[Bio] / Sprout / ERDB.pm Repository:
ViewVC logotype

Diff of /Sprout/ERDB.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.33, Sat Jan 28 09:36:47 2006 UTC revision 1.91, Wed May 2 05:51:48 2007 UTC
# Line 6  Line 6 
6      use Data::Dumper;      use Data::Dumper;
7      use XML::Simple;      use XML::Simple;
8      use DBQuery;      use DBQuery;
9      use DBObject;      use ERDBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use FIG;      use Digest::MD5 qw(md5_base64);
13        use CGI;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
16    
# Line 58  Line 59 
59  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
60  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.
61    
62  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
63  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
64  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
65  to generate documentation for the database.  for the database.
66    
67    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
68    in which case it will be used to generate a text search index in which the user searches for words
69    in the field instead of a particular field value.
70    
71  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
72  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
73  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
74    
 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.  
   
75  =head2 XML Database Description  =head2 XML Database Description
76    
77  =head3 Data Types  =head3 Data Types
# Line 90  Line 91 
91    
92  32-bit signed integer  32-bit signed integer
93    
94    =item counter
95    
96    32-bit unsigned integer
97    
98  =item date  =item date
99    
100  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 109  Line 114 
114  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
115  0 and 1.  0 and 1.
116    
117    =item id-string
118    
119    variable-length string, maximum 25 characters
120    
121  =item key-string  =item key-string
122    
123  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 134 
134    
135  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
136    
137    =item hash-string
138    
139    variable-length string, maximum 22 characters
140    
141  =back  =back
142    
143    The hash-string data type has a special meaning. The actual key passed into the loader will
144    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
145    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
146    digest. Therefore, it is presumed the keys will be unique. When the database is actually
147    in use, the hashed keys will be presented rather than the original values. For this reason,
148    they should not be used for entities where the key is meaningful.
149    
150  =head3 Global Tags  =head3 Global Tags
151    
152  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 190 
190    
191  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<->),
192  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
193  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,
194    the name C<search-relevance> has special meaning for full-text searches and should not be
195    used as a field name.
196    
197  =item type  =item type
198    
# Line 189  Line 211 
211  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
212  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.
213    
214    =item searchable
215    
216    If specified, then the field is a candidate for full-text searching. A single full-text
217    index will be created for each relation with at least one searchable field in it.
218    For best results, this option should only be used for string or text fields.
219    
220    =item special
221    
222    This attribute allows the subclass to assign special meaning for certain fields.
223    The interpretation is up to the subclass itself. Currently, only entity fields
224    can have this attribute.
225    
226  =back  =back
227    
228  =head3 Indexes  =head3 Indexes
229    
230  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
231  be from the primary relation. The alternate indexes assist in ordering results  index must all be from the same relation. The alternate indexes assist in searching
232  from a query. A relationship can have up to two indexes-- a I<to-index> and a  on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
233  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
234  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
235  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
236  the genomes of a contig. A relationship's index must specify only fields in  the genomes of a contig. In addition, it can have zero or more alternate
237    indexes. A relationship's index must specify only fields in
238  the relationship.  the relationship.
239    
240  The indexes for an entity must be listed inside the B<Indexes> tag. The from-index  The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
241  of a relationship is specified using the B<FromIndex> tag; the to-index is specified  The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
242  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
243    
244  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 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 266  Line 303 
303    
304  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
305  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306  fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing  fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
307  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
308    
309  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
310    
# Line 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 =>   1, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
350                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
351                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
352                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
353                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
355                                   indexMod =>   0, notes => "signed, 64-bit integer"},
356                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
357                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
358                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
359                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
360                     'hash-string' =>
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                     'long-string' =>
376                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
377                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
378                  );                  );
379    
380  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 324  Line 383 
383                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
384                   );                   );
385    
386  # Table for interpreting string patterns.  # Options for XML input and output.
387    
388    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
389                                      Entities => 'Entity',
390                                      Fields => 'Field',
391                                      Indexes => 'Index',
392                                      IndexFields => 'IndexField'
393                                    },
394                      KeyAttr =>    { Relationship => 'name',
395                                      Entity => 'name',
396                                      Field => 'name'
397                                    },
398                      SuppressEmpty => 1,
399                     );
400    
401  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
402                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
403                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
404                       'V' => "aeiou",                    NormalizeSpace => 2,
                      'K' => "bcdfghjklmnoprstvwxyz"  
405                     );                     );
406    my %XmlOutOpts = (
407                      RootName => 'Database',
408                      XMLDecl => 1,
409                     );
410    
411    
412  =head2 Public Methods  =head2 Public Methods
413    
# Line 402  Line 478 
478      # Write the HTML heading stuff.      # Write the HTML heading stuff.
479      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
480      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
481        # Write the documentation.
482        print HTMLOUT $self->DisplayMetaData();
483        # Close the document.
484        print HTMLOUT "</body>\n</html>\n";
485        # Close the file.
486        close HTMLOUT;
487    }
488    
489    =head3 DisplayMetaData
490    
491    C<< my $html = $erdb->DisplayMetaData(); >>
492    
493    Return an HTML description of the database. This description can be used to help users create
494    the data to be loaded into the relations and form queries. The output is raw includable HTML
495    without any HEAD or BODY tags.
496    
497    =over 4
498    
499    =item filename
500    
501    The name of the output file.
502    
503    =back
504    
505    =cut
506    
507    sub DisplayMetaData {
508        # Get the parameters.
509        my ($self) = @_;
510        # Get the metadata and the title string.
511        my $metadata = $self->{_metaData};
512        # Get the title string.
513        my $title = $metadata->{Title};
514        # Get the entity and relationship lists.
515        my $entityList = $metadata->{Entities};
516        my $relationshipList = $metadata->{Relationships};
517        # Declare the return variable.
518        my $retVal = "";
519        # Open the output file.
520        Trace("Building MetaData table of contents.") if T(4);
521      # 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
522      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
523      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";
524      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
525      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
526          # Display this item.          # Display this item.
527          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
528      }      }
529      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
530      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";
531      # Loop through the Relationships.      # Loop through the Relationships.
532      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
533          # Display this item.          # Display this item.
534          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
535          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
536      }      }
537      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
538      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";
539      # Close off the table of contents itself.      # Close off the table of contents itself.
540      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
541      # 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.
542      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
543      # Loop through the entities.      # Loop through the entities.
544      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
545          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
546          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
547          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
548          # Get the entity data.          # Get the entity data.
549          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
550          # If there's descriptive text, display it.          # If there's descriptive text, display it.
551          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
552              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
553          }          }
554          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
555          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
556            if ($relCount > 0) {
557                # First, we set up the relationship subsection.
558                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
559          # Loop through the relationships.          # Loop through the relationships.
560          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
561              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 565 
565                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
566                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
567                  # Display the relationship data.                  # Display the relationship data.
568                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
569              }              }
570          }          }
571          # Close off the relationship list.          # Close off the relationship list.
572          print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
573            }
574          # Get the entity's relations.          # Get the entity's relations.
575          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
576          # Create a header for the relation subsection.          # Create a header for the relation subsection.
577          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
578          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
579          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
580              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
581              print HTMLOUT $htmlString;              $retVal .= $htmlString;
582          }          }
583      }      }
584      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
585      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
586      # Loop through the relationships.      # Loop through the relationships.
587      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
588          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 590 
590          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
591          # Create the relationship header.          # Create the relationship header.
592          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
593          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
594          # Get the entity names.          # Get the entity names.
595          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
596          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 600 
600          # since both sentences will say the same thing.          # since both sentences will say the same thing.
601          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
602          if ($arity eq "11") {          if ($arity eq "11") {
603              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
604          } else {          } else {
605              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
606              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
607                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
608              }              }
609          }          }
610          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
611          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
612          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
613              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
614          }          }
615          # Generate the relationship's relation table.          # Generate the relationship's relation table.
616          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
617          print HTMLOUT $htmlString;          $retVal .= $htmlString;
618      }      }
619      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
620      # Denote we're starting the join table.      # Denote we're starting the join table.
621      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
622      # Create a table header.      # Create a table header.
623      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
624      # Loop through the joins.      # Loop through the joins.
625      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
626      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 513  Line 633 
633          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
634          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
635          # Display them in a table row.          # Display them in a table row.
636          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";
637      }      }
638      # Close the table.      # Close the table.
639      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
640      # Close the document.      Trace("Built MetaData HTML.") if T(3);
641      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
642      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
643  }  }
644    
645  =head3 DumpMetaData  =head3 DumpMetaData
# Line 539  Line 657 
657      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
658  }  }
659    
660    =head3 CreatePPO
661    
662    C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
663    
664    Create a PPO XML file from an ERDB data definition XML file. At the
665    current time, the PPO XML file can be used to create a database with
666    similar functionality. Eventually, the PPO will be able to use the
667    created XML to access the live ERDB database.
668    
669    =over 4
670    
671    =item erdbXMLFile
672    
673    Name of the XML data definition file for the ERDB database. This
674    file must exist.
675    
676    =item ppoXMLFile
677    
678    Output file for the PPO XML definition. If this file exists, it
679    will be overwritten.
680    
681    =back
682    
683    =cut
684    
685    sub CreatePPO {
686        # Get the parameters.
687        my ($erdbXMLFile, $ppoXMLFile) = @_;
688        # First, we want to slurp in the ERDB XML file in its raw form.
689        my $xml = ReadMetaXML($erdbXMLFile);
690        # Create a variable to hold all of the objects in the PPO project.
691        my @objects = ();
692        # Get the relationship hash.
693        my $relationships = $xml->{Relationships};
694        # Loop through the entities.
695        my $entities = $xml->{Entities};
696        for my $entityName (keys %{$entities}) {
697            # Get the entity's data structures.
698            my $entityObject = $entities->{$entityName};
699            # We put the object's fields in here, according to their type.
700            my (@object_refs, @scalars, @indexes, @arrays);
701            # Create the ID field for the entity. We get the key type from the
702            # entity object and compute the corresponding SQL type.
703            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
704            push @scalars, { label => 'id', type => $type };
705            # Loop through the entity fields.
706            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
707                # Get the field object.
708                my $fieldObject = $entityObject->{Fields}->{$fieldName};
709                # Convert it to a scalar tag.
710                my $scalar = _CreatePPOField($fieldName, $fieldObject);
711                # If we have a relation, this field is stored in an array.
712                # otherwise, it is a scalar. The array tag has scalars
713                # stored as an XML array. In ERDB, there is only ever one,
714                # but PPO can have more.
715                my $relation = $fieldObject->{relation};
716                if ($relation) {
717                    push @arrays, { scalar => [$scalar] };
718                } else {
719                    push @scalars, $scalar;
720                }
721            }
722            # Loop through the relationships. If this entity is the to-entity
723            # on a relationship of 1M arity, then it is implemented as a PPO
724            # object reference.
725            for my $relationshipName (keys %{$relationships}) {
726                # Get the relationship data.
727                my $relationshipData = $relationships->{$relationshipName};
728                # If we have a from for this entity and an arity of 1M, we
729                # have an object reference.
730                if ($relationshipData->{to} eq $entityName &&
731                    $relationshipData->{arity} eq '1M') {
732                    # Build the object reference tag.
733                    push @object_refs, { label => $relationshipName,
734                                         type => $relationshipData->{from} };
735                }
736            }
737            # Create the indexes.
738            my $indexList = $entityObject->{Indexes};
739            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
740            # Build the object XML tree.
741            my $object = { label => $entityName,
742                           object_ref => \@object_refs,
743                           scalar => \@scalars,
744                           index => \@indexes,
745                           array => \@arrays
746                          };
747            # Push the object onto the objects list.
748            push @objects, $object;
749        }
750        # Loop through the relationships, searching for MMs. The 1Ms were
751        # already handled by the entity search above.
752        for my $relationshipName (keys %{$relationships}) {
753            # Get this relationship's object.
754            my $relationshipObject = $relationships->{$relationshipName};
755            # Only proceed if it's many-to-many.
756            if ($relationshipObject->{arity} eq 'MM') {
757                # Create the tag lists for the relationship object.
758                my (@object_refs, @scalars, @indexes);
759                # The relationship will be created as an object with object
760                # references for its links to the participating entities.
761                my %links = ( from_link => $relationshipObject->{from},
762                              to_link => $relationshipObject->{to} );
763                for my $link (keys %links) {
764                    # Create an object_ref tag for this piece of the
765                    # relationship (from or to).
766                    my $object_ref = { label => $link,
767                                       type => $links{$link} };
768                    push @object_refs, $object_ref;
769                }
770                # Loop through the intersection data fields, creating scalar tags.
771                # There are no fancy array tags in a relationship.
772                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
773                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
774                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
775                }
776                # Finally, the indexes: currently we cannot support the to-index and
777                # from-index in PPO, so we just process the alternate indexes.
778                my $indexList = $relationshipObject->{Indexes};
779                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
780                # Wrap up all the stuff about this relationship.
781                my $object = { label => $relationshipName,
782                               scalar => \@scalars,
783                               object_ref => \@object_refs,
784                               index => \@indexes
785                             };
786                # Push it into the object list.
787                push @objects, $object;
788            }
789        }
790        # Compute a title.
791        my $title;
792        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
793            # Here we have a standard file name we can use for a title.
794            $title = $2;
795        } else {
796            # Here the file name is non-standard, so we carve up the
797            # database title.
798            $title = $xml->{Title}->{content};
799            $title =~ s/\s\.,//g;
800        }
801        # Wrap up the XML as a project.
802        my $ppoXML = { project => { label => $title,
803                                    object => \@objects }};
804        # Write out the results.
805        my $ppoString = XML::Simple::XMLout($ppoXML,
806                                            AttrIndent => 1,
807                                            KeepRoot => 1);
808        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
809    }
810    
811    =head3 FindIndexForEntity
812    
813    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
814    
815    This method locates the entry in an entity's index list that begins with the
816    specified attribute name. If the entity has no index list, one will be
817    created. This method works on raw XML, not a live ERDB object.
818    
819    =over 4
820    
821    =item xml
822    
823    The raw XML structure defining the database.
824    
825    =item entityName
826    
827    The name of the relevant entity.
828    
829    =item attributeName
830    
831    The name of the attribute relevant to the search.
832    
833    =item RETURN
834    
835    The numerical index in the index list of the index entry for the specified entity and
836    attribute, or C<undef> if no such index exists.
837    
838    =back
839    
840    =cut
841    
842    sub FindIndexForEntity {
843        # Get the parameters.
844        my ($xml, $entityName, $attributeName) = @_;
845        # Declare the return variable.
846        my $retVal;
847        # Get the named entity.
848        my $entityData = $xml->{Entities}->{$entityName};
849        if (! $entityData) {
850            Confess("Entity $entityName not found in DBD structure.");
851        } else {
852            # Insure it has an index list.
853            if (! exists $entityData->{Indexes}) {
854                $entityData->{Indexes} = [];
855            } else {
856                # Search for the desired index.
857                my $indexList = $entityData->{Indexes};
858                my $n = scalar @{$indexList};
859                Trace("Searching $n indexes in index list for $entityName.") if T(2);
860                # We use an indexed FOR here because we're returning an
861                # index number instead of an object. We do THAT so we can
862                # delete the index from the list if needed.
863                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
864                    my $index = $indexList->[$i];
865                    my $fields = $index->{IndexFields};
866                    # Technically this IF should be safe (that is, we are guaranteed
867                    # the existence of a "$fields->[0]"), because when we load the XML
868                    # we have SuppressEmpty specified.
869                    if ($fields->[0]->{name} eq $attributeName) {
870                        $retVal = $i;
871                    }
872                }
873            }
874        }
875        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
876        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
877        # Return the result.
878        return $retVal;
879    }
880    
881  =head3 CreateTables  =head3 CreateTables
882    
883  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 558  Line 897 
897      # Loop through the relations.      # Loop through the relations.
898      for my $relationName (@relNames) {      for my $relationName (@relNames) {
899          # Create a table for this relation.          # Create a table for this relation.
900          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
901          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
902      }      }
903  }  }
# Line 626  Line 965 
965      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
966      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
967      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
968      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
969        # index will not be built until the table has been loaded.
970      if ($indexFlag) {      if ($indexFlag) {
971          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
972      }      }
# Line 687  Line 1027 
1027      return $retVal;      return $retVal;
1028  }  }
1029    
1030    =head3 DigestFields
1031    
1032    C<< $erdb->DigestFields($relName, $fieldList); >>
1033    
1034    Digest the strings in the field list that correspond to data type C<hash-string> in the
1035    specified relation.
1036    
1037    =over 4
1038    
1039    =item relName
1040    
1041    Name of the relation to which the fields belong.
1042    
1043    =item fieldList
1044    
1045    List of field contents to be loaded into the relation.
1046    
1047    =back
1048    
1049    =cut
1050    #: Return Type ;
1051    sub DigestFields {
1052        # Get the parameters.
1053        my ($self, $relName, $fieldList) = @_;
1054        # Get the relation definition.
1055        my $relData = $self->_FindRelation($relName);
1056        # Get the list of field descriptors.
1057        my $fieldTypes = $relData->{Fields};
1058        my $fieldCount = scalar @{$fieldTypes};
1059        # Loop through the two lists.
1060        for (my $i = 0; $i < $fieldCount; $i++) {
1061            # Get the type of the current field.
1062            my $fieldType = $fieldTypes->[$i]->{type};
1063            # If it's a hash string, digest it in place.
1064            if ($fieldType eq 'hash-string') {
1065                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1066            }
1067        }
1068    }
1069    
1070    =head3 DigestKey
1071    
1072    C<< my $digested = $erdb->DigestKey($keyValue); >>
1073    
1074    Return the digested value of a symbolic key. The digested value can then be plugged into a
1075    key-based search into a table with key-type hash-string.
1076    
1077    Currently the digesting process is independent of the database structure, but that may not
1078    always be the case, so this is an instance method instead of a static method.
1079    
1080    =over 4
1081    
1082    =item keyValue
1083    
1084    Key value to digest.
1085    
1086    =item RETURN
1087    
1088    Digested value of the key.
1089    
1090    =back
1091    
1092    =cut
1093    
1094    sub DigestKey {
1095        # Get the parameters.
1096        my ($self, $keyValue) = @_;
1097        # Compute the digest.
1098        my $retVal = md5_base64($keyValue);
1099        # Return the result.
1100        return $retVal;
1101    }
1102    
1103  =head3 CreateIndex  =head3 CreateIndex
1104    
1105  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 710  Line 1123 
1123      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
1124          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
1125          # Get the index's field list.          # Get the index's field list.
1126          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
1127            # Get a hash of the relation's field types.
1128            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1129            # We need to check for text fields so we can append a length limitation for them. To do
1130            # that, we need the relation's field list.
1131            my $relFields = $relationData->{Fields};
1132            for (my $i = 0; $i <= $#rawFields; $i++) {
1133                # Get the field type.
1134                my $field = $rawFields[$i];
1135                my $type = $types{$field};
1136                # Ask if it requires using prefix notation for the index.
1137                my $mod = $TypeTable{$type}->{indexMod};
1138                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1139                if ($mod) {
1140                    # Append the prefix length to the field name,
1141                    $rawFields[$i] .= "($mod)";
1142                }
1143            }
1144            my @fieldList = _FixNames(@rawFields);
1145          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
1146          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
1147          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1148          # Create the index.          # Create the index.
1149          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1150                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
1151          if ($rv) {          if ($rv) {
1152              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1153          } else {          } else {
# Line 725  Line 1156 
1156      }      }
1157  }  }
1158    
1159  =head3 LoadTables  =head3 GetSecondaryFields
   
 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  
1160    
1161  This method will load the database tables from a directory. The tables must already have been created  C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
 in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  
 all of the relations to be loaded must have a file in the directory with the same name as the relation  
 (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each  
 line of the file will be loaded as a row of the target relation table. The field values should be in  
 the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is  
 erased before the new data is loaded in.  
1162    
1163  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and  This method will return a list of the name and type of each of the secondary
1164  tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must  fields for a specified entity. Secondary fields are stored in two-column tables
1165  be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.  in addition to the primary entity table. This enables the field to have no value
1166    or to have multiple values.
1167    
1168  =over 4  =over 4
1169    
1170  =item directoryName  =item entityName
   
 Name of the directory containing the relation files to be loaded.  
   
 =item rebuild  
1171    
1172  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the  Name of the entity whose secondary fields are desired.
 only way to erase existing data in the tables, since the TRUNCATE command is not supported  
 by all of the DB engines we use.  
1173    
1174  =item RETURN  =item RETURN
1175    
1176  Returns a statistical object describing the number of records read and a list of the error messages.  Returns a hash mapping the field names to their field types.
1177    
1178  =back  =back
1179    
1180  =cut  =cut
1181    
1182  sub LoadTables {  sub GetSecondaryFields {
1183      # Get the parameters.      # Get the parameters.
1184      my ($self, $directoryName, $rebuild) = @_;      my ($self, $entityName) = @_;
     # Start the timer.  
     my $startTime = gettimeofday;  
     # Clean any trailing slash from the directory name.  
     $directoryName =~ s!/\\$!!;  
1185      # Declare the return variable.      # Declare the return variable.
1186      my $retVal = Stats->new();      my %retVal = ();
1187      # Get the relation names.      # Look for the entity.
1188      my @relNames = $self->GetTableNames();      my $table = $self->GetFieldTable($entityName);
1189      for my $relationName (@relNames) {      # Loop through the fields, pulling out the secondaries.
1190          # Try to load this relation.      for my $field (sort keys %{$table}) {
1191          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);          if ($table->{$field}->{relation} ne $entityName) {
1192          # Accumulate the statistics.              # Here we have a secondary field.
1193          $retVal->Accumulate($result);              $retVal{$field} = $table->{$field}->{type};
1194      }      }
1195      # Add the duration of the load to the statistical object.      }
1196      $retVal->Add('duration', gettimeofday - $startTime);      # Return the result.
1197      # Return the accumulated statistics.      return %retVal;
     return $retVal;  
1198  }  }
1199    
1200    =head3 GetFieldRelationName
1201    
1202  =head3 GetTableNames  C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1203    
1204  C<< my @names = $erdb->GetTableNames; >>  Return the name of the relation containing a specified field.
1205    
1206  Return a list of the relations required to implement this database.  =over 4
1207    
1208  =cut  =item objectName
1209    
1210  sub GetTableNames {  Name of the entity or relationship containing the field.
     # Get the parameters.  
     my ($self) = @_;  
     # Get the relation list from the metadata.  
     my $relationTable = $self->{_metaData}->{RelationTable};  
     # Return the relation names.  
     return keys %{$relationTable};  
 }  
1211    
1212  =head3 GetEntityTypes  =item fieldName
1213    
1214  C<< my @names = $erdb->GetEntityTypes; >>  Name of the relevant field in that entity or relationship.
1215    
1216  Return a list of the entity type names.  =item RETURN
1217    
1218    Returns the name of the database relation containing the field, or C<undef> if
1219    the field does not exist.
1220    
1221    =back
1222    
1223  =cut  =cut
1224    
1225  sub GetEntityTypes {  sub GetFieldRelationName {
1226      # Get the database object.      # Get the parameters.
1227      my ($self) = @_;      my ($self, $objectName, $fieldName) = @_;
1228      # Get the entity list from the metadata object.      # Declare the return variable.
1229      my $entityList = $self->{_metaData}->{Entities};      my $retVal;
1230      # Return the list of entity names in alphabetical order.      # Get the object field table.
1231      return sort keys %{$entityList};      my $table = $self->GetFieldTable($objectName);
1232        # Only proceed if the field exists.
1233        if (exists $table->{$fieldName}) {
1234            # Determine the name of the relation that contains this field.
1235            $retVal = $table->{$fieldName}->{relation};
1236        }
1237        # Return the result.
1238        return $retVal;
1239  }  }
1240    
1241  =head3 IsEntity  =head3 DeleteValue
1242    
1243    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1244    
1245    Delete secondary field values from the database. This method can be used to delete all
1246    values of a specified field for a particular entity instance, or only a single value.
1247    
1248    Secondary fields are stored in two-column relations separate from an entity's primary
1249    table, and as a result a secondary field can legitimately have no value or multiple
1250    values. Therefore, it makes sense to talk about deleting secondary fields where it
1251    would not make sense for primary fields.
1252    
1253    =over 4
1254    
1255    =item entityName
1256    
1257    Name of the entity from which the fields are to be deleted.
1258    
1259    =item id
1260    
1261    ID of the entity instance to be processed. If the instance is not found, this
1262    method will have no effect. If C<undef> is specified, all values for all of
1263    the entity instances will be deleted.
1264    
1265    =item fieldName
1266    
1267    Name of the field whose values are to be deleted.
1268    
1269    =item fieldValue (optional)
1270    
1271    Value to be deleted. If not specified, then all values of the specified field
1272    will be deleted for the entity instance. If specified, then only the values which
1273    match this parameter will be deleted.
1274    
1275    =item RETURN
1276    
1277    Returns the number of rows deleted.
1278    
1279    =back
1280    
1281    =cut
1282    
1283    sub DeleteValue {
1284        # Get the parameters.
1285        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1286        # Declare the return value.
1287        my $retVal = 0;
1288        # We need to set up an SQL command to do the deletion. First, we
1289        # find the name of the field's relation.
1290        my $table = $self->GetFieldTable($entityName);
1291        my $field = $table->{$fieldName};
1292        my $relation = $field->{relation};
1293        # Make sure this is a secondary field.
1294        if ($relation eq $entityName) {
1295            Confess("Cannot delete values of $fieldName for $entityName.");
1296        } else {
1297            # Set up the SQL command to delete all values.
1298            my $sql = "DELETE FROM $relation";
1299            # Build the filter.
1300            my @filters = ();
1301            my @parms = ();
1302            # Check for a filter by ID.
1303            if (defined $id) {
1304                push @filters, "id = ?";
1305                push @parms, $id;
1306            }
1307            # Check for a filter by value.
1308            if (defined $fieldValue) {
1309                push @filters, "$fieldName = ?";
1310                push @parms, $fieldValue;
1311            }
1312            # Append the filters to the command.
1313            if (@filters) {
1314                $sql .= " WHERE " . join(" AND ", @filters);
1315            }
1316            # Execute the command.
1317            my $dbh = $self->{_dbh};
1318            $retVal = $dbh->SQL($sql, 0, @parms);
1319        }
1320        # Return the result.
1321        return $retVal;
1322    }
1323    
1324    =head3 LoadTables
1325    
1326    C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1327    
1328    This method will load the database tables from a directory. The tables must already have been created
1329    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1330    all of the relations to be loaded must have a file in the directory with the same name as the relation
1331    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1332    line of the file will be loaded as a row of the target relation table. The field values should be in
1333    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1334    erased before the new data is loaded in.
1335    
1336    A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1337    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1338    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1339    
1340    =over 4
1341    
1342    =item directoryName
1343    
1344    Name of the directory containing the relation files to be loaded.
1345    
1346    =item rebuild
1347    
1348    TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1349    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1350    by all of the DB engines we use.
1351    
1352    =item RETURN
1353    
1354    Returns a statistical object describing the number of records read and a list of the error messages.
1355    
1356    =back
1357    
1358    =cut
1359    
1360    sub LoadTables {
1361        # Get the parameters.
1362        my ($self, $directoryName, $rebuild) = @_;
1363        # Start the timer.
1364        my $startTime = gettimeofday;
1365        # Clean any trailing slash from the directory name.
1366        $directoryName =~ s!/\\$!!;
1367        # Declare the return variable.
1368        my $retVal = Stats->new();
1369        # Get the relation names.
1370        my @relNames = $self->GetTableNames();
1371        for my $relationName (@relNames) {
1372            # Try to load this relation.
1373            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1374            # Accumulate the statistics.
1375            $retVal->Accumulate($result);
1376        }
1377        # Add the duration of the load to the statistical object.
1378        $retVal->Add('duration', gettimeofday - $startTime);
1379        # Return the accumulated statistics.
1380        return $retVal;
1381    }
1382    
1383    
1384    =head3 GetTableNames
1385    
1386    C<< my @names = $erdb->GetTableNames; >>
1387    
1388    Return a list of the relations required to implement this database.
1389    
1390    =cut
1391    
1392    sub GetTableNames {
1393        # Get the parameters.
1394        my ($self) = @_;
1395        # Get the relation list from the metadata.
1396        my $relationTable = $self->{_metaData}->{RelationTable};
1397        # Return the relation names.
1398        return keys %{$relationTable};
1399    }
1400    
1401    =head3 GetEntityTypes
1402    
1403    C<< my @names = $erdb->GetEntityTypes; >>
1404    
1405    Return a list of the entity type names.
1406    
1407    =cut
1408    
1409    sub GetEntityTypes {
1410        # Get the database object.
1411        my ($self) = @_;
1412        # Get the entity list from the metadata object.
1413        my $entityList = $self->{_metaData}->{Entities};
1414        # Return the list of entity names in alphabetical order.
1415        return sort keys %{$entityList};
1416    }
1417    
1418    =head3 GetDataTypes
1419    
1420    C<< my %types = ERDB::GetDataTypes(); >>
1421    
1422    Return a table of ERDB data types. The table returned is a hash of hashes.
1423    The keys of the big hash are the datatypes. Each smaller hash has several
1424    values used to manage the data. The most interesting is the SQL type (key
1425    C<sqlType>) and the descriptive node (key C<notes>).
1426    
1427    Note that changing the values in the smaller hashes will seriously break
1428    things, so this data should be treated as read-only.
1429    
1430    =cut
1431    
1432    sub GetDataTypes {
1433        return %TypeTable;
1434    }
1435    
1436    
1437    =head3 IsEntity
1438    
1439  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
1440    
# Line 848  Line 1463 
1463    
1464  =head3 Get  =head3 Get
1465    
1466  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1467    
1468  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.
1469  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 856  Line 1471 
1471  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
1472  $genus.  $genus.
1473    
1474  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1475    
1476  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
1477  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 873  Line 1488 
1488  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
1489  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,
1490    
1491  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1492    
1493  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
1494  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.
1495  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
1496  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
1497  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  
1498  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,
1499  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.
1500    
1501    If an entity or relationship is mentioned twice, the name for the second occurrence will
1502    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1503    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1504    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1505    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1506    
1507  =over 4  =over 4
1508    
1509  =item objectNames  =item objectNames
# Line 913  Line 1533 
1533  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
1534  relation.  relation.
1535    
1536  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1537    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1538    a positive number. So, for example
1539    
1540    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1541    
1542  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
1543    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1544    use
1545    
1546    C<< "LIMIT 10" >>
1547    
1548    =item params
1549    
1550    Reference to a list of parameter values to be substituted into the filter clause.
1551    
1552  =item RETURN  =item RETURN
1553    
# Line 927  Line 1559 
1559    
1560  sub Get {  sub Get {
1561      # Get the parameters.      # Get the parameters.
1562      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1563      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1564      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1565      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1566      #      # Create the query.
1567      my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1568      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1569                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1570      # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1571      if ($filterClause) {      # and mapped name for each object in the query.
1572          # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1573          # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1574          my $filterString = $filterClause;          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command.  
         my %fromNames = ();  
         for my $objectName (@sortedNames) {  
             $fromNames{$objectName} = 1;  
         }  
         # We are ready to begin. We loop through the object names, replacing each  
         # object name's field references by the corresponding SQL field reference.  
         # Along the way, if we find a secondary relation, we will need to add it  
         # to the FROM clause.  
         for my $objectName (@sortedNames) {  
             # Get the length of the object name plus 2. This is the value we add to the  
             # size of the field name to determine the size of the field reference as a  
             # whole.  
             my $nameLength = 2 + length $objectName;  
             # Get the object's field list.  
             my $fieldList = $self->_GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                 # At this point, $1 contains the field name, and the current position  
                 # is set immediately after the final parenthesis. We pull out the name of  
                 # the field and the position and length of the field reference as a whole.  
                 my $fieldName = $1;  
                 my $len = $nameLength + length $fieldName;  
                 my $pos = pos($filterString) - $len;  
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
                 } else {  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$relationName}) {  
                         # Add the relation to the FROM clause.  
                         $command .= ", $relationName";  
                         # Create its join sub-clause.  
                         push @joinWhere, "$objectName.id = $relationName.id";  
                         # Denote we have it available for future fields.  
                         $fromNames{$relationName} = 1;  
                     }  
                     # Form an SQL field reference from the relation name and the field name.  
                     my $sqlReference = "$relationName." . _FixName($fieldName);  
                     # Put it into the filter string in place of the old value.  
                     substr($filterString, $pos, $len) = $sqlReference;  
                     # Reposition the search.  
                     pos $filterString = $pos + length $sqlReference;  
                 }  
             }  
         }  
         # The next step is to join the objects together. We only need to do this if there  
         # is more than one object in the object list. We start with the first object and  
         # run through the objects after it. Note also that we make a safety copy of the  
         # list before running through it.  
         my @objectList = @{$objectNames};  
         my $lastObject = shift @objectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisObject (@objectList) {  
             # Look for a join.  
             my $joinKey = "$lastObject/$thisObject";  
             if (!exists $joinTable->{$joinKey}) {  
                 # Here there's no join, so we throw an error.  
                 Confess("No join exists to connect from $lastObject to $thisObject.");  
             } else {  
                 # Get the join clause and add it to the WHERE list.  
                 push @joinWhere, $joinTable->{$joinKey};  
                 # Save this object as the last object for the next iteration.  
                 $lastObject = $thisObject;  
             }  
         }  
         # Now we need to handle the whole ORDER BY / LIMIT thing. The important part  
         # here is we want the filter clause to be empty if there's no WHERE filter.  
         # We'll put the ORDER BY / LIMIT clauses in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy  
         # operator so that we find the first occurrence of either verb.  
         if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {  
             # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = $2 . substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort or limit clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " $orderClause";  
         }  
1575      }      }
     Trace("SQL query: $command") if T(SQL => 4);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1576      # Return the statement object.      # Return the statement object.
1577      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1578      return $retVal;      return $retVal;
1579  }  }
1580    
 =head3 Delete  
1581    
 C<< my $stats = $erdb->Delete($entityName, $objectID); >>  
1582    
1583  Delete an entity instance from the database. The instance is deleted along with all entity and  =head3 Search
1584  relationship instances dependent on it. The idea of dependence here is recursive. An object is  
1585  always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1586  relationship connected to a dependent entity or the "to" entity connected to a 1-to-many  
1587  dependent relationship.  Perform a full text search with filtering. The search will be against a specified object
1588    in the object name list. That object will get an extra field containing the search
1589    relevance. Note that except for the search expression, the parameters of this method are
1590    the same as those for L</Get> and follow the same rules.
1591    
1592  =over 4  =over 4
1593    
1594  =item entityName  =item searchExpression
1595    
1596  Name of the entity type for the instance being deleted.  Boolean search expression for the text fields of the target object. The default mode for
1597    a Boolean search expression is OR, but we want the default to be AND, so we will
1598    add a C<+> operator to each word with no other operator before it.
1599    
1600  =item objectID  =item idx
1601    
1602  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  Index in the I<$objectNames> list of the table to be searched in full-text mode.
1603  then it is presumed to by a LIKE pattern.  
1604    =item objectNames
1605    
1606    List containing the names of the entity and relationship objects to be retrieved.
1607    
1608    =item filterClause
1609    
1610    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1611    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1612    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1613    in the filter clause should be added to the parameter list as additional parameters. The
1614    fields in a filter clause can come from primary entity relations, relationship relations,
1615    or secondary entity relations; however, all of the entities and relationships involved must
1616    be included in the list of object names.
1617    
1618  =item testFlag  =item params
1619    
1620  If TRUE, the delete statements will be traced without being executed.  Reference to a list of parameter values to be substituted into the filter clause.
1621    
1622  =item RETURN  =item RETURN
1623    
1624  Returns a statistics object indicating how many records of each particular table were  Returns a query object for the specified search.
 deleted.  
1625    
1626  =back  =back
1627    
1628  =cut  =cut
1629  #: Return Type $%;  
1630  sub Delete {  sub Search {
1631      # Get the parameters.      # Get the parameters.
1632      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1633      # Declare the return variable.      # Declare the return variable.
1634      my $retVal = Stats->new();      my $retVal;
1635      # Get the DBKernel object.      # Create a safety copy of the parameter list. Note we have to be careful to insure
1636        # a parameter list exists before we copy it.
1637        my @myParams = ();
1638        if (defined $params) {
1639            @myParams = @{$params};
1640        }
1641        # Get the first object's structure so we have access to the searchable fields.
1642        my $object1Name = $objectNames->[$idx];
1643        my $object1Structure = $self->_GetStructure($object1Name);
1644        # Get the field list.
1645        if (! exists $object1Structure->{searchFields}) {
1646            Confess("No searchable index for $object1Name.");
1647        } else {
1648            # Get the field list.
1649            my @fields = @{$object1Structure->{searchFields}};
1650            # Clean the search expression.
1651            my $actualKeywords = $self->CleanKeywords($searchExpression);
1652            # Prefix a "+" to each uncontrolled word. This converts the default
1653            # search mode from OR to AND.
1654            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1655            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1656            # We need two match expressions, one for the filter clause and one in the
1657            # query itself. Both will use a parameter mark, so we need to push the
1658            # search expression onto the front of the parameter list twice.
1659            unshift @myParams, $actualKeywords, $actualKeywords;
1660            # Build the match expression.
1661            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1662            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1663            # Process the SQL stuff.
1664            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1665                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1666            # Create the query. Note that the match clause is inserted at the front of
1667            # the select fields.
1668            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1669                ".* $suffix";
1670            my $sth = $self->_GetStatementHandle($command, \@myParams);
1671            # Now we create the relation map, which enables DBQuery to determine the order, name
1672            # and mapped name for each object in the query.
1673            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1674            # Return the statement object.
1675            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1676        }
1677        return $retVal;
1678    }
1679    
1680    =head3 GetFlat
1681    
1682    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1683    
1684    This is a variation of L</GetAll> that asks for only a single field per record and
1685    returns a single flattened list.
1686    
1687    =over 4
1688    
1689    =item objectNames
1690    
1691    List containing the names of the entity and relationship objects to be retrieved.
1692    
1693    =item filterClause
1694    
1695    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1696    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1697    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1698    parameter list as additional parameters. The fields in a filter clause can come from primary
1699    entity relations, relationship relations, or secondary entity relations; however, all of the
1700    entities and relationships involved must be included in the list of object names.
1701    
1702    =item parameterList
1703    
1704    List of the parameters to be substituted in for the parameters marks in the filter clause.
1705    
1706    =item field
1707    
1708    Name of the field to be used to get the elements of the list returned.
1709    
1710    =item RETURN
1711    
1712    Returns a list of values.
1713    
1714    =back
1715    
1716    =cut
1717    #: Return Type @;
1718    sub GetFlat {
1719        # Get the parameters.
1720        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1721        # Construct the query.
1722        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1723        # Create the result list.
1724        my @retVal = ();
1725        # Loop through the records, adding the field values found to the result list.
1726        while (my $row = $query->Fetch()) {
1727            push @retVal, $row->Value($field);
1728        }
1729        # Return the list created.
1730        return @retVal;
1731    }
1732    
1733    =head3 SpecialFields
1734    
1735    C<< my %specials = $erdb->SpecialFields($entityName); >>
1736    
1737    Return a hash mapping special fields in the specified entity to the value of their
1738    C<special> attribute. This enables the subclass to get access to the special field
1739    attributes without needed to plumb the internal ERDB data structures.
1740    
1741    =over 4
1742    
1743    =item entityName
1744    
1745    Name of the entity whose special fields are desired.
1746    
1747    =item RETURN
1748    
1749    Returns a hash. The keys of the hash are the special field names, and the values
1750    are the values from each special field's C<special> attribute.
1751    
1752    =back
1753    
1754    =cut
1755    
1756    sub SpecialFields {
1757        # Get the parameters.
1758        my ($self, $entityName) = @_;
1759        # Declare the return variable.
1760        my %retVal = ();
1761        # Find the entity's data structure.
1762        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1763        # Loop through its fields, adding each special field to the return hash.
1764        my $fieldHash = $entityData->{Fields};
1765        for my $fieldName (keys %{$fieldHash}) {
1766            my $fieldData = $fieldHash->{$fieldName};
1767            if (exists $fieldData->{special}) {
1768                $retVal{$fieldName} = $fieldData->{special};
1769            }
1770        }
1771        # Return the result.
1772        return %retVal;
1773    }
1774    
1775    =head3 Delete
1776    
1777    C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1778    
1779    Delete an entity instance from the database. The instance is deleted along with all entity and
1780    relationship instances dependent on it. The definition of I<dependence> is recursive.
1781    
1782    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1783    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1784    dependent relationship.
1785    
1786    =over 4
1787    
1788    =item entityName
1789    
1790    Name of the entity type for the instance being deleted.
1791    
1792    =item objectID
1793    
1794    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1795    then it is presumed to by a LIKE pattern.
1796    
1797    =item options
1798    
1799    A hash detailing the options for this delete operation.
1800    
1801    =item RETURN
1802    
1803    Returns a statistics object indicating how many records of each particular table were
1804    deleted.
1805    
1806    =back
1807    
1808    The permissible options for this method are as follows.
1809    
1810    =over 4
1811    
1812    =item testMode
1813    
1814    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1815    
1816    =item keepRoot
1817    
1818    If TRUE, then the entity instances will not be deleted, only the dependent records.
1819    
1820    =back
1821    
1822    =cut
1823    #: Return Type $%;
1824    sub Delete {
1825        # Get the parameters.
1826        my ($self, $entityName, $objectID, %options) = @_;
1827        # Declare the return variable.
1828        my $retVal = Stats->new();
1829        # Get the DBKernel object.
1830      my $db = $self->{_dbh};      my $db = $self->{_dbh};
1831      # We're going to generate all the paths branching out from the starting entity. One of      # We're going to generate all the paths branching out from the starting entity. One of
1832      # the things we have to be careful about is preventing loops. We'll use a hash to      # the things we have to be careful about is preventing loops. We'll use a hash to
# Line 1104  Line 1840 
1840      # FROM-relationships and entities.      # FROM-relationships and entities.
1841      my @fromPathList = ();      my @fromPathList = ();
1842      my @toPathList = ();      my @toPathList = ();
1843      # This final hash is used to remember what work still needs to be done. We push paths      # This final list is used to remember what work still needs to be done. We push paths
1844      # onto the list, then pop them off to extend the paths. We prime it with the starting      # onto the list, then pop them off to extend the paths. We prime it with the starting
1845      # point. Note that we will work hard to insure that the last item on a path in the      # point. Note that we will work hard to insure that the last item on a path in the
1846      # TODO list is always an entity.      # to-do list is always an entity.
1847      my @todoList = ([$entityName]);      my @todoList = ([$entityName]);
1848      while (@todoList) {      while (@todoList) {
1849          # Get the current path.          # Get the current path.
# Line 1115  Line 1851 
1851          # Copy it into a list.          # Copy it into a list.
1852          my @stackedPath = @{$current};          my @stackedPath = @{$current};
1853          # Pull off the last item on the path. It will always be an entity.          # Pull off the last item on the path. It will always be an entity.
1854          my $entityName = pop @stackedPath;          my $myEntityName = pop @stackedPath;
1855          # Add it to the alreadyFound list.          # Add it to the alreadyFound list.
1856          $alreadyFound{$entityName} = 1;          $alreadyFound{$myEntityName} = 1;
1857            # Figure out if we need to delete this entity.
1858            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1859          # Get the entity data.          # Get the entity data.
1860          my $entityData = $self->_GetStructure($entityName);              my $entityData = $self->_GetStructure($myEntityName);
1861          # The first task is to loop through the entity's relation. A DELETE command will              # Loop through the entity's relations. A DELETE command will be needed for each of them.
         # be needed for each of them.  
1862          my $relations = $entityData->{Relations};          my $relations = $entityData->{Relations};
1863          for my $relation (keys %{$relations}) {          for my $relation (keys %{$relations}) {
1864              my @augmentedList = (@stackedPath, $relation);              my @augmentedList = (@stackedPath, $relation);
1865              push @fromPathList, \@augmentedList;              push @fromPathList, \@augmentedList;
1866          }          }
1867            }
1868          # Now we need to look for relationships connected to this entity.          # Now we need to look for relationships connected to this entity.
1869          my $relationshipList = $self->{_metaData}->{Relationships};          my $relationshipList = $self->{_metaData}->{Relationships};
1870          for my $relationshipName (keys %{$relationshipList}) {          for my $relationshipName (keys %{$relationshipList}) {
1871              my $relationship = $relationshipList->{$relationshipName};              my $relationship = $relationshipList->{$relationshipName};
1872              # Check the FROM field. We're only interested if it's us.              # Check the FROM field. We're only interested if it's us.
1873              if ($relationship->{from} eq $entityName) {              if ($relationship->{from} eq $myEntityName) {
1874                  # Add the path to this relationship.                  # Add the path to this relationship.
1875                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1876                  push @fromPathList, \@augmentedList;                  push @fromPathList, \@augmentedList;
1877                  # Check the arity. If it's MM we're done. If it's 1M                  # Check the arity. If it's MM we're done. If it's 1M
1878                  # and the target hasn't been seen yet, we want to                  # and the target hasn't been seen yet, we want to
# Line 1146  Line 1884 
1884                          # the current entity, so we need to stack it.                          # the current entity, so we need to stack it.
1885                          my @stackList = (@augmentedList, $toEntity);                          my @stackList = (@augmentedList, $toEntity);
1886                          push @fromPathList, \@stackList;                          push @fromPathList, \@stackList;
1887                        } else {
1888                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1889                      }                      }
1890                  }                  }
1891              }              }
1892              # Now check the TO field. In this case only the relationship needs              # Now check the TO field. In this case only the relationship needs
1893              # deletion.              # deletion.
1894              if ($relationship->{to} eq $entityName) {              if ($relationship->{to} eq $myEntityName) {
1895                  my @augmentedList = (@stackedPath, $entityName, $relationshipName);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1896                  push @toPathList, \@augmentedList;                  push @toPathList, \@augmentedList;
1897              }              }
1898          }          }
1899      }      }
1900      # Create the first qualifier for the WHERE clause. This selects the      # Create the first qualifier for the WHERE clause. This selects the
1901      # keys of the primary entity records to be deleted. When we're deleting      # keys of the primary entity records to be deleted. When we're deleting
1902      # from a dependent table, we construct a join page from the first qualifier      # from a dependent table, we construct a join path from the first qualifier
1903      # to the table containing the dependent records to delete.      # to the table containing the dependent records to delete.
1904      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");      my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1905      # We need to make two passes. The first is through the to-list, and      # We need to make two passes. The first is through the to-list, and
# Line 1171  Line 1911 
1911      for my $keyName ('to_link', 'from_link') {      for my $keyName ('to_link', 'from_link') {
1912          # Get the list for this key.          # Get the list for this key.
1913          my @pathList = @{$stackList{$keyName}};          my @pathList = @{$stackList{$keyName}};
1914            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1915          # Loop through this list.          # Loop through this list.
1916          while (my $path = pop @pathList) {          while (my $path = pop @pathList) {
1917              # Get the table whose rows are to be deleted.              # Get the table whose rows are to be deleted.
1918              my @pathTables = @{$path};              my @pathTables = @{$path};
1919              # Start the DELETE statement.              # Start the DELETE statement. We need to call DBKernel because the
1920                # syntax of a DELETE-USING varies among DBMSs.
1921              my $target = $pathTables[$#pathTables];              my $target = $pathTables[$#pathTables];
1922              my $stmt = "DELETE FROM $target";              my $stmt = $db->SetUsing(@pathTables);
             # If there's more than just the one table, we need a USING clause.  
             if (@pathTables > 1) {  
                 $stmt .= " USING " . join(", ", @pathTables[0 .. ($#pathTables - 1)]);  
             }  
1923              # Now start the WHERE. The first thing is the ID field from the starting table. That              # Now start the WHERE. The first thing is the ID field from the starting table. That
1924              # starting table will either be the entity relation or one of the entity's              # starting table will either be the entity relation or one of the entity's
1925              # sub-relations.              # sub-relations.
# Line 1191  Line 1929 
1929                  # Connect the current relationship to the preceding entity.                  # Connect the current relationship to the preceding entity.
1930                  my ($entity, $rel) = @pathTables[$i-1,$i];                  my ($entity, $rel) = @pathTables[$i-1,$i];
1931                  # The style of connection depends on the direction of the relationship.                  # The style of connection depends on the direction of the relationship.
1932                  $stmt .= " AND $entity.id = $rel.from_link";                  $stmt .= " AND $entity.id = $rel.$keyName";
1933                  if ($i + 1 <= $#pathTables) {                  if ($i + 1 <= $#pathTables) {
1934                      # Here there's a next entity, so connect that to the relationship's                      # Here there's a next entity, so connect that to the relationship's
1935                      # to-link.                      # to-link.
1936                      my $entity2 = $pathTables[$i+1];                      my $entity2 = $pathTables[$i+1];
1937                      $stmt .= " AND $rel.$keyName = $entity2.id";                      $stmt .= " AND $rel.to_link = $entity2.id";
1938                  }                  }
1939              }              }
1940              # Now we have our desired DELETE statement.              # Now we have our desired DELETE statement.
1941              if ($testFlag) {              if ($options{testMode}) {
1942                  # Here the user wants to trace without executing.                  # Here the user wants to trace without executing.
1943                  Trace($stmt) if T(0);                  Trace($stmt) if T(0);
1944              } else {              } else {
1945                  # Here we can delete. Note that the SQL method dies with a confessing                  # Here we can delete. Note that the SQL method dies with a confession
1946                  # if an error occurs, so we just go ahead and do it.                  # if an error occurs, so we just go ahead and do it.
1947                  Trace("Executing delete: $stmt") if T(3);                  Trace("Executing delete from $target using '$objectID'.") if T(3);
1948                  my $rv = $db->SQL($stmt, 0, [$objectID]);                  my $rv = $db->SQL($stmt, 0, $objectID);
1949                  # Accumulate the statistics for this delete. The only rows deleted                  # Accumulate the statistics for this delete. The only rows deleted
1950                  # are from the target table, so we use its name to record the                  # are from the target table, so we use its name to record the
1951                  # statistic.                  # statistic.
# Line 1219  Line 1957 
1957      return $retVal;      return $retVal;
1958  }  }
1959    
1960    =head3 Disconnect
1961    
1962    C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1963    
1964    Disconnect an entity instance from all the objects to which it is related. This
1965    will delete each relationship instance that connects to the specified entity.
1966    
1967    =over 4
1968    
1969    =item relationshipName
1970    
1971    Name of the relationship whose instances are to be deleted.
1972    
1973    =item originEntityName
1974    
1975    Name of the entity that is to be disconnected.
1976    
1977    =item originEntityID
1978    
1979    ID of the entity that is to be disconnected.
1980    
1981    =back
1982    
1983    =cut
1984    
1985    sub Disconnect {
1986        # Get the parameters.
1987        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1988        # Get the relationship descriptor.
1989        my $structure = $self->_GetStructure($relationshipName);
1990        # Insure we have a relationship.
1991        if (! exists $structure->{from}) {
1992            Confess("$relationshipName is not a relationship in the database.");
1993        } else {
1994            # Get the database handle.
1995            my $dbh = $self->{_dbh};
1996            # We'll set this value to 1 if we find our entity.
1997            my $found = 0;
1998            # Loop through the ends of the relationship.
1999            for my $dir ('from', 'to') {
2000                if ($structure->{$dir} eq $originEntityName) {
2001                    # Delete all relationship instances on this side of the entity instance.
2002                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2003                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2004                    $found = 1;
2005                }
2006            }
2007            # Insure we found the entity on at least one end.
2008            if (! $found) {
2009                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2010            }
2011        }
2012    }
2013    
2014    =head3 DeleteRow
2015    
2016    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
2017    
2018    Delete a row from a relationship. In most cases, only the from-link and to-link are
2019    needed; however, for relationships with intersection data values can be specified
2020    for the other fields using a hash.
2021    
2022    =over 4
2023    
2024    =item relationshipName
2025    
2026    Name of the relationship from which the row is to be deleted.
2027    
2028    =item fromLink
2029    
2030    ID of the entity instance in the From direction.
2031    
2032    =item toLink
2033    
2034    ID of the entity instance in the To direction.
2035    
2036    =item values
2037    
2038    Reference to a hash of other values to be used for filtering the delete.
2039    
2040    =back
2041    
2042    =cut
2043    
2044    sub DeleteRow {
2045        # Get the parameters.
2046        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2047        # Create a hash of all the filter information.
2048        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2049        if (defined $values) {
2050            for my $key (keys %{$values}) {
2051                $filter{$key} = $values->{$key};
2052            }
2053        }
2054        # Build an SQL statement out of the hash.
2055        my @filters = ();
2056        my @parms = ();
2057        for my $key (keys %filter) {
2058            push @filters, _FixName($key) . " = ?";
2059            push @parms, $filter{$key};
2060        }
2061        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2062        my $command = "DELETE FROM $relationshipName WHERE " .
2063                      join(" AND ", @filters);
2064        # Execute it.
2065        my $dbh = $self->{_dbh};
2066        $dbh->SQL($command, undef, @parms);
2067    }
2068    
2069    =head3 DeleteLike
2070    
2071    C<< my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms); >>
2072    
2073    Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2074    filter, only fields from the relationship itself can be used.
2075    
2076    =over 4
2077    
2078    =item relName
2079    
2080    Name of the relationship whose records are to be deleted.
2081    
2082    =item filter
2083    
2084    A filter clause (L</Get>-style) for the delete query.
2085    
2086    =item parms
2087    
2088    Reference to a list of parameters for the filter clause.
2089    
2090    =item RETURN
2091    
2092    Returns a count of the number of rows deleted.
2093    
2094    =back
2095    
2096    =cut
2097    
2098    sub DeleteLike {
2099        # Get the parameters.
2100        my ($self, $objectName, $filter, $parms) = @_;
2101        # Declare the return variable.
2102        my $retVal;
2103        # Insure the parms argument is an array reference if the caller left it off.
2104        if (! defined($parms)) {
2105            $parms = [];
2106        }
2107        # Insure we have a relationship. The main reason for this is if we delete an entity
2108        # instance we have to yank out a bunch of other stuff with it.
2109        if ($self->IsEntity($objectName)) {
2110            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2111        } else {
2112            # Create the SQL command suffix to get the desierd records.
2113            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2114            # Convert it to a DELETE command.
2115            my $command = "DELETE $suffix";
2116            # Execute the command.
2117            my $dbh = $self->{_dbh};
2118            my $result = $dbh->SQL($command, 0, @{$parms});
2119            # Check the results. Note we convert the "0D0" result to a real zero.
2120            # A failure causes an abnormal termination, so the caller isn't going to
2121            # worry about it.
2122            if (! defined $result) {
2123                Confess("Error deleting from $objectName: " . $dbh->errstr());
2124            } elsif ($result == 0) {
2125                $retVal = 0;
2126            } else {
2127                $retVal = $result;
2128            }
2129        }
2130        # Return the result count.
2131        return $retVal;
2132    }
2133    
2134    =head3 SortNeeded
2135    
2136    C<< my $parms = $erdb->SortNeeded($relationName); >>
2137    
2138    Return the pipe command for the sort that should be applied to the specified
2139    relation when creating the load file.
2140    
2141    For example, if the load file should be sorted ascending by the first
2142    field, this method would return
2143    
2144        sort -k1 -t"\t"
2145    
2146    If the first field is numeric, the method would return
2147    
2148        sort -k1n -t"\t"
2149    
2150    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2151    keys using a sort.
2152    
2153    =over 4
2154    
2155    =item relationName
2156    
2157    Name of the relation to be examined.
2158    
2159    =item
2160    
2161    Returns the sort command to use for sorting the relation, suitable for piping.
2162    
2163    =back
2164    
2165    =cut
2166    #: Return Type $;
2167    sub SortNeeded {
2168        # Get the parameters.
2169        my ($self, $relationName) = @_;
2170        # Declare a descriptor to hold the names of the key fields.
2171        my @keyNames = ();
2172        # Get the relation structure.
2173        my $relationData = $self->_FindRelation($relationName);
2174        # Find out if the relation is a primary entity relation,
2175        # a relationship relation, or a secondary entity relation.
2176        my $entityTable = $self->{_metaData}->{Entities};
2177        my $relationshipTable = $self->{_metaData}->{Relationships};
2178        if (exists $entityTable->{$relationName}) {
2179            # Here we have a primary entity relation.
2180            push @keyNames, "id";
2181        } elsif (exists $relationshipTable->{$relationName}) {
2182            # Here we have a relationship. We sort using the FROM index.
2183            my $relationshipData = $relationshipTable->{$relationName};
2184            my $index = $relationData->{Indexes}->{idxFrom};
2185            push @keyNames, @{$index->{IndexFields}};
2186        } else {
2187            # Here we have a secondary entity relation, so we have a sort on the ID field.
2188            push @keyNames, "id";
2189        }
2190        # Now we parse the key names into sort parameters. First, we prime the return
2191        # string.
2192        my $retVal = "sort -t\"\t\" ";
2193        # Get the relation's field list.
2194        my @fields = @{$relationData->{Fields}};
2195        # Loop through the keys.
2196        for my $keyData (@keyNames) {
2197            # Get the key and the ordering.
2198            my ($keyName, $ordering);
2199            if ($keyData =~ /^([^ ]+) DESC/) {
2200                ($keyName, $ordering) = ($1, "descending");
2201            } else {
2202                ($keyName, $ordering) = ($keyData, "ascending");
2203            }
2204            # Find the key's position and type.
2205            my $fieldSpec;
2206            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2207                my $thisField = $fields[$i];
2208                if ($thisField->{name} eq $keyName) {
2209                    # Get the sort modifier for this field type. The modifier
2210                    # decides whether we're using a character, numeric, or
2211                    # floating-point sort.
2212                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2213                    # If the index is descending for this field, denote we want
2214                    # to reverse the sort order on this field.
2215                    if ($ordering eq 'descending') {
2216                        $modifier .= "r";
2217                    }
2218                    # Store the position and modifier into the field spec, which
2219                    # will stop the inner loop. Note that the field number is
2220                    # 1-based in the sort command, so we have to increment the
2221                    # index.
2222                    $fieldSpec = ($i + 1) . $modifier;
2223                }
2224            }
2225            # Add this field to the sort command.
2226            $retVal .= " -k$fieldSpec";
2227        }
2228        # Return the result.
2229        return $retVal;
2230    }
2231    
2232  =head3 GetList  =head3 GetList
2233    
2234  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2235    
2236  Return a list of object descriptors for the specified objects as determined by the  Return a list of object descriptors for the specified objects as determined by the
2237  specified filter clause.  specified filter clause.
# Line 1255  Line 2265 
2265  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
2266  relation.  relation.
2267    
2268  =item param1, param2, ..., paramN  =item params
2269    
2270  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
2271    
2272  =item RETURN  =item RETURN
2273    
2274  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of B<ERDBObject>s that satisfy the query conditions.
2275    
2276  =back  =back
2277    
# Line 1269  Line 2279 
2279  #: Return Type @%  #: Return Type @%
2280  sub GetList {  sub GetList {
2281      # Get the parameters.      # Get the parameters.
2282      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
2283      # Declare the return variable.      # Declare the return variable.
2284      my @retVal = ();      my @retVal = ();
2285      # Perform the query.      # Perform the query.
2286      my $query = $self->Get($objectNames, $filterClause, @params);      my $query = $self->Get($objectNames, $filterClause, $params);
2287      # Loop through the results.      # Loop through the results.
2288      while (my $object = $query->Fetch) {      while (my $object = $query->Fetch) {
2289          push @retVal, $object;          push @retVal, $object;
# Line 1282  Line 2292 
2292      return @retVal;      return @retVal;
2293  }  }
2294    
2295  =head3 ComputeObjectSentence  =head3 GetCount
2296    
2297  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2298    
2299  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return the number of rows found by a specified query. This method would
2300    normally be used to count the records in a single table. For example, in a
2301    genetics database
2302    
2303        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2304    
2305    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2306    to use it to return records based on a join. For example,
2307    
2308        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2309                                    ['homo %']);
2310    
2311    would return the number of features for genomes in the genus I<homo>. Note that
2312    only the rows from the first table are counted. If the above command were
2313    
2314        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2315                                    ['homo %']);
2316    
2317    it would return the number of genomes, not the number of genome/feature pairs.
2318    
2319  =over 4  =over 4
2320    
2321  =item objectName  =item objectNames
2322    
2323  Name of the entity or relationship.  Reference to a list of the objects (entities and relationships) included in the
2324    query.
2325    
2326    =item filter
2327    
2328    A filter clause for restricting the query. The rules are the same as for the L</Get>
2329    method.
2330    
2331    =item params
2332    
2333    Reference to a list of the parameter values to be substituted for the parameter marks
2334    in the filter.
2335    
2336  =item RETURN  =item RETURN
2337    
2338  Returns a string containing the entity name or a relationship sentence.  Returns a count of the number of records in the first table that would satisfy
2339    the query.
2340    
2341  =back  =back
2342    
2343  =cut  =cut
2344    
2345  sub ComputeObjectSentence {  sub GetCount {
2346      # Get the parameters.      # Get the parameters.
2347      my ($self, $objectName) = @_;      my ($self, $objectNames, $filter, $params) = @_;
2348      # Set the default return value.      # Insure the params argument is an array reference if the caller left it off.
2349      my $retVal = $objectName;      if (! defined($params)) {
2350            $params = [];
2351        }
2352        # Declare the return variable.
2353        my $retVal;
2354        # Find out if we're counting an entity or a relationship.
2355        my $countedField;
2356        if ($self->IsEntity($objectNames->[0])) {
2357            $countedField = "id";
2358        } else {
2359            # For a relationship we count the to-link because it's usually more
2360            # numerous. Note we're automatically converting to the SQL form
2361            # of the field name (to_link vs. to-link).
2362            $countedField = "to_link";
2363        }
2364        # Create the SQL command suffix to get the desired records.
2365        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2366                                                                                $filter);
2367        # Prefix it with text telling it we want a record count.
2368        my $firstObject = $mappedNameListRef->[0];
2369        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2370        # Prepare and execute the command.
2371        my $sth = $self->_GetStatementHandle($command, $params);
2372        # Get the count value.
2373        ($retVal) = $sth->fetchrow_array();
2374        # Check for a problem.
2375        if (! defined($retVal)) {
2376            if ($sth->err) {
2377                # Here we had an SQL error.
2378                Confess("Error retrieving row count: " . $sth->errstr());
2379            } else {
2380                # Here we have no result.
2381                Confess("No result attempting to retrieve row count.");
2382            }
2383        }
2384        # Return the result.
2385        return $retVal;
2386    }
2387    
2388    =head3 ComputeObjectSentence
2389    
2390    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2391    
2392    Check an object name, and if it is a relationship convert it to a relationship sentence.
2393    
2394    =over 4
2395    
2396    =item objectName
2397    
2398    Name of the entity or relationship.
2399    
2400    =item RETURN
2401    
2402    Returns a string containing the entity name or a relationship sentence.
2403    
2404    =back
2405    
2406    =cut
2407    
2408    sub ComputeObjectSentence {
2409        # Get the parameters.
2410        my ($self, $objectName) = @_;
2411        # Set the default return value.
2412        my $retVal = $objectName;
2413      # Look for the object as a relationship.      # Look for the object as a relationship.
2414      my $relTable = $self->{_metaData}->{Relationships};      my $relTable = $self->{_metaData}->{Relationships};
2415      if (exists $relTable->{$objectName}) {      if (exists $relTable->{$objectName}) {
# Line 1359  Line 2462 
2462      }      }
2463  }  }
2464    
2465    =head3 InsertValue
2466    
2467    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2468    
2469    This method will insert a new value into the database. The value must be one
2470    associated with a secondary relation, since primary values cannot be inserted:
2471    they occur exactly once. Secondary values, on the other hand, can be missing
2472    or multiply-occurring.
2473    
2474    =over 4
2475    
2476    =item entityID
2477    
2478    ID of the object that is to receive the new value.
2479    
2480    =item fieldName
2481    
2482    Field name for the new value-- this includes the entity name, since
2483    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2484    
2485    =item value
2486    
2487    New value to be put in the field.
2488    
2489    =back
2490    
2491    =cut
2492    
2493    sub InsertValue {
2494        # Get the parameters.
2495        my ($self, $entityID, $fieldName, $value) = @_;
2496        # Parse the entity name and the real field name.
2497        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2498            my $entityName = $1;
2499            my $fieldTitle = $2;
2500            # Get its descriptor.
2501            if (!$self->IsEntity($entityName)) {
2502                Confess("$entityName is not a valid entity.");
2503            } else {
2504                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2505                # Find the relation containing this field.
2506                my $fieldHash = $entityData->{Fields};
2507                if (! exists $fieldHash->{$fieldTitle}) {
2508                    Confess("$fieldTitle not found in $entityName.");
2509                } else {
2510                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2511                    if ($relation eq $entityName) {
2512                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2513                    } else {
2514                        # Now we can create an INSERT statement.
2515                        my $dbh = $self->{_dbh};
2516                        my $fixedName = _FixName($fieldTitle);
2517                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2518                        # Execute the command.
2519                        $dbh->SQL($statement, 0, $entityID, $value);
2520                    }
2521                }
2522            }
2523        } else {
2524            Confess("$fieldName is not a valid field name.");
2525        }
2526    }
2527    
2528  =head3 InsertObject  =head3 InsertObject
2529    
2530  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2531    
2532  Insert an object into the database. The object is defined by a type name and then a hash  Insert an object into the database. The object is defined by a type name and then a hash
2533  of field names to values. Field values in the primary relation are represented by scalars.  of field names to values. Field values in the primary relation are represented by scalars.
# Line 1375  Line 2541 
2541  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2542  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2543    
2544  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2545    
2546  =over 4  =over 4
2547    
# Line 1387  Line 2553 
2553    
2554  Hash of field names to values.  Hash of field names to values.
2555    
 =item RETURN  
   
 Returns 1 if successful, 0 if an error occurred.  
   
2556  =back  =back
2557    
2558  =cut  =cut
# Line 1489  Line 2651 
2651                  $retVal = $sth->execute(@parameterList);                  $retVal = $sth->execute(@parameterList);
2652                  if (!$retVal) {                  if (!$retVal) {
2653                      my $errorString = $sth->errstr();                      my $errorString = $sth->errstr();
2654                      Trace("Insert error: $errorString.") if T(0);                      Confess("Error inserting into $relationName: $errorString");
2655                    } else {
2656                        Trace("Insert successful using $parameterList[0].") if T(3);
2657                  }                  }
2658              }              }
2659          }          }
2660      }      }
2661      # Return the success indicator.      # Return a 1 for backward compatability.
2662      return $retVal;      return 1;
2663    }
2664    
2665    =head3 UpdateEntity
2666    
2667    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2668    
2669    Update the values of an entity. This is an unprotected update, so it should only be
2670    done if the database resides on a database server.
2671    
2672    =over 4
2673    
2674    =item entityName
2675    
2676    Name of the entity to update. (This is the entity type.)
2677    
2678    =item id
2679    
2680    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2681    
2682    =item fields
2683    
2684    Reference to a hash mapping field names to their new values. All of the fields named
2685    must be in the entity's primary relation, and they cannot any of them be the ID field.
2686    
2687    =back
2688    
2689    =cut
2690    
2691    sub UpdateEntity {
2692        # Get the parameters.
2693        my ($self, $entityName, $id, $fields) = @_;
2694        # Get a list of the field names being updated.
2695        my @fieldList = keys %{$fields};
2696        # Verify that the fields exist.
2697        my $checker = $self->GetFieldTable($entityName);
2698        for my $field (@fieldList) {
2699            if ($field eq 'id') {
2700                Confess("Cannot update the ID field for entity $entityName.");
2701            } elsif ($checker->{$field}->{relation} ne $entityName) {
2702                Confess("Cannot find $field in primary relation of $entityName.");
2703            }
2704        }
2705        # Build the SQL statement.
2706        my @sets = ();
2707        my @valueList = ();
2708        for my $field (@fieldList) {
2709            push @sets, _FixName($field) . " = ?";
2710            push @valueList, $fields->{$field};
2711        }
2712        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2713        # Add the ID to the list of binding values.
2714        push @valueList, $id;
2715        # Call SQL to do the work.
2716        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2717        # Check for errors.
2718        if ($rows == 0) {
2719            Confess("Entity $id of type $entityName not found.");
2720        }
2721  }  }
2722    
2723  =head3 LoadTable  =head3 LoadTable
2724    
2725  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2726    
2727  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2728  first.  first.
# Line 1547  Line 2769 
2769          # leave extra room. We postulate a minimum row count of 1000 to          # leave extra room. We postulate a minimum row count of 1000 to
2770          # prevent problems with incoming empty load files.          # prevent problems with incoming empty load files.
2771          my $rowSize = $self->EstimateRowSize($relationName);          my $rowSize = $self->EstimateRowSize($relationName);
2772          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);          my $estimate = $fileSize * 1.5 / $rowSize;
2773            if ($estimate < 1000) {
2774                $estimate = 1000;
2775            }
2776          # Re-create the table without its index.          # Re-create the table without its index.
2777          $self->CreateTable($relationName, 0, $estimate);          $self->CreateTable($relationName, 0, $estimate);
2778          # If this is a pre-index DBMS, create the index here.          # If this is a pre-index DBMS, create the index here.
# Line 1567  Line 2792 
2792      };      };
2793      if (!defined $rv) {      if (!defined $rv) {
2794          $retVal->AddMessage($@) if ($@);          $retVal->AddMessage($@) if ($@);
2795          $retVal->AddMessage("Table load failed for $relationName using $fileName.");          $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2796          Trace("Table load failed for $relationName.") if T(1);          Trace("Table load failed for $relationName.") if T(1);
2797      } else {      } else {
2798          # Here we successfully loaded the table.          # Here we successfully loaded the table.
# Line 1575  Line 2800 
2800          my $size = -s $fileName;          my $size = -s $fileName;
2801          Trace("$size bytes loaded into $relationName.") if T(2);          Trace("$size bytes loaded into $relationName.") if T(2);
2802          # If we're rebuilding, we need to create the table indexes.          # If we're rebuilding, we need to create the table indexes.
2803          if ($truncateFlag && ! $dbh->{_preIndex}) {          if ($truncateFlag) {
2804                # Indexes are created here for PostGres. For PostGres, indexes are
2805                # best built at the end. For MySQL, the reverse is true.
2806                if (! $dbh->{_preIndex}) {
2807              eval {              eval {
2808                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
2809              };              };
# Line 1583  Line 2811 
2811                  $retVal->AddMessage($@);                  $retVal->AddMessage($@);
2812              }              }
2813          }          }
2814                # The full-text index (if any) is always built last, even for MySQL.
2815                # First we need to see if this table has a full-text index. Only
2816                # primary relations are allowed that privilege.
2817                Trace("Checking for full-text index on $relationName.") if T(2);
2818                if ($self->_IsPrimary($relationName)) {
2819                    $self->CreateSearchIndex($relationName);
2820                }
2821            }
2822      }      }
2823      # Analyze the table to improve performance.      # Analyze the table to improve performance.
2824        Trace("Analyzing and compacting $relationName.") if T(3);
2825      $dbh->vacuum_it($relationName);      $dbh->vacuum_it($relationName);
2826        Trace("$relationName load completed.") if T(3);
2827      # Return the statistics.      # Return the statistics.
2828      return $retVal;      return $retVal;
2829  }  }
2830    
2831  =head3 GenerateEntity  =head3 CreateSearchIndex
2832    
2833  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< $erdb->CreateSearchIndex($objectName); >>
2834    
2835  Generate the data for a new entity instance. This method creates a field hash suitable for  Check for a full-text search index on the specified entity or relationship object, and
2836  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  if one is required, rebuild it.
 of the fields are generated using information in the database schema.  
   
 Each data type has a default algorithm for generating random test data. This can be overridden  
 by including a B<DataGen> element in the field. If this happens, the content of the element is  
 executed as a PERL program in the context of this module. The element may make use of a C<$this>  
 variable which contains the field hash as it has been built up to the current point. If any  
 fields are dependent on other fields, the C<pass> attribute can be used to control the order  
 in which the fields are generated. A field with a high data pass number will be generated after  
 a field with a lower one. If any external values are needed, they should be passed in via the  
 optional third parameter, which will be available to the data generation script under the name  
 C<$value>. Several useful utility methods are provided for generating random values, including  
 L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated  
 in the form of a timestamp number rather than a string.  
2837    
2838  =over 4  =over 4
2839    
2840  =item id  =item objectName
2841    
2842  ID to assign to the new entity.  Name of the entity or relationship to be indexed.
2843    
2844  =item type  =back
2845    
2846  Type name for the new entity.  =cut
2847    
2848  =item values  sub CreateSearchIndex {
2849        # Get the parameters.
2850        my ($self, $objectName) = @_;
2851        # Get the relation's entity/relationship structure.
2852        my $structure = $self->_GetStructure($objectName);
2853        # Get the database handle.
2854        my $dbh = $self->{_dbh};
2855        Trace("Checking for search fields in $objectName.") if T(3);
2856        # Check for a searchable fields list.
2857        if (exists $structure->{searchFields}) {
2858            # Here we know that we need to create a full-text search index.
2859            # Get an SQL-formatted field name list.
2860            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2861            # Create the index. If it already exists, it will be dropped.
2862            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2863                               flds => $fields, kind => 'fulltext');
2864            Trace("Index created for $fields in $objectName.") if T(2);
2865        }
2866    }
2867    
2868    =head3 DropRelation
2869    
2870    C<< $erdb->DropRelation($relationName); >>
2871    
2872  Hash containing additional values that might be needed by the data generation methods (optional).  Physically drop a relation from the database.
2873    
2874    =over 4
2875    
2876    =item relationName
2877    
2878    Name of the relation to drop. If it does not exist, this method will have
2879    no effect.
2880    
2881  =back  =back
2882    
2883  =cut  =cut
2884    
2885  sub GenerateEntity {  sub DropRelation {
2886      # Get the parameters.      # Get the parameters.
2887      my ($self, $id, $type, $values) = @_;      my ($self, $relationName) = @_;
2888      # Create the return hash.      # Get the database handle.
2889      my $this = { id => $id };      my $dbh = $self->{_dbh};
2890      # Get the metadata structure.      # Drop the relation. The method used here has no effect if the relation
2891      my $metadata = $self->{_metaData};      # does not exist.
2892      # Get this entity's list of fields.      Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2893      if (!exists $metadata->{Entities}->{$type}) {      $dbh->drop_table(tbl => $relationName);
2894          Confess("Unrecognized entity type $type in GenerateEntity.");  }
2895      } else {  
2896          my $entity = $metadata->{Entities}->{$type};  =head3 MatchSqlPattern
2897          my $fields = $entity->{Fields};  
2898          # Generate data from the fields.  C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2899          _GenerateFields($this, $fields, $type, $values);  
2900    Determine whether or not a specified value matches an SQL pattern. An SQL
2901    pattern has two wild card characters: C<%> that matches multiple characters,
2902    and C<_> that matches a single character. These can be escaped using a
2903    backslash (C<\>). We pull this off by converting the SQL pattern to a
2904    PERL regular expression. As per SQL rules, the match is case-insensitive.
2905    
2906    =over 4
2907    
2908    =item value
2909    
2910    Value to be matched against the pattern. Note that an undefined or empty
2911    value will not match anything.
2912    
2913    =item pattern
2914    
2915    SQL pattern against which to match the value. An undefined or empty pattern will
2916    match everything.
2917    
2918    =item RETURN
2919    
2920    Returns TRUE if the value and pattern match, else FALSE.
2921    
2922    =back
2923    
2924    =cut
2925    
2926    sub MatchSqlPattern {
2927        # Get the parameters.
2928        my ($value, $pattern) = @_;
2929        # Declare the return variable.
2930        my $retVal;
2931        # Insure we have a pattern.
2932        if (! defined($pattern) || $pattern eq "") {
2933            $retVal = 1;
2934        } else {
2935            # Break the pattern into pieces around the wildcard characters. Because we
2936            # use parentheses in the split function's delimiter expression, we'll get
2937            # list elements for the delimiters as well as the rest of the string.
2938            my @pieces = split /([_%]|\\[_%])/, $pattern;
2939            # Check some fast special cases.
2940            if ($pattern eq '%') {
2941                # A null pattern matches everything.
2942                $retVal = 1;
2943            } elsif (@pieces == 1) {
2944                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2945                $retVal = (lc($value) eq lc($pattern));
2946            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2947                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2948                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2949            } else {
2950                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2951                my $realPattern = "";
2952                for my $piece (@pieces) {
2953                    # Determine the type of piece.
2954                    if ($piece eq "") {
2955                        # Empty pieces are ignored.
2956                    } elsif ($piece eq "%") {
2957                        # Here we have a multi-character wildcard. Note that it can match
2958                        # zero or more characters.
2959                        $realPattern .= ".*"
2960                    } elsif ($piece eq "_") {
2961                        # Here we have a single-character wildcard.
2962                        $realPattern .= ".";
2963                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2964                        # This is an escape sequence (which is a rare thing, actually).
2965                        $realPattern .= substr($piece, 1, 1);
2966                    } else {
2967                        # Here we have raw text.
2968                        $realPattern .= quotemeta($piece);
2969      }      }
2970      # Return the hash created.              }
2971      return $this;              # Do the match.
2972                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2973            }
2974        }
2975        # Return the result.
2976        return $retVal;
2977  }  }
2978    
2979  =head3 GetEntity  =head3 GetEntity
# Line 1666  Line 2994 
2994    
2995  =item RETURN  =item RETURN
2996    
2997  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2998  instance is found with the specified key.  instance is found with the specified key.
2999    
3000  =back  =back
# Line 1677  Line 3005 
3005      # Get the parameters.      # Get the parameters.
3006      my ($self, $entityType, $ID) = @_;      my ($self, $entityType, $ID) = @_;
3007      # Create a query.      # Create a query.
3008      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3009      # Get the first (and only) object.      # Get the first (and only) object.
3010      my $retVal = $query->Fetch();      my $retVal = $query->Fetch();
3011      # Return the result.      # Return the result.
3012      return $retVal;      return $retVal;
3013  }  }
3014    
3015    =head3 GetChoices
3016    
3017    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
3018    
3019    Return a list of all the values for the specified field that are represented in the
3020    specified entity.
3021    
3022    Note that if the field is not indexed, then this will be a very slow operation.
3023    
3024    =over 4
3025    
3026    =item entityName
3027    
3028    Name of an entity in the database.
3029    
3030    =item fieldName
3031    
3032    Name of a field belonging to the entity. This is a raw field name without
3033    the standard parenthesized notation used in most calls.
3034    
3035    =item RETURN
3036    
3037    Returns a list of the distinct values for the specified field in the database.
3038    
3039    =back
3040    
3041    =cut
3042    
3043    sub GetChoices {
3044        # Get the parameters.
3045        my ($self, $entityName, $fieldName) = @_;
3046        # Declare the return variable.
3047        my @retVal;
3048        # Get the entity data structure.
3049        my $entityData = $self->_GetStructure($entityName);
3050        # Get the field.
3051        my $fieldHash = $entityData->{Fields};
3052        if (! exists $fieldHash->{$fieldName}) {
3053            Confess("$fieldName not found in $entityName.");
3054        } else {
3055            # Get the name of the relation containing the field.
3056            my $relation = $fieldHash->{$fieldName}->{relation};
3057            # Fix up the field name.
3058            my $realName = _FixName($fieldName);
3059            # Get the database handle.
3060            my $dbh = $self->{_dbh};
3061            # Query the database.
3062            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
3063            # Clean the results. They are stored as a list of lists, and we just want the one list.
3064            @retVal = sort map { $_->[0] } @{$results};
3065        }
3066        # Return the result.
3067        return @retVal;
3068    }
3069    
3070  =head3 GetEntityValues  =head3 GetEntityValues
3071    
3072  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
3073    
3074  Return a list of values from a specified entity instance.  Return a list of values from a specified entity instance. If the entity instance
3075    does not exist, an empty list is returned.
3076    
3077  =over 4  =over 4
3078    
# Line 1745  Line 3129 
3129  spreadsheet cell, and each feature will be represented by a list containing the  spreadsheet cell, and each feature will be represented by a list containing the
3130  feature ID followed by all of its aliases.  feature ID followed by all of its aliases.
3131    
3132  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
3133    
3134  =over 4  =over 4
3135    
# Line 1766  Line 3150 
3150    
3151  List of the parameters to be substituted in for the parameters marks in the filter clause.  List of the parameters to be substituted in for the parameters marks in the filter clause.
3152    
3153  =item fields  =item fields
3154    
3155    List of the fields to be returned in each element of the list returned.
3156    
3157    =item count
3158    
3159    Maximum number of records to return. If omitted or 0, all available records will be returned.
3160    
3161    =item RETURN
3162    
3163    Returns a list of list references. Each element of the return list contains the values for the
3164    fields specified in the B<fields> parameter.
3165    
3166    =back
3167    
3168    =cut
3169    #: Return Type @@;
3170    sub GetAll {
3171        # Get the parameters.
3172        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3173        # Translate the parameters from a list reference to a list. If the parameter
3174        # list is a scalar we convert it into a singleton list.
3175        my @parmList = ();
3176        if (ref $parameterList eq "ARRAY") {
3177            Trace("GetAll parm list is an array.") if T(4);
3178            @parmList = @{$parameterList};
3179        } else {
3180            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3181            push @parmList, $parameterList;
3182        }
3183        # Insure the counter has a value.
3184        if (!defined $count) {
3185            $count = 0;
3186        }
3187        # Add the row limit to the filter clause.
3188        if ($count > 0) {
3189            $filterClause .= " LIMIT $count";
3190        }
3191        # Create the query.
3192        my $query = $self->Get($objectNames, $filterClause, \@parmList);
3193        # Set up a counter of the number of records read.
3194        my $fetched = 0;
3195        # Loop through the records returned, extracting the fields. Note that if the
3196        # counter is non-zero, we stop when the number of records read hits the count.
3197        my @retVal = ();
3198        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3199            my @rowData = $row->Values($fields);
3200            push @retVal, \@rowData;
3201            $fetched++;
3202        }
3203        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3204        # Return the resulting list.
3205        return @retVal;
3206    }
3207    
3208    =head3 Exists
3209    
3210    C<< my $found = $sprout->Exists($entityName, $entityID); >>
3211    
3212    Return TRUE if an entity exists, else FALSE.
3213    
3214    =over 4
3215    
3216    =item entityName
3217    
3218    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3219    
3220    =item entityID
3221    
3222    ID of the entity instance whose existence is to be checked.
3223    
3224    =item RETURN
3225    
3226    Returns TRUE if the entity instance exists, else FALSE.
3227    
3228    =back
3229    
3230    =cut
3231    #: Return Type $;
3232    sub Exists {
3233        # Get the parameters.
3234        my ($self, $entityName, $entityID) = @_;
3235        # Check for the entity instance.
3236        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3237        my $testInstance = $self->GetEntity($entityName, $entityID);
3238        # Return an existence indicator.
3239        my $retVal = ($testInstance ? 1 : 0);
3240        return $retVal;
3241    }
3242    
3243    =head3 EstimateRowSize
3244    
3245    C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3246    
3247    Estimate the row size of the specified relation. The estimated row size is computed by adding
3248    up the average length for each data type.
3249    
3250    =over 4
3251    
3252    =item relName
3253    
3254    Name of the relation whose estimated row size is desired.
3255    
3256    =item RETURN
3257    
3258    Returns an estimate of the row size for the specified relation.
3259    
3260    =back
3261    
3262    =cut
3263    #: Return Type $;
3264    sub EstimateRowSize {
3265        # Get the parameters.
3266        my ($self, $relName) = @_;
3267        # Declare the return variable.
3268        my $retVal = 0;
3269        # Find the relation descriptor.
3270        my $relation = $self->_FindRelation($relName);
3271        # Get the list of fields.
3272        for my $fieldData (@{$relation->{Fields}}) {
3273            # Get the field type and add its length.
3274            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3275            $retVal += $fieldLen;
3276        }
3277        # Return the result.
3278        return $retVal;
3279    }
3280    
3281    =head3 GetFieldTable
3282    
3283    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3284    
3285    Get the field structure for a specified entity or relationship.
3286    
3287    =over 4
3288    
3289    =item objectName
3290    
3291    Name of the desired entity or relationship.
3292    
3293    =item RETURN
3294    
3295    The table containing the field descriptors for the specified object.
3296    
3297    =back
3298    
3299    =cut
3300    
3301    sub GetFieldTable {
3302        # Get the parameters.
3303        my ($self, $objectName) = @_;
3304        # Get the descriptor from the metadata.
3305        my $objectData = $self->_GetStructure($objectName);
3306        # Return the object's field table.
3307        return $objectData->{Fields};
3308    }
3309    
3310    =head3 SplitKeywords
3311    
3312    C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3313    
3314    This method returns a list of the positive keywords in the specified
3315    keyword string. All of the operators will have been stripped off,
3316    and if the keyword is preceded by a minus operator (C<->), it will
3317    not be in the list returned. The idea here is to get a list of the
3318    keywords the user wants to see. The list will be processed to remove
3319    duplicates.
3320    
3321    It is possible to create a string that confuses this method. For example
3322    
3323        frog toad -frog
3324    
3325    would return both C<frog> and C<toad>. If this is a problem we can deal
3326    with it later.
3327    
3328    =over 4
3329    
3330    =item keywordString
3331    
3332    The keyword string to be parsed.
3333    
3334    =item RETURN
3335    
3336    Returns a list of the words in the keyword string the user wants to
3337    see.
3338    
3339    =back
3340    
3341    =cut
3342    
3343    sub SplitKeywords {
3344        # Get the parameters.
3345        my ($keywordString) = @_;
3346        # Make a safety copy of the string. (This helps during debugging.)
3347        my $workString = $keywordString;
3348        # Convert operators we don't care about to spaces.
3349        $workString =~ tr/+"()<>/ /;
3350        # Split the rest of the string along space boundaries. Note that we
3351        # eliminate any words that are zero length or begin with a minus sign.
3352        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3353        # Use a hash to remove duplicates.
3354        my %words = map { $_ => 1 } @wordList;
3355        # Return the result.
3356        return sort keys %words;
3357    }
3358    
3359    =head3 ValidateFieldName
3360    
3361    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3362    
3363    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3364    be hyphenated words subject to certain restrictions.
3365    
3366    =over 4
3367    
3368    =item fieldName
3369    
3370    Field name to be validated.
3371    
3372    =item RETURN
3373    
3374    Returns TRUE if the field name is valid, else FALSE.
3375    
3376    =back
3377    
3378    =cut
3379    
3380    sub ValidateFieldName {
3381        # Get the parameters.
3382        my ($fieldName) = @_;
3383        # Declare the return variable. The field name is valid until we hear
3384        # differently.
3385        my $retVal = 1;
3386        # Compute the maximum name length.
3387        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3388        # Look for bad stuff in the name.
3389        if ($fieldName =~ /--/) {
3390            # Here we have a doubled minus sign.
3391            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3392            $retVal = 0;
3393        } elsif ($fieldName !~ /^[A-Za-z]/) {
3394            # Here the field name is missing the initial letter.
3395            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3396            $retVal = 0;
3397        } elsif (length($fieldName) > $maxLen) {
3398            # Here the field name is too long.
3399            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3400        } else {
3401            # Strip out the minus signs. Everything remaining must be a letter,
3402            # underscore, or digit.
3403            my $strippedName = $fieldName;
3404            $strippedName =~ s/-//g;
3405            if ($strippedName !~ /^(\w|\d)+$/) {
3406                Trace("Field name $fieldName contains illegal characters.") if T(1);
3407                $retVal = 0;
3408            }
3409        }
3410        # Return the result.
3411        return $retVal;
3412    }
3413    
3414    =head3 ReadMetaXML
3415    
3416    C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3417    
3418    This method reads a raw database definition XML file and returns it.
3419    Normally, the metadata used by the ERDB system has been processed and
3420    modified to make it easier to load and retrieve the data; however,
3421    this method can be used to get the data in its raw form.
3422    
3423    =over 4
3424    
3425    =item fileName
3426    
3427    Name of the XML file to read.
3428    
3429    =item RETURN
3430    
3431    Returns a hash reference containing the raw XML data from the specified file.
3432    
3433    =back
3434    
3435    =cut
3436    
3437    sub ReadMetaXML {
3438        # Get the parameters.
3439        my ($fileName) = @_;
3440        # Read the XML.
3441        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3442        Trace("XML metadata loaded from file $fileName.") if T(1);
3443        # Return the result.
3444        return $retVal;
3445    }
3446    
3447    =head3 GetEntityFieldHash
3448    
3449    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3450    
3451    Get the field hash of the named entity in the specified raw XML structure.
3452    The field hash may not exist, in which case we need to create it.
3453    
3454    =over 4
3455    
3456    =item structure
3457    
3458    Raw XML structure defininng the database. This is not the run-time XML used by
3459    an ERDB object, since that has all sorts of optimizations built-in.
3460    
3461    =item entityName
3462    
3463    Name of the entity whose field structure is desired.
3464    
3465    =item RETURN
3466    
3467    Returns the field hash used to define the entity's fields.
3468    
3469    =back
3470    
3471    =cut
3472    
3473    sub GetEntityFieldHash {
3474        # Get the parameters.
3475        my ($structure, $entityName) = @_;
3476        # Get the entity structure.
3477        my $entityData = $structure->{Entities}->{$entityName};
3478        # Look for a field structure.
3479        my $retVal = $entityData->{Fields};
3480        # If it doesn't exist, create it.
3481        if (! defined($retVal)) {
3482            $entityData->{Fields} = {};
3483            $retVal = $entityData->{Fields};
3484        }
3485        # Return the result.
3486        return $retVal;
3487    }
3488    
3489    =head3 WriteMetaXML
3490    
3491    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3492    
3493    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3494    used to update the database definition. It must be used with care, however, since it
3495    will only work on a raw structure, not on the processed structure created by an ERDB
3496    constructor.
3497    
3498    =over 4
3499    
3500    =item structure
3501    
3502    XML structure to be written to the file.
3503    
3504    =item fileName
3505    
3506    Name of the output file to which the updated XML should be stored.
3507    
3508    =back
3509    
3510    =cut
3511    
3512    sub WriteMetaXML {
3513        # Get the parameters.
3514        my ($structure, $fileName) = @_;
3515        # Compute the output.
3516        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3517        # Write it to the file.
3518        my $xmlOut = Open(undef, ">$fileName");
3519        print $xmlOut $fileString;
3520    }
3521    
3522    
3523    =head3 HTMLNote
3524    
3525    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3526    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3527    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3528    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3529    
3530    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3531    
3532    =over 4
3533    
3534    =item dataString
3535    
3536    String to convert to HTML.
3537    
3538    =item RETURN
3539    
3540    An HTML string derived from the input string.
3541    
3542    =back
3543    
3544    =cut
3545    
3546    sub HTMLNote {
3547        # Get the parameter.
3548        my ($dataString) = @_;
3549        # HTML-escape the text.
3550        my $retVal = CGI::escapeHTML($dataString);
3551        # Substitute the bulletin board codes.
3552        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3553        $retVal =~ s!\[p\]!</p><p>!g;
3554        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3555        $retVal =~ s!\[/link\]!</a>!g;
3556        # Return the result.
3557        return $retVal;
3558    }
3559    
3560    =head3 BeginTran
3561    
3562    C<< $erdb->BeginTran(); >>
3563    
3564    Start a database transaction.
3565    
3566    =cut
3567    
3568    sub BeginTran {
3569        my ($self) = @_;
3570        $self->{_dbh}->begin_tran();
3571    
3572    }
3573    
3574    =head3 CommitTran
3575    
3576    C<< $erdb->CommitTran(); >>
3577    
3578    Commit an active database transaction.
3579    
3580    =cut
3581    
3582    sub CommitTran {
3583        my ($self) = @_;
3584        $self->{_dbh}->commit_tran();
3585    }
3586    
3587    =head3 RollbackTran
3588    
3589    C<< $erdb->RollbackTran(); >>
3590    
3591    Roll back an active database transaction.
3592    
3593    =cut
3594    
3595    sub RollbackTran {
3596        my ($self) = @_;
3597        $self->{_dbh}->roll_tran();
3598    }
3599    
3600    =head3 UpdateField
3601    
3602    C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>
3603    
3604    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3605    returned.
3606    
3607    =over 4
3608    
3609    =item fieldName
3610    
3611    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3612    
3613    =item oldValue
3614    
3615    Value to be modified. All occurrences of this value in the named field will be replaced by the
3616    new value.
3617    
3618    =item newValue
3619    
3620    New value to be substituted for the old value when it's found.
3621    
3622    =item filter
3623    
3624    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3625    
3626    =item parms
3627    
3628    Reference to a list of parameter values in the filter.
3629    
3630    =item RETURN
3631    
3632    Returns the number of rows modified.
3633    
3634    =back
3635    
3636    =cut
3637    
3638    sub UpdateField {
3639        # Get the parameters.
3640        my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3641        # Get the object and field names from the field name parameter.
3642        $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3643        my $objectName = $1;
3644        my $realFieldName = _FixName($2);
3645        # Add the old value to the filter. Note we allow the possibility that no
3646        # filter was specified.
3647        my $realFilter = "$fieldName = ?";
3648        if ($filter) {
3649            $realFilter .= " AND $filter";
3650        }
3651        # Format the query filter.
3652        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3653            $self->_SetupSQL([$objectName], $realFilter);
3654        # Create the query. Since there is only one object name, the mapped-name data is not
3655        # necessary. Neither is the FROM clause.
3656        $suffix =~ s/^FROM.+WHERE\s+//;
3657        # Create the update statement.
3658        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3659        # Get the database handle.
3660        my $dbh = $self->{_dbh};
3661        # Add the old and new values to the parameter list. Note we allow the possibility that
3662        # there are no user-supplied parameters.
3663        my @params = ($newValue, $oldValue);
3664        if (defined $parms) {
3665            push @params, @{$parms};
3666        }
3667        # Execute the update.
3668        my $retVal = $dbh->SQL($command, 0, @params);
3669        # Make the funky zero a real zero.
3670        if ($retVal == 0) {
3671            $retVal = 0;
3672        }
3673        # Return the result.
3674        return $retVal;
3675    }
3676    
3677    
3678    =head2 Data Mining Methods
3679    
3680    =head3 GetUsefulCrossValues
3681    
3682    C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3683    
3684    Return a list of the useful attributes that would be returned by a B<Cross> call
3685    from an entity of the source entity type through the specified relationship. This
3686    means it will return the fields of the target entity type and the intersection data
3687    fields in the relationship. Only primary table fields are returned. In other words,
3688    the field names returned will be for fields where there is always one and only one
3689    value.
3690    
3691    =over 4
3692    
3693    =item sourceEntity
3694    
3695    Name of the entity from which the relationship crossing will start.
3696    
3697    =item relationship
3698    
3699    Name of the relationship being crossed.
3700    
3701    =item RETURN
3702    
3703    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3704    
3705    =back
3706    
3707    =cut
3708    #: Return Type @;
3709    sub GetUsefulCrossValues {
3710        # Get the parameters.
3711        my ($self, $sourceEntity, $relationship) = @_;
3712        # Declare the return variable.
3713        my @retVal = ();
3714        # Determine the target entity for the relationship. This is whichever entity is not
3715        # the source entity. So, if the source entity is the FROM, we'll get the name of
3716        # the TO, and vice versa.
3717        my $relStructure = $self->_GetStructure($relationship);
3718        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3719        my $targetEntity = $relStructure->{$targetEntityType};
3720        # Get the field table for the entity.
3721        my $entityFields = $self->GetFieldTable($targetEntity);
3722        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3723        # For the entity fields, the key aspect of the target structure is that the {relation} value
3724        # must match the entity name.
3725        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3726                            keys %{$entityFields};
3727        # Push the fields found onto the return variable.
3728        push @retVal, sort @fieldList;
3729        # Get the field table for the relationship.
3730        my $relationshipFields = $self->GetFieldTable($relationship);
3731        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3732        # This may end up being an empty set.
3733        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3734                            keys %{$relationshipFields};
3735        # Push these onto the return list.
3736        push @retVal, sort @fieldList2;
3737        # Return the result.
3738        return @retVal;
3739    }
3740    
3741    =head3 FindColumn
3742    
3743    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3744    
3745    Return the location a desired column in a data mining header line. The data
3746    mining header line is a tab-separated list of column names. The column
3747    identifier is either the numerical index of a column or the actual column
3748    name.
3749    
3750    =over 4
3751    
3752    =item headerLine
3753    
3754    The header line from a data mining command, which consists of a tab-separated
3755    list of column names.
3756    
3757    =item columnIdentifier
3758    
3759    Either the ordinal number of the desired column (1-based), or the name of the
3760    desired column.
3761    
3762    =item RETURN
3763    
3764    Returns the array index (0-based) of the desired column.
3765    
3766    =back
3767    
3768    =cut
3769    
3770    sub FindColumn {
3771        # Get the parameters.
3772        my ($headerLine, $columnIdentifier) = @_;
3773        # Declare the return variable.
3774        my $retVal;
3775        # Split the header line into column names.
3776        my @headers = ParseColumns($headerLine);
3777        # Determine whether we have a number or a name.
3778        if ($columnIdentifier =~ /^\d+$/) {
3779            # Here we have a number. Subtract 1 and validate the result.
3780            $retVal = $columnIdentifier - 1;
3781            if ($retVal < 0 || $retVal > $#headers) {
3782                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3783            }
3784        } else {
3785            # Here we have a name. We need to find it in the list.
3786            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3787                if ($headers[$i] eq $columnIdentifier) {
3788                    $retVal = $i;
3789                }
3790            }
3791            if (! defined($retVal)) {
3792                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3793            }
3794        }
3795        # Return the result.
3796        return $retVal;
3797    }
3798    
3799    =head3 ParseColumns
3800    
3801    C<< my @columns = ERDB::ParseColumns($line); >>
3802    
3803    Convert the specified data line to a list of columns.
3804    
3805    =over 4
3806    
3807    =item line
3808    
3809    A data mining input, consisting of a tab-separated list of columns terminated by a
3810    new-line.
3811    
3812    =item RETURN
3813    
3814    Returns a list consisting of the column values.
3815    
3816    =back
3817    
3818    =cut
3819    
3820    sub ParseColumns {
3821        # Get the parameters.
3822        my ($line) = @_;
3823        # Chop off the line-end.
3824        chomp $line;
3825        # Split it into a list.
3826        my @retVal = split(/\t/, $line);
3827        # Return the result.
3828        return @retVal;
3829    }
3830    
3831    =head2 Virtual Methods
3832    
3833    =head3 _CreatePPOIndex
3834    
3835    C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3836    
3837    Convert the XML for an ERDB index to the XML structure for a PPO
3838    index.
3839    
3840    =over 4
3841    
3842    ERDB XML structure for an index.
3843    
3844    =item RETURN
3845    
3846    PPO XML structure for the same index.
3847    
3848    =back
3849    
3850    =cut
3851    
3852    sub _CreatePPOIndex {
3853        # Get the parameters.
3854        my ($indexObject) = @_;
3855        # The incoming index contains a list of the index fields in the IndexFields
3856        # member. We loop through it to create the index tags.
3857        my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3858        # Wrap the fields in attribute tags.
3859        my $retVal = { attribute => \@fields };
3860        # Return the result.
3861        return $retVal;
3862    }
3863    
3864    =head3 _CreatePPOField
3865    
3866    C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3867    
3868    Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3869    
3870    =over 4
3871    
3872    =item fieldName
3873    
3874  List of the fields to be returned in each element of the list returned.  Name of the scalar field.
3875    
3876  =item count  =item fieldObject
3877    
3878  Maximum number of records to return. If omitted or 0, all available records will be returned.  ERDB XML structure describing the field.
3879    
3880  =item RETURN  =item RETURN
3881    
3882  Returns a list of list references. Each element of the return list contains the values for the  Returns a PPO XML structure for the same field.
 fields specified in the B<fields> parameter.  
3883    
3884  =back  =back
3885    
3886  =cut  =cut
3887  #: Return Type @@;  
3888  sub GetAll {  sub _CreatePPOField {
3889      # Get the parameters.      # Get the parameters.
3890      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      my ($fieldName, $fieldObject) = @_;
3891      # Translate the parameters from a list reference to a list. If the parameter      # Get the field type.
3892      # list is a scalar we convert it into a singleton list.      my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3893      my @parmList = ();      # Fix up the field name.
3894      if (ref $parameterList eq "ARRAY") {      $fieldName = _FixName($fieldName);
3895          @parmList = @{$parameterList};      # Build the scalar tag.
3896      } else {      my $retVal = { label => $fieldName, type => $type };
3897          push @parmList, $parameterList;      # Return the result.
3898      }      return $retVal;
     # Insure the counter has a value.  
     if (!defined $count) {  
         $count = 0;  
     }  
     # Add the row limit to the filter clause.  
     if ($count > 0) {  
         $filterClause .= " LIMIT $count";  
     }  
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, @parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
     # Loop through the records returned, extracting the fields. Note that if the  
     # counter is non-zero, we stop when the number of records read hits the count.  
     my @retVal = ();  
     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
         my @rowData = $row->Values($fields);  
         push @retVal, \@rowData;  
         $fetched++;  
     }  
     # Return the resulting list.  
     return @retVal;  
3899  }  }
3900    
3901  =head3 EstimateRowSize  =head3 CleanKeywords
3902    
3903  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3904    
3905  Estimate the row size of the specified relation. The estimated row size is computed by adding  Clean up a search expression or keyword list. This is a virtual method that may
3906  up the average length for each data type.  be overridden by the subclass. The base-class method removes extra spaces
3907    and converts everything to lower case.
3908    
3909  =over 4  =over 4
3910    
3911  =item relName  =item searchExpression
3912    
3913  Name of the relation whose estimated row size is desired.  Search expression or keyword list to clean. Note that a search expression may
3914    contain boolean operators which need to be preserved. This includes leading
3915    minus signs.
3916    
3917  =item RETURN  =item RETURN
3918    
3919  Returns an estimate of the row size for the specified relation.  Cleaned expression or keyword list.
3920    
3921  =back  =back
3922    
3923  =cut  =cut
3924  #: Return Type $;  
3925  sub EstimateRowSize {  sub CleanKeywords {
3926      # Get the parameters.      # Get the parameters.
3927      my ($self, $relName) = @_;      my ($self, $searchExpression) = @_;
3928      # Declare the return variable.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3929      my $retVal = 0;      # don't accidentally end up with an undefined value.
3930      # Find the relation descriptor.      my $retVal = lc($searchExpression || "");
3931      my $relation = $self->_FindRelation($relName);      # Remove extra spaces.
3932      # Get the list of fields.      $retVal =~ s/\s+/ /g;
3933      for my $fieldData (@{$relation->{Fields}}) {      $retVal =~ s/(^\s+)|(\s+$)//g;
         # Get the field type and add its length.  
         my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};  
         $retVal += $fieldLen;  
     }  
3934      # Return the result.      # Return the result.
3935      return $retVal;      return $retVal;
3936  }  }
3937    
3938    =head3 GetSourceObject
3939    
3940    C<< my $source = $erdb->GetSourceObject($entityName); >>
3941    
3942    Return the object to be used in loading special attributes of the specified entity. The
3943    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3944    XML
3945    
3946  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3947    
3948  =head3 GetLoadStats  =head3 _RelationMap
3949    
3950  Return a blank statistics object for use by the load methods.  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3951    
3952  This is a static method.  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3953    to determine how to interpret the results of the query.
3954    
3955  =cut  =over 4
3956    
3957  sub _GetLoadStats{  =item mappedNameHashRef
     return Stats->new();  
 }  
3958    
3959  =head3 GenerateFields  Reference to a hash that maps modified object names to real object names.
3960    
3961  Generate field values from a field structure and store in a specified table. The field names  =item mappedNameListRef
 are first sorted by pass count, certain pre-defined fields are removed from the list, and  
 then we rip through them evaluation the data generation string. Fields in the primary relation  
 are stored as scalars; fields in secondary relations are stored as value lists.  
3962    
3963  This is a static method.  Reference to a list of modified object names in the order they appear in the
3964    SELECT list.
3965    
3966  =over 4  =item RETURN
3967    
3968  =item this  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3969    query followed by the actual name of that object. This enables the B<ERDBObject> to
3970    determine the order of the tables in the query and which object name belongs to each
3971    mapped object name. Most of the time these two values are the same; however, if a
3972    relation occurs twice in the query, the relation name in the field list and WHERE
3973    clause will use a mapped name (generally the actual relation name with a numeric
3974    suffix) that does not match the actual relation name.
3975    
3976  Hash table into which the field values should be placed.  =back
3977    
3978  =item fields  =cut
3979    
3980  Field structure from which the field descriptors should be taken.  sub _RelationMap {
3981        # Get the parameters.
3982        my ($mappedNameHashRef, $mappedNameListRef) = @_;
3983        # Declare the return variable.
3984        my @retVal = ();
3985        # Build the map.
3986        for my $mappedName (@{$mappedNameListRef}) {
3987            push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3988        }
3989        # Return it.
3990        return @retVal;
3991    }
3992    
 =item type  
3993    
3994  Type name of the object whose fields are being generated.  =head3 _SetupSQL
3995    
3996    Process a list of object names and a filter clause so that they can be used to
3997    build an SQL statement. This method takes in a reference to a list of object names
3998    and a filter clause. It will return a corrected filter clause, a list of mapped
3999    names and the mapped name hash.
4000    
4001    This is an instance method.
4002    
4003    =over 4
4004    
4005    =item objectNames
4006    
4007    Reference to a list of the object names to be included in the query.
4008    
4009  =item values (optional)  =item filterClause
4010    
4011  Reference to a value structure from which additional values can be taken.  A string containing the WHERE clause for the query (without the C<WHERE>) and also
4012    optionally the C<ORDER BY> and C<LIMIT> clauses.
4013    
4014  =item from (optiona)  =item matchClause
4015    
4016  Reference to the source entity instance if relationship data is being generated.  An optional full-text search clause. If specified, it will be inserted at the
4017    front of the WHERE clause. It should already be SQL-formatted; that is, the
4018    field names should be in the form I<table>C<.>I<fieldName>.
4019    
4020  =item to (optional)  =item RETURN
4021    
4022  Reference to the target entity instance if relationship data is being generated.  Returns a three-element list. The first element is the SQL statement suffix, beginning
4023    with the FROM clause. The second element is a reference to a list of the names to be
4024    used in retrieving the fields. The third element is a hash mapping the names to the
4025    objects they represent.
4026    
4027  =back  =back
4028    
4029  =cut  =cut
4030    
4031  sub _GenerateFields {  sub _SetupSQL {
4032      # Get the parameters.      my ($self, $objectNames, $filterClause, $matchClause) = @_;
4033      my ($this, $fields, $type, $values, $from, $to) = @_;      # Adjust the list of object names to account for multiple occurrences of the
4034      # Sort the field names by pass number.      # same object. We start with a hash table keyed on object name that will
4035      my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};      # return the object suffix. The first time an object is encountered it will
4036      # Loop through the field names, generating data.      # not be found in the hash. The next time the hash will map the object name
4037      for my $name (@fieldNames) {      # to 2, then 3, and so forth.
4038          # Only proceed if this field needs to be generated.      my %objectHash = ();
4039          if (!exists $this->{$name}) {      # This list will contain the object names as they are to appear in the
4040              # Get this field's data generation descriptor.      # FROM list.
4041              my $fieldDescriptor = $fields->{$name};      my @fromList = ();
4042              my $data = $fieldDescriptor->{DataGen};      # This list contains the suffixed object name for each object. It is exactly
4043              # Get the code to generate the field value.      # parallel to the list in the $objectNames parameter.
4044              my $codeString = $data->{content};      my @mappedNameList = ();
4045              # Determine whether or not this field is in the primary relation.      # Finally, this hash translates from a mapped name to its original object name.
4046              if ($fieldDescriptor->{relation} eq $type) {      my %mappedNameHash = ();
4047                  # Here we have a primary relation field. Store the field value as      # Now we create the lists. Note that for every single name we push something into
4048                  # a scalar.      # @fromList and @mappedNameList. This insures that those two arrays are exactly
4049                  $this->{$name} = eval($codeString);      # parallel to $objectNames.
4050        for my $objectName (@{$objectNames}) {
4051            # Get the next suffix for this object.
4052            my $suffix = $objectHash{$objectName};
4053            if (! $suffix) {
4054                # Here we are seeing the object for the first time. The object name
4055                # is used as is.
4056                push @mappedNameList, $objectName;
4057                push @fromList, $objectName;
4058                $mappedNameHash{$objectName} = $objectName;
4059                # Denote the next suffix will be 2.
4060                $objectHash{$objectName} = 2;
4061            } else {
4062                # Here we've seen the object before. We construct a new name using
4063                # the suffix from the hash and update the hash.
4064                my $mappedName = "$objectName$suffix";
4065                $objectHash{$objectName} = $suffix + 1;
4066                # The FROM list has the object name followed by the mapped name. This
4067                # tells SQL it's still the same table, but we're using a different name
4068                # for it to avoid confusion.
4069                push @fromList, "$objectName $mappedName";
4070                # The mapped-name list contains the real mapped name.
4071                push @mappedNameList, $mappedName;
4072                # Finally, enable us to get back from the mapped name to the object name.
4073                $mappedNameHash{$mappedName} = $objectName;
4074            }
4075        }
4076        # Begin the SELECT suffix. It starts with
4077        #
4078        # FROM name1, name2, ... nameN
4079        #
4080        my $suffix = "FROM " . join(', ', @fromList);
4081        # Now for the WHERE. First, we need a place for the filter string.
4082        my $filterString = "";
4083        # We will also keep a list of conditions to add to the WHERE clause in order to link
4084        # entities and relationships as well as primary relations to secondary ones.
4085        my @joinWhere = ();
4086        # Check for a filter clause.
4087        if ($filterClause) {
4088            # Here we have one, so we convert its field names and add it to the query. First,
4089            # We create a copy of the filter string we can work with.
4090            $filterString = $filterClause;
4091            # Next, we sort the object names by length. This helps protect us from finding
4092            # object names inside other object names when we're doing our search and replace.
4093            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
4094            # The final preparatory step is to create a hash table of relation names. The
4095            # table begins with the relation names already in the SELECT command. We may
4096            # need to add relations later if there is filtering on a field in a secondary
4097            # relation. The secondary relations are the ones that contain multiply-
4098            # occurring or optional fields.
4099            my %fromNames = map { $_ => 1 } @sortedNames;
4100            # We are ready to begin. We loop through the object names, replacing each
4101            # object name's field references by the corresponding SQL field reference.
4102            # Along the way, if we find a secondary relation, we will need to add it
4103            # to the FROM clause.
4104            for my $mappedName (@sortedNames) {
4105                # Get the length of the object name plus 2. This is the value we add to the
4106                # size of the field name to determine the size of the field reference as a
4107                # whole.
4108                my $nameLength = 2 + length $mappedName;
4109                # Get the real object name for this mapped name.
4110                my $objectName = $mappedNameHash{$mappedName};
4111                Trace("Processing $mappedName for object $objectName.") if T(4);
4112                # Get the object's field list.
4113                my $fieldList = $self->GetFieldTable($objectName);
4114                # Find the field references for this object.
4115                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
4116                    # At this point, $1 contains the field name, and the current position
4117                    # is set immediately after the final parenthesis. We pull out the name of
4118                    # the field and the position and length of the field reference as a whole.
4119                    my $fieldName = $1;
4120                    my $len = $nameLength + length $fieldName;
4121                    my $pos = pos($filterString) - $len;
4122                    # Insure the field exists.
4123                    if (!exists $fieldList->{$fieldName}) {
4124                        Confess("Field $fieldName not found for object $objectName.");
4125                    } else {
4126                        Trace("Processing $fieldName at position $pos.") if T(4);
4127                        # Get the field's relation.
4128                        my $relationName = $fieldList->{$fieldName}->{relation};
4129                        # Now we have a secondary relation. We need to insure it matches the
4130                        # mapped name of the primary relation. First we peel off the suffix
4131                        # from the mapped name.
4132                        my $mappingSuffix = substr $mappedName, length($objectName);
4133                        # Put the mapping suffix onto the relation name to get the
4134                        # mapped relation name.
4135                        my $mappedRelationName = "$relationName$mappingSuffix";
4136                        # Insure the relation is in the FROM clause.
4137                        if (!exists $fromNames{$mappedRelationName}) {
4138                            # Add the relation to the FROM clause.
4139                            if ($mappedRelationName eq $relationName) {
4140                                # The name is un-mapped, so we add it without
4141                                # any frills.
4142                                $suffix .= ", $relationName";
4143                                push @joinWhere, "$objectName.id = $relationName.id";
4144                            } else {
4145                                # Here we have a mapping situation.
4146                                $suffix .= ", $relationName $mappedRelationName";
4147                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
4148                            }
4149                            # Denote we have this relation available for future fields.
4150                            $fromNames{$mappedRelationName} = 1;
4151                        }
4152                        # Form an SQL field reference from the relation name and the field name.
4153                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
4154                        # Put it into the filter string in place of the old value.
4155                        substr($filterString, $pos, $len) = $sqlReference;
4156                        # Reposition the search.
4157                        pos $filterString = $pos + length $sqlReference;
4158                    }
4159                }
4160            }
4161        }
4162        # The next step is to join the objects together. We only need to do this if there
4163        # is more than one object in the object list. We start with the first object and
4164        # run through the objects after it. Note also that we make a safety copy of the
4165        # list before running through it, because we shift off the first object before
4166        # processing the rest.
4167        my @mappedObjectList = @mappedNameList;
4168        my $lastMappedObject = shift @mappedObjectList;
4169        # Get the join table.
4170        my $joinTable = $self->{_metaData}->{Joins};
4171        # Loop through the object list.
4172        for my $thisMappedObject (@mappedObjectList) {
4173            # Look for a join using the real object names.
4174            my $lastObject = $mappedNameHash{$lastMappedObject};
4175            my $thisObject = $mappedNameHash{$thisMappedObject};
4176            my $joinKey = "$lastObject/$thisObject";
4177            if (!exists $joinTable->{$joinKey}) {
4178                # Here there's no join, so we throw an error.
4179                Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
4180              } else {              } else {
4181                  # Here we have a secondary relation field. Create a null list              # Get the join clause.
4182                  # and push the desired number of field values onto it.              my $unMappedJoin = $joinTable->{$joinKey};
4183                  my @fieldValues = ();              # Fix the names.
4184                  my $count = IntGen(0,$data->{testCount});              $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
4185                  for (my $i = 0; $i < $count; $i++) {              $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
4186                      my $newValue = eval($codeString);              push @joinWhere, $unMappedJoin;
4187                      push @fieldValues, $newValue;              # Save this object as the last object for the next iteration.
4188                $lastMappedObject = $thisMappedObject;
4189            }
4190        }
4191        # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
4192        # here is we want the filter clause to be empty if there's no WHERE filter.
4193        # We'll put the ORDER BY / LIMIT clauses in the following variable.
4194        my $orderClause = "";
4195        # This is only necessary if we have a filter string in which the ORDER BY
4196        # and LIMIT clauses can live.
4197        if ($filterString) {
4198            # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
4199            # operator so that we find the first occurrence of either verb.
4200            if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
4201                # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
4202                my $pos = pos $filterString;
4203                $orderClause = $2 . substr($filterString, $pos);
4204                $filterString = $1;
4205            }
4206                  }                  }
4207                  # Store the value list in the main hash.      # All the things that are supposed to be in the WHERE clause of the
4208                  $this->{$name} = \@fieldValues;      # SELECT command need to be put into @joinWhere so we can string them
4209        # together. We begin with the match clause. This is important,
4210        # because the match clause's parameter mark must precede any parameter
4211        # marks in the filter string.
4212        if ($matchClause) {
4213            push @joinWhere, $matchClause;
4214              }              }
4215        # Add the filter string. We put it in parentheses to avoid operator
4216        # precedence problems with the match clause or the joins.
4217        if ($filterString) {
4218            Trace("Filter string is \"$filterString\".") if T(4);
4219            push @joinWhere, "($filterString)";
4220        }
4221        # String it all together into a big filter clause.
4222        if (@joinWhere) {
4223            $suffix .= " WHERE " . join(' AND ', @joinWhere);
4224          }          }
4225        # Add the sort or limit clause (if any).
4226        if ($orderClause) {
4227            $suffix .= " $orderClause";
4228        }
4229        # Return the suffix, the mapped name list, and the mapped name hash.
4230        return ($suffix, \@mappedNameList, \%mappedNameHash);
4231    }
4232    
4233    =head3 _GetStatementHandle
4234    
4235    This method will prepare and execute an SQL query, returning the statement handle.
4236    The main reason for doing this here is so that everybody who does SQL queries gets
4237    the benefit of tracing.
4238    
4239    This is an instance method.
4240    
4241    =over 4
4242    
4243    =item command
4244    
4245    Command to prepare and execute.
4246    
4247    =item params
4248    
4249    Reference to a list of the values to be substituted in for the parameter marks.
4250    
4251    =item RETURN
4252    
4253    Returns a prepared and executed statement handle from which the caller can extract
4254    results.
4255    
4256    =back
4257    
4258    =cut
4259    
4260    sub _GetStatementHandle {
4261        # Get the parameters.
4262        my ($self, $command, $params) = @_;
4263        # Trace the query.
4264        Trace("SQL query: $command") if T(SQL => 3);
4265        Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
4266        # Get the database handle.
4267        my $dbh = $self->{_dbh};
4268        # Prepare the command.
4269        my $sth = $dbh->prepare_command($command);
4270        # Execute it with the parameters bound in.
4271        $sth->execute(@{$params}) || Confess("SELECT error:  " . $sth->errstr());
4272        # Return the statement handle.
4273        return $sth;
4274      }      }
4275    
4276    =head3 _GetLoadStats
4277    
4278    Return a blank statistics object for use by the load methods.
4279    
4280    This is a static method.
4281    
4282    =cut
4283    
4284    sub _GetLoadStats{
4285        return Stats->new();
4286  }  }
4287    
4288  =head3 DumpRelation  =head3 _DumpRelation
4289    
4290  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.
4291    
4292  This is an instance method.  This is an instance method.
4293    
# Line 1994  Line 4335 
4335      close DTXOUT;      close DTXOUT;
4336  }  }
4337    
4338  =head3 GetStructure  =head3 _GetStructure
4339    
4340  Get the data structure for a specified entity or relationship.  Get the data structure for a specified entity or relationship.
4341    
# Line 2033  Line 4374 
4374      return $retVal;      return $retVal;
4375  }  }
4376    
4377  =head3 GetRelationTable  
4378    
4379    =head3 _GetRelationTable
4380    
4381  Get the list of relations for a specified entity or relationship.  Get the list of relations for a specified entity or relationship.
4382    
# Line 2062  Line 4405 
4405      return $objectData->{Relations};      return $objectData->{Relations};
4406  }  }
4407    
4408  =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  
4409    
4410  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
4411  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 2118  Line 4432 
4432          for my $object (values %{$metadata->{$section}}) {          for my $object (values %{$metadata->{$section}}) {
4433              # Loop through the object's fields.              # Loop through the object's fields.
4434              for my $fieldName (keys %{$object->{Fields}}) {              for my $fieldName (keys %{$object->{Fields}}) {
4435                  # Now we make some initial validations.                  # If this field name is invalid, set the return value to zero
4436                  if ($fieldName =~ /--/) {                  # so we know we encountered an error.
4437                      # Here we have a doubled minus sign.                  if (! ValidateFieldName($fieldName)) {
                     print STDERR "Field name $fieldName has a doubled hyphen.\n";  
4438                      $retVal = 0;                      $retVal = 0;
                 } elsif ($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";  
                         $retVal = 0;  
                     }  
4439                  }                  }
4440              }              }
4441          }          }
# Line 2146  Line 4446 
4446      }      }
4447  }  }
4448    
4449  =head3 LoadRelation  =head3 _LoadRelation
4450    
4451  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
4452  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 2206  Line 4506 
4506      return $retVal;      return $retVal;
4507  }  }
4508    
4509  =head3 LoadMetaData  
4510    =head3 _LoadMetaData
4511    
4512    C<< my $metadata = ERDB::_LoadMetaData($filename); >>
4513    
4514  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.
4515  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 2231  Line 4534 
4534  sub _LoadMetaData {  sub _LoadMetaData {
4535      # Get the parameters.      # Get the parameters.
4536      my ($filename) = @_;      my ($filename) = @_;
4537      Trace("Reading Sprout DBD from $filename.") if T(2);      Trace("Reading DBD from $filename.") if T(2);
4538      # 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
4539      # get the exact structure we want.      # get the exact structure we want.
4540      my $metadata = XML::Simple::XMLin($filename,      my $metadata = ReadMetaXML($filename);
                                       GroupTags => { Relationships => 'Relationship',  
                                                      Entities => 'Entity',  
                                                      Fields => 'Field',  
                                                      Indexes => 'Index',  
                                                      IndexFields => 'IndexField'},  
                                       KeyAttr => { Relationship => 'name', &