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revision 1.26, Tue Oct 18 06:47:46 2005 UTC revision 1.80, Thu Nov 30 23:04:01 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 222  Line 257 
257    
258  =back  =back
259    
260  The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.  The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
261    have a B<Unique> attribute. If specified, the index will be generated as a unique
262    index.
263    
264  =head3 Object and Field Names  =head3 Object and Field Names
265    
# Line 300  Line 337 
337    
338  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
339  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
340  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "avgLen" is the average byte length for estimating
341  # string is specified in the field definition. "avgLen" is the average byte length for estimating  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
342  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
343  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
344                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
345                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
346                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
347                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
348                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
349                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   2, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
350                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
351                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
352                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
353                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
355                                   indexMod =>   0, notes => "signed, 64-bit integer"},
356                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
357                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
358                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
359                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
360                     'hash-string' =>
361                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
362                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
363                     'id-string' =>
364                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
365                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
366                   'key-string' =>                   'key-string' =>
367                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
368                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
369                   'name-string' =>                   'name-string' =>
370                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
371                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
372                   'medium-string' =>                   'medium-string' =>
373                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                  );                  );
376    
377  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 324  Line 380 
380                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
381                   );                   );
382    
383  # Table for interpreting string patterns.  # Options for XML input and output.
384    
385    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
386                                      Entities => 'Entity',
387                                      Fields => 'Field',
388                                      Indexes => 'Index',
389                                      IndexFields => 'IndexField'
390                                    },
391                      KeyAttr =>    { Relationship => 'name',
392                                      Entity => 'name',
393                                      Field => 'name'
394                                    },
395                      SuppressEmpty => 1,
396                     );
397    
398  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
399                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
400                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
401                       'V' => "aeiou",                    NormalizeSpace => 2,
                      'K' => "bcdfghjklmnoprstvwxyz"  
402                     );                     );
403    my %XmlOutOpts = (
404                      RootName => 'Database',
405                      XMLDecl => 1,
406                     );
407    
408    
409  =head2 Public Methods  =head2 Public Methods
410    
# Line 402  Line 475 
475      # Write the HTML heading stuff.      # Write the HTML heading stuff.
476      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
477      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
478        # Write the documentation.
479        print HTMLOUT $self->DisplayMetaData();
480        # Close the document.
481        print HTMLOUT "</body>\n</html>\n";
482        # Close the file.
483        close HTMLOUT;
484    }
485    
486    =head3 DisplayMetaData
487    
488    C<< my $html = $erdb->DisplayMetaData(); >>
489    
490    Return an HTML description of the database. This description can be used to help users create
491    the data to be loaded into the relations and form queries. The output is raw includable HTML
492    without any HEAD or BODY tags.
493    
494    =over 4
495    
496    =item filename
497    
498    The name of the output file.
499    
500    =back
501    
502    =cut
503    
504    sub DisplayMetaData {
505        # Get the parameters.
506        my ($self) = @_;
507        # Get the metadata and the title string.
508        my $metadata = $self->{_metaData};
509        # Get the title string.
510        my $title = $metadata->{Title};
511        # Get the entity and relationship lists.
512        my $entityList = $metadata->{Entities};
513        my $relationshipList = $metadata->{Relationships};
514        # Declare the return variable.
515        my $retVal = "";
516        # Open the output file.
517        Trace("Building MetaData table of contents.") if T(4);
518      # 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
519      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
520      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";
521      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
522      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
523          # Display this item.          # Display this item.
524          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
525      }      }
526      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
527      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";
528      # Loop through the Relationships.      # Loop through the Relationships.
529      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
530          # Display this item.          # Display this item.
531          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
532          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
533      }      }
534      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
535      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";
536      # Close off the table of contents itself.      # Close off the table of contents itself.
537      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
538      # 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.
539      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
540      # Loop through the entities.      # Loop through the entities.
541      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
542          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
543          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
544          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
545          # Get the entity data.          # Get the entity data.
546          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
547          # If there's descriptive text, display it.          # If there's descriptive text, display it.
548          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
549              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
550          }          }
551          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
552          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
553          # Loop through the relationships.          # Loop through the relationships.
554          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
555              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 559 
559                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
560                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
561                  # Display the relationship data.                  # Display the relationship data.
562                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
563              }              }
564          }          }
565          # Close off the relationship list.          # Close off the relationship list.
566          print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
567          # Get the entity's relations.          # Get the entity's relations.
568          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
569          # Create a header for the relation subsection.          # Create a header for the relation subsection.
570          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
571          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
572          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
573              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
574              print HTMLOUT $htmlString;              $retVal .= $htmlString;
575          }          }
576      }      }
577      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
578      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
579      # Loop through the relationships.      # Loop through the relationships.
580      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
581          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 583 
583          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
584          # Create the relationship header.          # Create the relationship header.
585          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
586          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
587          # Get the entity names.          # Get the entity names.
588          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
589          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 593 
593          # since both sentences will say the same thing.          # since both sentences will say the same thing.
594          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
595          if ($arity eq "11") {          if ($arity eq "11") {
596              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
597          } else {          } else {
598              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
599              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
600                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
601              }              }
602          }          }
603          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
604          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
605          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
606              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
607          }          }
608          # Generate the relationship's relation table.          # Generate the relationship's relation table.
609          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
610          print HTMLOUT $htmlString;          $retVal .= $htmlString;
611      }      }
612      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
613      # Denote we're starting the join table.      # Denote we're starting the join table.
614      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
615      # Create a table header.      # Create a table header.
616      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
617      # Loop through the joins.      # Loop through the joins.
618      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
619      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 508  Line 621 
621          # Separate out the source, the target, and the join clause.          # Separate out the source, the target, and the join clause.
622          $joinKey =~ m!^([^/]+)/(.+)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
623          my ($sourceRelation, $targetRelation) = ($1, $2);          my ($sourceRelation, $targetRelation) = ($1, $2);
624          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);
625          my $source = $self->ComputeObjectSentence($sourceRelation);          my $source = $self->ComputeObjectSentence($sourceRelation);
626          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
627          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
628          # Display them in a table row.          # Display them in a table row.
629          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";
630      }      }
631      # Close the table.      # Close the table.
632      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
633      # Close the document.      Trace("Built MetaData HTML.") if T(3);
634      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
635      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
636  }  }
637    
638  =head3 DumpMetaData  =head3 DumpMetaData
# Line 539  Line 650 
650      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
651  }  }
652    
653    =head3 FindIndexForEntity
654    
655    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
656    
657    This method locates the entry in an entity's index list that begins with the
658    specified attribute name. If the entity has no index list, one will be
659    created. This method works on raw XML, not a live ERDB object.
660    
661    =over 4
662    
663    =item xml
664    
665    The raw XML structure defining the database.
666    
667    =item entityName
668    
669    The name of the relevant entity.
670    
671    =item attributeName
672    
673    The name of the attribute relevant to the search.
674    
675    =item RETURN
676    
677    The numerical index in the index list of the index entry for the specified entity and
678    attribute, or C<undef> if no such index exists.
679    
680    =back
681    
682    =cut
683    
684    sub FindIndexForEntity {
685        # Get the parameters.
686        my ($xml, $entityName, $attributeName) = @_;
687        # Declare the return variable.
688        my $retVal;
689        # Get the named entity.
690        my $entityData = $xml->{Entities}->{$entityName};
691        if (! $entityData) {
692            Confess("Entity $entityName not found in DBD structure.");
693        } else {
694            # Insure it has an index list.
695            if (! exists $entityData->{Indexes}) {
696                $entityData->{Indexes} = [];
697            } else {
698                # Search for the desired index.
699                my $indexList = $entityData->{Indexes};
700                my $n = scalar @{$indexList};
701                Trace("Searching $n indexes in index list for $entityName.") if T(2);
702                # We use an indexed FOR here because we're returning an
703                # index number instead of an object. We do THAT so we can
704                # delete the index from the list if needed.
705                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
706                    my $index = $indexList->[$i];
707                    my $fields = $index->{IndexFields};
708                    # Technically this IF should be safe (that is, we are guaranteed
709                    # the existence of a "$fields->[0]"), because when we load the XML
710                    # we have SuppressEmpty specified.
711                    if ($fields->[0]->{name} eq $attributeName) {
712                        $retVal = $i;
713                    }
714                }
715            }
716        }
717        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
718        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
719        # Return the result.
720        return $retVal;
721    }
722    
723  =head3 CreateTables  =head3 CreateTables
724    
725  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 626  Line 807 
807      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
808      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
809      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
810      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
811        # index will not be built until the table has been loaded.
812      if ($indexFlag) {      if ($indexFlag) {
813          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
814      }      }
815  }  }
816    
817    =head3 VerifyFields
818    
819    C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
820    
821    Run through the list of proposed field values, insuring that all the character fields are
822    below the maximum length. If any fields are too long, they will be truncated in place.
823    
824    =over 4
825    
826    =item relName
827    
828    Name of the relation for which the specified fields are destined.
829    
830    =item fieldList
831    
832    Reference to a list, in order, of the fields to be put into the relation.
833    
834    =item RETURN
835    
836    Returns the number of fields truncated.
837    
838    =back
839    
840    =cut
841    
842    sub VerifyFields {
843        # Get the parameters.
844        my ($self, $relName, $fieldList) = @_;
845        # Initialize the return value.
846        my $retVal = 0;
847        # Get the relation definition.
848        my $relData = $self->_FindRelation($relName);
849        # Get the list of field descriptors.
850        my $fieldTypes = $relData->{Fields};
851        my $fieldCount = scalar @{$fieldTypes};
852        # Loop through the two lists.
853        for (my $i = 0; $i < $fieldCount; $i++) {
854            # Get the type of the current field.
855            my $fieldType = $fieldTypes->[$i]->{type};
856            # If it's a character field, verify the length.
857            if ($fieldType =~ /string/) {
858                my $maxLen = $TypeTable{$fieldType}->{maxLen};
859                my $oldString = $fieldList->[$i];
860                if (length($oldString) > $maxLen) {
861                    # Here it's too big, so we truncate it.
862                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
863                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
864                    $retVal++;
865                }
866            }
867        }
868        # Return the truncation count.
869        return $retVal;
870    }
871    
872    =head3 DigestFields
873    
874    C<< $erdb->DigestFields($relName, $fieldList); >>
875    
876    Digest the strings in the field list that correspond to data type C<hash-string> in the
877    specified relation.
878    
879    =over 4
880    
881    =item relName
882    
883    Name of the relation to which the fields belong.
884    
885    =item fieldList
886    
887    List of field contents to be loaded into the relation.
888    
889    =back
890    
891    =cut
892    #: Return Type ;
893    sub DigestFields {
894        # Get the parameters.
895        my ($self, $relName, $fieldList) = @_;
896        # Get the relation definition.
897        my $relData = $self->_FindRelation($relName);
898        # Get the list of field descriptors.
899        my $fieldTypes = $relData->{Fields};
900        my $fieldCount = scalar @{$fieldTypes};
901        # Loop through the two lists.
902        for (my $i = 0; $i < $fieldCount; $i++) {
903            # Get the type of the current field.
904            my $fieldType = $fieldTypes->[$i]->{type};
905            # If it's a hash string, digest it in place.
906            if ($fieldType eq 'hash-string') {
907                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
908            }
909        }
910    }
911    
912    =head3 DigestKey
913    
914    C<< my $digested = $erdb->DigestKey($keyValue); >>
915    
916    Return the digested value of a symbolic key. The digested value can then be plugged into a
917    key-based search into a table with key-type hash-string.
918    
919    Currently the digesting process is independent of the database structure, but that may not
920    always be the case, so this is an instance method instead of a static method.
921    
922    =over 4
923    
924    =item keyValue
925    
926    Key value to digest.
927    
928    =item RETURN
929    
930    Digested value of the key.
931    
932    =back
933    
934    =cut
935    
936    sub DigestKey {
937        # Get the parameters.
938        my ($self, $keyValue) = @_;
939        # Compute the digest.
940        my $retVal = md5_base64($keyValue);
941        # Return the result.
942        return $retVal;
943    }
944    
945  =head3 CreateIndex  =head3 CreateIndex
946    
947  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 655  Line 965 
965      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
966          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
967          # Get the index's field list.          # Get the index's field list.
968          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
969            # Get a hash of the relation's field types.
970            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
971            # We need to check for text fields so we can append a length limitation for them. To do
972            # that, we need the relation's field list.
973            my $relFields = $relationData->{Fields};
974            for (my $i = 0; $i <= $#rawFields; $i++) {
975                # Get the field type.
976                my $field = $rawFields[$i];
977                my $type = $types{$field};
978                # Ask if it requires using prefix notation for the index.
979                my $mod = $TypeTable{$type}->{indexMod};
980                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
981                if ($mod) {
982                    # Append the prefix length to the field name,
983                    $rawFields[$i] .= "($mod)";
984                }
985            }
986            my @fieldList = _FixNames(@rawFields);
987          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
988          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
989          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
990          # Create the index.          # Create the index.
991          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
992                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
993          if ($rv) {          if ($rv) {
994              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
995          } else {          } else {
# Line 670  Line 998 
998      }      }
999  }  }
1000    
1001    =head3 GetSecondaryFields
1002    
1003    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1004    
1005    This method will return a list of the name and type of each of the secondary
1006    fields for a specified entity. Secondary fields are stored in two-column tables
1007    in addition to the primary entity table. This enables the field to have no value
1008    or to have multiple values.
1009    
1010    =over 4
1011    
1012    =item entityName
1013    
1014    Name of the entity whose secondary fields are desired.
1015    
1016    =item RETURN
1017    
1018    Returns a hash mapping the field names to their field types.
1019    
1020    =back
1021    
1022    =cut
1023    
1024    sub GetSecondaryFields {
1025        # Get the parameters.
1026        my ($self, $entityName) = @_;
1027        # Declare the return variable.
1028        my %retVal = ();
1029        # Look for the entity.
1030        my $table = $self->GetFieldTable($entityName);
1031        # Loop through the fields, pulling out the secondaries.
1032        for my $field (sort keys %{$table}) {
1033            if ($table->{$field}->{relation} ne $entityName) {
1034                # Here we have a secondary field.
1035                $retVal{$field} = $table->{$field}->{type};
1036            }
1037        }
1038        # Return the result.
1039        return %retVal;
1040    }
1041    
1042    =head3 GetFieldRelationName
1043    
1044    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1045    
1046    Return the name of the relation containing a specified field.
1047    
1048    =over 4
1049    
1050    =item objectName
1051    
1052    Name of the entity or relationship containing the field.
1053    
1054    =item fieldName
1055    
1056    Name of the relevant field in that entity or relationship.
1057    
1058    =item RETURN
1059    
1060    Returns the name of the database relation containing the field, or C<undef> if
1061    the field does not exist.
1062    
1063    =back
1064    
1065    =cut
1066    
1067    sub GetFieldRelationName {
1068        # Get the parameters.
1069        my ($self, $objectName, $fieldName) = @_;
1070        # Declare the return variable.
1071        my $retVal;
1072        # Get the object field table.
1073        my $table = $self->GetFieldTable($objectName);
1074        # Only proceed if the field exists.
1075        if (exists $table->{$fieldName}) {
1076            # Determine the name of the relation that contains this field.
1077            $retVal = $table->{$fieldName}->{relation};
1078        }
1079        # Return the result.
1080        return $retVal;
1081    }
1082    
1083    =head3 DeleteValue
1084    
1085    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1086    
1087    Delete secondary field values from the database. This method can be used to delete all
1088    values of a specified field for a particular entity instance, or only a single value.
1089    
1090    Secondary fields are stored in two-column relations separate from an entity's primary
1091    table, and as a result a secondary field can legitimately have no value or multiple
1092    values. Therefore, it makes sense to talk about deleting secondary fields where it
1093    would not make sense for primary fields.
1094    
1095    =over 4
1096    
1097    =item entityName
1098    
1099    Name of the entity from which the fields are to be deleted.
1100    
1101    =item id
1102    
1103    ID of the entity instance to be processed. If the instance is not found, this
1104    method will have no effect. If C<undef> is specified, all values for all of
1105    the entity instances will be deleted.
1106    
1107    =item fieldName
1108    
1109    Name of the field whose values are to be deleted.
1110    
1111    =item fieldValue (optional)
1112    
1113    Value to be deleted. If not specified, then all values of the specified field
1114    will be deleted for the entity instance. If specified, then only the values which
1115    match this parameter will be deleted.
1116    
1117    =item RETURN
1118    
1119    Returns the number of rows deleted.
1120    
1121    =back
1122    
1123    =cut
1124    
1125    sub DeleteValue {
1126        # Get the parameters.
1127        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1128        # Declare the return value.
1129        my $retVal = 0;
1130        # We need to set up an SQL command to do the deletion. First, we
1131        # find the name of the field's relation.
1132        my $table = $self->GetFieldTable($entityName);
1133        my $field = $table->{$fieldName};
1134        my $relation = $field->{relation};
1135        # Make sure this is a secondary field.
1136        if ($relation eq $entityName) {
1137            Confess("Cannot delete values of $fieldName for $entityName.");
1138        } else {
1139            # Set up the SQL command to delete all values.
1140            my $sql = "DELETE FROM $relation";
1141            # Build the filter.
1142            my @filters = ();
1143            my @parms = ();
1144            # Check for a filter by ID.
1145            if (defined $id) {
1146                push @filters, "id = ?";
1147                push @parms, $id;
1148            }
1149            # Check for a filter by value.
1150            if (defined $fieldValue) {
1151                push @filters, "$fieldName = ?";
1152                push @parms, $fieldValue;
1153            }
1154            # Append the filters to the command.
1155            if (@filters) {
1156                $sql .= " WHERE " . join(" AND ", @filters);
1157            }
1158            # Execute the command.
1159            my $dbh = $self->{_dbh};
1160            $retVal = $dbh->SQL($sql, 0, @parms);
1161        }
1162        # Return the result.
1163        return $retVal;
1164    }
1165    
1166  =head3 LoadTables  =head3 LoadTables
1167    
1168  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
# Line 764  Line 1257 
1257      return sort keys %{$entityList};      return sort keys %{$entityList};
1258  }  }
1259    
1260    =head3 GetDataTypes
1261    
1262    C<< my %types = ERDB::GetDataTypes(); >>
1263    
1264    Return a table of ERDB data types. The table returned is a hash of hashes.
1265    The keys of the big hash are the datatypes. Each smaller hash has several
1266    values used to manage the data. The most interesting is the SQL type (key
1267    C<sqlType>) and the descriptive node (key C<notes>).
1268    
1269    Note that changing the values in the smaller hashes will seriously break
1270    things, so this data should be treated as read-only.
1271    
1272    =cut
1273    
1274    sub GetDataTypes {
1275        return %TypeTable;
1276    }
1277    
1278    
1279  =head3 IsEntity  =head3 IsEntity
1280    
1281  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
# Line 793  Line 1305 
1305    
1306  =head3 Get  =head3 Get
1307    
1308  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1309    
1310  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.
1311  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 801  Line 1313 
1313  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
1314  $genus.  $genus.
1315    
1316  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1317    
1318  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
1319  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 818  Line 1330 
1330  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
1331  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,
1332    
1333  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1334    
1335  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
1336  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.
1337  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
1338  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
1339  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  
1340  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,
1341  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.
1342    
1343    If an entity or relationship is mentioned twice, the name for the second occurrence will
1344    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1345    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1346    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1347    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1348    
1349  =over 4  =over 4
1350    
1351  =item objectNames  =item objectNames
# Line 851  Line 1368 
1368    
1369  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1370    
1371    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1372    be processed. The idea is to make it less likely to find the verb by accident.
1373    
1374  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
1375  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
1376  relation.  relation.
1377    
1378  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1379    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1380    a positive number. So, for example
1381    
1382    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1383    
1384  Parameter values to be substituted into the filter clause.  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1385    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1386    use
1387    
1388    C<< "LIMIT 10" >>
1389    
1390    =item params
1391    
1392    Reference to a list of parameter values to be substituted into the filter clause.
1393    
1394  =item RETURN  =item RETURN
1395    
# Line 869  Line 1401 
1401    
1402  sub Get {  sub Get {
1403      # Get the parameters.      # Get the parameters.
1404      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1405      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1406      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1407      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1408      #      # Create the query.
1409      my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1410      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1411                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1412      Trace("SQL = $command") if T(SQL => 4);      # Now we create the relation map, which enables DBQuery to determine the order, name
1413      # Check for a filter clause.      # and mapped name for each object in the query.
1414      if ($filterClause) {      my @relationMap = ();
1415          # Here we have one, so we convert its field names and add it to the query. First,      for my $mappedName (@{$mappedNameListRef}) {
1416          # We create a copy of the filter string we can work with.          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
         my $filterString = $filterClause;  
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($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";  
         }  
1417      }      }
     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());  
1418      # Return the statement object.      # Return the statement object.
1419      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1420      return $retVal;      return $retVal;
1421  }  }
1422    
 =head3 GetList  
1423    
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1424    
1425  Return a list of object descriptors for the specified objects as determined by the  =head3 Search
 specified filter clause.  
1426    
1427  This method is essentially the same as L</Get> except it returns a list of objects rather  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1428  than a query object that can be used to get the results one record at a time.  
1429    Perform a full text search with filtering. The search will be against a specified object
1430    in the object name list. That object will get an extra field containing the search
1431    relevance. Note that except for the search expression, the parameters of this method are
1432    the same as those for L</Get> and follow the same rules.
1433    
1434  =over 4  =over 4
1435    
1436    =item searchExpression
1437    
1438    Boolean search expression for the text fields of the target object. The default mode for
1439    a Boolean search expression is OR, but we want the default to be AND, so we will
1440    add a C<+> operator to each word with no other operator before it.
1441    
1442    =item idx
1443    
1444    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1445    
1446  =item objectNames  =item objectNames
1447    
1448  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 1018  Line 1457 
1457  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
1458  be included in the list of object names.  be included in the list of object names.
1459    
1460  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.  
1461    
1462  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  Reference to a list of parameter values to be substituted into the filter clause.
1463    
1464  The rules for field references in a sort order are the same as those for field references in the  =item RETURN
1465  filter clause in general; however, odd things may happen if a sort field is from a secondary  
1466  relation.  Returns a query object for the specified search.
1467    
1468    =back
1469    
1470    =cut
1471    
1472  =item param1, param2, ..., paramN  sub Search {
1473        # Get the parameters.
1474        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1475        # Declare the return variable.
1476        my $retVal;
1477        # Create a safety copy of the parameter list. Note we have to be careful to insure
1478        # a parameter list exists before we copy it.
1479        my @myParams = ();
1480        if (defined $params) {
1481            @myParams = @{$params};
1482        }
1483        # Get the first object's structure so we have access to the searchable fields.
1484        my $object1Name = $objectNames->[$idx];
1485        my $object1Structure = $self->_GetStructure($object1Name);
1486        # Get the field list.
1487        if (! exists $object1Structure->{searchFields}) {
1488            Confess("No searchable index for $object1Name.");
1489        } else {
1490            # Get the field list.
1491            my @fields = @{$object1Structure->{searchFields}};
1492            # Clean the search expression.
1493            my $actualKeywords = $self->CleanKeywords($searchExpression);
1494            # Prefix a "+" to each uncontrolled word. This converts the default
1495            # search mode from OR to AND.
1496            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1497            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1498            # We need two match expressions, one for the filter clause and one in the
1499            # query itself. Both will use a parameter mark, so we need to push the
1500            # search expression onto the front of the parameter list twice.
1501            unshift @myParams, $actualKeywords, $actualKeywords;
1502            # Build the match expression.
1503            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1504            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1505            # Process the SQL stuff.
1506            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1507                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1508            # Create the query. Note that the match clause is inserted at the front of
1509            # the select fields.
1510            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1511                ".* $suffix";
1512            my $sth = $self->_GetStatementHandle($command, \@myParams);
1513            # Now we create the relation map, which enables DBQuery to determine the order, name
1514            # and mapped name for each object in the query.
1515            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1516            # Return the statement object.
1517            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1518        }
1519        return $retVal;
1520    }
1521    
1522    =head3 GetFlat
1523    
1524    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1525    
1526    This is a variation of L</GetAll> that asks for only a single field per record and
1527    returns a single flattened list.
1528    
1529    =over 4
1530    
1531    =item objectNames
1532    
1533    List containing the names of the entity and relationship objects to be retrieved.
1534    
1535    =item filterClause
1536    
1537    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1538    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1539    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1540    parameter list as additional parameters. The fields in a filter clause can come from primary
1541    entity relations, relationship relations, or secondary entity relations; however, all of the
1542    entities and relationships involved must be included in the list of object names.
1543    
1544    =item parameterList
1545    
1546  Parameter values to be substituted into the filter clause.  List of the parameters to be substituted in for the parameters marks in the filter clause.
1547    
1548    =item field
1549    
1550    Name of the field to be used to get the elements of the list returned.
1551    
1552  =item RETURN  =item RETURN
1553    
1554  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of values.
1555    
1556  =back  =back
1557    
1558  =cut  =cut
1559  #: Return Type @%  #: Return Type @;
1560  sub GetList {  sub GetFlat {
1561      # Get the parameters.      # Get the parameters.
1562      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1563      # Declare the return variable.      # Construct the query.
1564        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1565        # Create the result list.
1566      my @retVal = ();      my @retVal = ();
1567      # Perform the query.      # Loop through the records, adding the field values found to the result list.
1568      my $query = $self->Get($objectNames, $filterClause, @params);      while (my $row = $query->Fetch()) {
1569      # Loop through the results.          push @retVal, $row->Value($field);
     while (my $object = $query->Fetch) {  
         push @retVal, $object;  
1570      }      }
1571      # Return the result.      # Return the list created.
1572      return @retVal;      return @retVal;
1573  }  }
1574    
1575  =head3 ComputeObjectSentence  =head3 SpecialFields
1576    
1577  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my %specials = $erdb->SpecialFields($entityName); >>
1578    
1579  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
1580    C<special> attribute. This enables the subclass to get access to the special field
1581    attributes without needed to plumb the internal ERDB data structures.
1582    
1583  =over 4  =over 4
1584    
1585  =item objectName  =item entityName
1586    
1587  Name of the entity or relationship.  Name of the entity whose special fields are desired.
1588    
1589  =item RETURN  =item RETURN
1590    
1591  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
1592    are the values from each special field's C<special> attribute.
1593    
1594  =back  =back
1595    
1596  =cut  =cut
1597    
1598  sub ComputeObjectSentence {  sub SpecialFields {
1599      # Get the parameters.      # Get the parameters.
1600      my ($self, $objectName) = @_;      my ($self, $entityName) = @_;
1601      # Set the default return value.      # Declare the return variable.
1602      my $retVal = $objectName;      my %retVal = ();
1603      # Look for the object as a relationship.      # Find the entity's data structure.
1604      my $relTable = $self->{_metaData}->{Relationships};      my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1605      if (exists $relTable->{$objectName}) {      # Loop through its fields, adding each special field to the return hash.
1606          # Get the relationship sentence.      my $fieldHash = $entityData->{Fields};
1607          $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});      for my $fieldName (keys %{$fieldHash}) {
1608            my $fieldData = $fieldHash->{$fieldName};
1609            if (exists $fieldData->{special}) {
1610                $retVal{$fieldName} = $fieldData->{special};
1611            }
1612      }      }
1613      # Return the result.      # Return the result.
1614      return $retVal;      return %retVal;
1615  }  }
1616    
1617  =head3 DumpRelations  =head3 Delete
1618    
1619  C<< $erdb->DumpRelations($outputDirectory); >>  C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1620    
1621  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
1622  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.
1623    
1624    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1625    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1626    dependent relationship.
1627    
1628  =over 4  =over 4
1629    
1630  =item outputDirectory  =item entityName
1631    
1632  Name of the directory into which the relation files should be dumped.  Name of the entity type for the instance being deleted.
1633    
1634    =item objectID
1635    
1636    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1637    then it is presumed to by a LIKE pattern.
1638    
1639    =item options
1640    
1641    A hash detailing the options for this delete operation.
1642    
1643    =item RETURN
1644    
1645    Returns a statistics object indicating how many records of each particular table were
1646    deleted.
1647    
1648  =back  =back
1649    
1650  =cut  The permissible options for this method are as follows.
1651    
1652  sub DumpRelations {  =over 4
1653    
1654    =item testMode
1655    
1656    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1657    
1658    =item keepRoot
1659    
1660    If TRUE, then the entity instances will not be deleted, only the dependent records.
1661    
1662    =back
1663    
1664    =cut
1665    #: Return Type $%;
1666    sub Delete {
1667      # Get the parameters.      # Get the parameters.
1668      my ($self, $outputDirectory) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1669      # Now we need to run through all the relations. First, we loop through the entities.      # Declare the return variable.
1670      my $metaData = $self->{_metaData};      my $retVal = Stats->new();
1671      my $entities = $metaData->{Entities};      # Get the DBKernel object.
1672      for my $entityName (keys %{$entities}) {      my $db = $self->{_dbh};
1673          my $entityStructure = $entities->{$entityName};      # We're going to generate all the paths branching out from the starting entity. One of
1674          # Get the entity's relations.      # the things we have to be careful about is preventing loops. We'll use a hash to
1675          my $relationList = $entityStructure->{Relations};      # determine if we've hit a loop.
1676          # Loop through the relations, dumping them.      my %alreadyFound = ();
1677          for my $relationName (keys %{$relationList}) {      # These next lists will serve as our result stack. We start by pushing object lists onto
1678              my $relation = $relationList->{$relationName};      # the stack, and then popping them off to do the deletes. This means the deletes will
1679              $self->_DumpRelation($outputDirectory, $relationName, $relation);      # start with the longer paths before getting to the shorter ones. That, in turn, makes
1680        # sure we don't delete records that might be needed to forge relationships back to the
1681        # original item. We have two lists-- one for TO-relationships, and one for
1682        # FROM-relationships and entities.
1683        my @fromPathList = ();
1684        my @toPathList = ();
1685        # This final list is used to remember what work still needs to be done. We push paths
1686        # onto the list, then pop them off to extend the paths. We prime it with the starting
1687        # point. Note that we will work hard to insure that the last item on a path in the
1688        # to-do list is always an entity.
1689        my @todoList = ([$entityName]);
1690        while (@todoList) {
1691            # Get the current path.
1692            my $current = pop @todoList;
1693            # Copy it into a list.
1694            my @stackedPath = @{$current};
1695            # Pull off the last item on the path. It will always be an entity.
1696            my $myEntityName = pop @stackedPath;
1697            # Add it to the alreadyFound list.
1698            $alreadyFound{$myEntityName} = 1;
1699            # Figure out if we need to delete this entity.
1700            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1701                # Get the entity data.
1702                my $entityData = $self->_GetStructure($myEntityName);
1703                # Loop through the entity's relations. A DELETE command will be needed for each of them.
1704                my $relations = $entityData->{Relations};
1705                for my $relation (keys %{$relations}) {
1706                    my @augmentedList = (@stackedPath, $relation);
1707                    push @fromPathList, \@augmentedList;
1708          }          }
1709      }      }
1710      # Next, we loop through the relationships.          # Now we need to look for relationships connected to this entity.
1711      my $relationships = $metaData->{Relationships};          my $relationshipList = $self->{_metaData}->{Relationships};
1712      for my $relationshipName (keys %{$relationships}) {          for my $relationshipName (keys %{$relationshipList}) {
1713          my $relationshipStructure = $relationships->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
1714          # Dump this relationship's relation.              # Check the FROM field. We're only interested if it's us.
1715          $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});              if ($relationship->{from} eq $myEntityName) {
1716                    # Add the path to this relationship.
1717                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1718                    push @fromPathList, \@augmentedList;
1719                    # Check the arity. If it's MM we're done. If it's 1M
1720                    # and the target hasn't been seen yet, we want to
1721                    # stack the entity for future processing.
1722                    if ($relationship->{arity} eq '1M') {
1723                        my $toEntity = $relationship->{to};
1724                        if (! exists $alreadyFound{$toEntity}) {
1725                            # Here we have a new entity that's dependent on
1726                            # the current entity, so we need to stack it.
1727                            my @stackList = (@augmentedList, $toEntity);
1728                            push @fromPathList, \@stackList;
1729                        } else {
1730                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1731      }      }
1732  }  }
1733                }
1734                # Now check the TO field. In this case only the relationship needs
1735                # deletion.
1736                if ($relationship->{to} eq $myEntityName) {
1737                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1738                    push @toPathList, \@augmentedList;
1739                }
1740            }
1741        }
1742        # Create the first qualifier for the WHERE clause. This selects the
1743        # keys of the primary entity records to be deleted. When we're deleting
1744        # from a dependent table, we construct a join path from the first qualifier
1745        # to the table containing the dependent records to delete.
1746        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1747        # We need to make two passes. The first is through the to-list, and
1748        # the second through the from-list. The from-list is second because
1749        # the to-list may need to pass through some of the entities the
1750        # from-list would delete.
1751        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1752        # Now it's time to do the deletes. We do it in two passes.
1753        for my $keyName ('to_link', 'from_link') {
1754            # Get the list for this key.
1755            my @pathList = @{$stackList{$keyName}};
1756            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1757            # Loop through this list.
1758            while (my $path = pop @pathList) {
1759                # Get the table whose rows are to be deleted.
1760                my @pathTables = @{$path};
1761                # Start the DELETE statement. We need to call DBKernel because the
1762                # syntax of a DELETE-USING varies among DBMSs.
1763                my $target = $pathTables[$#pathTables];
1764                my $stmt = $db->SetUsing(@pathTables);
1765                # Now start the WHERE. The first thing is the ID field from the starting table. That
1766                # starting table will either be the entity relation or one of the entity's
1767                # sub-relations.
1768                $stmt .= " WHERE $pathTables[0].id $qualifier";
1769                # Now we run through the remaining entities in the path, connecting them up.
1770                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1771                    # Connect the current relationship to the preceding entity.
1772                    my ($entity, $rel) = @pathTables[$i-1,$i];
1773                    # The style of connection depends on the direction of the relationship.
1774                    $stmt .= " AND $entity.id = $rel.$keyName";
1775                    if ($i + 1 <= $#pathTables) {
1776                        # Here there's a next entity, so connect that to the relationship's
1777                        # to-link.
1778                        my $entity2 = $pathTables[$i+1];
1779                        $stmt .= " AND $rel.to_link = $entity2.id";
1780                    }
1781                }
1782                # Now we have our desired DELETE statement.
1783                if ($options{testMode}) {
1784                    # Here the user wants to trace without executing.
1785                    Trace($stmt) if T(0);
1786                } else {
1787                    # Here we can delete. Note that the SQL method dies with a confession
1788                    # if an error occurs, so we just go ahead and do it.
1789                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1790                    my $rv = $db->SQL($stmt, 0, $objectID);
1791                    # Accumulate the statistics for this delete. The only rows deleted
1792                    # are from the target table, so we use its name to record the
1793                    # statistic.
1794                    $retVal->Add($target, $rv);
1795                }
1796            }
1797        }
1798        # Return the result.
1799        return $retVal;
1800    }
1801    
1802  =head3 InsertObject  =head3 Disconnect
   
 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  
   
 Insert an object into the database. The object is defined by a type name and then a hash  
 of field names to values. Field values in the primary relation are represented by scalars.  
 (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>.  
   
 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  
1803    
1804  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
1805    
1806  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  Disconnect an entity instance from all the objects to which it is related. This
1807    will delete each relationship instance that connects to the specified entity.
1808    
1809  =over 4  =over 4
1810    
1811  =item newObjectType  =item relationshipName
1812    
1813  Type name of the object to insert.  Name of the relationship whose instances are to be deleted.
1814    
1815  =item fieldHash  =item originEntityName
1816    
1817  Hash of field names to values.  Name of the entity that is to be disconnected.
1818    
1819  =item RETURN  =item originEntityID
1820    
1821  Returns 1 if successful, 0 if an error occurred.  ID of the entity that is to be disconnected.
1822    
1823  =back  =back
1824    
1825  =cut  =cut
1826    
1827  sub InsertObject {  sub Disconnect {
1828      # Get the parameters.      # Get the parameters.
1829      my ($self, $newObjectType, $fieldHash) = @_;      my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1830      # Denote that so far we appear successful.      # Get the relationship descriptor.
1831      my $retVal = 1;      my $structure = $self->_GetStructure($relationshipName);
1832        # Insure we have a relationship.
1833        if (! exists $structure->{from}) {
1834            Confess("$relationshipName is not a relationship in the database.");
1835        } else {
1836      # Get the database handle.      # Get the database handle.
1837      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
1838      # Get the relation list.          # We'll set this value to 1 if we find our entity.
1839      my $relationTable = $self->_GetRelationTable($newObjectType);          my $found = 0;
1840      # Loop through the relations. We'll build insert statements for each one. If a relation is          # Loop through the ends of the relationship.
1841      # secondary, we may end up generating multiple insert statements. If an error occurs, we          for my $dir ('from', 'to') {
1842      # stop the loop.              if ($structure->{$dir} eq $originEntityName) {
1843      my @relationList = keys %{$relationTable};                  # Delete all relationship instances on this side of the entity instance.
1844      for (my $i = 0; $retVal && $i <= $#relationList; $i++) {                  $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1845          my $relationName = $relationList[$i];                  $found = 1;
         my $relationDefinition = $relationTable->{$relationName};  
         # Get the relation's fields. For each field we will collect a value in the corresponding  
         # position of the @valueList array. If one of the fields is missing, we will add it to the  
         # @missing list.  
         my @fieldList = @{$relationDefinition->{Fields}};  
         my @fieldNameList = ();  
         my @valueList = ();  
         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;  
1846                      }                      }
1847                  }                  }
1848              } else {          # Insure we found the entity on at least one end.
1849                  # Here the field is not present. Flag it as missing.          if (! $found) {
1850                  push @missing, $fieldName;              Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1851              }              }
1852          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
1853          }          }
1854          # Only proceed if there are no missing fields.  
1855          if (@missing > 0) {  =head3 DeleteRow
1856              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .  
1857                  join(' ', @missing)) if T(1);  C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1858          } else {  
1859              # Build the INSERT statement.  Delete a row from a relationship. In most cases, only the from-link and to-link are
1860              my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .  needed; however, for relationships with intersection data values can be specified
1861                  ") VALUES (";  for the other fields using a hash.
1862              # Create a marker list of the proper size and put it in the statement.  
1863              my @markers = ();  =over 4
1864              while (@markers < @fieldNameList) { push @markers, '?'; }  
1865              $statement .= join(', ', @markers) . ")";  =item relationshipName
1866              # We have the insert statement, so prepare it.  
1867              my $sth = $dbh->prepare_command($statement);  Name of the relationship from which the row is to be deleted.
1868              Trace("Insert statement prepared: $statement") if T(3);  
1869              # Now we loop through the values. If a value is scalar, we use it unmodified. If it's  =item fromLink
1870              # a list, we use the current element. The values are stored in the @parameterList array.  
1871              my $done = 0;  ID of the entity instance in the From direction.
1872              for (my $i = 0; $i < $recordCount; $i++) {  
1873                  # Clear the parameter list array.  =item toLink
1874                  my @parameterList = ();  
1875                  # Loop through the values.  ID of the entity instance in the To direction.
1876                  for my $value (@valueList) {  
1877                      # Check to see if this is a scalar value.  =item values
1878                      if (ref $value eq "ARRAY") {  
1879                          # Here we have a list value. Pull the current entry.  Reference to a hash of other values to be used for filtering the delete.
1880                          push @parameterList, $value->[$i];  
1881                      } else {  =back
1882                          # Here we have a scalar value. Use it unmodified.  
1883                          push @parameterList, $value;  =cut
1884    
1885    sub DeleteRow {
1886        # Get the parameters.
1887        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1888        # Create a hash of all the filter information.
1889        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1890        if (defined $values) {
1891            for my $key (keys %{$values}) {
1892                $filter{$key} = $values->{$key};
1893                      }                      }
1894                  }                  }
1895                  # Execute the INSERT statement with the specified parameter list.      # Build an SQL statement out of the hash.
1896                  $retVal = $sth->execute(@parameterList);      my @filters = ();
1897                  if (!$retVal) {      my @parms = ();
1898                      my $errorString = $sth->errstr();      for my $key (keys %filter) {
1899                      Trace("Insert error: $errorString.") if T(0);          push @filters, _FixName($key) . " = ?";
1900            push @parms, $filter{$key};
1901        }
1902        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1903        my $command = "DELETE FROM $relationshipName WHERE " .
1904                      join(" AND ", @filters);
1905        # Execute it.
1906        my $dbh = $self->{_dbh};
1907        $dbh->SQL($command, undef, @parms);
1908    }
1909    
1910    =head3 SortNeeded
1911    
1912    C<< my $parms = $erdb->SortNeeded($relationName); >>
1913    
1914    Return the pipe command for the sort that should be applied to the specified
1915    relation when creating the load file.
1916    
1917    For example, if the load file should be sorted ascending by the first
1918    field, this method would return
1919    
1920        sort -k1 -t"\t"
1921    
1922    If the first field is numeric, the method would return
1923    
1924        sort -k1n -t"\t"
1925    
1926    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1927    keys using a sort.
1928    
1929    =over 4
1930    
1931    =item relationName
1932    
1933    Name of the relation to be examined.
1934    
1935    =item
1936    
1937    Returns the sort command to use for sorting the relation, suitable for piping.
1938    
1939    =back
1940    
1941    =cut
1942    #: Return Type $;
1943    sub SortNeeded {
1944        # Get the parameters.
1945        my ($self, $relationName) = @_;
1946        # Declare a descriptor to hold the names of the key fields.
1947        my @keyNames = ();
1948        # Get the relation structure.
1949        my $relationData = $self->_FindRelation($relationName);
1950        # Find out if the relation is a primary entity relation,
1951        # a relationship relation, or a secondary entity relation.
1952        my $entityTable = $self->{_metaData}->{Entities};
1953        my $relationshipTable = $self->{_metaData}->{Relationships};
1954        if (exists $entityTable->{$relationName}) {
1955            # Here we have a primary entity relation.
1956            push @keyNames, "id";
1957        } elsif (exists $relationshipTable->{$relationName}) {
1958            # Here we have a relationship. We sort using the FROM index.
1959            my $relationshipData = $relationshipTable->{$relationName};
1960            my $index = $relationData->{Indexes}->{idxFrom};
1961            push @keyNames, @{$index->{IndexFields}};
1962        } else {
1963            # Here we have a secondary entity relation, so we have a sort on the ID field.
1964            push @keyNames, "id";
1965        }
1966        # Now we parse the key names into sort parameters. First, we prime the return
1967        # string.
1968        my $retVal = "sort -t\"\t\" ";
1969        # Get the relation's field list.
1970        my @fields = @{$relationData->{Fields}};
1971        # Loop through the keys.
1972        for my $keyData (@keyNames) {
1973            # Get the key and the ordering.
1974            my ($keyName, $ordering);
1975            if ($keyData =~ /^([^ ]+) DESC/) {
1976                ($keyName, $ordering) = ($1, "descending");
1977            } else {
1978                ($keyName, $ordering) = ($keyData, "ascending");
1979                  }                  }
1980            # Find the key's position and type.
1981            my $fieldSpec;
1982            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1983                my $thisField = $fields[$i];
1984                if ($thisField->{name} eq $keyName) {
1985                    # Get the sort modifier for this field type. The modifier
1986                    # decides whether we're using a character, numeric, or
1987                    # floating-point sort.
1988                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1989                    # If the index is descending for this field, denote we want
1990                    # to reverse the sort order on this field.
1991                    if ($ordering eq 'descending') {
1992                        $modifier .= "r";
1993                    }
1994                    # Store the position and modifier into the field spec, which
1995                    # will stop the inner loop. Note that the field number is
1996                    # 1-based in the sort command, so we have to increment the
1997                    # index.
1998                    $fieldSpec = ($i + 1) . $modifier;
1999              }              }
2000          }          }
2001            # Add this field to the sort command.
2002            $retVal .= " -k$fieldSpec";
2003      }      }
2004      # Return the success indicator.      # Return the result.
2005      return $retVal;      return $retVal;
2006  }  }
2007    
2008  =head3 LoadTable  =head3 GetList
2009    
2010  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2011    
2012  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Return a list of object descriptors for the specified objects as determined by the
2013  first.  specified filter clause.
2014    
2015    This method is essentially the same as L</Get> except it returns a list of objects rather
2016    than a query object that can be used to get the results one record at a time.
2017    
2018  =over 4  =over 4
2019    
2020  =item fileName  =item objectNames
2021    
2022  Name of the file from which the table data should be loaded.  List containing the names of the entity and relationship objects to be retrieved.
2023    
2024  =item relationName  =item filterClause
2025    
2026  Name of the relation to be loaded. This is the same as the table name.  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2027    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2028    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2029    in the filter clause should be added to the parameter list as additional parameters. The
2030    fields in a filter clause can come from primary entity relations, relationship relations,
2031    or secondary entity relations; however, all of the entities and relationships involved must
2032    be included in the list of object names.
2033    
2034  =item truncateFlag  The filter clause can also specify a sort order. To do this, simply follow the filter string
2035    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2036    particular genus and sorts them by species name.
2037    
2038  TRUE if the table should be dropped and re-created, else FALSE  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2039    
2040    The rules for field references in a sort order are the same as those for field references in the
2041    filter clause in general; however, odd things may happen if a sort field is from a secondary
2042    relation.
2043    
2044    =item params
2045    
2046    Reference to a list of parameter values to be substituted into the filter clause.
2047    
2048  =item RETURN  =item RETURN
2049    
2050  Returns a statistical object containing the number of records read and a list of  Returns a list of B<DBObject>s that satisfy the query conditions.
 the error messages.  
2051    
2052  =back  =back
2053    
2054  =cut  =cut
2055  sub LoadTable {  #: Return Type @%
2056    sub GetList {
2057      # Get the parameters.      # Get the parameters.
2058      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
2059      # Create the statistical return object.      # Declare the return variable.
2060      my $retVal = _GetLoadStats();      my @retVal = ();
2061      # Trace the fact of the load.      # Perform the query.
2062      Trace("Loading table $relationName from $fileName") if T(2);      my $query = $self->Get($objectNames, $filterClause, $params);
2063      # Get the database handle.      # Loop through the results.
2064      my $dbh = $self->{_dbh};      while (my $object = $query->Fetch) {
2065      # Get the input file size.          push @retVal, $object;
     my $fileSize = -s $fileName;  
     # Get the relation data.  
     my $relation = $self->_FindRelation($relationName);  
     # 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 $estimate = FIG::max($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 ($@) {  
                 $retVal->AddMessage($@);  
2066              }              }
2067        # Return the result.
2068        return @retVal;
2069          }          }
2070    
2071    =head3 GetCount
2072    
2073    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2074    
2075    Return the number of rows found by a specified query. This method would
2076    normally be used to count the records in a single table. For example, in a
2077    genetics database
2078    
2079        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2080    
2081    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2082    to use it to return records based on a join. For example,
2083    
2084        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2085                                    ['homo %']);
2086    
2087    would return the number of features for genomes in the genus I<homo>. Note that
2088    only the rows from the first table are counted. If the above command were
2089    
2090        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2091                                    ['homo %']);
2092    
2093    it would return the number of genomes, not the number of genome/feature pairs.
2094    
2095    =over 4
2096    
2097    =item objectNames
2098    
2099    Reference to a list of the objects (entities and relationships) included in the
2100    query.
2101    
2102    =item filter
2103    
2104    A filter clause for restricting the query. The rules are the same as for the L</Get>
2105    method.
2106    
2107    =item params
2108    
2109    Reference to a list of the parameter values to be substituted for the parameter marks
2110    in the filter.
2111    
2112    =item RETURN
2113    
2114    Returns a count of the number of records in the first table that would satisfy
2115    the query.
2116    
2117    =back
2118    
2119    =cut
2120    
2121    sub GetCount {
2122        # Get the parameters.
2123        my ($self, $objectNames, $filter, $params) = @_;
2124        # Insure the params argument is an array reference if the caller left it off.
2125        if (! defined($params)) {
2126            $params = [];
2127      }      }
2128      # Load the table.      # Declare the return variable.
2129      my $rv;      my $retVal;
2130      eval {      # Find out if we're counting an entity or a relationship.
2131          $rv = $dbh->load_table(file => $fileName, tbl => $relationName);      my $countedField;
2132      };      if ($self->IsEntity($objectNames->[0])) {
2133      if (!defined $rv) {          $countedField = "id";
         $retVal->AddMessage($@) if ($@);  
         $retVal->AddMessage("Table load failed for $relationName using $fileName.");  
         Trace("Table load failed for $relationName.") if T(1);  
2134      } else {      } else {
2135          # Here we successfully loaded the table.          # For a relationship we count the to-link because it's usually more
2136          $retVal->Add("tables");          # numerous. Note we're automatically converting to the SQL form
2137          my $size = -s $fileName;          # of the field name (to_link vs. to-link).
2138          Trace("$size bytes loaded into $relationName.") if T(2);          $countedField = "to_link";
2139          # If we're rebuilding, we need to create the table indexes.      }
2140          if ($truncateFlag && ! $dbh->{_preIndex}) {      # Create the SQL command suffix to get the desired records.
2141              eval {      my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2142                  $self->CreateIndex($relationName);                                                                              $filter);
2143              };      # Prefix it with text telling it we want a record count.
2144              if ($@) {      my $firstObject = $mappedNameListRef->[0];
2145                  $retVal->AddMessage($@);      my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2146        # Prepare and execute the command.
2147        my $sth = $self->_GetStatementHandle($command, $params);
2148        # Get the count value.
2149        ($retVal) = $sth->fetchrow_array();
2150        # Check for a problem.
2151        if (! defined($retVal)) {
2152            if ($sth->err) {
2153                # Here we had an SQL error.
2154                Confess("Error retrieving row count: " . $sth->errstr());
2155            } else {
2156                # Here we have no result.
2157                Confess("No result attempting to retrieve row count.");
2158              }              }
2159          }          }
2160        # Return the result.
2161        return $retVal;
2162      }      }
2163      # Analyze the table to improve performance.  
2164      $dbh->vacuum_it($relationName);  =head3 ComputeObjectSentence
2165      # Return the statistics.  
2166    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2167    
2168    Check an object name, and if it is a relationship convert it to a relationship sentence.
2169    
2170    =over 4
2171    
2172    =item objectName
2173    
2174    Name of the entity or relationship.
2175    
2176    =item RETURN
2177    
2178    Returns a string containing the entity name or a relationship sentence.
2179    
2180    =back
2181    
2182    =cut
2183    
2184    sub ComputeObjectSentence {
2185        # Get the parameters.
2186        my ($self, $objectName) = @_;
2187        # Set the default return value.
2188        my $retVal = $objectName;
2189        # Look for the object as a relationship.
2190        my $relTable = $self->{_metaData}->{Relationships};
2191        if (exists $relTable->{$objectName}) {
2192            # Get the relationship sentence.
2193            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2194        }
2195        # Return the result.
2196        return $retVal;
2197    }
2198    
2199    =head3 DumpRelations
2200    
2201    C<< $erdb->DumpRelations($outputDirectory); >>
2202    
2203    Write the contents of all the relations to tab-delimited files in the specified directory.
2204    Each file will have the same name as the relation dumped, with an extension of DTX.
2205    
2206    =over 4
2207    
2208    =item outputDirectory
2209    
2210    Name of the directory into which the relation files should be dumped.
2211    
2212    =back
2213    
2214    =cut
2215    
2216    sub DumpRelations {
2217        # Get the parameters.
2218        my ($self, $outputDirectory) = @_;
2219        # Now we need to run through all the relations. First, we loop through the entities.
2220        my $metaData = $self->{_metaData};
2221        my $entities = $metaData->{Entities};
2222        for my $entityName (keys %{$entities}) {
2223            my $entityStructure = $entities->{$entityName};
2224            # Get the entity's relations.
2225            my $relationList = $entityStructure->{Relations};
2226            # Loop through the relations, dumping them.
2227            for my $relationName (keys %{$relationList}) {
2228                my $relation = $relationList->{$relationName};
2229                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2230            }
2231        }
2232        # Next, we loop through the relationships.
2233        my $relationships = $metaData->{Relationships};
2234        for my $relationshipName (keys %{$relationships}) {
2235            my $relationshipStructure = $relationships->{$relationshipName};
2236            # Dump this relationship's relation.
2237            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2238        }
2239    }
2240    
2241    =head3 InsertValue
2242    
2243    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2244    
2245    This method will insert a new value into the database. The value must be one
2246    associated with a secondary relation, since primary values cannot be inserted:
2247    they occur exactly once. Secondary values, on the other hand, can be missing
2248    or multiply-occurring.
2249    
2250    =over 4
2251    
2252    =item entityID
2253    
2254    ID of the object that is to receive the new value.
2255    
2256    =item fieldName
2257    
2258    Field name for the new value-- this includes the entity name, since
2259    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2260    
2261    =item value
2262    
2263    New value to be put in the field.
2264    
2265    =back
2266    
2267    =cut
2268    
2269    sub InsertValue {
2270        # Get the parameters.
2271        my ($self, $entityID, $fieldName, $value) = @_;
2272        # Parse the entity name and the real field name.
2273        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2274            my $entityName = $1;
2275            my $fieldTitle = $2;
2276            # Get its descriptor.
2277            if (!$self->IsEntity($entityName)) {
2278                Confess("$entityName is not a valid entity.");
2279            } else {
2280                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2281                # Find the relation containing this field.
2282                my $fieldHash = $entityData->{Fields};
2283                if (! exists $fieldHash->{$fieldTitle}) {
2284                    Confess("$fieldTitle not found in $entityName.");
2285                } else {
2286                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2287                    if ($relation eq $entityName) {
2288                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2289                    } else {
2290                        # Now we can create an INSERT statement.
2291                        my $dbh = $self->{_dbh};
2292                        my $fixedName = _FixName($fieldTitle);
2293                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2294                        # Execute the command.
2295                        $dbh->SQL($statement, 0, $entityID, $value);
2296                    }
2297                }
2298            }
2299        } else {
2300            Confess("$fieldName is not a valid field name.");
2301        }
2302    }
2303    
2304    =head3 InsertObject
2305    
2306    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2307    
2308    Insert an object into the database. The object is defined by a type name and then a hash
2309    of field names to values. Field values in the primary relation are represented by scalars.
2310    (Note that for relationships, the primary relation is the B<only> relation.)
2311    Field values for the other relations comprising the entity are always list references. For
2312    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2313    C<ZP_00210270.1> and C<gi|46206278>.
2314    
2315    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2316    
2317    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2318    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2319    
2320    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2321    
2322    =over 4
2323    
2324    =item newObjectType
2325    
2326    Type name of the object to insert.
2327    
2328    =item fieldHash
2329    
2330    Hash of field names to values.
2331    
2332    =back
2333    
2334    =cut
2335    
2336    sub InsertObject {
2337        # Get the parameters.
2338        my ($self, $newObjectType, $fieldHash) = @_;
2339        # Denote that so far we appear successful.
2340        my $retVal = 1;
2341        # Get the database handle.
2342        my $dbh = $self->{_dbh};
2343        # Get the relation list.
2344        my $relationTable = $self->_GetRelationTable($newObjectType);
2345        # Loop through the relations. We'll build insert statements for each one. If a relation is
2346        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2347        # stop the loop.
2348        my @relationList = keys %{$relationTable};
2349        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2350            my $relationName = $relationList[$i];
2351            my $relationDefinition = $relationTable->{$relationName};
2352            # Get the relation's fields. For each field we will collect a value in the corresponding
2353            # position of the @valueList array. If one of the fields is missing, we will add it to the
2354            # @missing list.
2355            my @fieldList = @{$relationDefinition->{Fields}};
2356            my @fieldNameList = ();
2357            my @valueList = ();
2358            my @missing = ();
2359            my $recordCount = 1;
2360            for my $fieldDescriptor (@fieldList) {
2361                # Get the field name and save it. Note we need to fix it up so the hyphens
2362                # are converted to underscores.
2363                my $fieldName = $fieldDescriptor->{name};
2364                push @fieldNameList, _FixName($fieldName);
2365                # Look for the named field in the incoming structure. Note that we are looking
2366                # for the real field name, not the fixed-up one!
2367                if (exists $fieldHash->{$fieldName}) {
2368                    # Here we found the field. Stash it in the value list.
2369                    my $value = $fieldHash->{$fieldName};
2370                    push @valueList, $value;
2371                    # If the value is a list, we may need to increment the record count.
2372                    if (ref $value eq "ARRAY") {
2373                        my $thisCount = @{$value};
2374                        if ($recordCount == 1) {
2375                            # Here we have our first list, so we save its count.
2376                            $recordCount = $thisCount;
2377                        } elsif ($recordCount != $thisCount) {
2378                            # Here we have a second list, so its length has to match the
2379                            # previous lists.
2380                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2381                            $retVal = 0;
2382                        }
2383                    }
2384                } else {
2385                    # Here the field is not present. Flag it as missing.
2386                    push @missing, $fieldName;
2387                }
2388            }
2389            # If we are the primary relation, add the new-record flag.
2390            if ($relationName eq $newObjectType) {
2391                push @valueList, 1;
2392                push @fieldNameList, "new_record";
2393            }
2394            # Only proceed if there are no missing fields.
2395            if (@missing > 0) {
2396                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2397                    join(' ', @missing)) if T(1);
2398            } else {
2399                # Build the INSERT statement.
2400                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2401                    ") VALUES (";
2402                # Create a marker list of the proper size and put it in the statement.
2403                my @markers = ();
2404                while (@markers < @fieldNameList) { push @markers, '?'; }
2405                $statement .= join(', ', @markers) . ")";
2406                # We have the insert statement, so prepare it.
2407                my $sth = $dbh->prepare_command($statement);
2408                Trace("Insert statement prepared: $statement") if T(3);
2409                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2410                # a list, we use the current element. The values are stored in the @parameterList array.
2411                my $done = 0;
2412                for (my $i = 0; $i < $recordCount; $i++) {
2413                    # Clear the parameter list array.
2414                    my @parameterList = ();
2415                    # Loop through the values.
2416                    for my $value (@valueList) {
2417                        # Check to see if this is a scalar value.
2418                        if (ref $value eq "ARRAY") {
2419                            # Here we have a list value. Pull the current entry.
2420                            push @parameterList, $value->[$i];
2421                        } else {
2422                            # Here we have a scalar value. Use it unmodified.
2423                            push @parameterList, $value;
2424                        }
2425                    }
2426                    # Execute the INSERT statement with the specified parameter list.
2427                    $retVal = $sth->execute(@parameterList);
2428                    if (!$retVal) {
2429                        my $errorString = $sth->errstr();
2430                        Confess("Error inserting into $relationName: $errorString");
2431                    }
2432                }
2433            }
2434        }
2435        # Return a 1 for backward compatability.
2436        return 1;
2437    }
2438    
2439    =head3 UpdateEntity
2440    
2441    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2442    
2443    Update the values of an entity. This is an unprotected update, so it should only be
2444    done if the database resides on a database server.
2445    
2446    =over 4
2447    
2448    =item entityName
2449    
2450    Name of the entity to update. (This is the entity type.)
2451    
2452    =item id
2453    
2454    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2455    
2456    =item fields
2457    
2458    Reference to a hash mapping field names to their new values. All of the fields named
2459    must be in the entity's primary relation, and they cannot any of them be the ID field.
2460    
2461    =back
2462    
2463    =cut
2464    
2465    sub UpdateEntity {
2466        # Get the parameters.
2467        my ($self, $entityName, $id, $fields) = @_;
2468        # Get a list of the field names being updated.
2469        my @fieldList = keys %{$fields};
2470        # Verify that the fields exist.
2471        my $checker = $self->GetFieldTable($entityName);
2472        for my $field (@fieldList) {
2473            if ($field eq 'id') {
2474                Confess("Cannot update the ID field for entity $entityName.");
2475            } elsif ($checker->{$field}->{relation} ne $entityName) {
2476                Confess("Cannot find $field in primary relation of $entityName.");
2477            }
2478        }
2479        # Build the SQL statement.
2480        my @sets = ();
2481        my @valueList = ();
2482        for my $field (@fieldList) {
2483            push @sets, _FixName($field) . " = ?";
2484            push @valueList, $fields->{$field};
2485        }
2486        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2487        # Add the ID to the list of binding values.
2488        push @valueList, $id;
2489        # Call SQL to do the work.
2490        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2491        # Check for errors.
2492        if ($rows == 0) {
2493            Confess("Entity $id of type $entityName not found.");
2494        }
2495    }
2496    
2497    =head3 LoadTable
2498    
2499    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2500    
2501    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2502    first.
2503    
2504    =over 4
2505    
2506    =item fileName
2507    
2508    Name of the file from which the table data should be loaded.
2509    
2510    =item relationName
2511    
2512    Name of the relation to be loaded. This is the same as the table name.
2513    
2514    =item truncateFlag
2515    
2516    TRUE if the table should be dropped and re-created, else FALSE
2517    
2518    =item RETURN
2519    
2520    Returns a statistical object containing a list of the error messages.
2521    
2522    =back
2523    
2524    =cut
2525    sub LoadTable {
2526        # Get the parameters.
2527        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2528        # Create the statistical return object.
2529        my $retVal = _GetLoadStats();
2530        # Trace the fact of the load.
2531        Trace("Loading table $relationName from $fileName") if T(2);
2532        # Get the database handle.
2533        my $dbh = $self->{_dbh};
2534        # Get the input file size.
2535        my $fileSize = -s $fileName;
2536        # Get the relation data.
2537        my $relation = $self->_FindRelation($relationName);
2538        # Check the truncation flag.
2539        if ($truncateFlag) {
2540            Trace("Creating table $relationName") if T(2);
2541            # Compute the row count estimate. We take the size of the load file,
2542            # divide it by the estimated row size, and then multiply by 1.5 to
2543            # leave extra room. We postulate a minimum row count of 1000 to
2544            # prevent problems with incoming empty load files.
2545            my $rowSize = $self->EstimateRowSize($relationName);
2546            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2547            # Re-create the table without its index.
2548            $self->CreateTable($relationName, 0, $estimate);
2549            # If this is a pre-index DBMS, create the index here.
2550            if ($dbh->{_preIndex}) {
2551                eval {
2552                    $self->CreateIndex($relationName);
2553                };
2554                if ($@) {
2555                    $retVal->AddMessage($@);
2556                }
2557            }
2558        }
2559        # Load the table.
2560        my $rv;
2561        eval {
2562            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2563        };
2564        if (!defined $rv) {
2565            $retVal->AddMessage($@) if ($@);
2566            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2567            Trace("Table load failed for $relationName.") if T(1);
2568        } else {
2569            # Here we successfully loaded the table.
2570            $retVal->Add("tables");
2571            my $size = -s $fileName;
2572            Trace("$size bytes loaded into $relationName.") if T(2);
2573            # If we're rebuilding, we need to create the table indexes.
2574            if ($truncateFlag) {
2575                # Indexes are created here for PostGres. For PostGres, indexes are
2576                # best built at the end. For MySQL, the reverse is true.
2577                if (! $dbh->{_preIndex}) {
2578                    eval {
2579                        $self->CreateIndex($relationName);
2580                    };
2581                    if ($@) {
2582                        $retVal->AddMessage($@);
2583                    }
2584                }
2585                # The full-text index (if any) is always built last, even for MySQL.
2586                # First we need to see if this table has a full-text index. Only
2587                # primary relations are allowed that privilege.
2588                if ($self->_IsPrimary($relationName)) {
2589                    # Get the relation's entity/relationship structure.
2590                    my $structure = $self->_GetStructure($relationName);
2591                    # Check for a searchable fields list.
2592                    if (exists $structure->{searchFields}) {
2593                        # Here we know that we need to create a full-text search index.
2594                        # Get an SQL-formatted field name list.
2595                        my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2596                        # Create the index.
2597                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2598                                           flds => $fields, kind => 'fulltext');
2599                    }
2600                }
2601            }
2602        }
2603        # Analyze the table to improve performance.
2604        Trace("Analyzing and compacting $relationName.") if T(3);
2605        $dbh->vacuum_it($relationName);
2606        Trace("$relationName load completed.") if T(3);
2607        # Return the statistics.
2608        return $retVal;
2609    }
2610    
2611    =head3 DropRelation
2612    
2613    C<< $erdb->DropRelation($relationName); >>
2614    
2615    Physically drop a relation from the database.
2616    
2617    =over 4
2618    
2619    =item relationName
2620    
2621    Name of the relation to drop. If it does not exist, this method will have
2622    no effect.
2623    
2624    =back
2625    
2626    =cut
2627    
2628    sub DropRelation {
2629        # Get the parameters.
2630        my ($self, $relationName) = @_;
2631        # Get the database handle.
2632        my $dbh = $self->{_dbh};
2633        # Drop the relation. The method used here has no effect if the relation
2634        # does not exist.
2635        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2636        $dbh->drop_table(tbl => $relationName);
2637    }
2638    
2639    =head3 MatchSqlPattern
2640    
2641    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2642    
2643    Determine whether or not a specified value matches an SQL pattern. An SQL
2644    pattern has two wild card characters: C<%> that matches multiple characters,
2645    and C<_> that matches a single character. These can be escaped using a
2646    backslash (C<\>). We pull this off by converting the SQL pattern to a
2647    PERL regular expression. As per SQL rules, the match is case-insensitive.
2648    
2649    =over 4
2650    
2651    =item value
2652    
2653    Value to be matched against the pattern. Note that an undefined or empty
2654    value will not match anything.
2655    
2656    =item pattern
2657    
2658    SQL pattern against which to match the value. An undefined or empty pattern will
2659    match everything.
2660    
2661    =item RETURN
2662    
2663    Returns TRUE if the value and pattern match, else FALSE.
2664    
2665    =back
2666    
2667    =cut
2668    
2669    sub MatchSqlPattern {
2670        # Get the parameters.
2671        my ($value, $pattern) = @_;
2672        # Declare the return variable.
2673        my $retVal;
2674        # Insure we have a pattern.
2675        if (! defined($pattern) || $pattern eq "") {
2676            $retVal = 1;
2677        } else {
2678            # Break the pattern into pieces around the wildcard characters. Because we
2679            # use parentheses in the split function's delimiter expression, we'll get
2680            # list elements for the delimiters as well as the rest of the string.
2681            my @pieces = split /([_%]|\\[_%])/, $pattern;
2682            # Check some fast special cases.
2683            if ($pattern eq '%') {
2684                # A null pattern matches everything.
2685                $retVal = 1;
2686            } elsif (@pieces == 1) {
2687                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2688                $retVal = (lc($value) eq lc($pattern));
2689            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2690                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2691                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2692            } else {
2693                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2694                my $realPattern = "";
2695                for my $piece (@pieces) {
2696                    # Determine the type of piece.
2697                    if ($piece eq "") {
2698                        # Empty pieces are ignored.
2699                    } elsif ($piece eq "%") {
2700                        # Here we have a multi-character wildcard. Note that it can match
2701                        # zero or more characters.
2702                        $realPattern .= ".*"
2703                    } elsif ($piece eq "_") {
2704                        # Here we have a single-character wildcard.
2705                        $realPattern .= ".";
2706                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2707                        # This is an escape sequence (which is a rare thing, actually).
2708                        $realPattern .= substr($piece, 1, 1);
2709                    } else {
2710                        # Here we have raw text.
2711                        $realPattern .= quotemeta($piece);
2712                    }
2713                }
2714                # Do the match.
2715                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2716            }
2717        }
2718        # Return the result.
2719        return $retVal;
2720    }
2721    
2722    =head3 GetEntity
2723    
2724    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2725    
2726    Return an object describing the entity instance with a specified ID.
2727    
2728    =over 4
2729    
2730    =item entityType
2731    
2732    Entity type name.
2733    
2734    =item ID
2735    
2736    ID of the desired entity.
2737    
2738    =item RETURN
2739    
2740    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2741    instance is found with the specified key.
2742    
2743    =back
2744    
2745    =cut
2746    
2747    sub GetEntity {
2748        # Get the parameters.
2749        my ($self, $entityType, $ID) = @_;
2750        # Create a query.
2751        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2752        # Get the first (and only) object.
2753        my $retVal = $query->Fetch();
2754        # Return the result.
2755        return $retVal;
2756    }
2757    
2758    =head3 GetChoices
2759    
2760    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2761    
2762    Return a list of all the values for the specified field that are represented in the
2763    specified entity.
2764    
2765    Note that if the field is not indexed, then this will be a very slow operation.
2766    
2767    =over 4
2768    
2769    =item entityName
2770    
2771    Name of an entity in the database.
2772    
2773    =item fieldName
2774    
2775    Name of a field belonging to the entity. This is a raw field name without
2776    the standard parenthesized notation used in most calls.
2777    
2778    =item RETURN
2779    
2780    Returns a list of the distinct values for the specified field in the database.
2781    
2782    =back
2783    
2784    =cut
2785    
2786    sub GetChoices {
2787        # Get the parameters.
2788        my ($self, $entityName, $fieldName) = @_;
2789        # Declare the return variable.
2790        my @retVal;
2791        # Get the entity data structure.
2792        my $entityData = $self->_GetStructure($entityName);
2793        # Get the field.
2794        my $fieldHash = $entityData->{Fields};
2795        if (! exists $fieldHash->{$fieldName}) {
2796            Confess("$fieldName not found in $entityName.");
2797        } else {
2798            # Get the name of the relation containing the field.
2799            my $relation = $fieldHash->{$fieldName}->{relation};
2800            # Fix up the field name.
2801            my $realName = _FixName($fieldName);
2802            # Get the database handle.
2803            my $dbh = $self->{_dbh};
2804            # Query the database.
2805            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2806            # Clean the results. They are stored as a list of lists, and we just want the one list.
2807            @retVal = sort map { $_->[0] } @{$results};
2808        }
2809        # Return the result.
2810        return @retVal;
2811    }
2812    
2813    =head3 GetEntityValues
2814    
2815    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2816    
2817    Return a list of values from a specified entity instance. If the entity instance
2818    does not exist, an empty list is returned.
2819    
2820    =over 4
2821    
2822    =item entityType
2823    
2824    Entity type name.
2825    
2826    =item ID
2827    
2828    ID of the desired entity.
2829    
2830    =item fields
2831    
2832    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2833    
2834    =item RETURN
2835    
2836    Returns a flattened list of the values of the specified fields for the specified entity.
2837    
2838    =back
2839    
2840    =cut
2841    
2842    sub GetEntityValues {
2843        # Get the parameters.
2844        my ($self, $entityType, $ID, $fields) = @_;
2845        # Get the specified entity.
2846        my $entity = $self->GetEntity($entityType, $ID);
2847        # Declare the return list.
2848        my @retVal = ();
2849        # If we found the entity, push the values into the return list.
2850        if ($entity) {
2851            push @retVal, $entity->Values($fields);
2852        }
2853        # Return the result.
2854        return @retVal;
2855    }
2856    
2857    =head3 GetAll
2858    
2859    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2860    
2861    Return a list of values taken from the objects returned by a query. The first three
2862    parameters correspond to the parameters of the L</Get> method. The final parameter is
2863    a list of the fields desired from each record found by the query. The field name
2864    syntax is the standard syntax used for fields in the B<ERDB> system--
2865    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2866    or relationship and I<fieldName> is the name of the field.
2867    
2868    The list returned will be a list of lists. Each element of the list will contain
2869    the values returned for the fields specified in the fourth parameter. If one of the
2870    fields specified returns multiple values, they are flattened in with the rest. For
2871    example, the following call will return a list of the features in a particular
2872    spreadsheet cell, and each feature will be represented by a list containing the
2873    feature ID followed by all of its aliases.
2874    
2875    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2876    
2877    =over 4
2878    
2879    =item objectNames
2880    
2881    List containing the names of the entity and relationship objects to be retrieved.
2882    
2883    =item filterClause
2884    
2885    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2886    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2887    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2888    parameter list as additional parameters. The fields in a filter clause can come from primary
2889    entity relations, relationship relations, or secondary entity relations; however, all of the
2890    entities and relationships involved must be included in the list of object names.
2891    
2892    =item parameterList
2893    
2894    List of the parameters to be substituted in for the parameters marks in the filter clause.
2895    
2896    =item fields
2897    
2898    List of the fields to be returned in each element of the list returned.
2899    
2900    =item count
2901    
2902    Maximum number of records to return. If omitted or 0, all available records will be returned.
2903    
2904    =item RETURN
2905    
2906    Returns a list of list references. Each element of the return list contains the values for the
2907    fields specified in the B<fields> parameter.
2908    
2909    =back
2910    
2911    =cut
2912    #: Return Type @@;
2913    sub GetAll {
2914        # Get the parameters.
2915        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2916        # Translate the parameters from a list reference to a list. If the parameter
2917        # list is a scalar we convert it into a singleton list.
2918        my @parmList = ();
2919        if (ref $parameterList eq "ARRAY") {
2920            Trace("GetAll parm list is an array.") if T(4);
2921            @parmList = @{$parameterList};
2922        } else {
2923            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2924            push @parmList, $parameterList;
2925        }
2926        # Insure the counter has a value.
2927        if (!defined $count) {
2928            $count = 0;
2929        }
2930        # Add the row limit to the filter clause.
2931        if ($count > 0) {
2932            $filterClause .= " LIMIT $count";
2933        }
2934        # Create the query.
2935        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2936        # Set up a counter of the number of records read.
2937        my $fetched = 0;
2938        # Loop through the records returned, extracting the fields. Note that if the
2939        # counter is non-zero, we stop when the number of records read hits the count.
2940        my @retVal = ();
2941        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2942            my @rowData = $row->Values($fields);
2943            push @retVal, \@rowData;
2944            $fetched++;
2945        }
2946        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2947        # Return the resulting list.
2948        return @retVal;
2949    }
2950    
2951    =head3 Exists
2952    
2953    C<< my $found = $sprout->Exists($entityName, $entityID); >>
2954    
2955    Return TRUE if an entity exists, else FALSE.
2956    
2957    =over 4
2958    
2959    =item entityName
2960    
2961    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2962    
2963    =item entityID
2964    
2965    ID of the entity instance whose existence is to be checked.
2966    
2967    =item RETURN
2968    
2969    Returns TRUE if the entity instance exists, else FALSE.
2970    
2971    =back
2972    
2973    =cut
2974    #: Return Type $;
2975    sub Exists {
2976        # Get the parameters.
2977        my ($self, $entityName, $entityID) = @_;
2978        # Check for the entity instance.
2979        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2980        my $testInstance = $self->GetEntity($entityName, $entityID);
2981        # Return an existence indicator.
2982        my $retVal = ($testInstance ? 1 : 0);
2983        return $retVal;
2984    }
2985    
2986    =head3 EstimateRowSize
2987    
2988    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2989    
2990    Estimate the row size of the specified relation. The estimated row size is computed by adding
2991    up the average length for each data type.
2992    
2993    =over 4
2994    
2995    =item relName
2996    
2997    Name of the relation whose estimated row size is desired.
2998    
2999    =item RETURN
3000    
3001    Returns an estimate of the row size for the specified relation.
3002    
3003    =back
3004    
3005    =cut
3006    #: Return Type $;
3007    sub EstimateRowSize {
3008        # Get the parameters.
3009        my ($self, $relName) = @_;
3010        # Declare the return variable.
3011        my $retVal = 0;
3012        # Find the relation descriptor.
3013        my $relation = $self->_FindRelation($relName);
3014        # Get the list of fields.
3015        for my $fieldData (@{$relation->{Fields}}) {
3016            # Get the field type and add its length.
3017            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3018            $retVal += $fieldLen;
3019        }
3020        # Return the result.
3021        return $retVal;
3022    }
3023    
3024    =head3 GetFieldTable
3025    
3026    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3027    
3028    Get the field structure for a specified entity or relationship.
3029    
3030    =over 4
3031    
3032    =item objectName
3033    
3034    Name of the desired entity or relationship.
3035    
3036    =item RETURN
3037    
3038    The table containing the field descriptors for the specified object.
3039    
3040    =back
3041    
3042    =cut
3043    
3044    sub GetFieldTable {
3045        # Get the parameters.
3046        my ($self, $objectName) = @_;
3047        # Get the descriptor from the metadata.
3048        my $objectData = $self->_GetStructure($objectName);
3049        # Return the object's field table.
3050        return $objectData->{Fields};
3051    }
3052    
3053    =head3 SplitKeywords
3054    
3055    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3056    
3057    This method returns a list of the positive keywords in the specified
3058    keyword string. All of the operators will have been stripped off,
3059    and if the keyword is preceded by a minus operator (C<->), it will
3060    not be in the list returned. The idea here is to get a list of the
3061    keywords the user wants to see. The list will be processed to remove
3062    duplicates.
3063    
3064    It is possible to create a string that confuses this method. For example
3065    
3066        frog toad -frog
3067    
3068    would return both C<frog> and C<toad>. If this is a problem we can deal
3069    with it later.
3070    
3071    =over 4
3072    
3073    =item keywordString
3074    
3075    The keyword string to be parsed.
3076    
3077    =item RETURN
3078    
3079    Returns a list of the words in the keyword string the user wants to
3080    see.
3081    
3082    =back
3083    
3084    =cut
3085    
3086    sub SplitKeywords {
3087        # Get the parameters.
3088        my ($keywordString) = @_;
3089        # Make a safety copy of the string. (This helps during debugging.)
3090        my $workString = $keywordString;
3091        # Convert operators we don't care about to spaces.
3092        $workString =~ tr/+"()<>/ /;
3093        # Split the rest of the string along space boundaries. Note that we
3094        # eliminate any words that are zero length or begin with a minus sign.
3095        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3096        # Use a hash to remove duplicates.
3097        my %words = map { $_ => 1 } @wordList;
3098        # Return the result.
3099        return sort keys %words;
3100    }
3101    
3102    =head3 ValidateFieldName
3103    
3104    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3105    
3106    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3107    be hyphenated words subject to certain restrictions.
3108    
3109    =over 4
3110    
3111    =item fieldName
3112    
3113    Field name to be validated.
3114    
3115    =item RETURN
3116    
3117    Returns TRUE if the field name is valid, else FALSE.
3118    
3119    =back
3120    
3121    =cut
3122    
3123    sub ValidateFieldName {
3124        # Get the parameters.
3125        my ($fieldName) = @_;
3126        # Declare the return variable. The field name is valid until we hear
3127        # differently.
3128        my $retVal = 1;
3129        # Compute the maximum name length.
3130        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3131        # Look for bad stuff in the name.
3132        if ($fieldName =~ /--/) {
3133            # Here we have a doubled minus sign.
3134            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3135            $retVal = 0;
3136        } elsif ($fieldName !~ /^[A-Za-z]/) {
3137            # Here the field name is missing the initial letter.
3138            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3139            $retVal = 0;
3140        } elsif (length($fieldName) > $maxLen) {
3141            # Here the field name is too long.
3142            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3143        } else {
3144            # Strip out the minus signs. Everything remaining must be a letter,
3145            # underscore, or digit.
3146            my $strippedName = $fieldName;
3147            $strippedName =~ s/-//g;
3148            if ($strippedName !~ /^(\w|\d)+$/) {
3149                Trace("Field name $fieldName contains illegal characters.") if T(1);
3150                $retVal = 0;
3151            }
3152        }
3153        # Return the result.
3154        return $retVal;
3155    }
3156    
3157    =head3 ReadMetaXML
3158    
3159    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3160    
3161    This method reads a raw database definition XML file and returns it.
3162    Normally, the metadata used by the ERDB system has been processed and
3163    modified to make it easier to load and retrieve the data; however,
3164    this method can be used to get the data in its raw form.
3165    
3166    =over 4
3167    
3168    =item fileName
3169    
3170    Name of the XML file to read.
3171    
3172    =item RETURN
3173    
3174    Returns a hash reference containing the raw XML data from the specified file.
3175    
3176    =back
3177    
3178    =cut
3179    
3180    sub ReadMetaXML {
3181        # Get the parameters.
3182        my ($fileName) = @_;
3183        # Read the XML.
3184        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3185        Trace("XML metadata loaded from file $fileName.") if T(1);
3186        # Return the result.
3187        return $retVal;
3188    }
3189    
3190    =head3 GetEntityFieldHash
3191    
3192    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3193    
3194    Get the field hash of the named entity in the specified raw XML structure.
3195    The field hash may not exist, in which case we need to create it.
3196    
3197    =over 4
3198    
3199    =item structure
3200    
3201    Raw XML structure defininng the database. This is not the run-time XML used by
3202    an ERDB object, since that has all sorts of optimizations built-in.
3203    
3204    =item entityName
3205    
3206    Name of the entity whose field structure is desired.
3207    
3208    =item RETURN
3209    
3210    Returns the field hash used to define the entity's fields.
3211    
3212    =back
3213    
3214    =cut
3215    
3216    sub GetEntityFieldHash {
3217        # Get the parameters.
3218        my ($structure, $entityName) = @_;
3219        # Get the entity structure.
3220        my $entityData = $structure->{Entities}->{$entityName};
3221        # Look for a field structure.
3222        my $retVal = $entityData->{Fields};
3223        # If it doesn't exist, create it.
3224        if (! defined($retVal)) {
3225            $entityData->{Fields} = {};
3226            $retVal = $entityData->{Fields};
3227        }
3228        # Return the result.
3229        return $retVal;
3230    }
3231    
3232    =head3 WriteMetaXML
3233    
3234    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3235    
3236    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3237    used to update the database definition. It must be used with care, however, since it
3238    will only work on a raw structure, not on the processed structure created by an ERDB
3239    constructor.
3240    
3241    =over 4
3242    
3243    =item structure
3244    
3245    XML structure to be written to the file.
3246    
3247    =item fileName
3248    
3249    Name of the output file to which the updated XML should be stored.
3250    
3251    =back
3252    
3253    =cut
3254    
3255    sub WriteMetaXML {
3256        # Get the parameters.
3257        my ($structure, $fileName) = @_;
3258        # Compute the output.
3259        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3260        # Write it to the file.
3261        my $xmlOut = Open(undef, ">$fileName");
3262        print $xmlOut $fileString;
3263    }
3264    
3265    
3266    =head3 HTMLNote
3267    
3268    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3269    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3270    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3271    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3272    
3273    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3274    
3275    =over 4
3276    
3277    =item dataString
3278    
3279    String to convert to HTML.
3280    
3281    =item RETURN
3282    
3283    An HTML string derived from the input string.
3284    
3285    =back
3286    
3287    =cut
3288    
3289    sub HTMLNote {
3290        # Get the parameter.
3291        my ($dataString) = @_;
3292        # HTML-escape the text.
3293        my $retVal = CGI::escapeHTML($dataString);
3294        # Substitute the bulletin board codes.
3295        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3296        $retVal =~ s!\[p\]!</p><p>!g;
3297        # Return the result.
3298        return $retVal;
3299    }
3300    
3301    
3302    =head2 Data Mining Methods
3303    
3304    =head3 GetUsefulCrossValues
3305    
3306    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3307    
3308    Return a list of the useful attributes that would be returned by a B<Cross> call
3309    from an entity of the source entity type through the specified relationship. This
3310    means it will return the fields of the target entity type and the intersection data
3311    fields in the relationship. Only primary table fields are returned. In other words,
3312    the field names returned will be for fields where there is always one and only one
3313    value.
3314    
3315    =over 4
3316    
3317    =item sourceEntity
3318    
3319    Name of the entity from which the relationship crossing will start.
3320    
3321    =item relationship
3322    
3323    Name of the relationship being crossed.
3324    
3325    =item RETURN
3326    
3327    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3328    
3329    =back
3330    
3331    =cut
3332    #: Return Type @;
3333    sub GetUsefulCrossValues {
3334        # Get the parameters.
3335        my ($self, $sourceEntity, $relationship) = @_;
3336        # Declare the return variable.
3337        my @retVal = ();
3338        # Determine the target entity for the relationship. This is whichever entity is not
3339        # the source entity. So, if the source entity is the FROM, we'll get the name of
3340        # the TO, and vice versa.
3341        my $relStructure = $self->_GetStructure($relationship);
3342        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3343        my $targetEntity = $relStructure->{$targetEntityType};
3344        # Get the field table for the entity.
3345        my $entityFields = $self->GetFieldTable($targetEntity);
3346        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3347        # For the entity fields, the key aspect of the target structure is that the {relation} value
3348        # must match the entity name.
3349        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3350                            keys %{$entityFields};
3351        # Push the fields found onto the return variable.
3352        push @retVal, sort @fieldList;
3353        # Get the field table for the relationship.
3354        my $relationshipFields = $self->GetFieldTable($relationship);
3355        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3356        # This may end up being an empty set.
3357        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3358                            keys %{$relationshipFields};
3359        # Push these onto the return list.
3360        push @retVal, sort @fieldList2;
3361        # Return the result.
3362        return @retVal;
3363    }
3364    
3365    =head3 FindColumn
3366    
3367    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3368    
3369    Return the location a desired column in a data mining header line. The data
3370    mining header line is a tab-separated list of column names. The column
3371    identifier is either the numerical index of a column or the actual column
3372    name.
3373    
3374    =over 4
3375    
3376    =item headerLine
3377    
3378    The header line from a data mining command, which consists of a tab-separated
3379    list of column names.
3380    
3381    =item columnIdentifier
3382    
3383    Either the ordinal number of the desired column (1-based), or the name of the
3384    desired column.
3385    
3386    =item RETURN
3387    
3388    Returns the array index (0-based) of the desired column.
3389    
3390    =back
3391    
3392    =cut
3393    
3394    sub FindColumn {
3395        # Get the parameters.
3396        my ($headerLine, $columnIdentifier) = @_;
3397        # Declare the return variable.
3398        my $retVal;
3399        # Split the header line into column names.
3400        my @headers = ParseColumns($headerLine);
3401        # Determine whether we have a number or a name.
3402        if ($columnIdentifier =~ /^\d+$/) {
3403            # Here we have a number. Subtract 1 and validate the result.
3404            $retVal = $columnIdentifier - 1;
3405            if ($retVal < 0 || $retVal > $#headers) {
3406                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3407            }
3408        } else {
3409            # Here we have a name. We need to find it in the list.
3410            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3411                if ($headers[$i] eq $columnIdentifier) {
3412                    $retVal = $i;
3413                }
3414            }
3415            if (! defined($retVal)) {
3416                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3417            }
3418        }
3419        # Return the result.
3420      return $retVal;      return $retVal;
3421  }  }
3422    
3423  =head3 GenerateEntity  =head3 ParseColumns
3424    
3425  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3426    
3427  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.  
3428    
3429  =over 4  =over 4
3430    
3431  =item id  =item line
   
 ID to assign to the new entity.  
   
 =item type  
3432    
3433  Type name for the new entity.  A data mining input, consisting of a tab-separated list of columns terminated by a
3434    new-line.
3435    
3436  =item values  =item RETURN
3437    
3438  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a list consisting of the column values.
3439    
3440  =back  =back
3441    
3442  =cut  =cut
3443    
3444  sub GenerateEntity {  sub ParseColumns {
3445      # Get the parameters.      # Get the parameters.
3446      my ($self, $id, $type, $values) = @_;      my ($line) = @_;
3447      # Create the return hash.      # Chop off the line-end.
3448      my $this = { id => $id };      chomp $line;
3449      # Get the metadata structure.      # Split it into a list.
3450      my $metadata = $self->{_metaData};      my @retVal = split(/\t/, $line);
3451      # Get this entity's list of fields.      # Return the result.
3452      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;  
3453  }  }
3454    
3455  =head3 GetEntity  =head2 Virtual Methods
   
 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>  
3456    
3457  Return an object describing the entity instance with a specified ID.  =head3 CleanKeywords
3458    
3459  =over 4  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3460    
3461  =item entityType  Clean up a search expression or keyword list. This is a virtual method that may
3462    be overridden by the subclass. The base-class method removes extra spaces
3463    and converts everything to lower case.
3464    
3465  Entity type name.  =over 4
3466    
3467  =item ID  =item searchExpression
3468    
3469  ID of the desired entity.  Search expression or keyword list to clean. Note that a search expression may
3470    contain boolean operators which need to be preserved. This includes leading
3471    minus signs.
3472    
3473  =item RETURN  =item RETURN
3474    
3475  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.  
3476    
3477  =back  =back
3478    
3479  =cut  =cut
3480    
3481  sub GetEntity {  sub CleanKeywords {
3482      # Get the parameters.      # Get the parameters.
3483      my ($self, $entityType, $ID) = @_;      my ($self, $searchExpression) = @_;
3484      # Create a query.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3485      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      # don't accidentally end up with an undefined value.
3486      # Get the first (and only) object.      my $retVal = lc($searchExpression || "");
3487      my $retVal = $query->Fetch();      # Remove extra spaces.
3488        $retVal =~ s/\s+/ /g;
3489        $retVal =~ s/(^\s+)|(\s+$)//g;
3490      # Return the result.      # Return the result.
3491      return $retVal;      return $retVal;
3492  }  }
3493    
3494  =head3 GetEntityValues  =head3 GetSourceObject
3495    
3496  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my $source = $erdb->GetSourceObject($entityName); >>
3497    
3498  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
3499    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3500    XML
3501    
3502  =over 4  =head2 Internal Utility Methods
3503    
3504  =item entityType  =head3 _RelationMap
3505    
3506  Entity type name.  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3507    
3508  =item ID  Create the relation map for an SQL query. The relation map is used by B<DBObject>
3509    to determine how to interpret the results of the query.
3510    
3511  ID of the desired entity.  =over 4
3512    
3513  =item fields  =item mappedNameHashRef
3514    
3515  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  Reference to a hash that maps modified object names to real object names.
3516    
3517    =item mappedNameListRef
3518    
3519    Reference to a list of modified object names in the order they appear in the
3520    SELECT list.
3521    
3522  =item RETURN  =item RETURN
3523    
3524  Returns a flattened list of the values of the specified fields for the specified entity.  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3525    query followed by the actual name of that object. This enables the B<DBObject> to
3526    determine the order of the tables in the query and which object name belongs to each
3527    mapped object name. Most of the time these two values are the same; however, if a
3528    relation occurs twice in the query, the relation name in the field list and WHERE
3529    clause will use a mapped name (generally the actual relation name with a numeric
3530    suffix) that does not match the actual relation name.
3531    
3532  =back  =back
3533    
3534  =cut  =cut
3535    
3536  sub GetEntityValues {  sub _RelationMap {
3537      # Get the parameters.      # Get the parameters.
3538      my ($self, $entityType, $ID, $fields) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
3539      # Get the specified entity.      # Declare the return variable.
     my $entity = $self->GetEntity($entityType, $ID);  
     # Declare the return list.  
3540      my @retVal = ();      my @retVal = ();
3541      # If we found the entity, push the values into the return list.      # Build the map.
3542      if ($entity) {      for my $mappedName (@{$mappedNameListRef}) {
3543          push @retVal, $entity->Values($fields);          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3544      }      }
3545      # Return the result.      # Return it.
3546      return @retVal;      return @retVal;
3547  }  }
3548    
 =head3 GetAll  
   
 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
3549    
3550  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.  
3551    
3552  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
3553  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
3554  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
3555  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.  
3556    
3557  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  This is an instance method.
3558    
3559  =over 4  =over 4
3560    
3561  =item objectNames  =item objectNames
3562    
3563  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.
3564    
3565  =item filterClause  =item filterClause
3566    
3567  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
3568  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.  
3569    
3570  =item count  =item matchClause
3571    
3572  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
3573    front of the WHERE clause. It should already be SQL-formatted; that is, the
3574    field names should be in the form I<table>C<.>I<fieldName>.
3575    
3576  =item RETURN  =item RETURN
3577    
3578  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
3579  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
3580    used in retrieving the fields. The third element is a hash mapping the names to the
3581    objects they represent.
3582    
3583  =back  =back
3584    
3585  =cut  =cut
3586  #: Return Type @@;  
3587  sub GetAll {  sub _SetupSQL {
3588      # Get the parameters.      my ($self, $objectNames, $filterClause, $matchClause) = @_;
3589      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Adjust the list of object names to account for multiple occurrences of the
3590      # 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
3591      # list is a scalar we convert it into a singleton list.      # return the object suffix. The first time an object is encountered it will
3592      my @parmList = ();      # not be found in the hash. The next time the hash will map the object name
3593      if (ref $parameterList eq "ARRAY") {      # to 2, then 3, and so forth.
3594          @parmList = @{$parameterList};      my %objectHash = ();
3595        # This list will contain the object names as they are to appear in the
3596        # FROM list.
3597        my @fromList = ();
3598        # This list contains the suffixed object name for each object. It is exactly
3599        # parallel to the list in the $objectNames parameter.
3600        my @mappedNameList = ();
3601        # Finally, this hash translates from a mapped name to its original object name.
3602        my %mappedNameHash = ();
3603        # Now we create the lists. Note that for every single name we push something into
3604        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3605        # parallel to $objectNames.
3606        for my $objectName (@{$objectNames}) {
3607            # Get the next suffix for this object.
3608            my $suffix = $objectHash{$objectName};
3609            if (! $suffix) {
3610                # Here we are seeing the object for the first time. The object name
3611                # is used as is.
3612                push @mappedNameList, $objectName;
3613                push @fromList, $objectName;
3614                $mappedNameHash{$objectName} = $objectName;
3615                # Denote the next suffix will be 2.
3616                $objectHash{$objectName} = 2;
3617      } else {      } else {
3618          push @parmList, $parameterList;              # Here we've seen the object before. We construct a new name using
3619                # the suffix from the hash and update the hash.
3620                my $mappedName = "$objectName$suffix";
3621                $objectHash{$objectName} = $suffix + 1;
3622                # The FROM list has the object name followed by the mapped name. This
3623                # tells SQL it's still the same table, but we're using a different name
3624                # for it to avoid confusion.
3625                push @fromList, "$objectName $mappedName";
3626                # The mapped-name list contains the real mapped name.
3627                push @mappedNameList, $mappedName;
3628                # Finally, enable us to get back from the mapped name to the object name.
3629                $mappedNameHash{$mappedName} = $objectName;
3630      }      }
     # 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) {  
         $count = 0;  
3631      }      }
3632      # Loop through the records returned, extracting the fields. Note that if the      # Begin the SELECT suffix. It starts with
3633      # counter is non-zero, we stop when the number of records read hits the count.      #
3634      my @retVal = ();      # FROM name1, name2, ... nameN
3635      while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {      #
3636          my @rowData = $row->Values($fields);      my $suffix = "FROM " . join(', ', @fromList);
3637          push @retVal, \@rowData;      # Now for the WHERE. First, we need a place for the filter string.
3638          $fetched++;      my $filterString = "";
3639        # We will also keep a list of conditions to add to the WHERE clause in order to link
3640        # entities and relationships as well as primary relations to secondary ones.
3641        my @joinWhere = ();
3642        # Check for a filter clause.
3643        if ($filterClause) {
3644            # Here we have one, so we convert its field names and add it to the query. First,
3645            # We create a copy of the filter string we can work with.
3646            $filterString = $filterClause;
3647            # Next, we sort the object names by length. This helps protect us from finding
3648            # object names inside other object names when we're doing our search and replace.
3649            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3650            # The final preparatory step is to create a hash table of relation names. The
3651            # table begins with the relation names already in the SELECT command. We may
3652            # need to add relations later if there is filtering on a field in a secondary
3653            # relation. The secondary relations are the ones that contain multiply-
3654            # occurring or optional fields.
3655            my %fromNames = map { $_ => 1 } @sortedNames;
3656            # We are ready to begin. We loop through the object names, replacing each
3657            # object name's field references by the corresponding SQL field reference.
3658            # Along the way, if we find a secondary relation, we will need to add it
3659            # to the FROM clause.
3660            for my $mappedName (@sortedNames) {
3661                # Get the length of the object name plus 2. This is the value we add to the
3662                # size of the field name to determine the size of the field reference as a
3663                # whole.
3664                my $nameLength = 2 + length $mappedName;
3665                # Get the real object name for this mapped name.
3666                my $objectName = $mappedNameHash{$mappedName};
3667                Trace("Processing $mappedName for object $objectName.") if T(4);
3668                # Get the object's field list.
3669                my $fieldList = $self->GetFieldTable($objectName);
3670                # Find the field references for this object.
3671                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3672                    # At this point, $1 contains the field name, and the current position
3673                    # is set immediately after the final parenthesis. We pull out the name of
3674                    # the field and the position and length of the field reference as a whole.
3675                    my $fieldName = $1;
3676                    my $len = $nameLength + length $fieldName;
3677                    my $pos = pos($filterString) - $len;
3678                    # Insure the field exists.
3679                    if (!exists $fieldList->{$fieldName}) {
3680                        Confess("Field $fieldName not found for object $objectName.");
3681                    } else {
3682                        Trace("Processing $fieldName at position $pos.") if T(4);
3683                        # Get the field's relation.
3684                        my $relationName = $fieldList->{$fieldName}->{relation};
3685                        # Now we have a secondary relation. We need to insure it matches the
3686                        # mapped name of the primary relation. First we peel off the suffix
3687                        # from the mapped name.
3688                        my $mappingSuffix = substr $mappedName, length($objectName);
3689                        # Put the mapping suffix onto the relation name to get the
3690                        # mapped relation name.
3691                        my $mappedRelationName = "$relationName$mappingSuffix";
3692                        # Insure the relation is in the FROM clause.
3693                        if (!exists $fromNames{$mappedRelationName}) {
3694                            # Add the relation to the FROM clause.
3695                            if ($mappedRelationName eq $relationName) {
3696                                # The name is un-mapped, so we add it without
3697                                # any frills.
3698                                $suffix .= ", $relationName";
3699                                push @joinWhere, "$objectName.id = $relationName.id";
3700                            } else {
3701                                # Here we have a mapping situation.
3702                                $suffix .= ", $relationName $mappedRelationName";
3703                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3704                            }
3705                            # Denote we have this relation available for future fields.
3706                            $fromNames{$mappedRelationName} = 1;
3707                        }
3708                        # Form an SQL field reference from the relation name and the field name.
3709                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3710                        # Put it into the filter string in place of the old value.
3711                        substr($filterString, $pos, $len) = $sqlReference;
3712                        # Reposition the search.
3713                        pos $filterString = $pos + length $sqlReference;
3714      }      }
3715      # Return the resulting list.              }
3716      return @retVal;          }
3717        }
3718        # The next step is to join the objects together. We only need to do this if there
3719        # is more than one object in the object list. We start with the first object and
3720        # run through the objects after it. Note also that we make a safety copy of the
3721        # list before running through it, because we shift off the first object before
3722        # processing the rest.
3723        my @mappedObjectList = @mappedNameList;
3724        my $lastMappedObject = shift @mappedObjectList;
3725        # Get the join table.
3726        my $joinTable = $self->{_metaData}->{Joins};
3727        # Loop through the object list.
3728        for my $thisMappedObject (@mappedObjectList) {
3729            # Look for a join using the real object names.
3730            my $lastObject = $mappedNameHash{$lastMappedObject};
3731            my $thisObject = $mappedNameHash{$thisMappedObject};
3732            my $joinKey = "$lastObject/$thisObject";
3733            if (!exists $joinTable->{$joinKey}) {
3734                # Here there's no join, so we throw an error.
3735                Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3736            } else {
3737                # Get the join clause.
3738                my $unMappedJoin = $joinTable->{$joinKey};
3739                # Fix the names.
3740                $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3741                $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3742                push @joinWhere, $unMappedJoin;
3743                # Save this object as the last object for the next iteration.
3744                $lastMappedObject = $thisMappedObject;
3745            }
3746        }
3747        # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3748        # here is we want the filter clause to be empty if there's no WHERE filter.
3749        # We'll put the ORDER BY / LIMIT clauses in the following variable.
3750        my $orderClause = "";
3751        # This is only necessary if we have a filter string in which the ORDER BY
3752        # and LIMIT clauses can live.
3753        if ($filterString) {
3754            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3755            # operator so that we find the first occurrence of either verb.
3756            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3757                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3758                my $pos = pos $filterString;
3759                $orderClause = $2 . substr($filterString, $pos);
3760                $filterString = $1;
3761            }
3762        }
3763        # All the things that are supposed to be in the WHERE clause of the
3764        # SELECT command need to be put into @joinWhere so we can string them
3765        # together. We begin with the match clause. This is important,
3766        # because the match clause's parameter mark must precede any parameter
3767        # marks in the filter string.
3768        if ($matchClause) {
3769            push @joinWhere, $matchClause;
3770        }
3771        # Add the filter string. We put it in parentheses to avoid operator
3772        # precedence problems with the match clause or the joins.
3773        if ($filterString) {
3774            Trace("Filter string is \"$filterString\".") if T(4);
3775            push @joinWhere, "($filterString)";
3776        }
3777        # String it all together into a big filter clause.
3778        if (@joinWhere) {
3779            $suffix .= " WHERE " . join(' AND ', @joinWhere);
3780        }
3781        # Add the sort or limit clause (if any).
3782        if ($orderClause) {
3783            $suffix .= " $orderClause";
3784        }
3785        # Return the suffix, the mapped name list, and the mapped name hash.
3786        return ($suffix, \@mappedNameList, \%mappedNameHash);
3787  }  }
3788    
3789  =head3 EstimateRowSize  =head3 _GetStatementHandle
3790    
3791  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  This method will prepare and execute an SQL query, returning the statement handle.
3792    The main reason for doing this here is so that everybody who does SQL queries gets
3793    the benefit of tracing.
3794    
3795  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.  
3796    
3797  =over 4  =over 4
3798    
3799  =item relName  =item command
3800    
3801  Name of the relation whose estimated row size is desired.  Command to prepare and execute.
3802    
3803    =item params
3804    
3805    Reference to a list of the values to be substituted in for the parameter marks.
3806    
3807  =item RETURN  =item RETURN
3808    
3809  Returns an estimate of the row size for the specified relation.  Returns a prepared and executed statement handle from which the caller can extract
3810    results.
3811    
3812  =back  =back
3813    
3814  =cut  =cut
3815  #: Return Type $;  
3816  sub EstimateRowSize {  sub _GetStatementHandle {
3817      # Get the parameters.      # Get the parameters.
3818      my ($self, $relName) = @_;      my ($self, $command, $params) = @_;
3819      # Declare the return variable.      # Trace the query.
3820      my $retVal = 0;      Trace("SQL query: $command") if T(SQL => 3);
3821      # Find the relation descriptor.      Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3822      my $relation = $self->_FindRelation($relName);      # Get the database handle.
3823      # Get the list of fields.      my $dbh = $self->{_dbh};
3824      for my $fieldData (@{$relation->{Fields}}) {      # Prepare the command.
3825          # Get the field type and add its length.      my $sth = $dbh->prepare_command($command);
3826          my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};      # Execute it with the parameters bound in.
3827          $retVal += $fieldLen;      $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
3828      }      # Return the statement handle.
3829      # Return the result.      return $sth;
     return $retVal;  
3830  }  }
3831    
3832  =head2 Internal Utility Methods  =head3 _GetLoadStats
   
 =head3 GetLoadStats  
3833    
3834  Return a blank statistics object for use by the load methods.  Return a blank statistics object for use by the load methods.
3835    
3836  This is a static method.  This is a static method.
3837    
3838  =cut  =cut
3839    
3840  sub _GetLoadStats {  sub _GetLoadStats{
3841      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;  
             }  
         }  
     }  
3842  }  }
3843    
3844  =head3 DumpRelation  =head3 _DumpRelation
3845    
3846  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.
3847    
3848  This is an instance method.  This is an instance method.
3849    
# Line 1764  Line 3891 
3891      close DTXOUT;      close DTXOUT;
3892  }  }
3893    
3894  =head3 GetStructure  =head3 _GetStructure
3895    
3896  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
3897    
# Line 1803  Line 3930 
3930      return $retVal;      return $retVal;
3931  }  }
3932    
3933  =head3 GetRelationTable  
3934    
3935    =head3 _GetRelationTable
3936    
3937  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
3938    
# Line 1832  Line 3961 
3961      return $objectData->{Relations};      return $objectData->{Relations};
3962  }  }
3963    
3964  =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  
3965    
3966  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
3967  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 1888  Line 3988 
3988          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
3989              # Loop through the object's fields.              # Loop through the object's fields.
3990              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
3991                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
3992                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
3993                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($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";  
3994                          $retVal = 0;                          $retVal = 0;
3995                      }                      }
3996                  }                  }
3997              }              }
3998          }          }
     }  
3999      # If an error was found, fail.      # If an error was found, fail.
4000      if ($retVal  == 0) {      if ($retVal  == 0) {
4001          Confess("Errors found in field names.");          Confess("Errors found in field names.");
4002      }      }
4003  }  }
4004    
4005  =head3 LoadRelation  =head3 _LoadRelation
4006    
4007  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
4008  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 1976  Line 4062 
4062      return $retVal;      return $retVal;
4063  }  }
4064    
4065  =head3 LoadMetaData  
4066    =head3 _LoadMetaData
4067    
4068  This method loads the data describing this database from an XML file into a metadata structure.  This method loads the data describing this database from an XML file into a metadata structure.
4069  The resulting structure is a set of nested hash tables containing all the information needed to  The resulting structure is a set of nested hash tables containing all the information needed to
# Line 2001  Line 4088 
4088  sub _LoadMetaData {  sub _LoadMetaData {
4089      # Get the parameters.      # Get the parameters.
4090      my ($filename) = @_;      my ($filename) = @_;
4091      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4092      # 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
4093      # get the exact structure we want.      # get the exact structure we want.
4094      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 $filename.") if T(1);  
4095      # Before we go any farther, we need to validate the field and object names. If an error is found,      # Before we go any farther, we need to validate the field and object names. If an error is found,
4096      # the method below will fail.      # the method below will fail.
4097      _ValidateFieldNames($metadata);      _ValidateFieldNames($metadata);
# Line 2147  Line 4221 
4221              my $count = 0;              my $count = 0;
4222              for my $index (@{$indexList}) {              for my $index (@{$indexList}) {
4223                  # Add this index to the index table.                  # Add this index to the index table.
4224                  _AddIndex("idx$relationName$count", $relation, $index);                  _AddIndex("idx$count", $relation, $index);
4225                  # Increment the counter so that the next index has a different name.                  # Increment the counter so that the next index has a different name.
4226                  $count++;                  $count++;
4227              }              }
# Line 2214  Line 4288 
4288              # 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.
4289              my $fromEntity = $relationship->{from};              my $fromEntity = $relationship->{from};
4290              my $toEntity = $relationship->{to};              my $toEntity = $relationship->{to};
4291              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(4);              Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4292              if ($fromEntity eq $entityName) {              if ($fromEntity eq $entityName) {
4293                  if ($toEntity eq $entityName) {                  if ($toEntity eq $entityName) {
4294                      # Here the relationship is recursive.                      # Here the relationship is recursive.
# Line 2303  Line 4377 
4377      return $metadata;      return $metadata;
4378  }  }
4379    
4380  =head3 CreateRelationshipIndex  =head3 _CreateRelationshipIndex
4381    
4382  Create an index for a relationship's relation.  Create an index for a relationship's relation.
4383    
# Line 2345  Line 4419 
4419          $newIndex->{Unique} = 'true';          $newIndex->{Unique} = 'true';
4420      }      }
4421      # Add the index to the relation.      # Add the index to the relation.
4422      _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);      _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4423  }  }
4424    
4425  =head3 AddIndex  =head3 _AddIndex
4426    
4427  Add an index to a relation structure.  Add an index to a relation structure.
4428    
# Line 2394  Line 4468 
4468      $relationStructure->{Indexes}->{$indexName} = $newIndex;      $relationStructure->{Indexes}->{$indexName} = $newIndex;
4469  }  }
4470    
4471  =head3 FixupFields  =head3 _FixupFields
4472    
4473  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
4474  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 2432  Line 4506 
4506          # Here it doesn't, so we create a new one.          # Here it doesn't, so we create a new one.
4507          $structure->{Fields} = { };          $structure->{Fields} = { };
4508      } else {      } else {
4509          # 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
4510            # create a list for stashing them.
4511            my @textFields = ();
4512            # Loop through the fields.
4513          my $fieldStructures = $structure->{Fields};          my $fieldStructures = $structure->{Fields};
4514          for my $fieldName (keys %{$fieldStructures}) {          for my $fieldName (keys %{$fieldStructures}) {
4515              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);              Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
# Line 2441  Line 4518 
4518              my $type = $fieldData->{type};              my $type = $fieldData->{type};
4519              # Plug in a relation name if it is needed.              # Plug in a relation name if it is needed.
4520              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });              Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4521              # Plug in a data generator if we need one.              # Check for searchability.
4522              if (!exists $fieldData->{DataGen}) {