title string.
508        my $title = $metadata->{Title};
509        # Get the entity and relationship lists.
510        my $entityList = $metadata->{Entities};
511        my $relationshipList = $metadata->{Relationships};
512        # Declare the return variable.
513        my $retVal = "";
514        # Open the output file.
515        Trace("Building MetaData table of contents.") if T(4);
516      # Here we do the table of contents. It starts as an unordered list of section names. Each      # Here we do the table of contents. It starts as an unordered list of section names. Each
517      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
518      print HTMLOUT "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";      $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
519      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
520      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
521          # Display this item.          # Display this item.
522          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
523      }      }
524      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
525      print HTMLOUT "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";      $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
526      # Loop through the Relationships.      # Loop through the Relationships.
527      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
528          # Display this item.          # Display this item.
529          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
530          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
531      }      }
532      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
533      print HTMLOUT "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";      $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
534      # Close off the table of contents itself.      # Close off the table of contents itself.
535      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
536      # Now we start with the actual data. Denote we're starting the entity section.      # Now we start with the actual data. Denote we're starting the entity section.
537      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
538      # Loop through the entities.      # Loop through the entities.
539      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
540          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
541          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
542          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
543          # Get the entity data.          # Get the entity data.
544          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
545          # If there's descriptive text, display it.          # If there's descriptive text, display it.
546          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
547              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
548          }          }
549          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
550          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
551          # Loop through the relationships.          # Loop through the relationships.
552          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
553              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 557 
557                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
558                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
559                  # Display the relationship data.                  # Display the relationship data.
560                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
561              }              }
562          }          }
563          # Close off the relationship list.          # Close off the relationship list.
564          print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
565          # Get the entity's relations.          # Get the entity's relations.
566          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
567          # Create a header for the relation subsection.          # Create a header for the relation subsection.
568          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
569          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
570          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
571              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
572              print HTMLOUT $htmlString;              $retVal .= $htmlString;
573          }          }
574      }      }
575      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
576      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
577      # Loop through the relationships.      # Loop through the relationships.
578      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
579          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 581 
581          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
582          # Create the relationship header.          # Create the relationship header.
583          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
584          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
585          # Get the entity names.          # Get the entity names.
586          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
587          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 591 
591          # since both sentences will say the same thing.          # since both sentences will say the same thing.
592          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
593          if ($arity eq "11") {          if ($arity eq "11") {
594              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
595          } else {          } else {
596              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
597              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
598                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
599              }              }
600          }          }
601          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
602          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
603          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
604              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
605          }          }
606          # Generate the relationship's relation table.          # Generate the relationship's relation table.
607          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
608          print HTMLOUT $htmlString;          $retVal .= $htmlString;
609      }      }
610      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
611      # Denote we're starting the join table.      # Denote we're starting the join table.
612      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
613      # Create a table header.      # Create a table header.
614      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
615      # Loop through the joins.      # Loop through the joins.
616      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
617      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 508  Line 619 
619          # Separate out the source, the target, and the join clause.          # Separate out the source, the target, and the join clause.
620          $joinKey =~ m!^([^/]+)/(.+)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
621          my ($sourceRelation, $targetRelation) = ($1, $2);          my ($sourceRelation, $targetRelation) = ($1, $2);
622          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
623          my $source = $self->ComputeObjectSentence($sourceRelation);          my $source = $self->ComputeObjectSentence($sourceRelation);
624          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
625          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
626          # Display them in a table row.          # Display them in a table row.
627          print HTMLOUT "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";          $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
628      }      }
629      # Close the table.      # Close the table.
630      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
631      # Close the document.      Trace("Built MetaData HTML.") if T(3);
632      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
633      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
634  }  }
635    
636  =head3 DumpMetaData  =head3 DumpMetaData
# Line 539  Line 648 
648      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
649  }  }
650    
651    =head3 FindIndexForEntity
652    
653    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
654    
655    This method locates the entry in an entity's index list that begins with the
656    specified attribute name. If the entity has no index list, one will be
657    created. This method works on raw XML, not a live ERDB object.
658    
659    =over 4
660    
661    =item xml
662    
663    The raw XML structure defining the database.
664    
665    =item entityName
666    
667    The name of the relevant entity.
668    
669    =item attributeName
670    
671    The name of the attribute relevant to the search.
672    
673    =item RETURN
674    
675    The numerical index in the index list of the index entry for the specified entity and
676    attribute, or C<undef> if no such index exists.
677    
678    =back
679    
680    =cut
681    
682    sub FindIndexForEntity {
683        # Get the parameters.
684        my ($xml, $entityName, $attributeName) = @_;
685        # Declare the return variable.
686        my $retVal;
687        # Get the named entity.
688        my $entityData = $xml->{Entities}->{$entityName};
689        if (! $entityData) {
690            Confess("Entity $entityName not found in DBD structure.");
691        } else {
692            # Insure it has an index list.
693            if (! exists $entityData->{Indexes}) {
694                $entityData->{Indexes} = [];
695            } else {
696                # Search for the desired index.
697                my $indexList = $entityData->{Indexes};
698                my $n = scalar @{$indexList};
699                Trace("Searching $n indexes in index list for $entityName.") if T(2);
700                # We use an indexed FOR here because we're returning an
701                # index number instead of an object. We do THAT so we can
702                # delete the index from the list if needed.
703                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
704                    my $index = $indexList->[$i];
705                    my $fields = $index->{IndexFields};
706                    # Technically this IF should be safe (that is, we are guaranteed
707                    # the existence of a "$fields->[0]"), because when we load the XML
708                    # we have SuppressEmpty specified.
709                    if ($fields->[0]->{name} eq $attributeName) {
710                        $retVal = $i;
711                    }
712                }
713            }
714        }
715        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
716        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
717        # Return the result.
718        return $retVal;
719    }
720    
721  =head3 CreateTables  =head3 CreateTables
722    
723  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 553  Line 732 
732  sub CreateTables {  sub CreateTables {
733      # Get the parameters.      # Get the parameters.
734      my ($self) = @_;      my ($self) = @_;
735      my $metadata = $self->{_metaData};      # Get the relation names.
736      my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
737      # Loop through the entities.      # Loop through the relations.
738      my $entityHash = $metadata->{Entities};      for my $relationName (@relNames) {
     for my $entityName (keys %{$entityHash}) {  
         my $entityData = $entityHash->{$entityName};  
         # Tell the user what we're doing.  
         Trace("Creating relations for entity $entityName.") if T(1);  
         # Loop through the entity's relations.  
         for my $relationName (keys %{$entityData->{Relations}}) {  
739              # Create a table for this relation.              # Create a table for this relation.
740              $self->CreateTable($relationName);              $self->CreateTable($relationName);
741              Trace("Relation $relationName created.") if T(1);          Trace("Relation $relationName created.") if T(2);
         }  
     }  
     # Loop through the relationships.  
     my $relationshipTable = $metadata->{Relationships};  
     for my $relationshipName (keys %{$metadata->{Relationships}}) {  
         # Create a table for this relationship.  
         Trace("Creating relationship $relationshipName.") if T(1);  
         $self->CreateTable($relationshipName);  
742      }      }
743  }  }
744    
# Line 640  Line 805 
805      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
806      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
807      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
808      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
809        # index will not be built until the table has been loaded.
810      if ($indexFlag) {      if ($indexFlag) {
811          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
812      }      }
813  }  }
814    
815    =head3 VerifyFields
816    
817    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
818    
819    Run through the list of proposed field values, insuring that all the character fields are
820    below the maximum length. If any fields are too long, they will be truncated in place.
821    
822    =over 4
823    
824    =item relName
825    
826    Name of the relation for which the specified fields are destined.
827    
828    =item fieldList
829    
830    Reference to a list, in order, of the fields to be put into the relation.
831    
832    =item RETURN
833    
834    Returns the number of fields truncated.
835    
836    =back
837    
838    =cut
839    
840    sub VerifyFields {
841        # Get the parameters.
842        my ($self, $relName, $fieldList) = @_;
843        # Initialize the return value.
844        my $retVal = 0;
845        # Get the relation definition.
846        my $relData = $self->_FindRelation($relName);
847        # Get the list of field descriptors.
848        my $fieldTypes = $relData->{Fields};
849        my $fieldCount = scalar @{$fieldTypes};
850        # Loop through the two lists.
851        for (my $i = 0; $i < $fieldCount; $i++) {
852            # Get the type of the current field.
853            my $fieldType = $fieldTypes->[$i]->{type};
854            # If it's a character field, verify the length.
855            if ($fieldType =~ /string/) {
856                my $maxLen = $TypeTable{$fieldType}->{maxLen};
857                my $oldString = $fieldList->[$i];
858                if (length($oldString) > $maxLen) {
859                    # Here it's too big, so we truncate it.
860                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
861                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
862                    $retVal++;
863                }
864            }
865        }
866        # Return the truncation count.
867        return $retVal;
868    }
869    
870    =head3 DigestFields
871    
872    C<< $erdb->DigestFields($relName, $fieldList); >>
873    
874    Digest the strings in the field list that correspond to data type C<hash-string> in the
875    specified relation.
876    
877    =over 4
878    
879    =item relName
880    
881    Name of the relation to which the fields belong.
882    
883    =item fieldList
884    
885    List of field contents to be loaded into the relation.
886    
887    =back
888    
889    =cut
890    #: Return Type ;
891    sub DigestFields {
892        # Get the parameters.
893        my ($self, $relName, $fieldList) = @_;
894        # Get the relation definition.
895        my $relData = $self->_FindRelation($relName);
896        # Get the list of field descriptors.
897        my $fieldTypes = $relData->{Fields};
898        my $fieldCount = scalar @{$fieldTypes};
899        # Loop through the two lists.
900        for (my $i = 0; $i < $fieldCount; $i++) {
901            # Get the type of the current field.
902            my $fieldType = $fieldTypes->[$i]->{type};
903            # If it's a hash string, digest it in place.
904            if ($fieldType eq 'hash-string') {
905                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
906            }
907        }
908    }
909    
910    =head3 DigestKey
911    
912    C<< my $digested = $erdb->DigestKey($keyValue); >>
913    
914    Return the digested value of a symbolic key. The digested value can then be plugged into a
915    key-based search into a table with key-type hash-string.
916    
917    Currently the digesting process is independent of the database structure, but that may not
918    always be the case, so this is an instance method instead of a static method.
919    
920    =over 4
921    
922    =item keyValue
923    
924    Key value to digest.
925    
926    =item RETURN
927    
928    Digested value of the key.
929    
930    =back
931    
932    =cut
933    
934    sub DigestKey {
935        # Get the parameters.
936        my ($self, $keyValue) = @_;
937        # Compute the digest.
938        my $retVal = md5_base64($keyValue);
939        # Return the result.
940        return $retVal;
941    }
942    
943  =head3 CreateIndex  =head3 CreateIndex
944    
945  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 669  Line 963 
963      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
964          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
965          # Get the index's field list.          # Get the index's field list.
966          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
967            # Get a hash of the relation's field types.
968            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
969            # We need to check for text fields. We need a append a length limitation for them. To do
970            # that, we need the relation's field list.
971            my $relFields = $relationData->{Fields};
972            for (my $i = 0; $i <= $#rawFields; $i++) {
973                # Get the field type.
974                my $field = $rawFields[$i];
975                my $type = $types{$field};
976                # Ask if it requires using prefix notation for the index.
977                my $mod = $TypeTable{$type}->{indexMod};
978                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
979                if ($mod) {
980                    # Append the prefix length to the field name,
981                    $rawFields[$i] .= "($mod)";
982                }
983            }
984            my @fieldList = _FixNames(@rawFields);
985          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
986          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
987          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
988          # Create the index.          # Create the index.
989          $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
990                                        flds => $flds, kind => $unique);
991            if ($rv) {
992          Trace("Index created: $indexName for $relationName ($flds)") if T(1);          Trace("Index created: $indexName for $relationName ($flds)") if T(1);
993            } else {
994                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
995            }
996        }
997    }
998    
999    =head3 GetSecondaryFields
1000    
1001    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1002    
1003    This method will return a list of the name and type of each of the secondary
1004    fields for a specified entity. Secondary fields are stored in two-column tables
1005    in addition to the primary entity table. This enables the field to have no value
1006    or to have multiple values.
1007    
1008    =over 4
1009    
1010    =item entityName
1011    
1012    Name of the entity whose secondary fields are desired.
1013    
1014    =item RETURN
1015    
1016    Returns a hash mapping the field names to their field types.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub GetSecondaryFields {
1023        # Get the parameters.
1024        my ($self, $entityName) = @_;
1025        # Declare the return variable.
1026        my %retVal = ();
1027        # Look for the entity.
1028        my $table = $self->GetFieldTable($entityName);
1029        # Loop through the fields, pulling out the secondaries.
1030        for my $field (sort keys %{$table}) {
1031            if ($table->{$field}->{relation} ne $entityName) {
1032                # Here we have a secondary field.
1033                $retVal{$field} = $table->{$field}->{type};
1034            }
1035        }
1036        # Return the result.
1037        return %retVal;
1038    }
1039    
1040    =head3 GetFieldRelationName
1041    
1042    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1043    
1044    Return the name of the relation containing a specified field.
1045    
1046    =over 4
1047    
1048    =item objectName
1049    
1050    Name of the entity or relationship containing the field.
1051    
1052    =item fieldName
1053    
1054    Name of the relevant field in that entity or relationship.
1055    
1056    =item RETURN
1057    
1058    Returns the name of the database relation containing the field, or C<undef> if
1059    the field does not exist.
1060    
1061    =back
1062    
1063    =cut
1064    
1065    sub GetFieldRelationName {
1066        # Get the parameters.
1067        my ($self, $objectName, $fieldName) = @_;
1068        # Declare the return variable.
1069        my $retVal;
1070        # Get the object field table.
1071        my $table = $self->GetFieldTable($objectName);
1072        # Only proceed if the field exists.
1073        if (exists $table->{$fieldName}) {
1074            # Determine the name of the relation that contains this field.
1075            $retVal = $table->{$fieldName}->{relation};
1076        }
1077        # Return the result.
1078        return $retVal;
1079    }
1080    
1081    =head3 DeleteValue
1082    
1083    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1084    
1085    Delete secondary field values from the database. This method can be used to delete all
1086    values of a specified field for a particular entity instance, or only a single value.
1087    
1088    Secondary fields are stored in two-column relations separate from an entity's primary
1089    table, and as a result a secondary field can legitimately have no value or multiple
1090    values. Therefore, it makes sense to talk about deleting secondary fields where it
1091    would not make sense for primary fields.
1092    
1093    =over 4
1094    
1095    =item entityName
1096    
1097    Name of the entity from which the fields are to be deleted.
1098    
1099    =item id
1100    
1101    ID of the entity instance to be processed. If the instance is not found, this
1102    method will have no effect. If C<undef> is specified, all values for all of
1103    the entity instances will be deleted.
1104    
1105    =item fieldName
1106    
1107    Name of the field whose values are to be deleted.
1108    
1109    =item fieldValue (optional)
1110    
1111    Value to be deleted. If not specified, then all values of the specified field
1112    will be deleted for the entity instance. If specified, then only the values which
1113    match this parameter will be deleted.
1114    
1115    =item RETURN
1116    
1117    Returns the number of rows deleted.
1118    
1119    =back
1120    
1121    =cut
1122    
1123    sub DeleteValue {
1124        # Get the parameters.
1125        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1126        # Declare the return value.
1127        my $retVal = 0;
1128        # We need to set up an SQL command to do the deletion. First, we
1129        # find the name of the field's relation.
1130        my $table = $self->GetFieldTable($entityName);
1131        my $field = $table->{$fieldName};
1132        my $relation = $field->{relation};
1133        # Make sure this is a secondary field.
1134        if ($relation eq $entityName) {
1135            Confess("Cannot delete values of $fieldName for $entityName.");
1136        } else {
1137            # Set up the SQL command to delete all values.
1138            my $sql = "DELETE FROM $relation";
1139            # Build the filter.
1140            my @filters = ();
1141            my @parms = ();
1142            # Check for a filter by ID.
1143            if (defined $id) {
1144                push @filters, "id = ?";
1145                push @parms, $id;
1146            }
1147            # Check for a filter by value.
1148            if (defined $fieldValue) {
1149                push @filters, "$fieldName = ?";
1150                push @parms, $fieldValue;
1151            }
1152            # Append the filters to the command.
1153            if (@filters) {
1154                $sql .= " WHERE " . join(" AND ", @filters);
1155            }
1156            # Execute the command.
1157            my $dbh = $self->{_dbh};
1158            $retVal = $dbh->SQL($sql, 0, @parms);
1159      }      }
1160        # Return the result.
1161        return $retVal;
1162  }  }
1163    
1164  =head3 LoadTables  =head3 LoadTables
# Line 724  Line 1206 
1206      $directoryName =~ s!/\\$!!;      $directoryName =~ s!/\\$!!;
1207      # Declare the return variable.      # Declare the return variable.
1208      my $retVal = Stats->new();      my $retVal = Stats->new();
1209      # Get the metadata structure.      # Get the relation names.
1210      my $metaData = $self->{_metaData};      my @relNames = $self->GetTableNames();
1211      # Loop through the entities.      for my $relationName (@relNames) {
     for my $entity (values %{$metaData->{Entities}}) {  
         # Loop through the entity's relations.  
         for my $relationName (keys %{$entity->{Relations}}) {  
1212              # Try to load this relation.              # Try to load this relation.
1213              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1214              # Accumulate the statistics.              # Accumulate the statistics.
1215              $retVal->Accumulate($result);              $retVal->Accumulate($result);
1216          }          }
     }  
     # Loop through the relationships.  
     for my $relationshipName (keys %{$metaData->{Relationships}}) {  
         # Try to load this relationship's relation.  
         my $result = $self->_LoadRelation($directoryName, $relationshipName, $rebuild);  
         # Accumulate the statistics.  
         $retVal->Accumulate($result);  
     }  
1217      # Add the duration of the load to the statistical object.      # Add the duration of the load to the statistical object.
1218      $retVal->Add('duration', gettimeofday - $startTime);      $retVal->Add('duration', gettimeofday - $startTime);
1219      # Return the accumulated statistics.      # Return the accumulated statistics.
1220      return $retVal;      return $retVal;
1221  }  }
1222    
1223    
1224  =head3 GetTableNames  =head3 GetTableNames
1225    
1226  C<< my @names = $erdb->GetTableNames; >>  C<< my @names = $erdb->GetTableNames; >>
# Line 783  Line 1255 
1255      return sort keys %{$entityList};      return sort keys %{$entityList};
1256  }  }
1257    
1258    =head3 GetDataTypes
1259    
1260    C<< my %types = ERDB::GetDataTypes(); >>
1261    
1262    Return a table of ERDB data types. The table returned is a hash of hashes.
1263    The keys of the big hash are the datatypes. Each smaller hash has several
1264    values used to manage the data. The most interesting is the SQL type (key
1265    C<sqlType>) and the descriptive node (key C<notes>).
1266    
1267    Note that changing the values in the smaller hashes will seriously break
1268    things, so this data should be treated as read-only.
1269    
1270    =cut
1271    
1272    sub GetDataTypes {
1273        return %TypeTable;
1274    }
1275    
1276    
1277  =head3 IsEntity  =head3 IsEntity
1278    
1279  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
# Line 812  Line 1303 
1303    
1304  =head3 Get  =head3 Get
1305    
1306  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1307    
1308  This method returns a query object for entities of a specified type using a specified filter.  This method returns a query object for entities of a specified type using a specified filter.
1309  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 820  Line 1311 
1311  following call requests all B<Genome> objects for the genus specified in the variable  following call requests all B<Genome> objects for the genus specified in the variable
1312  $genus.  $genus.
1313    
1314  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1315    
1316  The WHERE clause contains a single question mark, so there is a single additional  The WHERE clause contains a single question mark, so there is a single additional
1317  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
# Line 837  Line 1328 
1328  It is possible to specify multiple entity and relationship names in order to retrieve more than  It is possible to specify multiple entity and relationship names in order to retrieve more than
1329  one object's data at the same time, which allows highly complex joined queries. For example,  one object's data at the same time, which allows highly complex joined queries. For example,
1330    
1331  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1332    
1333  If multiple names are specified, then the query processor will automatically determine a  If multiple names are specified, then the query processor will automatically determine a
1334  join path between the entities and relationships. The algorithm used is very simplistic.  join path between the entities and relationships. The algorithm used is very simplistic.
1335  In particular, you can't specify any entity or relationship more than once, and if a  In particular, if a relationship is recursive, the path is determined by the order in which
1336  relationship is recursive, the path is determined by the order in which the entity  the entity and the relationship appear. For example, consider a recursive relationship
1337  and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
 which relates B<People> objects to other B<People> objects. If the join path is  
1338  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1339  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1340    
1341    If an entity or relationship is mentioned twice, the name for the second occurrence will
1342    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1343    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1344    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1345    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1346    
1347  =over 4  =over 4
1348    
1349  =item objectNames  =item objectNames
# Line 870  Line 1366 
1366    
1367  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1368    
1369    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1370    be processed. The idea is to make it less likely to find the verb by accident.
1371    
1372  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
1373  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1374  relation.  relation.
1375    
1376  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1377    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1378    a positive number. So, for example
1379    
1380    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1381    
1382    will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1383    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1384    use
1385    
1386  Parameter values to be substituted into the filter clause.  C<< "LIMIT 10" >>
1387    
1388    =item params
1389    
1390    Reference to a list of parameter values to be substituted into the filter clause.
1391    
1392  =item RETURN  =item RETURN
1393    
# Line 888  Line 1399 
1399    
1400  sub Get {  sub Get {
1401      # Get the parameters.      # Get the parameters.
1402      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1403      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1404      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1405      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1406      #      # Create the query.
1407      my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1408      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1409                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1410      # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1411      if ($filterClause) {      # and mapped name for each object in the query.
1412          # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1413          # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1414          my $filterString = $filterClause;          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
         # 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 = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command.  
         my %fromNames = ();  
         for my $objectName (@sortedNames) {  
             $fromNames{$objectName} = 1;  
         }  
         # We are ready to begin. We loop through the object names, replacing each  
         # object name's field references by the corresponding SQL field reference.  
         # Along the way, if we find a secondary relation, we will need to add it  
         # to the FROM clause.  
         for my $objectName (@sortedNames) {  
             # Get the length of the object name plus 2. This is the value we add to the  
             # size of the field name to determine the size of the field reference as a  
             # whole.  
             my $nameLength = 2 + length $objectName;  
             # Get the object's field list.  
             my $fieldList = $self->_GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                 # At this point, $1 contains the field name, and the current position  
                 # is set immediately after the final parenthesis. We pull out the name of  
                 # the field and the position and length of the field reference as a whole.  
                 my $fieldName = $1;  
                 my $len = $nameLength + length $fieldName;  
                 my $pos = pos($filterString) - $len;  
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
                 } else {  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$relationName}) {  
                         # Add the relation to the FROM clause.  
                         $command .= ", $relationName";  
                         # Create its join sub-clause.  
                         push @joinWhere, "$objectName.id = $relationName.id";  
                         # Denote we have it available for future fields.  
                         $fromNames{$relationName} = 1;  
                     }  
                     # Form an SQL field reference from the relation name and the field name.  
                     my $sqlReference = "$relationName." . _FixName($fieldName);  
                     # Put it into the filter string in place of the old value.  
                     substr($filterString, $pos, $len) = $sqlReference;  
                     # Reposition the search.  
                     pos $filterString = $pos + length $sqlReference;  
                 }  
             }  
         }  
         # The next step is to join the objects together. We only need to do this if there  
         # is more than one object in the object list. We start with the first object and  
         # run through the objects after it. Note also that we make a safety copy of the  
         # list before running through it.  
         my @objectList = @{$objectNames};  
         my $lastObject = shift @objectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisObject (@objectList) {  
             # Look for a join.  
             my $joinKey = "$lastObject/$thisObject";  
             if (!exists $joinTable->{$joinKey}) {  
                 # Here there's no join, so we throw an error.  
                 Confess("No join exists to connect from $lastObject to $thisObject.");  
             } else {  
                 # Get the join clause and add it to the WHERE list.  
                 push @joinWhere, $joinTable->{$joinKey};  
                 # Save this object as the last object for the next iteration.  
                 $lastObject = $thisObject;  
             }  
         }  
         # Now we need to handle the whole ORDER BY thing. We'll put the order by clause  
         # in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY verb (if any).  
         if ($filterString =~ m/^(.*)ORDER BY/g) {  
             # Here we have an ORDER BY verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " ORDER BY $orderClause";  
         }  
1415      }      }
     Trace("SQL query: $command") if T(3);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1416      # Return the statement object.      # Return the statement object.
1417      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1418      return $retVal;      return $retVal;
1419  }  }
1420    
1421  =head3 GetList  =head3 Search
   
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1422    
1423  Return a list of object descriptors for the specified objects as determined by the  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
 specified filter clause.  
1424    
1425  This method is essentially the same as L</Get> except it returns a list of objects rather  Perform a full text search with filtering. The search will be against a specified object
1426  than a query object that can be used to get the results one record at a time.  in the object name list. That object will get an extra field containing the search
1427    relevance. Note that except for the search expression, the parameters of this method are
1428    the same as those for L</Get> and follow the same rules.
1429    
1430  =over 4  =over 4
1431    
1432    =item searchExpression
1433    
1434    Boolean search expression for the text fields of the target object. The default mode for
1435    a Boolean search expression is OR, but we want the default to be AND, so we will
1436    add a C<+> operator to each word with no other operator before it.
1437    
1438    =item idx
1439    
1440    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1441    
1442  =item objectNames  =item objectNames
1443    
1444  List containing the names of the entity and relationship objects to be retrieved.  List containing the names of the entity and relationship objects to be retrieved.
# Line 1036  Line 1453 
1453  or secondary entity relations; however, all of the entities and relationships involved must  or secondary entity relations; however, all of the entities and relationships involved must
1454  be included in the list of object names.  be included in the list of object names.
1455    
1456  The filter clause can also specify a sort order. To do this, simply follow the filter string  =item params
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
1457    
1458  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  Reference to a list of parameter values to be substituted into the filter clause.
1459    
1460  The rules for field references in a sort order are the same as those for field references in the  =item RETURN
1461  filter clause in general; however, odd things may happen if a sort field is from a secondary  
1462  relation.  Returns a query object for the specified search.
1463    
1464    =back
1465    
1466    =cut
1467    
1468    sub Search {
1469        # Get the parameters.
1470        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1471        # Declare the return variable.
1472        my $retVal;
1473        # Create a safety copy of the parameter list. Note we have to be careful to insure
1474        # a parameter list exists before we copy it.
1475        my @myParams = ();
1476        if (defined $params) {
1477            @myParams = @{$params};
1478        }
1479        # Get the first object's structure so we have access to the searchable fields.
1480        my $object1Name = $objectNames->[$idx];
1481        my $object1Structure = $self->_GetStructure($object1Name);
1482        # Get the field list.
1483        if (! exists $object1Structure->{searchFields}) {
1484            Confess("No searchable index for $object1Name.");
1485        } else {
1486            # Get the field list.
1487            my @fields = @{$object1Structure->{searchFields}};
1488            # Clean the search expression.
1489            my $actualKeywords = $self->CleanKeywords($searchExpression);
1490            # Prefix a "+" to each uncontrolled word. This converts the default
1491            # search mode from OR to AND.
1492            $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;
1493            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1494            # We need two match expressions, one for the filter clause and one in the
1495            # query itself. Both will use a parameter mark, so we need to push the
1496            # search expression onto the front of the parameter list twice.
1497            unshift @myParams, $actualKeywords, $actualKeywords;
1498            # Build the match expression.
1499            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1500            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1501            # Process the SQL stuff.
1502            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1503                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1504            # Create the query. Note that the match clause is inserted at the front of
1505            # the select fields.
1506            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1507                ".* $suffix";
1508            my $sth = $self->_GetStatementHandle($command, \@myParams);
1509            # Now we create the relation map, which enables DBQuery to determine the order, name
1510            # and mapped name for each object in the query.
1511            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1512            # Return the statement object.
1513            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1514        }
1515        return $retVal;
1516    }
1517    
1518    =head3 GetFlat
1519    
1520    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1521    
1522    This is a variation of L</GetAll> that asks for only a single field per record and
1523    returns a single flattened list.
1524    
1525    =over 4
1526    
1527    =item objectNames
1528    
1529    List containing the names of the entity and relationship objects to be retrieved.
1530    
1531    =item filterClause
1532    
1533    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1534    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1535    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1536    parameter list as additional parameters. The fields in a filter clause can come from primary
1537    entity relations, relationship relations, or secondary entity relations; however, all of the
1538    entities and relationships involved must be included in the list of object names.
1539    
1540    =item parameterList
1541    
1542  =item param1, param2, ..., paramN  List of the parameters to be substituted in for the parameters marks in the filter clause.
1543    
1544    =item field
1545    
1546  Parameter values to be substituted into the filter clause.  Name of the field to be used to get the elements of the list returned.
1547    
1548  =item RETURN  =item RETURN
1549    
1550  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of values.
1551    
1552  =back  =back
1553    
1554  =cut  =cut
1555  #: Return Type @%  #: Return Type @;
1556  sub GetList {  sub GetFlat {
1557      # Get the parameters.      # Get the parameters.
1558      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1559      # Declare the return variable.      # Construct the query.
1560        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1561        # Create the result list.
1562      my @retVal = ();      my @retVal = ();
1563      # Perform the query.      # Loop through the records, adding the field values found to the result list.
1564      my $query = $self->Get($objectNames, $filterClause, @params);      while (my $row = $query->Fetch()) {
1565      # Loop through the results.          push @retVal, $row->Value($field);
     while (my $object = $query->Fetch) {  
         push @retVal, $object;  
1566      }      }
1567      # Return the result.      # Return the list created.
1568      return @retVal;      return @retVal;
1569  }  }
1570    
1571  =head3 ComputeObjectSentence  =head3 SpecialFields
1572    
1573  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my %specials = $erdb->SpecialFields($entityName); >>
1574    
1575  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return a hash mapping special fields in the specified entity to the value of their
1576    C<special> attribute. This enables the subclass to get access to the special field
1577    attributes without needed to plumb the internal ERDB data structures.
1578    
1579  =over 4  =over 4
1580    
1581  =item objectName  =item entityName
1582    
1583  Name of the entity or relationship.  Name of the entity whose special fields are desired.
1584    
1585  =item RETURN  =item RETURN
1586    
1587  Returns a string containing the entity name or a relationship sentence.  Returns a hash. The keys of the hash are the special field names, and the values
1588    are the values from each special field's C<special> attribute.
1589    
1590  =back  =back
1591    
1592  =cut  =cut
1593    
1594  sub ComputeObjectSentence {  sub SpecialFields {
1595      # Get the parameters.      # Get the parameters.
1596      my ($self, $objectName) = @_;      my ($self, $entityName) = @_;
1597      # Set the default return value.      # Declare the return variable.
1598      my $retVal = $objectName;      my %retVal = ();
1599      # Look for the object as a relationship.      # Find the entity's data structure.
1600      my $relTable = $self->{_metaData}->{Relationships};      my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1601      if (exists $relTable->{$objectName}) {      # Loop through its fields, adding each special field to the return hash.
1602          # Get the relationship sentence.      my $fieldHash = $entityData->{Fields};
1603          $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});      for my $fieldName (keys %{$fieldHash}) {
1604            my $fieldData = $fieldHash->{$fieldName};
1605            if (exists $fieldData->{special}) {
1606                $retVal{$fieldName} = $fieldData->{special};
1607            }
1608      }      }
1609      # Return the result.      # Return the result.
1610      return $retVal;      return %retVal;
1611  }  }
1612    
1613  =head3 DumpRelations  =head3 Delete
1614    
1615  C<< $erdb->DumpRelations($outputDirectory); >>  C<< my $stats = $erdb->Delete($entityName, $objectID, $testFlag); >>
1616    
1617  Write the contents of all the relations to tab-delimited files in the specified directory.  Delete an entity instance from the database. The instance is deleted along with all entity and
1618  Each file will have the same name as the relation dumped, with an extension of DTX.  relationship instances dependent on it. The definition of I<dependence> is recursive.
1619    
1620    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1621    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1622    dependent relationship.
1623    
1624  =over 4  =over 4
1625    
1626  =item outputDirectory  =item entityName
1627    
1628  Name of the directory into which the relation files should be dumped.  Name of the entity type for the instance being deleted.
1629    
1630    =item objectID
1631    
1632    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1633    then it is presumed to by a LIKE pattern.
1634    
1635    =item testFlag
1636    
1637    If TRUE, the delete statements will be traced without being executed.
1638    
1639    =item RETURN
1640    
1641    Returns a statistics object indicating how many records of each particular table were
1642    deleted.
1643    
1644  =back  =back
1645    
1646  =cut  =cut
1647    #: Return Type $%;
1648  sub DumpRelations {  sub Delete {
1649      # Get the parameters.      # Get the parameters.
1650      my ($self, $outputDirectory) = @_;      my ($self, $entityName, $objectID, $testFlag) = @_;
1651      # Now we need to run through all the relations. First, we loop through the entities.      # Declare the return variable.
1652      my $metaData = $self->{_metaData};      my $retVal = Stats->new();
1653      my $entities = $metaData->{Entities};      # Get the DBKernel object.
1654      for my $entityName (keys %{$entities}) {      my $db = $self->{_dbh};
1655          my $entityStructure = $entities->{$entityName};      # We're going to generate all the paths branching out from the starting entity. One of
1656          # Get the entity's relations.      # the things we have to be careful about is preventing loops. We'll use a hash to
1657          my $relationList = $entityStructure->{Relations};      # determine if we've hit a loop.
1658          # Loop through the relations, dumping them.      my %alreadyFound = ();
1659          for my $relationName (keys %{$relationList}) {      # These next lists will serve as our result stack. We start by pushing object lists onto
1660              my $relation = $relationList->{$relationName};      # the stack, and then popping them off to do the deletes. This means the deletes will
1661              $self->_DumpRelation($outputDirectory, $relationName, $relation);      # start with the longer paths before getting to the shorter ones. That, in turn, makes
1662        # sure we don't delete records that might be needed to forge relationships back to the
1663        # original item. We have two lists-- one for TO-relationships, and one for
1664        # FROM-relationships and entities.
1665        my @fromPathList = ();
1666        my @toPathList = ();
1667        # This final hash is used to remember what work still needs to be done. We push paths
1668        # onto the list, then pop them off to extend the paths. We prime it with the starting
1669        # point. Note that we will work hard to insure that the last item on a path in the
1670        # to-do list is always an entity.
1671        my @todoList = ([$entityName]);
1672        while (@todoList) {
1673            # Get the current path.
1674            my $current = pop @todoList;
1675            # Copy it into a list.
1676            my @stackedPath = @{$current};
1677            # Pull off the last item on the path. It will always be an entity.
1678            my $entityName = pop @stackedPath;
1679            # Add it to the alreadyFound list.
1680            $alreadyFound{$entityName} = 1;
1681            # Get the entity data.
1682            my $entityData = $self->_GetStructure($entityName);
1683            # The first task is to loop through the entity's relation. A DELETE command will
1684            # be needed for each of them.
1685            my $relations = $entityData->{Relations};
1686            for my $relation (keys %{$relations}) {
1687                my @augmentedList = (@stackedPath, $relation);
1688                push @fromPathList, \@augmentedList;
1689          }          }
1690            # Now we need to look for relationships connected to this entity.
1691            my $relationshipList = $self->{_metaData}->{Relationships};
1692            for my $relationshipName (keys %{$relationshipList}) {
1693                my $relationship = $relationshipList->{$relationshipName};
1694                # Check the FROM field. We're only interested if it's us.
1695                if ($relationship->{from} eq $entityName) {
1696                    # Add the path to this relationship.
1697                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1698                    push @fromPathList, \@augmentedList;
1699                    # Check the arity. If it's MM we're done. If it's 1M
1700                    # and the target hasn't been seen yet, we want to
1701                    # stack the entity for future processing.
1702                    if ($relationship->{arity} eq '1M') {
1703                        my $toEntity = $relationship->{to};
1704                        if (! exists $alreadyFound{$toEntity}) {
1705                            # Here we have a new entity that's dependent on
1706                            # the current entity, so we need to stack it.
1707                            my @stackList = (@augmentedList, $toEntity);
1708                            push @fromPathList, \@stackList;
1709                        } else {
1710                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1711      }      }
     # Next, we loop through the relationships.  
     my $relationships = $metaData->{Relationships};  
     for my $relationshipName (keys %{$relationships}) {  
         my $relationshipStructure = $relationships->{$relationshipName};  
         # Dump this relationship's relation.  
         $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
1712      }      }
1713  }  }
1714                # Now check the TO field. In this case only the relationship needs
1715                # deletion.
1716                if ($relationship->{to} eq $entityName) {
1717                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1718                    push @toPathList, \@augmentedList;
1719                }
1720            }
1721        }
1722        # Create the first qualifier for the WHERE clause. This selects the
1723        # keys of the primary entity records to be deleted. When we're deleting
1724        # from a dependent table, we construct a join page from the first qualifier
1725        # to the table containing the dependent records to delete.
1726        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1727        # We need to make two passes. The first is through the to-list, and
1728        # the second through the from-list. The from-list is second because
1729        # the to-list may need to pass through some of the entities the
1730        # from-list would delete.
1731        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1732        # Now it's time to do the deletes. We do it in two passes.
1733        for my $keyName ('to_link', 'from_link') {
1734            # Get the list for this key.
1735            my @pathList = @{$stackList{$keyName}};
1736            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1737            # Loop through this list.
1738            while (my $path = pop @pathList) {
1739                # Get the table whose rows are to be deleted.
1740                my @pathTables = @{$path};
1741                # Start the DELETE statement. We need to call DBKernel because the
1742                # syntax of a DELETE-USING varies among DBMSs.
1743                my $target = $pathTables[$#pathTables];
1744                my $stmt = $db->SetUsing(@pathTables);
1745                # Now start the WHERE. The first thing is the ID field from the starting table. That
1746                # starting table will either be the entity relation or one of the entity's
1747                # sub-relations.
1748                $stmt .= " WHERE $pathTables[0].id $qualifier";
1749                # Now we run through the remaining entities in the path, connecting them up.
1750                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1751                    # Connect the current relationship to the preceding entity.
1752                    my ($entity, $rel) = @pathTables[$i-1,$i];
1753                    # The style of connection depends on the direction of the relationship.
1754                    $stmt .= " AND $entity.id = $rel.$keyName";
1755                    if ($i + 1 <= $#pathTables) {
1756                        # Here there's a next entity, so connect that to the relationship's
1757                        # to-link.
1758                        my $entity2 = $pathTables[$i+1];
1759                        $stmt .= " AND $rel.to_link = $entity2.id";
1760                    }
1761                }
1762                # Now we have our desired DELETE statement.
1763                if ($testFlag) {
1764                    # Here the user wants to trace without executing.
1765                    Trace($stmt) if T(0);
1766                } else {
1767                    # Here we can delete. Note that the SQL method dies with a confession
1768                    # if an error occurs, so we just go ahead and do it.
1769                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1770                    my $rv = $db->SQL($stmt, 0, $objectID);
1771                    # Accumulate the statistics for this delete. The only rows deleted
1772                    # are from the target table, so we use its name to record the
1773                    # statistic.
1774                    $retVal->Add($target, $rv);
1775                }
1776            }
1777        }
1778        # Return the result.
1779        return $retVal;
1780    }
1781    
1782  =head3 InsertObject  =head3 SortNeeded
1783    
1784  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  C<< my $parms = $erdb->SortNeeded($relationName); >>
1785    
1786  Insert an object into the database. The object is defined by a type name and then a hash  Return the pipe command for the sort that should be applied to the specified
1787  of field names to values. Field values in the primary relation are represented by scalars.  relation when creating the load file.
 (Note that for relationships, the primary relation is the B<only> relation.)  
 Field values for the other relations comprising the entity are always list references. For  
 example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  
 C<ZP_00210270.1> and C<gi|46206278>.  
1788    
1789  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  For example, if the load file should be sorted ascending by the first
1790    field, this method would return
1791    
1792  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and      sort -k1 -t"\t"
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
1793    
1794  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  If the first field is numeric, the method would return
1795    
1796  =over 4      sort -k1n -t"\t"
1797    
1798  =item newObjectType  Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1799    keys using a sort.
1800    
1801  Type name of the object to insert.  =over 4
1802    
1803  =item fieldHash  =item relationName
1804    
1805  Hash of field names to values.  Name of the relation to be examined.
1806    
1807  =item RETURN  =item
1808    
1809  Returns 1 if successful, 0 if an error occurred.  Returns the sort command to use for sorting the relation, suitable for piping.
1810    
1811  =back  =back
1812    
1813  =cut  =cut
1814    #: Return Type $;
1815  sub InsertObject {  sub SortNeeded {
1816      # Get the parameters.      # Get the parameters.
1817      my ($self, $newObjectType, $fieldHash) = @_;      my ($self, $relationName) = @_;
1818      # Denote that so far we appear successful.      # Declare a descriptor to hold the names of the key fields.
1819      my $retVal = 1;      my @keyNames = ();
1820      # Get the database handle.      # Get the relation structure.
1821      my $dbh = $self->{_dbh};      my $relationData = $self->_FindRelation($relationName);
1822      # Get the relation list.      # Find out if the relation is a primary entity relation,
1823      my $relationTable = $self->_GetRelationTable($newObjectType);      # a relationship relation, or a secondary entity relation.
1824      # Loop through the relations. We'll build insert statements for each one. If a relation is      my $entityTable = $self->{_metaData}->{Entities};
1825      # secondary, we may end up generating multiple insert statements. If an error occurs, we      my $relationshipTable = $self->{_metaData}->{Relationships};
1826      # stop the loop.      if (exists $entityTable->{$relationName}) {
1827      my @relationList = keys %{$relationTable};          # Here we have a primary entity relation.
1828      for (my $i = 0; $retVal && $i <= $#relationList; $i++) {          push @keyNames, "id";
1829          my $relationName = $relationList[$i];      } elsif (exists $relationshipTable->{$relationName}) {
1830          my $relationDefinition = $relationTable->{$relationName};          # Here we have a relationship. We sort using the FROM index.
1831          # Get the relation's fields. For each field we will collect a value in the corresponding          my $relationshipData = $relationshipTable->{$relationName};
1832          # position of the @valueList array. If one of the fields is missing, we will add it to the          my $index = $relationData->{Indexes}->{idxFrom};
1833          # @missing list.          push @keyNames, @{$index->{IndexFields}};
1834          my @fieldList = @{$relationDefinition->{Fields}};      } else {
1835          my @fieldNameList = ();          # Here we have a secondary entity relation, so we have a sort on the ID field.
1836          my @valueList = ();          push @keyNames, "id";
         my @missing = ();  
         my $recordCount = 1;  
         for my $fieldDescriptor (@fieldList) {  
             # Get the field name and save it. Note we need to fix it up so the hyphens  
             # are converted to underscores.  
             my $fieldName = $fieldDescriptor->{name};  
             push @fieldNameList, _FixName($fieldName);  
             # Look for the named field in the incoming structure. Note that we are looking  
             # for the real field name, not the fixed-up one!  
             if (exists $fieldHash->{$fieldName}) {  
                 # Here we found the field. Stash it in the value list.  
                 my $value = $fieldHash->{$fieldName};  
                 push @valueList, $value;  
                 # If the value is a list, we may need to increment the record count.  
                 if (ref $value eq "ARRAY") {  
                     my $thisCount = @{$value};  
                     if ($recordCount == 1) {  
                         # Here we have our first list, so we save its count.  
                         $recordCount = $thisCount;  
                     } elsif ($recordCount != $thisCount) {  
                         # Here we have a second list, so its length has to match the  
                         # previous lists.  
                         Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);  
                         $retVal = 0;  
                     }  
1837                  }                  }
1838        # Now we parse the key names into sort parameters. First, we prime the return
1839        # string.
1840        my $retVal = "sort -t\"\t\" ";
1841        # Get the relation's field list.
1842        my @fields = @{$relationData->{Fields}};
1843        # Loop through the keys.
1844        for my $keyData (@keyNames) {
1845            # Get the key and the ordering.
1846            my ($keyName, $ordering);
1847            if ($keyData =~ /^([^ ]+) DESC/) {
1848                ($keyName, $ordering) = ($1, "descending");
1849              } else {              } else {
1850                  # Here the field is not present. Flag it as missing.              ($keyName, $ordering) = ($keyData, "ascending");
                 push @missing, $fieldName;  
1851              }              }
1852            # Find the key's position and type.
1853            my $fieldSpec;
1854            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1855                my $thisField = $fields[$i];
1856                if ($thisField->{name} eq $keyName) {
1857                    # Get the sort modifier for this field type. The modifier
1858                    # decides whether we're using a character, numeric, or
1859                    # floating-point sort.
1860                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1861                    # If the index is descending for this field, denote we want
1862                    # to reverse the sort order on this field.
1863                    if ($ordering eq 'descending') {
1864                        $modifier .= "r";
1865                    }
1866                    # Store the position and modifier into the field spec, which
1867                    # will stop the inner loop. Note that the field number is
1868                    # 1-based in the sort command, so we have to increment the
1869                    # index.
1870                    $fieldSpec = ($i + 1) . $modifier;
1871          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
1872          }          }
1873          # Only proceed if there are no missing fields.          # Add this field to the sort command.
1874          if (@missing > 0) {          $retVal .= " -k$fieldSpec";
1875              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .      }
1876                  join(' ', @missing)) if T(1);      # Return the result.
1877        return $retVal;
1878    }
1879    
1880    =head3 GetList
1881    
1882    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1883    
1884    Return a list of object descriptors for the specified objects as determined by the
1885    specified filter clause.
1886    
1887    This method is essentially the same as L</Get> except it returns a list of objects rather
1888    than a query object that can be used to get the results one record at a time.
1889    
1890    =over 4
1891    
1892    =item objectNames
1893    
1894    List containing the names of the entity and relationship objects to be retrieved.
1895    
1896    =item filterClause
1897    
1898    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1899    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1900    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1901    in the filter clause should be added to the parameter list as additional parameters. The
1902    fields in a filter clause can come from primary entity relations, relationship relations,
1903    or secondary entity relations; however, all of the entities and relationships involved must
1904    be included in the list of object names.
1905    
1906    The filter clause can also specify a sort order. To do this, simply follow the filter string
1907    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1908    particular genus and sorts them by species name.
1909    
1910    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1911    
1912    The rules for field references in a sort order are the same as those for field references in the
1913    filter clause in general; however, odd things may happen if a sort field is from a secondary
1914    relation.
1915    
1916    =item params
1917    
1918    Reference to a list of parameter values to be substituted into the filter clause.
1919    
1920    =item RETURN
1921    
1922    Returns a list of B<DBObject>s that satisfy the query conditions.
1923    
1924    =back
1925    
1926    =cut
1927    #: Return Type @%
1928    sub GetList {
1929        # Get the parameters.
1930        my ($self, $objectNames, $filterClause, $params) = @_;
1931        # Declare the return variable.
1932        my @retVal = ();
1933        # Perform the query.
1934        my $query = $self->Get($objectNames, $filterClause, $params);
1935        # Loop through the results.
1936        while (my $object = $query->Fetch) {
1937            push @retVal, $object;
1938        }
1939        # Return the result.
1940        return @retVal;
1941    }
1942    
1943    =head3 GetCount
1944    
1945    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1946    
1947    Return the number of rows found by a specified query. This method would
1948    normally be used to count the records in a single table. For example, in a
1949    genetics database
1950    
1951        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1952    
1953    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1954    to use it to return records based on a join. For example,
1955    
1956        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1957                                    ['homo %']);
1958    
1959    would return the number of features for genomes in the genus I<homo>. Note that
1960    only the rows from the first table are counted. If the above command were
1961    
1962        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1963                                    ['homo %']);
1964    
1965    it would return the number of genomes, not the number of genome/feature pairs.
1966    
1967    =over 4
1968    
1969    =item objectNames
1970    
1971    Reference to a list of the objects (entities and relationships) included in the
1972    query.
1973    
1974    =item filter
1975    
1976    A filter clause for restricting the query. The rules are the same as for the L</Get>
1977    method.
1978    
1979    =item params
1980    
1981    Reference to a list of the parameter values to be substituted for the parameter marks
1982    in the filter.
1983    
1984    =item RETURN
1985    
1986    Returns a count of the number of records in the first table that would satisfy
1987    the query.
1988    
1989    =back
1990    
1991    =cut
1992    
1993    sub GetCount {
1994        # Get the parameters.
1995        my ($self, $objectNames, $filter, $params) = @_;
1996        # Insure the params argument is an array reference if the caller left it off.
1997        if (! defined($params)) {
1998            $params = [];
1999        }
2000        # Declare the return variable.
2001        my $retVal;
2002        # Find out if we're counting an entity or a relationship.
2003        my $countedField;
2004        if ($self->IsEntity($objectNames->[0])) {
2005            $countedField = "id";
2006          } else {          } else {
2007              # Build the INSERT statement.          # For a relationship we count the to-link because it's usually more
2008              my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .          # numerous. Note we're automatically converting to the SQL form
2009                  ") VALUES (";          # of the field name (to_link vs. to-link).
2010              # Create a marker list of the proper size and put it in the statement.          $countedField = "to_link";
2011              my @markers = ();      }
2012              while (@markers < @fieldNameList) { push @markers, '?'; }      # Create the SQL command suffix to get the desired records.
2013              $statement .= join(', ', @markers) . ")";      my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2014              # We have the insert statement, so prepare it.                                                                              $filter);
2015              my $sth = $dbh->prepare_command($statement);      # Prefix it with text telling it we want a record count.
2016              Trace("Insert statement prepared: $statement") if T(3);      my $firstObject = $mappedNameListRef->[0];
2017              # Now we loop through the values. If a value is scalar, we use it unmodified. If it's      my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2018              # a list, we use the current element. The values are stored in the @parameterList array.      # Prepare and execute the command.
2019              my $done = 0;      my $sth = $self->_GetStatementHandle($command, $params);
2020              for (my $i = 0; $i < $recordCount; $i++) {      # Get the count value.
2021                  # Clear the parameter list array.      ($retVal) = $sth->fetchrow_array();
2022                  my @parameterList = ();      # Check for a problem.
2023                  # Loop through the values.      if (! defined($retVal)) {
2024                  for my $value (@valueList) {          if ($sth->err) {
2025                      # Check to see if this is a scalar value.              # Here we had an SQL error.
2026                      if (ref $value eq "ARRAY") {              Confess("Error retrieving row count: " . $sth->errstr());
                         # Here we have a list value. Pull the current entry.  
                         push @parameterList, $value->[$i];  
2027                      } else {                      } else {
2028                          # Here we have a scalar value. Use it unmodified.              # Here we have no result.
2029                          push @parameterList, $value;              Confess("No result attempting to retrieve row count.");
2030            }
2031        }
2032        # Return the result.
2033        return $retVal;
2034    }
2035    
2036    =head3 ComputeObjectSentence
2037    
2038    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2039    
2040    Check an object name, and if it is a relationship convert it to a relationship sentence.
2041    
2042    =over 4
2043    
2044    =item objectName
2045    
2046    Name of the entity or relationship.
2047    
2048    =item RETURN
2049    
2050    Returns a string containing the entity name or a relationship sentence.
2051    
2052    =back
2053    
2054    =cut
2055    
2056    sub ComputeObjectSentence {
2057        # Get the parameters.
2058        my ($self, $objectName) = @_;
2059        # Set the default return value.
2060        my $retVal = $objectName;
2061        # Look for the object as a relationship.
2062        my $relTable = $self->{_metaData}->{Relationships};
2063        if (exists $relTable->{$objectName}) {
2064            # Get the relationship sentence.
2065            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2066        }
2067        # Return the result.
2068        return $retVal;
2069    }
2070    
2071    =head3 DumpRelations
2072    
2073    C<< $erdb->DumpRelations($outputDirectory); >>
2074    
2075    Write the contents of all the relations to tab-delimited files in the specified directory.
2076    Each file will have the same name as the relation dumped, with an extension of DTX.
2077    
2078    =over 4
2079    
2080    =item outputDirectory
2081    
2082    Name of the directory into which the relation files should be dumped.
2083    
2084    =back
2085    
2086    =cut
2087    
2088    sub DumpRelations {
2089        # Get the parameters.
2090        my ($self, $outputDirectory) = @_;
2091        # Now we need to run through all the relations. First, we loop through the entities.
2092        my $metaData = $self->{_metaData};
2093        my $entities = $metaData->{Entities};
2094        for my $entityName (keys %{$entities}) {
2095            my $entityStructure = $entities->{$entityName};
2096            # Get the entity's relations.
2097            my $relationList = $entityStructure->{Relations};
2098            # Loop through the relations, dumping them.
2099            for my $relationName (keys %{$relationList}) {
2100                my $relation = $relationList->{$relationName};
2101                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2102            }
2103        }
2104        # Next, we loop through the relationships.
2105        my $relationships = $metaData->{Relationships};
2106        for my $relationshipName (keys %{$relationships}) {
2107            my $relationshipStructure = $relationships->{$relationshipName};
2108            # Dump this relationship's relation.
2109            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2110        }
2111    }
2112    
2113    =head3 InsertValue
2114    
2115    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2116    
2117    This method will insert a new value into the database. The value must be one
2118    associated with a secondary relation, since primary values cannot be inserted:
2119    they occur exactly once. Secondary values, on the other hand, can be missing
2120    or multiply-occurring.
2121    
2122    =over 4
2123    
2124    =item entityID
2125    
2126    ID of the object that is to receive the new value.
2127    
2128    =item fieldName
2129    
2130    Field name for the new value-- this includes the entity name, since
2131    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2132    
2133    =item value
2134    
2135    New value to be put in the field.
2136    
2137    =back
2138    
2139    =cut
2140    
2141    sub InsertValue {
2142        # Get the parameters.
2143        my ($self, $entityID, $fieldName, $value) = @_;
2144        # Parse the entity name and the real field name.
2145        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2146            my $entityName = $1;
2147            my $fieldTitle = $2;
2148            # Get its descriptor.
2149            if (!$self->IsEntity($entityName)) {
2150                Confess("$entityName is not a valid entity.");
2151            } else {
2152                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2153                # Find the relation containing this field.
2154                my $fieldHash = $entityData->{Fields};
2155                if (! exists $fieldHash->{$fieldTitle}) {
2156                    Confess("$fieldTitle not found in $entityName.");
2157                } else {
2158                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2159                    if ($relation eq $entityName) {
2160                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2161                    } else {
2162                        # Now we can create an INSERT statement.
2163                        my $dbh = $self->{_dbh};
2164                        my $fixedName = _FixName($fieldTitle);
2165                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2166                        # Execute the command.
2167                        $dbh->SQL($statement, 0, $entityID, $value);
2168                    }
2169                }
2170            }
2171        } else {
2172            Confess("$fieldName is not a valid field name.");
2173        }
2174    }
2175    
2176    =head3 InsertObject
2177    
2178    C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2179    
2180    Insert an object into the database. The object is defined by a type name and then a hash
2181    of field names to values. Field values in the primary relation are represented by scalars.
2182    (Note that for relationships, the primary relation is the B<only> relation.)
2183    Field values for the other relations comprising the entity are always list references. For
2184    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2185    C<ZP_00210270.1> and C<gi|46206278>.
2186    
2187    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2188    
2189    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2190    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2191    
2192    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2193    
2194    =over 4
2195    
2196    =item newObjectType
2197    
2198    Type name of the object to insert.
2199    
2200    =item fieldHash
2201    
2202    Hash of field names to values.
2203    
2204    =item RETURN
2205    
2206    Returns 1 if successful, 0 if an error occurred.
2207    
2208    =back
2209    
2210    =cut
2211    
2212    sub InsertObject {
2213        # Get the parameters.
2214        my ($self, $newObjectType, $fieldHash) = @_;
2215        # Denote that so far we appear successful.
2216        my $retVal = 1;
2217        # Get the database handle.
2218        my $dbh = $self->{_dbh};
2219        # Get the relation list.
2220        my $relationTable = $self->_GetRelationTable($newObjectType);
2221        # Loop through the relations. We'll build insert statements for each one. If a relation is
2222        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2223        # stop the loop.
2224        my @relationList = keys %{$relationTable};
2225        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2226            my $relationName = $relationList[$i];
2227            my $relationDefinition = $relationTable->{$relationName};
2228            # Get the relation's fields. For each field we will collect a value in the corresponding
2229            # position of the @valueList array. If one of the fields is missing, we will add it to the
2230            # @missing list.
2231            my @fieldList = @{$relationDefinition->{Fields}};
2232            my @fieldNameList = ();
2233            my @valueList = ();
2234            my @missing = ();
2235            my $recordCount = 1;
2236            for my $fieldDescriptor (@fieldList) {
2237                # Get the field name and save it. Note we need to fix it up so the hyphens
2238                # are converted to underscores.
2239                my $fieldName = $fieldDescriptor->{name};
2240                push @fieldNameList, _FixName($fieldName);
2241                # Look for the named field in the incoming structure. Note that we are looking
2242                # for the real field name, not the fixed-up one!
2243                if (exists $fieldHash->{$fieldName}) {
2244                    # Here we found the field. Stash it in the value list.
2245                    my $value = $fieldHash->{$fieldName};
2246                    push @valueList, $value;
2247                    # If the value is a list, we may need to increment the record count.
2248                    if (ref $value eq "ARRAY") {
2249                        my $thisCount = @{$value};
2250                        if ($recordCount == 1) {
2251                            # Here we have our first list, so we save its count.
2252                            $recordCount = $thisCount;
2253                        } elsif ($recordCount != $thisCount) {
2254                            # Here we have a second list, so its length has to match the
2255                            # previous lists.
2256                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2257                            $retVal = 0;
2258                        }
2259                    }
2260                } else {
2261                    # Here the field is not present. Flag it as missing.
2262                    push @missing, $fieldName;
2263                }
2264            }
2265            # If we are the primary relation, add the new-record flag.
2266            if ($relationName eq $newObjectType) {
2267                push @valueList, 1;
2268                push @fieldNameList, "new_record";
2269            }
2270            # Only proceed if there are no missing fields.
2271            if (@missing > 0) {
2272                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2273                    join(' ', @missing)) if T(1);
2274            } else {
2275                # Build the INSERT statement.
2276                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2277                    ") VALUES (";
2278                # Create a marker list of the proper size and put it in the statement.
2279                my @markers = ();
2280                while (@markers < @fieldNameList) { push @markers, '?'; }
2281                $statement .= join(', ', @markers) . ")";
2282                # We have the insert statement, so prepare it.
2283                my $sth = $dbh->prepare_command($statement);
2284                Trace("Insert statement prepared: $statement") if T(3);
2285                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2286                # a list, we use the current element. The values are stored in the @parameterList array.
2287                my $done = 0;
2288                for (my $i = 0; $i < $recordCount; $i++) {
2289                    # Clear the parameter list array.
2290                    my @parameterList = ();
2291                    # Loop through the values.
2292                    for my $value (@valueList) {
2293                        # Check to see if this is a scalar value.
2294                        if (ref $value eq "ARRAY") {
2295                            # Here we have a list value. Pull the current entry.
2296                            push @parameterList, $value->[$i];
2297                        } else {
2298                            # Here we have a scalar value. Use it unmodified.
2299                            push @parameterList, $value;
2300                        }
2301                    }
2302                    # Execute the INSERT statement with the specified parameter list.
2303                    $retVal = $sth->execute(@parameterList);
2304                    if (!$retVal) {
2305                        my $errorString = $sth->errstr();
2306                        Trace("Insert error: $errorString.") if T(0);
2307                    }
2308                }
2309            }
2310        }
2311        # Return the success indicator.
2312        return $retVal;
2313    }
2314    
2315    =head3 LoadTable
2316    
2317    C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2318    
2319    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2320    first.
2321    
2322    =over 4
2323    
2324    =item fileName
2325    
2326    Name of the file from which the table data should be loaded.
2327    
2328    =item relationName
2329    
2330    Name of the relation to be loaded. This is the same as the table name.
2331    
2332    =item truncateFlag
2333    
2334    TRUE if the table should be dropped and re-created, else FALSE
2335    
2336    =item RETURN
2337    
2338    Returns a statistical object containing a list of the error messages.
2339    
2340    =back
2341    
2342    =cut
2343    sub LoadTable {
2344        # Get the parameters.
2345        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2346        # Create the statistical return object.
2347        my $retVal = _GetLoadStats();
2348        # Trace the fact of the load.
2349        Trace("Loading table $relationName from $fileName") if T(2);
2350        # Get the database handle.
2351        my $dbh = $self->{_dbh};
2352        # Get the input file size.
2353        my $fileSize = -s $fileName;
2354        # Get the relation data.
2355        my $relation = $self->_FindRelation($relationName);
2356        # Check the truncation flag.
2357        if ($truncateFlag) {
2358            Trace("Creating table $relationName") if T(2);
2359            # Compute the row count estimate. We take the size of the load file,
2360            # divide it by the estimated row size, and then multiply by 1.5 to
2361            # leave extra room. We postulate a minimum row count of 1000 to
2362            # prevent problems with incoming empty load files.
2363            my $rowSize = $self->EstimateRowSize($relationName);
2364            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2365            # Re-create the table without its index.
2366            $self->CreateTable($relationName, 0, $estimate);
2367            # If this is a pre-index DBMS, create the index here.
2368            if ($dbh->{_preIndex}) {
2369                eval {
2370                    $self->CreateIndex($relationName);
2371                };
2372                if ($@) {
2373                    $retVal->AddMessage($@);
2374                }
2375            }
2376        }
2377        # Load the table.
2378        my $rv;
2379        eval {
2380            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2381        };
2382        if (!defined $rv) {
2383            $retVal->AddMessage($@) if ($@);
2384            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2385            Trace("Table load failed for $relationName.") if T(1);
2386        } else {
2387            # Here we successfully loaded the table.
2388            $retVal->Add("tables");
2389            my $size = -s $fileName;
2390            Trace("$size bytes loaded into $relationName.") if T(2);
2391            # If we're rebuilding, we need to create the table indexes.
2392            if ($truncateFlag) {
2393                # Indexes are created here for PostGres. For PostGres, indexes are
2394                # best built at the end. For MySQL, the reverse is true.
2395                if (! $dbh->{_preIndex}) {
2396                    eval {
2397                        $self->CreateIndex($relationName);
2398                    };
2399                    if ($@) {
2400                        $retVal->AddMessage($@);
2401                    }
2402                }
2403                # The full-text index (if any) is always built last, even for MySQL.
2404                # First we need to see if this table has a full-text index. Only
2405                # primary relations are allowed that privilege.
2406                if ($self->_IsPrimary($relationName)) {
2407                    # Get the relation's entity/relationship structure.
2408                    my $structure = $self->_GetStructure($relationName);
2409                    # Check for a searchable fields list.
2410                    if (exists $structure->{searchFields}) {
2411                        # Here we know that we need to create a full-text search index.
2412                        # Get an SQL-formatted field name list.
2413                        my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2414                        # Create the index.
2415                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2416                                           flds => $fields, kind => 'fulltext');
2417                    }
2418                }
2419            }
2420        }
2421        # Analyze the table to improve performance.
2422        Trace("Analyzing and compacting $relationName.") if T(3);
2423        $dbh->vacuum_it($relationName);
2424        Trace("$relationName load completed.") if T(3);
2425        # Return the statistics.
2426        return $retVal;
2427    }
2428    
2429    =head3 DropRelation
2430    
2431    C<< $erdb->DropRelation($relationName); >>
2432    
2433    Physically drop a relation from the database.
2434    
2435    =over 4
2436    
2437    =item relationName
2438    
2439    Name of the relation to drop. If it does not exist, this method will have
2440    no effect.
2441    
2442    =back
2443    
2444    =cut
2445    
2446    sub DropRelation {
2447        # Get the parameters.
2448        my ($self, $relationName) = @_;
2449        # Get the database handle.
2450        my $dbh = $self->{_dbh};
2451        # Drop the relation. The method used here has no effect if the relation
2452        # does not exist.
2453        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2454        $dbh->drop_table(tbl => $relationName);
2455    }
2456    
2457    =head3 GetEntity
2458    
2459    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2460    
2461    Return an object describing the entity instance with a specified ID.
2462    
2463    =over 4
2464    
2465    =item entityType
2466    
2467    Entity type name.
2468    
2469    =item ID
2470    
2471    ID of the desired entity.
2472    
2473    =item RETURN
2474    
2475    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2476    instance is found with the specified key.
2477    
2478    =back
2479    
2480    =cut
2481    
2482    sub GetEntity {
2483        # Get the parameters.
2484        my ($self, $entityType, $ID) = @_;
2485        # Create a query.
2486        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2487        # Get the first (and only) object.
2488        my $retVal = $query->Fetch();
2489        # Return the result.
2490        return $retVal;
2491    }
2492    
2493    =head3 GetChoices
2494    
2495    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2496    
2497    Return a list of all the values for the specified field that are represented in the
2498    specified entity.
2499    
2500    Note that if the field is not indexed, then this will be a very slow operation.
2501    
2502    =over 4
2503    
2504    =item entityName
2505    
2506    Name of an entity in the database.
2507    
2508    =item fieldName
2509    
2510    Name of a field belonging to the entity. This is a raw field name without
2511    the standard parenthesized notation used in most calls.
2512    
2513    =item RETURN
2514    
2515    Returns a list of the distinct values for the specified field in the database.
2516    
2517    =back
2518    
2519    =cut
2520    
2521    sub GetChoices {
2522        # Get the parameters.
2523        my ($self, $entityName, $fieldName) = @_;
2524        # Declare the return variable.
2525        my @retVal;
2526        # Get the entity data structure.
2527        my $entityData = $self->_GetStructure($entityName);
2528        # Get the field.
2529        my $fieldHash = $entityData->{Fields};
2530        if (! exists $fieldHash->{$fieldName}) {
2531            Confess("$fieldName not found in $entityName.");
2532        } else {
2533            # Get the name of the relation containing the field.
2534            my $relation = $fieldHash->{$fieldName}->{relation};
2535            # Fix up the field name.
2536            my $realName = _FixName($fieldName);
2537            # Get the database handle.
2538            my $dbh = $self->{_dbh};
2539            # Query the database.
2540            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2541            # Clean the results. They are stored as a list of lists, and we just want the one list.
2542            @retVal = sort map { $_->[0] } @{$results};
2543        }
2544        # Return the result.
2545        return @retVal;
2546    }
2547    
2548    =head3 GetEntityValues
2549    
2550    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2551    
2552    Return a list of values from a specified entity instance. If the entity instance
2553    does not exist, an empty list is returned.
2554    
2555    =over 4
2556    
2557    =item entityType
2558    
2559    Entity type name.
2560    
2561    =item ID
2562    
2563    ID of the desired entity.
2564    
2565    =item fields
2566    
2567    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2568    
2569    =item RETURN
2570    
2571    Returns a flattened list of the values of the specified fields for the specified entity.
2572    
2573    =back
2574    
2575    =cut
2576    
2577    sub GetEntityValues {
2578        # Get the parameters.
2579        my ($self, $entityType, $ID, $fields) = @_;
2580        # Get the specified entity.
2581        my $entity = $self->GetEntity($entityType, $ID);
2582        # Declare the return list.
2583        my @retVal = ();
2584        # If we found the entity, push the values into the return list.
2585        if ($entity) {
2586            push @retVal, $entity->Values($fields);
2587        }
2588        # Return the result.
2589        return @retVal;
2590    }
2591    
2592    =head3 GetAll
2593    
2594    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2595    
2596    Return a list of values taken from the objects returned by a query. The first three
2597    parameters correspond to the parameters of the L</Get> method. The final parameter is
2598    a list of the fields desired from each record found by the query. The field name
2599    syntax is the standard syntax used for fields in the B<ERDB> system--
2600    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2601    or relationship and I<fieldName> is the name of the field.
2602    
2603    The list returned will be a list of lists. Each element of the list will contain
2604    the values returned for the fields specified in the fourth parameter. If one of the
2605    fields specified returns multiple values, they are flattened in with the rest. For
2606    example, the following call will return a list of the features in a particular
2607    spreadsheet cell, and each feature will be represented by a list containing the
2608    feature ID followed by all of its aliases.
2609    
2610    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2611    
2612    =over 4
2613    
2614    =item objectNames
2615    
2616    List containing the names of the entity and relationship objects to be retrieved.
2617    
2618    =item filterClause
2619    
2620    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2621    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2622    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2623    parameter list as additional parameters. The fields in a filter clause can come from primary
2624    entity relations, relationship relations, or secondary entity relations; however, all of the
2625    entities and relationships involved must be included in the list of object names.
2626    
2627    =item parameterList
2628    
2629    List of the parameters to be substituted in for the parameters marks in the filter clause.
2630    
2631    =item fields
2632    
2633    List of the fields to be returned in each element of the list returned.
2634    
2635    =item count
2636    
2637    Maximum number of records to return. If omitted or 0, all available records will be returned.
2638    
2639    =item RETURN
2640    
2641    Returns a list of list references. Each element of the return list contains the values for the
2642    fields specified in the B<fields> parameter.
2643    
2644    =back
2645    
2646    =cut
2647    #: Return Type @@;
2648    sub GetAll {
2649        # Get the parameters.
2650        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2651        # Translate the parameters from a list reference to a list. If the parameter
2652        # list is a scalar we convert it into a singleton list.
2653        my @parmList = ();
2654        if (ref $parameterList eq "ARRAY") {
2655            Trace("GetAll parm list is an array.") if T(4);
2656            @parmList = @{$parameterList};
2657        } else {
2658            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2659            push @parmList, $parameterList;
2660        }
2661        # Insure the counter has a value.
2662        if (!defined $count) {
2663            $count = 0;
2664        }
2665        # Add the row limit to the filter clause.
2666        if ($count > 0) {
2667            $filterClause .= " LIMIT $count";
2668        }
2669        # Create the query.
2670        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2671        # Set up a counter of the number of records read.
2672        my $fetched = 0;
2673        # Loop through the records returned, extracting the fields. Note that if the
2674        # counter is non-zero, we stop when the number of records read hits the count.
2675        my @retVal = ();
2676        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2677            my @rowData = $row->Values($fields);
2678            push @retVal, \@rowData;
2679            $fetched++;
2680        }
2681        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2682        # Return the resulting list.
2683        return @retVal;
2684    }
2685    
2686    =head3 Exists
2687    
2688    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2689    
2690    Return TRUE if an entity exists, else FALSE.
2691    
2692    =over 4
2693    
2694    =item entityName
2695    
2696    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2697    
2698    =item entityID
2699    
2700    ID of the entity instance whose existence is to be checked.
2701    
2702    =item RETURN
2703    
2704    Returns TRUE if the entity instance exists, else FALSE.
2705    
2706    =back
2707    
2708    =cut
2709    #: Return Type $;
2710    sub Exists {
2711        # Get the parameters.
2712        my ($self, $entityName, $entityID) = @_;
2713        # Check for the entity instance.
2714        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2715        my $testInstance = $self->GetEntity($entityName, $entityID);
2716        # Return an existence indicator.
2717        my $retVal = ($testInstance ? 1 : 0);
2718        return $retVal;
2719    }
2720    
2721    =head3 EstimateRowSize
2722    
2723    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2724    
2725    Estimate the row size of the specified relation. The estimated row size is computed by adding
2726    up the average length for each data type.
2727    
2728    =over 4
2729    
2730    =item relName
2731    
2732    Name of the relation whose estimated row size is desired.
2733    
2734    =item RETURN
2735    
2736    Returns an estimate of the row size for the specified relation.
2737    
2738    =back
2739    
2740    =cut
2741    #: Return Type $;
2742    sub EstimateRowSize {
2743        # Get the parameters.
2744        my ($self, $relName) = @_;
2745        # Declare the return variable.
2746        my $retVal = 0;
2747        # Find the relation descriptor.
2748        my $relation = $self->_FindRelation($relName);
2749        # Get the list of fields.
2750        for my $fieldData (@{$relation->{Fields}}) {
2751            # Get the field type and add its length.
2752            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2753            $retVal += $fieldLen;
2754                      }                      }
2755        # Return the result.
2756        return $retVal;
2757                  }                  }
2758                  # Execute the INSERT statement with the specified parameter list.  
2759                  $retVal = $sth->execute(@parameterList);  =head3 GetFieldTable
2760                  if (!$retVal) {  
2761                      my $errorString = $sth->errstr();  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2762                      Trace("Insert error: $errorString.") if T(0);  
2763    Get the field structure for a specified entity or relationship.
2764    
2765    =over 4
2766    
2767    =item objectName
2768    
2769    Name of the desired entity or relationship.
2770    
2771    =item RETURN
2772    
2773    The table containing the field descriptors for the specified object.
2774    
2775    =back
2776    
2777    =cut
2778    
2779    sub GetFieldTable {
2780        # Get the parameters.
2781        my ($self, $objectName) = @_;
2782        # Get the descriptor from the metadata.
2783        my $objectData = $self->_GetStructure($objectName);
2784        # Return the object's field table.
2785        return $objectData->{Fields};
2786                  }                  }
2787    
2788    =head3 SplitKeywords
2789    
2790    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2791    
2792    This method returns a list of the positive keywords in the specified
2793    keyword string. All of the operators will have been stripped off,
2794    and if the keyword is preceded by a minus operator (C<->), it will
2795    not be in the list returned. The idea here is to get a list of the
2796    keywords the user wants to see. The list will be processed to remove
2797    duplicates.
2798    
2799    It is possible to create a string that confuses this method. For example
2800    
2801        frog toad -frog
2802    
2803    would return both C<frog> and C<toad>. If this is a problem we can deal
2804    with it later.
2805    
2806    =over 4
2807    
2808    =item keywordString
2809    
2810    The keyword string to be parsed.
2811    
2812    =item RETURN
2813    
2814    Returns a list of the words in the keyword string the user wants to
2815    see.
2816    
2817    =back
2818    
2819    =cut
2820    
2821    sub SplitKeywords {
2822        # Get the parameters.
2823        my ($keywordString) = @_;
2824        # Make a safety copy of the string. (This helps during debugging.)
2825        my $workString = $keywordString;
2826        # Convert operators we don't care about to spaces.
2827        $workString =~ tr/+"()<>/ /;
2828        # Split the rest of the string along space boundaries. Note that we
2829        # eliminate any words that are zero length or begin with a minus sign.
2830        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2831        # Use a hash to remove duplicates.
2832        my %words = map { $_ => 1 } @wordList;
2833        # Return the result.
2834        return sort keys %words;
2835              }              }
2836    
2837    =head3 ValidateFieldName
2838    
2839    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2840    
2841    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2842    be hyphenated words subject to certain restrictions.
2843    
2844    =over 4
2845    
2846    =item fieldName
2847    
2848    Field name to be validated.
2849    
2850    =item RETURN
2851    
2852    Returns TRUE if the field name is valid, else FALSE.
2853    
2854    =back
2855    
2856    =cut
2857    
2858    sub ValidateFieldName {
2859        # Get the parameters.
2860        my ($fieldName) = @_;
2861        # Declare the return variable. The field name is valid until we hear
2862        # differently.
2863        my $retVal = 1;
2864        # Look for bad stuff in the name.
2865        if ($fieldName =~ /--/) {
2866            # Here we have a doubled minus sign.
2867            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2868            $retVal = 0;
2869        } elsif ($fieldName !~ /^[A-Za-z]/) {
2870            # Here the field name is missing the initial letter.
2871            Trace("Field name $fieldName does not begin with a letter.") if T(1);
2872            $retVal = 0;
2873        } else {
2874            # Strip out the minus signs. Everything remaining must be a letter,
2875            # underscore, or digit.
2876            my $strippedName = $fieldName;
2877            $strippedName =~ s/-//g;
2878            if ($strippedName !~ /^(\w|\d)+$/) {
2879                Trace("Field name $fieldName contains illegal characters.") if T(1);
2880                $retVal = 0;
2881          }          }
2882      }      }
2883      # Return the success indicator.      # Return the result.
2884      return $retVal;      return $retVal;
2885  }  }
2886    
2887  =head3 LoadTable  =head3 ReadMetaXML
2888    
2889  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2890    
2891  Load data from a tab-delimited file into a specified table, optionally re-creating the table  This method reads a raw database definition XML file and returns it.
2892  first.  Normally, the metadata used by the ERDB system has been processed and
2893    modified to make it easier to load and retrieve the data; however,
2894    this method can be used to get the data in its raw form.
2895    
2896  =over 4  =over 4
2897    
2898  =item fileName  =item fileName
2899    
2900  Name of the file from which the table data should be loaded.  Name of the XML file to read.
2901    
2902  =item relationName  =item RETURN
2903    
2904  Name of the relation to be loaded. This is the same as the table name.  Returns a hash reference containing the raw XML data from the specified file.
2905    
2906  =item truncateFlag  =back
2907    
2908  TRUE if the table should be dropped and re-created, else FALSE  =cut
2909    
2910    sub ReadMetaXML {
2911        # Get the parameters.
2912        my ($fileName) = @_;
2913        # Read the XML.
2914        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2915        Trace("XML metadata loaded from file $fileName.") if T(1);
2916        # Return the result.
2917        return $retVal;
2918    }
2919    
2920    =head3 GetEntityFieldHash
2921    
2922    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2923    
2924    Get the field hash of the named entity in the specified raw XML structure.
2925    The field hash may not exist, in which case we need to create it.
2926    
2927    =over 4
2928    
2929    =item structure
2930    
2931    Raw XML structure defininng the database. This is not the run-time XML used by
2932    an ERDB object, since that has all sorts of optimizations built-in.
2933    
2934    =item entityName
2935    
2936    Name of the entity whose field structure is desired.
2937    
2938  =item RETURN  =item RETURN
2939    
2940  Returns a statistical object containing the number of records read and a list of  Returns the field hash used to define the entity's fields.
 the error messages.  
2941    
2942  =back  =back
2943    
2944  =cut  =cut
2945  sub LoadTable {  
2946    sub GetEntityFieldHash {
2947      # Get the parameters.      # Get the parameters.
2948      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($structure, $entityName) = @_;
2949      # Create the statistical return object.      # Get the entity structure.
2950      my $retVal = _GetLoadStats();      my $entityData = $structure->{Entities}->{$entityName};
2951      # Trace the fact of the load.      # Look for a field structure.
2952      Trace("Loading table $relationName from $fileName") if T(2);      my $retVal = $entityData->{Fields};
2953      # Get the database handle.      # If it doesn't exist, create it.
2954      my $dbh = $self->{_dbh};      if (! defined($retVal)) {
2955      # Get the relation data.          $entityData->{Fields} = {};
2956      my $relation = $self->_FindRelation($relationName);          $retVal = $entityData->{Fields};
     # Check the truncation flag.  
     if ($truncateFlag) {  
         Trace("Creating table $relationName") if T(2);  
         # Compute the row count estimate. We take the size of the load file,  
         # divide it by the estimated row size, and then multiply by 1.5 to  
         # leave extra room. We postulate a minimum row count of 1000 to  
         # prevent problems with incoming empty load files.  
         my $rowSize = $self->EstimateRowSize($relationName);  
         my $fileSize = -s $fileName;  
         my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);  
         # Re-create the table without its index.  
         $self->CreateTable($relationName, 0, $estimate);  
         # If this is a pre-index DBMS, create the index here.  
         if ($dbh->{_preIndex}) {  
             eval {  
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
2957              }              }
2958        # Return the result.
2959        return $retVal;
2960          }          }
2961    
2962    =head3 WriteMetaXML
2963    
2964    C<< ERDB::WriteMetaXML($structure, $fileName); >>
2965    
2966    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2967    used to update the database definition. It must be used with care, however, since it
2968    will only work on a raw structure, not on the processed structure created by an ERDB
2969    constructor.
2970    
2971    =over 4
2972    
2973    =item structure
2974    
2975    XML structure to be written to the file.
2976    
2977    =item fileName
2978    
2979    Name of the output file to which the updated XML should be stored.
2980    
2981    =back
2982    
2983    =cut
2984    
2985    sub WriteMetaXML {
2986        # Get the parameters.
2987        my ($structure, $fileName) = @_;
2988        # Compute the output.
2989        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2990        # Write it to the file.
2991        my $xmlOut = Open(undef, ">$fileName");
2992        print $xmlOut $fileString;
2993    }
2994    
2995    
2996    =head3 HTMLNote
2997    
2998    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2999    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3000    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3001    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3002    
3003    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3004    
3005    =over 4
3006    
3007    =item dataString
3008    
3009    String to convert to HTML.
3010    
3011    =item RETURN
3012    
3013    An HTML string derived from the input string.
3014    
3015    =back
3016    
3017    =cut
3018    
3019    sub HTMLNote {
3020        # Get the parameter.
3021        my ($dataString) = @_;
3022        # HTML-escape the text.
3023        my $retVal = CGI::escapeHTML($dataString);
3024        # Substitute the bulletin board codes.
3025        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3026        $retVal =~ s!\[p\]!</p><p>!g;
3027        # Return the result.
3028        return $retVal;
3029    }
3030    
3031    
3032    =head2 Data Mining Methods
3033    
3034    =head3 GetUsefulCrossValues
3035    
3036    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3037    
3038    Return a list of the useful attributes that would be returned by a B<Cross> call
3039    from an entity of the source entity type through the specified relationship. This
3040    means it will return the fields of the target entity type and the intersection data
3041    fields in the relationship. Only primary table fields are returned. In other words,
3042    the field names returned will be for fields where there is always one and only one
3043    value.
3044    
3045    =over 4
3046    
3047    =item sourceEntity
3048    
3049    Name of the entity from which the relationship crossing will start.
3050    
3051    =item relationship
3052    
3053    Name of the relationship being crossed.
3054    
3055    =item RETURN
3056    
3057    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3058    
3059    =back
3060    
3061    =cut
3062    #: Return Type @;
3063    sub GetUsefulCrossValues {
3064        # Get the parameters.
3065        my ($self, $sourceEntity, $relationship) = @_;
3066        # Declare the return variable.
3067        my @retVal = ();
3068        # Determine the target entity for the relationship. This is whichever entity is not
3069        # the source entity. So, if the source entity is the FROM, we'll get the name of
3070        # the TO, and vice versa.
3071        my $relStructure = $self->_GetStructure($relationship);
3072        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3073        my $targetEntity = $relStructure->{$targetEntityType};
3074        # Get the field table for the entity.
3075        my $entityFields = $self->GetFieldTable($targetEntity);
3076        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3077        # For the entity fields, the key aspect of the target structure is that the {relation} value
3078        # must match the entity name.
3079        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3080                            keys %{$entityFields};
3081        # Push the fields found onto the return variable.
3082        push @retVal, sort @fieldList;
3083        # Get the field table for the relationship.
3084        my $relationshipFields = $self->GetFieldTable($relationship);
3085        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3086        # This may end up being an empty set.
3087        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3088                            keys %{$relationshipFields};
3089        # Push these onto the return list.
3090        push @retVal, sort @fieldList2;
3091        # Return the result.
3092        return @retVal;
3093    }
3094    
3095    =head3 FindColumn
3096    
3097    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3098    
3099    Return the location a desired column in a data mining header line. The data
3100    mining header line is a tab-separated list of column names. The column
3101    identifier is either the numerical index of a column or the actual column
3102    name.
3103    
3104    =over 4
3105    
3106    =item headerLine
3107    
3108    The header line from a data mining command, which consists of a tab-separated
3109    list of column names.
3110    
3111    =item columnIdentifier
3112    
3113    Either the ordinal number of the desired column (1-based), or the name of the
3114    desired column.
3115    
3116    =item RETURN
3117    
3118    Returns the array index (0-based) of the desired column.
3119    
3120    =back
3121    
3122    =cut
3123    
3124    sub FindColumn {
3125        # Get the parameters.
3126        my ($headerLine, $columnIdentifier) = @_;
3127        # Declare the return variable.
3128        my $retVal;
3129        # Split the header line into column names.
3130        my @headers = ParseColumns($headerLine);
3131        # Determine whether we have a number or a name.
3132        if ($columnIdentifier =~ /^\d+$/) {
3133            # Here we have a number. Subtract 1 and validate the result.
3134            $retVal = $columnIdentifier - 1;
3135            if ($retVal < 0 || $retVal > $#headers) {
3136                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3137      }      }
     # Load the table.  
     my $rv;  
     eval {  
         $rv = $dbh->load_table(file => $fileName, tbl => $relationName);  
     };  
     if (!defined $rv) {  
         $retVal->AddMessage($@) if ($@);  
         $retVal->AddMessage("Table load failed for $relationName using $fileName.");  
         Trace("Table load failed for $relationName.") if T(1);  
3138      } else {      } else {
3139          # Here we successfully loaded the table. Trace the number of records loaded.          # Here we have a name. We need to find it in the list.
3140          Trace("$retVal->{records} records read for $relationName.") if T(2);          for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3141          # If we're rebuilding, we need to create the table indexes.              if ($headers[$i] eq $columnIdentifier) {
3142          if ($truncateFlag && ! $dbh->{_preIndex}) {                  $retVal = $i;
             eval {  
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
3143              }              }
3144          }          }
3145            if (! defined($retVal)) {
3146                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3147      }      }
3148      # Commit the database changes.      }
3149      $dbh->commit_tran;      # Return the result.
     # Analyze the table to improve performance.  
     $dbh->vacuum_it($relationName);  
     # Return the statistics.  
3150      return $retVal;      return $retVal;
3151  }  }
3152    
3153  =head3 GenerateEntity  =head3 ParseColumns
3154    
3155  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3156    
3157  Generate the data for a new entity instance. This method creates a field hash suitable for  Convert the specified data line to a list of columns.
 passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  
 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.  
3158    
3159  =over 4  =over 4
3160    
3161  =item id  =item line
   
 ID to assign to the new entity.  
   
 =item type  
3162    
3163  Type name for the new entity.  A data mining input, consisting of a tab-separated list of columns terminated by a
3164    new-line.
3165    
3166  =item values  =item RETURN
3167    
3168  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a list consisting of the column values.
3169    
3170  =back  =back
3171    
3172  =cut  =cut
3173    
3174  sub GenerateEntity {  sub ParseColumns {
3175      # Get the parameters.      # Get the parameters.
3176      my ($self, $id, $type, $values) = @_;      my ($line) = @_;
3177      # Create the return hash.      # Chop off the line-end.
3178      my $this = { id => $id };      chomp $line;
3179      # Get the metadata structure.      # Split it into a list.
3180      my $metadata = $self->{_metaData};      my @retVal = split(/\t/, $line);
3181      # Get this entity's list of fields.      # Return the result.
3182      if (!exists $metadata->{Entities}->{$type}) {      return @retVal;
         Confess("Unrecognized entity type $type in GenerateEntity.");  
     } else {  
         my $entity = $metadata->{Entities}->{$type};  
         my $fields = $entity->{Fields};  
         # Generate data from the fields.  
         _GenerateFields($this, $fields, $type, $values);  
     }  
     # Return the hash created.  
     return $this;  
3183  }  }
3184    
3185  =head3 GetEntity  =head2 Virtual Methods
   
 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>  
3186    
3187  Return an object describing the entity instance with a specified ID.  =head3 CleanKeywords
3188    
3189  =over 4  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3190    
3191  =item entityType  Clean up a search expression or keyword list. This is a virtual method that may
3192    be overridden by the subclass. The base-class method removes extra spaces
3193    and converts everything to lower case.
3194    
3195  Entity type name.  =over 4
3196    
3197  =item ID  =item searchExpression
3198    
3199  ID of the desired entity.  Search expression or keyword list to clean. Note that a search expression may
3200    contain boolean operators which need to be preserved. This includes leading
3201    minus signs.
3202    
3203  =item RETURN  =item RETURN
3204    
3205  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Cleaned expression or keyword list.
 instance is found with the specified key.  
3206    
3207  =back  =back
3208    
3209  =cut  =cut
3210    
3211  sub GetEntity {  sub CleanKeywords {
3212      # Get the parameters.      # Get the parameters.
3213      my ($self, $entityType, $ID) = @_;      my ($self, $searchExpression) = @_;
3214      # Create a query.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3215      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      # don't accidentally end up with an undefined value.
3216      # Get the first (and only) object.      my $retVal = lc($searchExpression || "");
3217      my $retVal = $query->Fetch();      # Remove extra spaces.
3218        $retVal =~ s/\s+/ /g;
3219        $retVal =~ s/(^\s+)|(\s+$)//g;
3220      # Return the result.      # Return the result.
3221      return $retVal;      return $retVal;
3222  }  }
3223    
3224  =head3 GetEntityValues  =head3 GetSourceObject
3225    
3226  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my $source = $erdb->GetSourceObject($entityName); >>
3227    
3228  Return a list of values from a specified entity instance.  Return the object to be used in loading special attributes of the specified entity. The
3229    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3230    XML
3231    
3232  =over 4  =head2 Internal Utility Methods
3233    
3234  =item entityType  =head3 _RelationMap
3235    
3236  Entity type name.  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3237    
3238  =item ID  Create the relation map for an SQL query. The relation map is used by B<DBObject>
3239    to determine how to interpret the results of the query.
3240    
3241  ID of the desired entity.  =over 4
3242    
3243  =item fields  =item mappedNameHashRef
3244    
3245  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  Reference to a hash that maps modified object names to real object names.
3246    
3247    =item mappedNameListRef
3248    
3249    Reference to a list of modified object names in the order they appear in the
3250    SELECT list.
3251    
3252  =item RETURN  =item RETURN
3253    
3254  Returns a flattened list of the values of the specified fields for the specified entity.  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3255    query followed by the actual name of that object. This enables the B<DBObject> to
3256    determine the order of the tables in the query and which object name belongs to each
3257    mapped object name. Most of the time these two values are the same; however, if a
3258    relation occurs twice in the query, the relation name in the field list and WHERE
3259    clause will use a mapped name (generally the actual relation name with a numeric
3260    suffix) that does not match the actual relation name.
3261    
3262  =back  =back
3263    
3264  =cut  =cut
3265    
3266  sub GetEntityValues {  sub _RelationMap {
3267      # Get the parameters.      # Get the parameters.
3268      my ($self, $entityType, $ID, $fields) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
3269      # Get the specified entity.      # Declare the return variable.
     my $entity = $self->GetEntity($entityType, $ID);  
     # Declare the return list.  
3270      my @retVal = ();      my @retVal = ();
3271      # If we found the entity, push the values into the return list.      # Build the map.
3272      if ($entity) {      for my $mappedName (@{$mappedNameListRef}) {
3273          push @retVal, $entity->Values($fields);          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3274      }      }
3275      # Return the result.      # Return it.
3276      return @retVal;      return @retVal;
3277  }  }
3278    
 =head3 GetAll  
   
 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
3279    
3280  Return a list of values taken from the objects returned by a query. The first three  =head3 _SetupSQL
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
3281    
3282  The list returned will be a list of lists. Each element of the list will contain  Process a list of object names and a filter clause so that they can be used to
3283  the values returned for the fields specified in the fourth parameter. If one of the  build an SQL statement. This method takes in a reference to a list of object names
3284  fields specified returns multiple values, they are flattened in with the rest. For  and a filter clause. It will return a corrected filter clause, a list of mapped
3285  example, the following call will return a list of the features in a particular  names and the mapped name hash.
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
3286    
3287  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  This is an instance method.
3288    
3289  =over 4  =over 4
3290    
3291  =item objectNames  =item objectNames
3292    
3293  List containing the names of the entity and relationship objects to be retrieved.  Reference to a list of the object names to be included in the query.
3294    
3295  =item filterClause  =item filterClause
3296    
3297  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  A string containing the WHERE clause for the query (without the C<WHERE>) and also
3298  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  optionally the C<ORDER BY> and C<LIMIT> clauses.
 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.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item fields  
   
 List of the fields to be returned in each element of the list returned.  
3299    
3300  =item count  =item matchClause
3301    
3302  Maximum number of records to return. If omitted or 0, all available records will be returned.  An optional full-text search clause. If specified, it will be inserted at the
3303    front of the WHERE clause. It should already be SQL-formatted; that is, the
3304    field names should be in the form I<table>C<.>I<fieldName>.
3305    
3306  =item RETURN  =item RETURN
3307    
3308  Returns a list of list references. Each element of the return list contains the values for the  Returns a three-element list. The first element is the SQL statement suffix, beginning
3309  fields specified in the B<fields> parameter.  with the FROM clause. The second element is a reference to a list of the names to be
3310    used in retrieving the fields. The third element is a hash mapping the names to the
3311    objects they represent.
3312    
3313  =back  =back
3314    
3315  =cut  =cut
3316  #: Return Type @@;  
3317  sub GetAll {  sub _SetupSQL {
3318      # Get the parameters.      my ($self, $objectNames, $filterClause, $matchClause) = @_;
3319      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Adjust the list of object names to account for multiple occurrences of the
3320      # Translate the parameters from a list reference to a list. If the parameter      # same object. We start with a hash table keyed on object name that will
3321      # list is a scalar we convert it into a singleton list.      # return the object suffix. The first time an object is encountered it will
3322      my @parmList = ();      # not be found in the hash. The next time the hash will map the object name
3323      if (ref $parameterList eq "ARRAY") {      # to 2, then 3, and so forth.
3324          @parmList = @{$parameterList};      my %objectHash = ();
3325        # This list will contain the object names as they are to appear in the
3326        # FROM list.
3327        my @fromList = ();
3328        # This list contains the suffixed object name for each object. It is exactly
3329        # parallel to the list in the $objectNames parameter.
3330        my @mappedNameList = ();
3331        # Finally, this hash translates from a mapped name to its original object name.
3332        my %mappedNameHash = ();
3333        # Now we create the lists. Note that for every single name we push something into
3334        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3335        # parallel to $objectNames.
3336        for my $objectName (@{$objectNames}) {
3337            # Get the next suffix for this object.
3338            my $suffix = $objectHash{$objectName};
3339            if (! $suffix) {
3340                # Here we are seeing the object for the first time. The object name
3341                # is used as is.
3342                push @mappedNameList, $objectName;
3343                push @fromList, $objectName;
3344                $mappedNameHash{$objectName} = $objectName;
3345                # Denote the next suffix will be 2.
3346                $objectHash{$objectName} = 2;
3347      } else {      } else {
3348          push @parmList, $parameterList;              # Here we've seen the object before. We construct a new name using
3349                # the suffix from the hash and update the hash.
3350                my $mappedName = "$objectName$suffix";
3351                $objectHash{$objectName} = $suffix + 1;
3352                # The FROM list has the object name followed by the mapped name. This
3353                # tells SQL it's still the same table, but we're using a different name
3354                # for it to avoid confusion.
3355                push @fromList, "$objectName $mappedName";
3356                # The mapped-name list contains the real mapped name.
3357                push @mappedNameList, $mappedName;
3358                # Finally, enable us to get back from the mapped name to the object name.
3359                $mappedNameHash{$mappedName} = $objectName;
3360      }      }
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, @parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
     # Insure the counter has a value.  
     if (!defined $count) {  
         $count = 0;  
3361      }      }
3362      # Loop through the records returned, extracting the fields. Note that if the      # Begin the SELECT suffix. It starts with
3363      # counter is non-zero, we stop when the number of records read hits the count.      #
3364      my @retVal = ();      # FROM name1, name2, ... nameN
3365      while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {      #
3366          my @rowData = $row->Values($fields);      my $suffix = "FROM " . join(', ', @fromList);
3367          push @retVal, \@rowData;      # Now for the WHERE. First, we need a place for the filter string.
3368          $fetched++;      my $filterString = "";
3369        # We will also keep a list of conditions to add to the WHERE clause in order to link
3370        # entities and relationships as well as primary relations to secondary ones.
3371        my @joinWhere = ();
3372        # Check for a filter clause.
3373        if ($filterClause) {
3374            # Here we have one, so we convert its field names and add it to the query. First,
3375            # We create a copy of the filter string we can work with.
3376            $filterString = $filterClause;
3377            # Next, we sort the object names by length. This helps protect us from finding
3378            # object names inside other object names when we're doing our search and replace.
3379            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3380            # The final preparatory step is to create a hash table of relation names. The
3381            # table begins with the relation names already in the SELECT command. We may
3382            # need to add relations later if there is filtering on a field in a secondary
3383            # relation. The secondary relations are the ones that contain multiply-
3384            # occurring or optional fields.
3385            my %fromNames = map { $_ => 1 } @sortedNames;
3386            # We are ready to begin. We loop through the object names, replacing each
3387            # object name's field references by the corresponding SQL field reference.
3388            # Along the way, if we find a secondary relation, we will need to add it
3389            # to the FROM clause.
3390            for my $mappedName (@sortedNames) {
3391                # Get the length of the object name plus 2. This is the value we add to the
3392                # size of the field name to determine the size of the field reference as a
3393                # whole.
3394                my $nameLength = 2 + length $mappedName;
3395                # Get the real object name for this mapped name.
3396                my $objectName = $mappedNameHash{$mappedName};
3397                Trace("Processing $mappedName for object $objectName.") if T(4);
3398                # Get the object's field list.
3399                my $fieldList = $self->GetFieldTable($objectName);
3400                # Find the field references for this object.
3401                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3402                    # At this point, $1 contains the field name, and the current position
3403                    # is set immediately after the final parenthesis. We pull out the name of
3404                    # the field and the position and length of the field reference as a whole.
3405                    my $fieldName = $1;
3406                    my $len = $nameLength + length $fieldName;
3407                    my $pos = pos($filterString) - $len;
3408                    # Insure the field exists.
3409                    if (!exists $fieldList->{$fieldName}) {
3410                        Confess("Field $fieldName not found for object $objectName.");
3411                    } else {
3412                        Trace("Processing $fieldName at position $pos.") if T(4);
3413                        # Get the field's relation.
3414                        my $relationName = $fieldList->{$fieldName}->{relation};
3415                        # Now we have a secondary relation. We need to insure it matches the
3416                        # mapped name of the primary relation. First we peel off the suffix
3417                        # from the mapped name.
3418                        my $mappingSuffix = substr $mappedName, length($objectName);
3419                        # Put the mapping suffix onto the relation name to get the
3420                        # mapped relation name.
3421                        my $mappedRelationName = "$relationName$mappingSuffix";
3422                        # Insure the relation is in the FROM clause.
3423                        if (!exists $fromNames{$mappedRelationName}) {
3424                            # Add the relation to the FROM clause.
3425                            if ($mappedRelationName eq $relationName) {
3426                                # The name is un-mapped, so we add it without
3427                                # any frills.
3428                                $suffix .= ", $relationName";
3429                                push @joinWhere, "$objectName.id = $relationName.id";
3430                            } else {
3431                                # Here we have a mapping situation.
3432                                $suffix .= ", $relationName $mappedRelationName";
3433                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3434                            }
3435                            # Denote we have this relation available for future fields.
3436                            $fromNames{$mappedRelationName} = 1;
3437                        }
3438                        # Form an SQL field reference from the relation name and the field name.
3439                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3440                        # Put it into the filter string in place of the old value.
3441                        substr($filterString, $pos, $len) = $sqlReference;
3442                        # Reposition the search.
3443                        pos $filterString = $pos + length $sqlReference;
3444      }      }
3445      # Return the resulting list.              }
3446      return @retVal;          }
3447        }
3448        # The next step is to join the objects together. We only need to do this if there
3449        # is more than one object in the object list. We start with the first object and
3450        # run through the objects after it. Note also that we make a safety copy of the
3451        # list before running through it, because we shift off the first object before
3452        # processing the rest.
3453        my @mappedObjectList = @mappedNameList;
3454        my $lastMappedObject = shift @mappedObjectList;
3455        # Get the join table.
3456        my $joinTable = $self->{_metaData}->{Joins};
3457        # Loop through the object list.
3458        for my $thisMappedObject (@mappedObjectList) {
3459            # Look for a join using the real object names.
3460            my $lastObject = $mappedNameHash{$lastMappedObject};
3461            my $thisObject = $mappedNameHash{$thisMappedObject};
3462            my $joinKey = "$lastObject/$thisObject";
3463            if (!exists $joinTable->{$joinKey}) {
3464                # Here there's no join, so we throw an error.
3465                Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3466            } else {
3467                # Get the join clause.
3468                my $unMappedJoin = $joinTable->{$joinKey};
3469                # Fix the names.
3470                $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3471                $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3472                push @joinWhere, $unMappedJoin;
3473                # Save this object as the last object for the next iteration.
3474                $lastMappedObject = $thisMappedObject;
3475            }
3476        }
3477        # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3478        # here is we want the filter clause to be empty if there's no WHERE filter.
3479        # We'll put the ORDER BY / LIMIT clauses in the following variable.
3480        my $orderClause = "";
3481        # This is only necessary if we have a filter string in which the ORDER BY
3482        # and LIMIT clauses can live.
3483        if ($filterString) {
3484            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3485            # operator so that we find the first occurrence of either verb.
3486            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3487                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3488                my $pos = pos $filterString;
3489                $orderClause = $2 . substr($filterString, $pos);
3490                $filterString = $1;
3491            }
3492        }
3493        # All the things that are supposed to be in the WHERE clause of the
3494        # SELECT command need to be put into @joinWhere so we can string them
3495        # together. We begin with the match clause. This is important,
3496        # because the match clause's parameter mark must precede any parameter
3497        # marks in the filter string.
3498        if ($matchClause) {
3499            push @joinWhere, $matchClause;
3500        }
3501        # Add the filter string. We put it in parentheses to avoid operator
3502        # precedence problems with the match clause or the joins.
3503        if ($filterString) {
3504            Trace("Filter string is \"$filterString\".") if T(4);
3505            push @joinWhere, "($filterString)";
3506        }
3507        # String it all together into a big filter clause.
3508        if (@joinWhere) {
3509            $suffix .= " WHERE " . join(' AND ', @joinWhere);
3510        }
3511        # Add the sort or limit clause (if any).
3512        if ($orderClause) {
3513            $suffix .= " $orderClause";
3514        }
3515        # Return the suffix, the mapped name list, and the mapped name hash.
3516        return ($suffix, \@mappedNameList, \%mappedNameHash);
3517  }  }
3518    
3519  =head3 EstimateRowSize  =head3 _GetStatementHandle
3520    
3521  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  This method will prepare and execute an SQL query, returning the statement handle.
3522    The main reason for doing this here is so that everybody who does SQL queries gets
3523    the benefit of tracing.
3524    
3525  Estimate the row size of the specified relation. The estimated row size is computed by adding  This is an instance method.
 up the average length for each data type.  
3526    
3527  =over 4  =over 4
3528    
3529  =item relName  =item command
3530    
3531  Name of the relation whose estimated row size is desired.  Command to prepare and execute.
3532    
3533    =item params
3534    
3535    Reference to a list of the values to be substituted in for the parameter marks.
3536    
3537  =item RETURN  =item RETURN
3538    
3539  Returns an estimate of the row size for the specified relation.  Returns a prepared and executed statement handle from which the caller can extract
3540    results.
3541    
3542  =back  =back
3543    
3544  =cut  =cut
3545  #: Return Type $;  
3546  sub EstimateRowSize {  sub _GetStatementHandle {
3547      # Get the parameters.      # Get the parameters.
3548      my ($self, $relName) = @_;      my ($self, $command, $params) = @_;
3549      # Declare the return variable.      # Trace the query.
3550      my $retVal = 0;      Trace("SQL query: $command") if T(SQL => 3);
3551      # Find the relation descriptor.      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3552      my $relation = $self->_FindRelation($relName);      # Get the database handle.
3553      # Get the list of fields.      my $dbh = $self->{_dbh};
3554      for my $fieldData (@{$relation->{Fields}}) {      # Prepare the command.
3555          # Get the field type and add its length.      my $sth = $dbh->prepare_command($command);
3556          my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};      # Execute it with the parameters bound in.
3557          $retVal += $fieldLen;      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
3558      }      # Return the statement handle.
3559      # Return the result.      return $sth;
     return $retVal;  
3560  }  }
3561    
3562  =head2 Internal Utility Methods  =head3 _GetLoadStats
   
 =head3 GetLoadStats  
3563    
3564  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
3565    
3566  This is a static method.  This is a static method.
3567    
3568  =cut  =cut
3569    
3570  sub _GetLoadStats {  sub _GetLoadStats{
3571      return Stats->new('records');      return Stats->new();
 }  
   
 =head3 GenerateFields  
   
 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;  
             }  
         }  
     }  
3572  }  }
3573    
3574  =head3 DumpRelation  =head3 _DumpRelation
3575    
3576  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.
3577    
3578  This is an instance method.  This is an instance method.
3579    
# Line 1781  Line 3621 
3621      close DTXOUT;      close DTXOUT;
3622  }  }
3623    
3624  =head3 GetStructure  =head3 _GetStructure
3625    
3626  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
3627    
# Line 1820  Line 3660 
3660      return $retVal;      return $retVal;
3661  }  }
3662    
3663  =head3 GetRelationTable  
3664    
3665    =head3 _GetRelationTable
3666    
3667  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
3668    
# Line 1849  Line 3691 
3691      return $objectData->{Relations};      return $objectData->{Relations};
3692  }  }
3693    
3694  =head3 GetFieldTable  =head3 _ValidateFieldNames
   
 Get the field structure for a specified entity or relationship.  
   
 This is an instance method.  
   
 =over 4  
   
 =item objectName  
   
 Name of the desired entity or relationship.  
   
 =item RETURN  
   
 The table containing the field descriptors for the specified object.  
   
 =back  
   
 =cut  
   
 sub _GetFieldTable {  
     # Get the parameters.  
     my ($self, $objectName) = @_;  
     # Get the descriptor from the metadata.  
     my $objectData = $self->_GetStructure($objectName);  
     # Return the object's field table.  
     return $objectData->{Fields};  
 }  
   
 =head3 ValidateFieldNames  
3695    
3696  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
3697  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 1905  Line 3718 
3718          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
3719              # Loop through the object's fields.              # Loop through the object's fields.
3720              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
3721                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
3722                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
3723                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($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";  
3724                          $retVal = 0;                          $retVal = 0;
3725                      }                      }
3726                  }                  }
3727              }              }
3728          }          }
     }  
3729      # If an error was found, fail.      # If an error was found, fail.
3730      if ($retVal  == 0) {      if ($retVal  == 0) {
3731          Confess("Errors found in field names.");          Confess("Errors found in field names.");
3732      }      }
3733  }  }
3734    
3735  =head3 LoadRelation  =head3 _LoadRelation
3736    
3737  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
3738  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 1993  Line 3792 
3792      return $retVal;      return $retVal;
3793  }  }
3794    
3795  =head3 LoadMetaData  
3796    =head3 _LoadMetaData
3797    
3798  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
3799  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 2018  Line 3818 
3818  sub _LoadMetaData {  sub _LoadMetaData {
3819      # Get the parameters.      # Get the parameters.
3820      my ($filename) = @_;      my ($filename) = @_;
3821      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
3822      # 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
3823      # get the exact structure we want.      # get the exact structure we want.
3824      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 $filename.") if T(1);  
3825      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
3826      # the method below will fail.      # the method below will fail.
3827      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 2164  Line 3951 
3951              my $count = 0;              my $count = 0;
3952              for my $index (@{$indexList}) {              for my $index (@{$indexList}) {
3953                  # Add this index to the index table.                  # Add this index to the index table.
3954                  _AddIndex("idx$relationName$count", $relation, $index);                  _AddIndex("idx$count", $relation, $index);
3955                  # Increment the counter so that the next index has a different name.                  # Increment the counter so that the next index has a different name.
3956                  $count++;                  $count++;
3957              }              }
# Line 2225  Line 4012 
4012          my @fromList = ();          my @fromList = ();
4013          my @toList = ();          my @toList = ();
4014          my @bothList = ();          my @bothList = ();
4015          Trace("Join table build for $entityName.") if T(4);          Trace("Join table build for $entityName.") if T(metadata => 4);
4016          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
4017              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
4018              # Determine if this relationship has our entity in one of its link fields.              # Determine if this relationship has our entity in one of its link fields.
4019              my $fromEntity = $relationship->{from};              my $fromEntity = $relationship->{from};
4020              my $toEntity = $relationship->{to};              my $toEntity = $relationship->{to};
4021              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4022              if ($fromEntity eq $entityName) {              if ($fromEntity eq $entityName) {
4023                  if ($toEntity eq $entityName) {                  if ($toEntity eq $entityName) {
4024                      # Here the relationship is recursive.                      # Here the relationship is recursive.
4025                      push @bothList, $relationshipName;                      push @bothList, $relationshipName;
4026                      Trace("Relationship $relationshipName put in both-list.") if T(4);                      Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
4027                  } else {                  } else {
4028                      # Here the relationship comes from the entity.                      # Here the relationship comes from the entity.
4029                      push @fromList, $relationshipName;                      push @fromList, $relationshipName;
4030                      Trace("Relationship $relationshipName put in from-list.") if T(4);                      Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
4031                  }                  }
4032              } elsif ($toEntity eq $entityName) {              } elsif ($toEntity eq $entityName) {
4033                  # Here the relationship goes to the entity.                  # Here the relationship goes to the entity.
4034                  push @toList, $relationshipName;                  push @toList, $relationshipName;
4035                  Trace("Relationship $relationshipName put in to-list.") if T(4);                  Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
4036              }              }
4037          }          }
4038          # Create the nonrecursive joins. Note that we build two hashes for running          # Create the nonrecursive joins. Note that we build two hashes for running
# Line 2261  Line 4048 
4048                  # Create joins between the entity and this relationship.                  # Create joins between the entity and this relationship.
4049                  my $linkField = "$relationshipName.${linkType}_link";                  my $linkField = "$relationshipName.${linkType}_link";
4050                  my $joinClause = "$entityName.id = $linkField";                  my $joinClause = "$entityName.id = $linkField";
4051                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(4);                  Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
4052                  $joinTable{"$entityName/$relationshipName"} = $joinClause;                  $joinTable{"$entityName/$relationshipName"} = $joinClause;
4053                  $joinTable{"$relationshipName/$entityName"} = $joinClause;                  $joinTable{"$relationshipName/$entityName"} = $joinClause;
4054                  # Create joins between this relationship and the other relationships.                  # Create joins between this relationship and the other relationships.
# Line 2282  Line 4069 
4069                              # relationship and itself are prohibited.                              # relationship and itself are prohibited.
4070                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";                              my $relJoinClause = "$otherName.${otherType}_link = $linkField";
4071                              $joinTable{$joinKey} = $relJoinClause;                              $joinTable{$joinKey} = $relJoinClause;
4072                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(4);                              Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
4073                          }                          }
4074                      }                      }
4075                  }                  }
# Line 2291  Line 4078 
4078                  # relationship can only be ambiguous with another recursive relationship,                  # relationship can only be ambiguous with another recursive relationship,
4079                  # and the incoming relationship from the outer loop is never recursive.                  # and the incoming relationship from the outer loop is never recursive.
4080                  for my $otherName (@bothList) {                  for my $otherName (@bothList) {
4081                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(4);                      Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
4082                      # Join from the left.                      # Join from the left.
4083                      $joinTable{"$relationshipName/$otherName"} =                      $joinTable{"$relationshipName/$otherName"} =
4084                          "$linkField = $otherName.from_link";                          "$linkField = $otherName.from_link";
# Line 2306  Line 4093 
4093          # rise to situations where we can't create the path we want; however, it is always          # rise to situations where we can't create the path we want; however, it is always
4094          # possible to get the same effect using multiple queries.          # possible to get the same effect using multiple queries.
4095          for my $relationshipName (@bothList) {          for my $relationshipName (@bothList) {
4096              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(4);              Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
4097              # Join to the entity from each direction.              # Join to the entity from each direction.
4098              $joinTable{"$entityName/$relationshipName"} =              $joinTable{"$entityName/$relationshipName"} =
4099                  "$entityName.id = $relationshipName.from_link";                  "$entityName.id = $relationshipName.from_link";
# Line 2320  Line 4107 
4107      return $metadata;      return $metadata;
4108  }  }
4109    
4110  =head3 CreateRelationshipIndex  =head3 _CreateRelationshipIndex
4111    
4112  Create an index for a relationship's relation.  Create an index for a relationship's relation.
4113    
# Line 2362  Line 4149 
4149          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
4150      }      }
4151      # Add the index to the relation.      # Add the index to the relation.
4152      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4153  }  }
4154    
4155  =head3 AddIndex  =head3 _AddIndex
4156    
4157  Add an index to a relation structure.  Add an index to a relation structure.
4158    
# Line 2411  Line 4198 
4198      $relationStructure->{Indexes}->{$indexName} = $newIndex;      $relationStructure->{Indexes}->{$indexName} = $newIndex;
4199  }  }
4200    
4201  =head3 FixupFields  =head3 _FixupFields
4202    
4203  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
4204  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 2449  Line 4236 
4236          # Here it doesn't, so we create a new one.          # Here it doesn't, so we create a new one.
4237          $structure->{Fields} = { };          $structure->{Fields} = { };
4238      } else {      } else {
4239          # 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
4240            # create a list for stashing them.
4241            my @textFields = ();
4242            # Loop through the fields.
4243          my $fieldStructures = $structure->{Fields};          my $fieldStructures = $structure->{Fields};
4244          for my $fieldName (keys %{$fieldStructures}) {          for my $fieldName (keys %{$fieldStructures}) {
4245              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
# Line 2458  Line 4248 
4248              my $type = $fieldData->{type};              my $type = $fieldData->{type};
4249              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
4250              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4251              # Plug in a data generator if we need one.              # Check for searchability.
4252              if (!exists $fieldData->{DataGen}) {              if ($fieldData->{searchable}) {
4253                  # The data generator will use the default for the field's type.                  # Only allow this for a primary relation.
4254                  $fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };                  if ($fieldData->{relation} ne $defaultRelationName) {
4255                        Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4256                    } else {
4257                        push @textFields, $fieldName;
4258                    }
4259              }              }
             # Plug in the defaults for the optional data generation parameters.  
             Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });  
4260              # Add the PrettySortValue.              # Add the PrettySortValue.
4261              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);              $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4262          }          }
4263            # If there are searchable fields, remember the fact.
4264            if (@textFields) {
4265                $structure->{searchFields} = \@textFields;
4266            }
4267      }      }
4268  }  }
4269    
4270  =head3 FixName  =head3 _FixName
4271    
4272  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.
4273    
# Line 2500  Line 4296 
4296      return $fieldName;      return $fieldName;
4297  }  }
4298    
4299  =head3 FixNames  =head3 _FixNames
4300    
4301  Fix all the field names in a list.  Fix all the field names in a list.
4302    
# Line 2531  Line 4327 
4327      return @result;      return @result;
4328  }  }
4329    
4330  =head3 AddField  =head3 _AddField
4331    
4332  Add a field to a field list.  Add a field to a field list.
4333    
# Line 2566  Line 4362 
4362      $fieldList->{$fieldName} = $fieldStructure;      $fieldList->{$fieldName} = $fieldStructure;
4363  }  }
4364    
4365  =head3 ReOrderRelationTable  =head3 _ReOrderRelationTable
4366    
4367  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
4368  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 2627  Line 4423 
4423    
4424  }  }
4425    
4426  =head3 IsPrimary  =head3 _IsPrimary
4427    
4428  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
4429  if it has the same name as an entity or relationship.  if it has the same name as an entity or relationship.
# Line 2663  Line 4459 
4459      return $retVal;      return $retVal;
4460  }  }
4461    
4462  =head3 FindRelation  =head3 _FindRelation
4463    
4464  Return the descriptor for the specified relation.  Return the descriptor for the specified relation.
4465    
# Line 2694  Line 4490 
4490    
4491  =head2 HTML Documentation Utility Methods  =head2 HTML Documentation Utility Methods
4492    
4493  =head3 ComputeRelationshipSentence  =head3 _ComputeRelationshipSentence
4494    
4495  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
4496  two related entities and an arity indicator.  two related entities and an arity indicator.
# Line 2732  Line 4528 
4528      return $result;      return $result;
4529  }  }
4530    
4531  =head3 ComputeRelationshipHeading  =head3 _ComputeRelationshipHeading
4532    
4533  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity  The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
4534  names hyperlinked to the appropriate entity sections of the document.  names hyperlinked to the appropriate entity sections of the document.
# Line 2769  Line 4565 
4565      return $result;      return $result;
4566  }  }
4567    
4568  =head3 ShowRelationTable  =head3 _ShowRelationTable
4569    
4570  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
4571  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 2819  Line 4615 
4615          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";          $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
4616          # Add any note text.          # Add any note text.
4617          if (my $note = $indexData->{Notes}) {          if (my $note = $indexData->{Notes}) {
4618              $htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";              $htmlString .= "<li>" . HTMLNote($note->{content}) . "</li>\n";
4619          }          }
4620          # Add the fiield list.          # Add the fiield list.
4621          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";          $htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
# Line 2830  Line 4626 
4626      $htmlString .= "</ul>\n";      $htmlString .= "</ul>\n";
4627  }  }
4628    
4629  =head3 OpenFieldTable  =head3 _OpenFieldTable
4630    
4631  This method creates the header string for the field table generated by L</ShowMetaData>.  This method creates the header string for the field table generated by L</ShowMetaData>.
4632    
# Line 2855  Line 4651 
4651      return _OpenTable($tablename, 'Field', 'Type', 'Description');      return _OpenTable($tablename, 'Field', 'Type', 'Description');
4652  }  }
4653    
4654  =head3 OpenTable  =head3 _OpenTable
4655    
4656  This method creates the header string for an HTML table.  This method creates the header string for an HTML table.
4657    
# Line 2895  Line 4691 
4691      return $htmlString;      return $htmlString;
4692  }  }
4693    
4694  =head3 CloseTable  =head3 _CloseTable
4695    
4696  This method returns the HTML for closing a table.  This method returns the HTML for closing a table.
4697    
# Line 2907  Line 4703 
4703      return "</table></p>\n";      return "</table></p>\n";
4704  }  }
4705    
4706  =head3 ShowField  =head3 _ShowField
4707    
4708  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.
4709    
# Line 2934  Line 4730 
4730      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>";
4731      # If we have content, add it as a third column.      # If we have content, add it as a third column.
4732      if (exists $fieldData->{Notes}) {      if (exists $fieldData->{Notes}) {
4733          $htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";          $htmlString .= "<td>" . HTMLNote($fieldData->{Notes}->{content}) . "</td>";
4734      }      }
4735      # Close off the row.      # Close off the row.
4736      $htmlString .= "</tr>\n";      $htmlString .= "</tr>\n";
# Line 2942  Line 4738 
4738      return $htmlString;      return $htmlString;
4739  }  }
4740    
 =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