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revision 1.26, Tue Oct 18 06:47:46 2005 UTC revision 1.96, Tue Feb 5 04:52:24 2008 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        use WikiTools;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 58  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
 To facilitate testing, the ERDB module supports automatic generation of test data. This process  
 is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
 fully implemented.  
   
76  =head2 XML Database Description  =head2 XML Database Description
77    
78  =head3 Data Types  =head3 Data Types
# Line 90  Line 92 
92    
93  32-bit signed integer  32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99  =item date  =item date
100    
101  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 109  Line 115 
115  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
116  0 and 1.  0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122  =item key-string  =item key-string
123    
124  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 135 
135    
136  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142  =back  =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151  =head3 Global Tags  =head3 Global Tags
152    
153  The entire database definition must be inside a B<Database> tag. The display name of  The entire database definition must be inside a B<Database> tag. The display name of
# Line 170  Line 191 
191    
192  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
194  with the respect to field names, so a best practice is to use lower-case letters only.  with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198  =item type  =item type
199    
# Line 189  Line 212 
212  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
213  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227  =back  =back
228    
229  =head3 Indexes  =head3 Indexes
230    
231  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
232  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
233  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
234  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
235  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236  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
237  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
238    indexes. A relationship's index must specify only fields in
239  the relationship.  the relationship.
240    
241  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.
242  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
243  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
244    
245  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>
246  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 258 
258    
259  =back  =back
260    
261  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
262    have a B<Unique> attribute. If specified, the index will be generated as a unique
263    index.
264    
265  =head3 Object and Field Names  =head3 Object and Field Names
266    
# Line 266  Line 304 
304    
305  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
306  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
307  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
308  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
309    
310  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
311    
# Line 300  Line 338 
338    
339  # 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.
340  # "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
341  # 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
342  # 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,
343  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
344  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
345                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
346                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
347                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
348                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
349                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
350                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   2, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
351                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
352                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
353                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
354                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
355                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
356                                   indexMod =>   0, notes => "signed, 64-bit integer"},
357                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
358                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
359                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
360                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
361                     'hash-string' =>
362                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
363                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
364                     'id-string' =>
365                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
367                   'key-string' =>                   'key-string' =>
368                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
370                   'name-string' =>                   'name-string' =>
371                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
373                   'medium-string' =>                   'medium-string' =>
374                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
375                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
376                     'long-string' =>
377                                 { sqlType => 'VARCHAR(500)',       maxLen => 500,          avglen => 255, sort => "",
378                                   indexMod =>   0, notes => "character string, 0 to 500 characters"},
379                  );                  );
380    
381  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 324  Line 384 
384                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
385                   );                   );
386    
387  # Table for interpreting string patterns.  # Options for XML input and output.
388    
389    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
390                                      Entities => 'Entity',
391                                      Fields => 'Field',
392                                      Indexes => 'Index',
393                                      IndexFields => 'IndexField'
394                                    },
395                      KeyAttr =>    { Relationship => 'name',
396                                      Entity => 'name',
397                                      Field => 'name'
398                                    },
399                      SuppressEmpty => 1,
400                     );
401    
402  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
403                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
404                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
405                       'V' => "aeiou",                    NormalizeSpace => 2,
                      'K' => "bcdfghjklmnoprstvwxyz"  
406                     );                     );
407    my %XmlOutOpts = (
408                      RootName => 'Database',
409                      XMLDecl => 1,
410                     );
411    
412    
413  =head2 Public Methods  =head2 Public Methods
414    
415  =head3 new  =head3 new
416    
417  C<< my $database = ERDB->new($dbh, $metaFileName); >>      my $database = ERDB->new($dbh, $metaFileName);
418    
419  Create a new ERDB object.  Create a new ERDB object.
420    
# Line 357  Line 434 
434    
435  sub new {  sub new {
436      # Get the parameters.      # Get the parameters.
437      my ($class, $dbh, $metaFileName, $options) = @_;      my ($class, $dbh, $metaFileName, %options) = @_;
438      # Load the meta-data.      # Load the meta-data.
439      my $metaData = _LoadMetaData($metaFileName);      my $metaData = _LoadMetaData($metaFileName);
440      # Create the object.      # Create the object.
# Line 371  Line 448 
448    
449  =head3 ShowMetaData  =head3 ShowMetaData
450    
451  C<< $erdb->ShowMetaData($fileName); >>      $erdb->ShowMetaData($fileName);
452    
453  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
454  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 402  Line 479 
479      # Write the HTML heading stuff.      # Write the HTML heading stuff.
480      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
481      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
482        # Write the documentation.
483        print HTMLOUT $self->DisplayMetaData();
484        # Close the document.
485        print HTMLOUT "</body>\n</html>\n";
486        # Close the file.
487        close HTMLOUT;
488    }
489    
490    =head3 DisplayMetaData
491    
492        my $html = $erdb->DisplayMetaData();
493    
494    Return an HTML description of the database. This description can be used to help users create
495    the data to be loaded into the relations and form queries. The output is raw includable HTML
496    without any HEAD or BODY tags.
497    
498    =over 4
499    
500    =item filename
501    
502    The name of the output file.
503    
504    =back
505    
506    =cut
507    
508    sub DisplayMetaData {
509        # Get the parameters.
510        my ($self) = @_;
511        # Get the metadata and the title string.
512        my $metadata = $self->{_metaData};
513        # Get the title string.
514        my $title = $metadata->{Title};
515        # Get the entity and relationship lists.
516        my $entityList = $metadata->{Entities};
517        my $relationshipList = $metadata->{Relationships};
518        # Declare the return variable.
519        my $retVal = "";
520        # Open the output file.
521        Trace("Building MetaData table of contents.") if T(4);
522      # 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
523      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
524      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";
525      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
526      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
527          # Display this item.          # Display this item.
528          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
529      }      }
530      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
531      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";
532      # Loop through the Relationships.      # Loop through the Relationships.
533      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
534          # Display this item.          # Display this item.
535          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
536          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
537      }      }
538      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
539      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";
540      # Close off the table of contents itself.      # Close off the table of contents itself.
541      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
542      # 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.
543      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
544      # Loop through the entities.      # Loop through the entities.
545      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
546          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
547          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
548          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
549          # Get the entity data.          # Get the entity data.
550          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
551          # If there's descriptive text, display it.          # If there's descriptive text, display it.
552          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
553              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
554          }          }
555          # 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.
556          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
557            if ($relCount > 0) {
558                # First, we set up the relationship subsection.
559                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
560          # Loop through the relationships.          # Loop through the relationships.
561          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
562              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 566 
566                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
567                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
568                  # Display the relationship data.                  # Display the relationship data.
569                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
570              }              }
571          }          }
572          # Close off the relationship list.          # Close off the relationship list.
573          print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
574            }
575          # Get the entity's relations.          # Get the entity's relations.
576          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
577          # Create a header for the relation subsection.          # Create a header for the relation subsection.
578          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
579          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
580          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
581              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
582              print HTMLOUT $htmlString;              $retVal .= $htmlString;
583          }          }
584      }      }
585      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
586      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
587      # Loop through the relationships.      # Loop through the relationships.
588      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
589          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 591 
591          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
592          # Create the relationship header.          # Create the relationship header.
593          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
594          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
595          # Get the entity names.          # Get the entity names.
596          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
597          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 601 
601          # since both sentences will say the same thing.          # since both sentences will say the same thing.
602          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
603          if ($arity eq "11") {          if ($arity eq "11") {
604              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
605          } else {          } else {
606              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
607              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
608                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
609              }              }
610          }          }
611          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
612          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
613          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
614              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
615          }          }
616          # Generate the relationship's relation table.          # Generate the relationship's relation table.
617          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
618          print HTMLOUT $htmlString;          $retVal .= $htmlString;
619      }      }
620      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
621      # Denote we're starting the join table.      # Denote we're starting the join table.
622      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
623      # Create a table header.      # Create a table header.
624      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
625      # Loop through the joins.      # Loop through the joins.
626      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
627      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 508  Line 629 
629          # Separate out the source, the target, and the join clause.          # Separate out the source, the target, and the join clause.
630          $joinKey =~ m!^([^/]+)/(.+)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
631          my ($sourceRelation, $targetRelation) = ($1, $2);          my ($sourceRelation, $targetRelation) = ($1, $2);
632          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(4);          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
633          my $source = $self->ComputeObjectSentence($sourceRelation);          my $source = $self->ComputeObjectSentence($sourceRelation);
634          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
635          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
636          # Display them in a table row.          # Display them in a table row.
637          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";
638      }      }
639      # Close the table.      # Close the table.
640      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
641      # Close the document.      Trace("Built MetaData HTML.") if T(3);
642      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
643      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
644  }  }
645    
646  =head3 DumpMetaData  =head3 DumpMetaData
647    
648  C<< $erdb->DumpMetaData(); >>      $erdb->DumpMetaData();
649    
650  Return a dump of the metadata structure.  Return a dump of the metadata structure.
651    
# Line 539  Line 658 
658      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
659  }  }
660    
661    =head3 GenerateWikiData
662    
663        my @wikiLines = $erdb->GenerateWikiData();
664    
665    Build a description of the database for the wiki. The database will be
666    organized into a single page, with sections for each entity and relationship.
667    The return value is a list of text lines.
668    
669    =cut
670    
671    sub GenerateWikiData {
672        # Get the parameters.
673        my ($self) = @_;
674        # We'll build the wiki text in here.
675        my @retVal = ();
676        # Get the metadata object.
677        my $metadata = $self->{_metaData};
678        # Get the title string. This will become the page name.
679        my $title = $metadata->{Title}->{content};
680        # Get the entity and relationship lists.
681        my $entityList = $metadata->{Entities};
682        my $relationshipList = $metadata->{Relationships};
683        # Start with the introductory text.
684        push @retVal, WikiTools::Heading(2, "Introduction");
685        if (my $notes = $metadata->{Notes}) {
686            push @retVal, WikiNote($notes->{content});
687        }
688        # Start the entity section.
689        push @retVal, WikiTools::Heading(2, "Entities");
690        # Loop through the entities. Note that unlike the situation with HTML, we
691        # don't need to generate the table of contents manually, just the data
692        # itself.
693        for my $key (sort keys %$entityList) {
694            # Create a header for this entity.
695            push @retVal, "", WikiTools::Heading(3, $key);
696            # Get the entity data.
697            my $entityData = $entityList->{$key};
698            # Plant the notes here, if there are any.
699            if (my $notes = $entityData->{Notes}) {
700                push @retVal, "", WikiNote($notes->{content});
701            }
702            # Get the entity's relations.
703            my $relationList = $entityData->{Relations};
704            # Loop through the relations, displaying them.
705            for my $relation (sort keys %{$relationList}) {
706                my $wikiString = _WikiRelationTable($relation, $relationList->{$relation});
707                push @retVal, $wikiString;
708            }
709            # Now we list the entity's relationships (if any). First, we build a list
710            # of the relationships relevant to this entity.
711            my @rels = ();
712            for my $rel (sort keys %$relationshipList) {
713                my $relStructure = $relationshipList->{$rel};
714                if ($relStructure->{from} eq $key || $relStructure->{to} eq $key) {
715                    # Get the relationship sentence.
716                    my $relSentence = _ComputeRelationshipSentence($rel, $relStructure);
717                    # Linkify it.
718                    my $linkedRel = WikiTools::LinkMarkup("#$rel", $rel);
719                    $relSentence =~ s/$rel/$linkedRel/;
720                    push @rels, $relSentence;
721                }
722            }
723            # Add the relationships as a Wiki list.
724            push @retVal, WikiTools::List(@rels);
725        }
726        # Now the entities are documented. Next we do the relationships.
727        push @retVal, WikiTools::Heading(2, "Relationships");
728        for my $key (sort keys %$relationshipList) {
729            my $relationshipData = $relationshipList->{$key};
730            # Create the relationship heading.
731            push @retVal, WikiTools::Heading(3, $key);
732            # Describe the relationship arity. Note there's a bit of trickiness involving recursive
733            # many-to-many relationships. In a normal many-to-many we use two sentences to describe
734            # the arity (one for each direction). This is a bad idea for a recursive relationship,
735            # since both sentences will say the same thing.
736            my $arity = $relationshipData->{arity};
737            my $fromEntity = $relationshipData->{from};
738            my $toEntity = $relationshipData->{to};
739            my @listElements = ();
740            my $boldCode = WikiTools::BoldCode();
741            if ($arity eq "11") {
742                push @listElements, "Each $boldCode$fromEntity$boldCode relates to at most one $boldCode$toEntity$boldCode.";
743            } else {
744                push @listElements, "Each $boldCode$fromEntity$boldCode relates to multiple $boldCode${toEntity}s$boldCode.\n";
745                if ($arity eq "MM" && $fromEntity ne $toEntity) {
746                    push @listElements, "Each $boldCode$toEntity$boldCode relates to multiple $boldCode${fromEntity}s$boldCode.\n";
747                }
748            }
749            push @retVal, WikiTools::List(@listElements);
750            # Plant the notes here, if there are any.
751            if (my $notes = $relationshipData->{Notes}) {
752                push @retVal, "", WikiNote($notes->{content});
753            }
754            # Finally, the relationship table.
755            my $wikiString = _WikiRelationTable($key, $relationshipData->{Relations}->{$key});
756            push @retVal, $wikiString;
757        }
758        # All done. Return the lines.
759        return @retVal;
760    }
761    
762    
763    =head3 CreatePPO
764    
765        ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile);
766    
767    Create a PPO XML file from an ERDB data definition XML file. At the
768    current time, the PPO XML file can be used to create a database with
769    similar functionality. Eventually, the PPO will be able to use the
770    created XML to access the live ERDB database.
771    
772    =over 4
773    
774    =item erdbXMLFile
775    
776    Name of the XML data definition file for the ERDB database. This
777    file must exist.
778    
779    =item ppoXMLFile
780    
781    Output file for the PPO XML definition. If this file exists, it
782    will be overwritten.
783    
784    =back
785    
786    =cut
787    
788    sub CreatePPO {
789        # Get the parameters.
790        my ($erdbXMLFile, $ppoXMLFile) = @_;
791        # First, we want to slurp in the ERDB XML file in its raw form.
792        my $xml = ReadMetaXML($erdbXMLFile);
793        # Create a variable to hold all of the objects in the PPO project.
794        my @objects = ();
795        # Get the relationship hash.
796        my $relationships = $xml->{Relationships};
797        # Loop through the entities.
798        my $entities = $xml->{Entities};
799        for my $entityName (keys %{$entities}) {
800            # Get the entity's data structures.
801            my $entityObject = $entities->{$entityName};
802            # We put the object's fields in here, according to their type.
803            my (@object_refs, @scalars, @indexes, @arrays);
804            # Create the ID field for the entity. We get the key type from the
805            # entity object and compute the corresponding SQL type.
806            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
807            push @scalars, { label => 'id', type => $type };
808            # Loop through the entity fields.
809            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
810                # Get the field object.
811                my $fieldObject = $entityObject->{Fields}->{$fieldName};
812                # Convert it to a scalar tag.
813                my $scalar = _CreatePPOField($fieldName, $fieldObject);
814                # If we have a relation, this field is stored in an array.
815                # otherwise, it is a scalar. The array tag has scalars
816                # stored as an XML array. In ERDB, there is only ever one,
817                # but PPO can have more.
818                my $relation = $fieldObject->{relation};
819                if ($relation) {
820                    push @arrays, { scalar => [$scalar] };
821                } else {
822                    push @scalars, $scalar;
823                }
824            }
825            # Loop through the relationships. If this entity is the to-entity
826            # on a relationship of 1M arity, then it is implemented as a PPO
827            # object reference.
828            for my $relationshipName (keys %{$relationships}) {
829                # Get the relationship data.
830                my $relationshipData = $relationships->{$relationshipName};
831                # If we have a from for this entity and an arity of 1M, we
832                # have an object reference.
833                if ($relationshipData->{to} eq $entityName &&
834                    $relationshipData->{arity} eq '1M') {
835                    # Build the object reference tag.
836                    push @object_refs, { label => $relationshipName,
837                                         type => $relationshipData->{from} };
838                }
839            }
840            # Create the indexes.
841            my $indexList = $entityObject->{Indexes};
842            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
843            # Build the object XML tree.
844            my $object = { label => $entityName,
845                           object_ref => \@object_refs,
846                           scalar => \@scalars,
847                           index => \@indexes,
848                           array => \@arrays
849                          };
850            # Push the object onto the objects list.
851            push @objects, $object;
852        }
853        # Loop through the relationships, searching for MMs. The 1Ms were
854        # already handled by the entity search above.
855        for my $relationshipName (keys %{$relationships}) {
856            # Get this relationship's object.
857            my $relationshipObject = $relationships->{$relationshipName};
858            # Only proceed if it's many-to-many.
859            if ($relationshipObject->{arity} eq 'MM') {
860                # Create the tag lists for the relationship object.
861                my (@object_refs, @scalars, @indexes);
862                # The relationship will be created as an object with object
863                # references for its links to the participating entities.
864                my %links = ( from_link => $relationshipObject->{from},
865                              to_link => $relationshipObject->{to} );
866                for my $link (keys %links) {
867                    # Create an object_ref tag for this piece of the
868                    # relationship (from or to).
869                    my $object_ref = { label => $link,
870                                       type => $links{$link} };
871                    push @object_refs, $object_ref;
872                }
873                # Loop through the intersection data fields, creating scalar tags.
874                # There are no fancy array tags in a relationship.
875                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
876                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
877                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
878                }
879                # Finally, the indexes: currently we cannot support the to-index and
880                # from-index in PPO, so we just process the alternate indexes.
881                my $indexList = $relationshipObject->{Indexes};
882                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
883                # Wrap up all the stuff about this relationship.
884                my $object = { label => $relationshipName,
885                               scalar => \@scalars,
886                               object_ref => \@object_refs,
887                               index => \@indexes
888                             };
889                # Push it into the object list.
890                push @objects, $object;
891            }
892        }
893        # Compute a title.
894        my $title;
895        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
896            # Here we have a standard file name we can use for a title.
897            $title = $2;
898        } else {
899            # Here the file name is non-standard, so we carve up the
900            # database title.
901            $title = $xml->{Title}->{content};
902            $title =~ s/\s\.,//g;
903        }
904        # Wrap up the XML as a project.
905        my $ppoXML = { project => { label => $title,
906                                    object => \@objects }};
907        # Write out the results.
908        my $ppoString = XML::Simple::XMLout($ppoXML,
909                                            AttrIndent => 1,
910                                            KeepRoot => 1);
911        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
912    }
913    
914    =head3 FindIndexForEntity
915    
916        my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName);
917    
918    This method locates the entry in an entity's index list that begins with the
919    specified attribute name. If the entity has no index list, one will be
920    created. This method works on raw XML, not a live ERDB object.
921    
922    =over 4
923    
924    =item xml
925    
926    The raw XML structure defining the database.
927    
928    =item entityName
929    
930    The name of the relevant entity.
931    
932    =item attributeName
933    
934    The name of the attribute relevant to the search.
935    
936    =item RETURN
937    
938    The numerical index in the index list of the index entry for the specified entity and
939    attribute, or C<undef> if no such index exists.
940    
941    =back
942    
943    =cut
944    
945    sub FindIndexForEntity {
946        # Get the parameters.
947        my ($xml, $entityName, $attributeName) = @_;
948        # Declare the return variable.
949        my $retVal;
950        # Get the named entity.
951        my $entityData = $xml->{Entities}->{$entityName};
952        if (! $entityData) {
953            Confess("Entity $entityName not found in DBD structure.");
954        } else {
955            # Insure it has an index list.
956            if (! exists $entityData->{Indexes}) {
957                $entityData->{Indexes} = [];
958            } else {
959                # Search for the desired index.
960                my $indexList = $entityData->{Indexes};
961                my $n = scalar @{$indexList};
962                Trace("Searching $n indexes in index list for $entityName.") if T(2);
963                # We use an indexed FOR here because we're returning an
964                # index number instead of an object. We do THAT so we can
965                # delete the index from the list if needed.
966                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
967                    my $index = $indexList->[$i];
968                    my $fields = $index->{IndexFields};
969                    # Technically this IF should be safe (that is, we are guaranteed
970                    # the existence of a "$fields->[0]"), because when we load the XML
971                    # we have SuppressEmpty specified.
972                    if ($fields->[0]->{name} eq $attributeName) {
973                        $retVal = $i;
974                    }
975                }
976            }
977        }
978        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
979        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
980        # Return the result.
981        return $retVal;
982    }
983    
984  =head3 CreateTables  =head3 CreateTables
985    
986  C<< $erdb->CreateTables(); >>      $erdb->CreateTables();
987    
988  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
989  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 558  Line 1000 
1000      # Loop through the relations.      # Loop through the relations.
1001      for my $relationName (@relNames) {      for my $relationName (@relNames) {
1002          # Create a table for this relation.          # Create a table for this relation.
1003          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
1004          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
1005      }      }
1006  }  }
1007    
1008  =head3 CreateTable  =head3 CreateTable
1009    
1010  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>      $erdb->CreateTable($tableName, $indexFlag, $estimatedRows);
1011    
1012  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
1013    
# Line 621  Line 1063 
1063      my $estimation = undef;      my $estimation = undef;
1064      if ($estimatedRows) {      if ($estimatedRows) {
1065          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];          $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
1066            Trace("$estimation->[1] rows of $estimation->[0] bytes each.") if T(3);
1067      }      }
1068      # Create the table.      # Create the table.
1069      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
1070      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
1071      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
1072      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
1073        # index will not be built until the table has been loaded.
1074      if ($indexFlag) {      if ($indexFlag) {
1075          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
1076      }      }
1077  }  }
1078    
1079    =head3 VerifyFields
1080    
1081        my $count = $erdb->VerifyFields($relName, \@fieldList);
1082    
1083    Run through the list of proposed field values, insuring that all the character fields are
1084    below the maximum length. If any fields are too long, they will be truncated in place.
1085    
1086    =over 4
1087    
1088    =item relName
1089    
1090    Name of the relation for which the specified fields are destined.
1091    
1092    =item fieldList
1093    
1094    Reference to a list, in order, of the fields to be put into the relation.
1095    
1096    =item RETURN
1097    
1098    Returns the number of fields truncated.
1099    
1100    =back
1101    
1102    =cut
1103    
1104    sub VerifyFields {
1105        # Get the parameters.
1106        my ($self, $relName, $fieldList) = @_;
1107        # Initialize the return value.
1108        my $retVal = 0;
1109        # Get the relation definition.
1110        my $relData = $self->_FindRelation($relName);
1111        # Get the list of field descriptors.
1112        my $fieldTypes = $relData->{Fields};
1113        my $fieldCount = scalar @{$fieldTypes};
1114        # Loop through the two lists.
1115        for (my $i = 0; $i < $fieldCount; $i++) {
1116            # Get the type of the current field.
1117            my $fieldType = $fieldTypes->[$i]->{type};
1118            # If it's a character field, verify the length.
1119            if ($fieldType =~ /string/) {
1120                my $maxLen = $TypeTable{$fieldType}->{maxLen};
1121                my $oldString = $fieldList->[$i];
1122                if (length($oldString) > $maxLen) {
1123                    # Here it's too big, so we truncate it.
1124                    Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1125                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
1126                    $retVal++;
1127                }
1128            }
1129        }
1130        # Return the truncation count.
1131        return $retVal;
1132    }
1133    
1134    =head3 DigestFields
1135    
1136        $erdb->DigestFields($relName, $fieldList);
1137    
1138    Digest the strings in the field list that correspond to data type C<hash-string> in the
1139    specified relation.
1140    
1141    =over 4
1142    
1143    =item relName
1144    
1145    Name of the relation to which the fields belong.
1146    
1147    =item fieldList
1148    
1149    List of field contents to be loaded into the relation.
1150    
1151    =back
1152    
1153    =cut
1154    #: Return Type ;
1155    sub DigestFields {
1156        # Get the parameters.
1157        my ($self, $relName, $fieldList) = @_;
1158        # Get the relation definition.
1159        my $relData = $self->_FindRelation($relName);
1160        # Get the list of field descriptors.
1161        my $fieldTypes = $relData->{Fields};
1162        my $fieldCount = scalar @{$fieldTypes};
1163        # Loop through the two lists.
1164        for (my $i = 0; $i < $fieldCount; $i++) {
1165            # Get the type of the current field.
1166            my $fieldType = $fieldTypes->[$i]->{type};
1167            # If it's a hash string, digest it in place.
1168            if ($fieldType eq 'hash-string') {
1169                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1170            }
1171        }
1172    }
1173    
1174    =head3 DigestKey
1175    
1176        my $digested = $erdb->DigestKey($keyValue);
1177    
1178    Return the digested value of a symbolic key. The digested value can then be plugged into a
1179    key-based search into a table with key-type hash-string.
1180    
1181    Currently the digesting process is independent of the database structure, but that may not
1182    always be the case, so this is an instance method instead of a static method.
1183    
1184    =over 4
1185    
1186    =item keyValue
1187    
1188    Key value to digest.
1189    
1190    =item RETURN
1191    
1192    Digested value of the key.
1193    
1194    =back
1195    
1196    =cut
1197    
1198    sub DigestKey {
1199        # Get the parameters.
1200        my ($self, $keyValue) = @_;
1201        # Compute the digest.
1202        my $retVal = md5_base64($keyValue);
1203        # Return the result.
1204        return $retVal;
1205    }
1206    
1207  =head3 CreateIndex  =head3 CreateIndex
1208    
1209  C<< $erdb->CreateIndex($relationName); >>      $erdb->CreateIndex($relationName);
1210    
1211  Create the indexes for a relation. If a table is being loaded from a large source file (as  Create the indexes for a relation. If a table is being loaded from a large source file (as
1212  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.  is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
# Line 655  Line 1227 
1227      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
1228          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
1229          # Get the index's field list.          # Get the index's field list.
1230          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
1231            # Get a hash of the relation's field types.
1232            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1233            # We need to check for text fields so we can append a length limitation for them. To do
1234            # that, we need the relation's field list.
1235            my $relFields = $relationData->{Fields};
1236            for (my $i = 0; $i <= $#rawFields; $i++) {
1237                # Get the field type.
1238                my $field = $rawFields[$i];
1239                my $type = $types{$field};
1240                # Ask if it requires using prefix notation for the index.
1241                my $mod = $TypeTable{$type}->{indexMod};
1242                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1243                if ($mod) {
1244                    # Append the prefix length to the field name,
1245                    $rawFields[$i] .= "($mod)";
1246                }
1247            }
1248            my @fieldList = _FixNames(@rawFields);
1249          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
1250          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
1251          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1252          # Create the index.          # Create the index.
1253          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1254                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
1255          if ($rv) {          if ($rv) {
1256              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1257          } else {          } else {
# Line 670  Line 1260 
1260      }      }
1261  }  }
1262    
1263  =head3 LoadTables  =head3 GetSecondaryFields
   
 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  
1264    
1265  This method will load the database tables from a directory. The tables must already have been created      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.  
1266    
1267  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
1268  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
1269  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
1270    or to have multiple values.
1271    
1272  =over 4  =over 4
1273    
1274  =item directoryName  =item entityName
   
 Name of the directory containing the relation files to be loaded.  
   
 =item rebuild  
1275    
1276  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.  
1277    
1278  =item RETURN  =item RETURN
1279    
1280  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.
1281    
1282  =back  =back
1283    
1284  =cut  =cut
1285    
1286  sub LoadTables {  sub GetSecondaryFields {
1287      # Get the parameters.      # Get the parameters.
1288      my ($self, $directoryName, $rebuild) = @_;      my ($self, $entityName) = @_;
1289      # Start the timer.      # Declare the return variable.
1290      my $startTime = gettimeofday;      my %retVal = ();
1291      # Clean any trailing slash from the directory name.      # Look for the entity.
1292      $directoryName =~ s!/\\$!!;      my $table = $self->GetFieldTable($entityName);
1293        # Loop through the fields, pulling out the secondaries.
1294        for my $field (sort keys %{$table}) {
1295            if ($table->{$field}->{relation} ne $entityName) {
1296                # Here we have a secondary field.
1297                $retVal{$field} = $table->{$field}->{type};
1298            }
1299        }
1300        # Return the result.
1301        return %retVal;
1302    }
1303    
1304    =head3 GetFieldRelationName
1305    
1306        my $name = $erdb->GetFieldRelationName($objectName, $fieldName);
1307    
1308    Return the name of the relation containing a specified field.
1309    
1310    =over 4
1311    
1312    =item objectName
1313    
1314    Name of the entity or relationship containing the field.
1315    
1316    =item fieldName
1317    
1318    Name of the relevant field in that entity or relationship.
1319    
1320    =item RETURN
1321    
1322    Returns the name of the database relation containing the field, or C<undef> if
1323    the field does not exist.
1324    
1325    =back
1326    
1327    =cut
1328    
1329    sub GetFieldRelationName {
1330        # Get the parameters.
1331        my ($self, $objectName, $fieldName) = @_;
1332        # Declare the return variable.
1333        my $retVal;
1334        # Get the object field table.
1335        my $table = $self->GetFieldTable($objectName);
1336        # Only proceed if the field exists.
1337        if (exists $table->{$fieldName}) {
1338            # Determine the name of the relation that contains this field.
1339            $retVal = $table->{$fieldName}->{relation};
1340        }
1341        # Return the result.
1342        return $retVal;
1343    }
1344    
1345    =head3 DeleteValue
1346    
1347        my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue);
1348    
1349    Delete secondary field values from the database. This method can be used to delete all
1350    values of a specified field for a particular entity instance, or only a single value.
1351    
1352    Secondary fields are stored in two-column relations separate from an entity's primary
1353    table, and as a result a secondary field can legitimately have no value or multiple
1354    values. Therefore, it makes sense to talk about deleting secondary fields where it
1355    would not make sense for primary fields.
1356    
1357    =over 4
1358    
1359    =item entityName
1360    
1361    Name of the entity from which the fields are to be deleted.
1362    
1363    =item id
1364    
1365    ID of the entity instance to be processed. If the instance is not found, this
1366    method will have no effect. If C<undef> is specified, all values for all of
1367    the entity instances will be deleted.
1368    
1369    =item fieldName
1370    
1371    Name of the field whose values are to be deleted.
1372    
1373    =item fieldValue (optional)
1374    
1375    Value to be deleted. If not specified, then all values of the specified field
1376    will be deleted for the entity instance. If specified, then only the values which
1377    match this parameter will be deleted.
1378    
1379    =item RETURN
1380    
1381    Returns the number of rows deleted.
1382    
1383    =back
1384    
1385    =cut
1386    
1387    sub DeleteValue {
1388        # Get the parameters.
1389        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1390        # Declare the return value.
1391        my $retVal = 0;
1392        # We need to set up an SQL command to do the deletion. First, we
1393        # find the name of the field's relation.
1394        my $table = $self->GetFieldTable($entityName);
1395        my $field = $table->{$fieldName};
1396        my $relation = $field->{relation};
1397        # Make sure this is a secondary field.
1398        if ($relation eq $entityName) {
1399            Confess("Cannot delete values of $fieldName for $entityName.");
1400        } else {
1401            # Set up the SQL command to delete all values.
1402            my $sql = "DELETE FROM $relation";
1403            # Build the filter.
1404            my @filters = ();
1405            my @parms = ();
1406            # Check for a filter by ID.
1407            if (defined $id) {
1408                push @filters, "id = ?";
1409                push @parms, $id;
1410            }
1411            # Check for a filter by value.
1412            if (defined $fieldValue) {
1413                push @filters, "$fieldName = ?";
1414                push @parms, $fieldValue;
1415            }
1416            # Append the filters to the command.
1417            if (@filters) {
1418                $sql .= " WHERE " . join(" AND ", @filters);
1419            }
1420            # Execute the command.
1421            my $dbh = $self->{_dbh};
1422            $retVal = $dbh->SQL($sql, 0, @parms);
1423        }
1424        # Return the result.
1425        return $retVal;
1426    }
1427    
1428    =head3 LoadTables
1429    
1430        my $stats = $erdb->LoadTables($directoryName, $rebuild);
1431    
1432    This method will load the database tables from a directory. The tables must already have been created
1433    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1434    all of the relations to be loaded must have a file in the directory with the same name as the relation
1435    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1436    line of the file will be loaded as a row of the target relation table. The field values should be in
1437    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1438    erased before the new data is loaded in.
1439    
1440    A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1441    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1442    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1443    
1444    =over 4
1445    
1446    =item directoryName
1447    
1448    Name of the directory containing the relation files to be loaded.
1449    
1450    =item rebuild
1451    
1452    TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1453    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1454    by all of the DB engines we use.
1455    
1456    =item RETURN
1457    
1458    Returns a statistical object describing the number of records read and a list of the error messages.
1459    
1460    =back
1461    
1462    =cut
1463    
1464    sub LoadTables {
1465        # Get the parameters.
1466        my ($self, $directoryName, $rebuild) = @_;
1467        # Start the timer.
1468        my $startTime = gettimeofday;
1469        # Clean any trailing slash from the directory name.
1470        $directoryName =~ s!/\\$!!;
1471      # Declare the return variable.      # Declare the return variable.
1472      my $retVal = Stats->new();      my $retVal = Stats->new();
1473      # Get the relation names.      # Get the relation names.
# Line 732  Line 1487 
1487    
1488  =head3 GetTableNames  =head3 GetTableNames
1489    
1490  C<< my @names = $erdb->GetTableNames; >>      my @names = $erdb->GetTableNames;
1491    
1492  Return a list of the relations required to implement this database.  Return a list of the relations required to implement this database.
1493    
# Line 749  Line 1504 
1504    
1505  =head3 GetEntityTypes  =head3 GetEntityTypes
1506    
1507  C<< my @names = $erdb->GetEntityTypes; >>      my @names = $erdb->GetEntityTypes;
1508    
1509  Return a list of the entity type names.  Return a list of the entity type names.
1510    
# Line 764  Line 1519 
1519      return sort keys %{$entityList};      return sort keys %{$entityList};
1520  }  }
1521    
1522    =head3 GetDataTypes
1523    
1524        my %types = ERDB::GetDataTypes();
1525    
1526    Return a table of ERDB data types. The table returned is a hash of hashes.
1527    The keys of the big hash are the datatypes. Each smaller hash has several
1528    values used to manage the data. The most interesting is the SQL type (key
1529    C<sqlType>) and the descriptive node (key C<notes>).
1530    
1531    Note that changing the values in the smaller hashes will seriously break
1532    things, so this data should be treated as read-only.
1533    
1534    =cut
1535    
1536    sub GetDataTypes {
1537        return %TypeTable;
1538    }
1539    
1540    
1541  =head3 IsEntity  =head3 IsEntity
1542    
1543  C<< my $flag = $erdb->IsEntity($entityName); >>      my $flag = $erdb->IsEntity($entityName);
1544    
1545  Return TRUE if the parameter is an entity name, else FALSE.  Return TRUE if the parameter is an entity name, else FALSE.
1546    
# Line 793  Line 1567 
1567    
1568  =head3 Get  =head3 Get
1569    
1570  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>      my $query = $erdb->Get(\@objectNames, $filterClause, \@params);
1571    
1572  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.
1573  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 801  Line 1575 
1575  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
1576  $genus.  $genus.
1577    
1578  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]);
1579    
1580  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
1581  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1582    
1583  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>      $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'");
1584    
1585  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1586  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 818  Line 1592 
1592  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
1593  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,
1594    
1595  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>      $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]);
1596    
1597  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
1598  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.
1599  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
1600  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
1601  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  
1602  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,
1603  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.
1604    
1605    If an entity or relationship is mentioned twice, the name for the second occurrence will
1606    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1607    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1608    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1609    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1610    
1611  =over 4  =over 4
1612    
1613  =item objectNames  =item objectNames
# Line 849  Line 1628 
1628  with an ORDER BY clause. For example, the following filter string gets all genomes for a  with an ORDER BY clause. For example, the following filter string gets all genomes for a
1629  particular genus and sorts them by species name.  particular genus and sorts them by species name.
1630    
1631  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>      "Genome(genus) = ? ORDER BY Genome(species)"
1632    
1633    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1634    be processed. The idea is to make it less likely to find the verb by accident.
1635    
1636  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
1637  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
1638  relation.  relation.
1639    
1640  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1641    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1642    a positive number. So, for example
1643    
1644        "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10"
1645    
1646  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
1647    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1648    use
1649    
1650        "LIMIT 10"
1651    
1652    =item params
1653    
1654    Reference to a list of parameter values to be substituted into the filter clause.
1655    
1656  =item RETURN  =item RETURN
1657    
# Line 869  Line 1663 
1663    
1664  sub Get {  sub Get {
1665      # Get the parameters.      # Get the parameters.
1666      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1667      # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1668      #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1669      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1670      #      # Create the query.
1671      my $dbh = $self->{_dbh};      my $command = "SELECT " . join(".*, ", @{$mappedNameListRef}) .
1672      my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1673                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1674      Trace("SQL = $command") if T(SQL => 4);      # Now we create the relation map, which enables DBQuery to determine the order, name
1675      # Check for a filter clause.      # and mapped name for each object in the query.
1676      if ($filterClause) {      my @relationMap = ();
1677          # Here we have one, so we convert its field names and add it to the query. First,      for my $mappedName (@{$mappedNameListRef}) {
1678          # We create a copy of the filter string we can work with.          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
         my $filterString = $filterClause;  
         # Next, we sort the object names by length. This helps protect us from finding  
         # object names inside other object names when we're doing our search and replace.  
         my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
         # We will also keep a list of conditions to add to the WHERE clause in order to link  
         # entities and relationships as well as primary relations to secondary ones.  
         my @joinWhere = ();  
         # The final preparatory step is to create a hash table of relation names. The  
         # table begins with the relation names already in the SELECT command.  
         my %fromNames = ();  
         for my $objectName (@sortedNames) {  
             $fromNames{$objectName} = 1;  
         }  
         # We are ready to begin. We loop through the object names, replacing each  
         # object name's field references by the corresponding SQL field reference.  
         # Along the way, if we find a secondary relation, we will need to add it  
         # to the FROM clause.  
         for my $objectName (@sortedNames) {  
             # Get the length of the object name plus 2. This is the value we add to the  
             # size of the field name to determine the size of the field reference as a  
             # whole.  
             my $nameLength = 2 + length $objectName;  
             # Get the object's field list.  
             my $fieldList = $self->_GetFieldTable($objectName);  
             # Find the field references for this object.  
             while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  
                 # At this point, $1 contains the field name, and the current position  
                 # is set immediately after the final parenthesis. We pull out the name of  
                 # the field and the position and length of the field reference as a whole.  
                 my $fieldName = $1;  
                 my $len = $nameLength + length $fieldName;  
                 my $pos = pos($filterString) - $len;  
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
                 } else {  
                     # Get the field's relation.  
                     my $relationName = $fieldList->{$fieldName}->{relation};  
                     # Insure the relation is in the FROM clause.  
                     if (!exists $fromNames{$relationName}) {  
                         # Add the relation to the FROM clause.  
                         $command .= ", $relationName";  
                         # Create its join sub-clause.  
                         push @joinWhere, "$objectName.id = $relationName.id";  
                         # Denote we have it available for future fields.  
                         $fromNames{$relationName} = 1;  
                     }  
                     # Form an SQL field reference from the relation name and the field name.  
                     my $sqlReference = "$relationName." . _FixName($fieldName);  
                     # Put it into the filter string in place of the old value.  
                     substr($filterString, $pos, $len) = $sqlReference;  
                     # Reposition the search.  
                     pos $filterString = $pos + length $sqlReference;  
                 }  
             }  
         }  
         # The next step is to join the objects together. We only need to do this if there  
         # is more than one object in the object list. We start with the first object and  
         # run through the objects after it. Note also that we make a safety copy of the  
         # list before running through it.  
         my @objectList = @{$objectNames};  
         my $lastObject = shift @objectList;  
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisObject (@objectList) {  
             # Look for a join.  
             my $joinKey = "$lastObject/$thisObject";  
             if (!exists $joinTable->{$joinKey}) {  
                 # Here there's no join, so we throw an error.  
                 Confess("No join exists to connect from $lastObject to $thisObject.");  
             } else {  
                 # Get the join clause and add it to the WHERE list.  
                 push @joinWhere, $joinTable->{$joinKey};  
                 # Save this object as the last object for the next iteration.  
                 $lastObject = $thisObject;  
             }  
         }  
         # Now we need to handle the whole ORDER BY thing. We'll put the order by clause  
         # in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY verb (if any).  
         if ($filterString =~ m/^(.*)ORDER BY/g) {  
             # Here we have an ORDER BY verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = substr($filterString, $pos);  
             $filterString = $1;  
         }  
         # Add the filter and the join clauses (if any) to the SELECT command.  
         if ($filterString) {  
             push @joinWhere, "($filterString)";  
         }  
         if (@joinWhere) {  
             $command .= " WHERE " . join(' AND ', @joinWhere);  
         }  
         # Add the sort clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " ORDER BY $orderClause";  
         }  
1679      }      }
     Trace("SQL query: $command") if T(3);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
1680      # Return the statement object.      # Return the statement object.
1681      my $retVal = DBQuery::_new($self, $sth, @{$objectNames});      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1682      return $retVal;      return $retVal;
1683  }  }
1684    
 =head3 GetList  
1685    
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
1686    
1687  Return a list of object descriptors for the specified objects as determined by the  =head3 Search
 specified filter clause.  
1688    
1689  This method is essentially the same as L</Get> except it returns a list of objects rather      my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params);
1690  than a query object that can be used to get the results one record at a time.  
1691    Perform a full text search with filtering. The search will be against a specified object
1692    in the object name list. That object will get an extra field containing the search
1693    relevance. Note that except for the search expression, the parameters of this method are
1694    the same as those for L</Get> and follow the same rules.
1695    
1696  =over 4  =over 4
1697    
1698    =item searchExpression
1699    
1700    Boolean search expression for the text fields of the target object. The default mode for
1701    a Boolean search expression is OR, but we want the default to be AND, so we will
1702    add a C<+> operator to each word with no other operator before it.
1703    
1704    =item idx
1705    
1706    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1707    
1708  =item objectNames  =item objectNames
1709    
1710  List containing the names of the entity and relationship objects to be retrieved.  List containing the names of the entity and relationship objects to be retrieved.
# Line 1018  Line 1719 
1719  or secondary entity relations; however, all of the entities and relationships involved must  or secondary entity relations; however, all of the entities and relationships involved must
1720  be included in the list of object names.  be included in the list of object names.
1721    
1722  The filter clause can also specify a sort order. To do this, simply follow the filter string  =item params
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
   
 C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  
   
 The rules for field references in a sort order are the same as those for field references in the  
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
   
 =item param1, param2, ..., paramN  
1723    
1724  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1725    
1726  =item RETURN  =item RETURN
1727    
1728  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a query object for the specified search.
1729    
1730  =back  =back
1731    
1732  =cut  =cut
1733  #: Return Type @%  
1734  sub GetList {  sub Search {
1735      # Get the parameters.      # Get the parameters.
1736      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1737      # Declare the return variable.      # Declare the return variable.
1738      my @retVal = ();      my $retVal;
1739      # Perform the query.      # Create a safety copy of the parameter list. Note we have to be careful to insure
1740      my $query = $self->Get($objectNames, $filterClause, @params);      # a parameter list exists before we copy it.
1741      # Loop through the results.      my @myParams = ();
1742      while (my $object = $query->Fetch) {      if (defined $params) {
1743          push @retVal, $object;          @myParams = @{$params};
1744        }
1745        # Get the first object's structure so we have access to the searchable fields.
1746        my $object1Name = $objectNames->[$idx];
1747        my $object1Structure = $self->_GetStructure($object1Name);
1748        # Get the field list.
1749        if (! exists $object1Structure->{searchFields}) {
1750            Confess("No searchable index for $object1Name.");
1751        } else {
1752            # Get the field list.
1753            my @fields = @{$object1Structure->{searchFields}};
1754            # Clean the search expression.
1755            my $actualKeywords = $self->CleanKeywords($searchExpression);
1756            # Prefix a "+" to each uncontrolled word. This converts the default
1757            # search mode from OR to AND.
1758            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1759            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1760            # We need two match expressions, one for the filter clause and one in the
1761            # query itself. Both will use a parameter mark, so we need to push the
1762            # search expression onto the front of the parameter list twice.
1763            unshift @myParams, $actualKeywords, $actualKeywords;
1764            # Build the match expression.
1765            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1766            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1767            # Process the SQL stuff.
1768            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1769                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1770            # Create the query. Note that the match clause is inserted at the front of
1771            # the select fields.
1772            my $command = "SELECT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1773                ".* $suffix";
1774            my $sth = $self->_GetStatementHandle($command, \@myParams);
1775            # Now we create the relation map, which enables DBQuery to determine the order, name
1776            # and mapped name for each object in the query.
1777            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1778            # Return the statement object.
1779            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1780      }      }
1781      # Return the result.      return $retVal;
     return @retVal;  
1782  }  }
1783    
1784  =head3 ComputeObjectSentence  =head3 GetFlat
1785    
1786  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>      my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field);
1787    
1788  Check an object name, and if it is a relationship convert it to a relationship sentence.  This is a variation of L</GetAll> that asks for only a single field per record and
1789    returns a single flattened list.
1790    
1791  =over 4  =over 4
1792    
1793  =item objectName  =item objectNames
1794    
1795  Name of the entity or relationship.  List containing the names of the entity and relationship objects to be retrieved.
1796    
1797    =item filterClause
1798    
1799    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1800    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1801    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1802    parameter list as additional parameters. The fields in a filter clause can come from primary
1803    entity relations, relationship relations, or secondary entity relations; however, all of the
1804    entities and relationships involved must be included in the list of object names.
1805    
1806    =item parameterList
1807    
1808    List of the parameters to be substituted in for the parameters marks in the filter clause.
1809    
1810    =item field
1811    
1812    Name of the field to be used to get the elements of the list returned.
1813    
1814  =item RETURN  =item RETURN
1815    
1816  Returns a string containing the entity name or a relationship sentence.  Returns a list of values.
1817    
1818  =back  =back
1819    
1820  =cut  =cut
1821    #: Return Type @;
1822  sub ComputeObjectSentence {  sub GetFlat {
1823      # Get the parameters.      # Get the parameters.
1824      my ($self, $objectName) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1825      # Set the default return value.      # Construct the query.
1826      my $retVal = $objectName;      my $query = $self->Get($objectNames, $filterClause, $parameterList);
1827      # Look for the object as a relationship.      # Create the result list.
1828      my $relTable = $self->{_metaData}->{Relationships};      my @retVal = ();
1829      if (exists $relTable->{$objectName}) {      # Loop through the records, adding the field values found to the result list.
1830          # Get the relationship sentence.      while (my $row = $query->Fetch()) {
1831          $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          push @retVal, $row->Value($field);
1832      }      }
1833      # Return the result.      # Return the list created.
1834      return $retVal;      return @retVal;
1835  }  }
1836    
1837  =head3 DumpRelations  =head3 SpecialFields
1838    
1839  C<< $erdb->DumpRelations($outputDirectory); >>      my %specials = $erdb->SpecialFields($entityName);
1840    
1841  Write the contents of all the relations to tab-delimited files in the specified directory.  Return a hash mapping special fields in the specified entity to the value of their
1842  Each file will have the same name as the relation dumped, with an extension of DTX.  C<special> attribute. This enables the subclass to get access to the special field
1843    attributes without needed to plumb the internal ERDB data structures.
1844    
1845  =over 4  =over 4
1846    
1847  =item outputDirectory  =item entityName
1848    
1849  Name of the directory into which the relation files should be dumped.  Name of the entity whose special fields are desired.
1850    
1851    =item RETURN
1852    
1853    Returns a hash. The keys of the hash are the special field names, and the values
1854    are the values from each special field's C<special> attribute.
1855    
1856  =back  =back
1857    
1858  =cut  =cut
1859    
1860  sub DumpRelations {  sub SpecialFields {
1861      # Get the parameters.      # Get the parameters.
1862      my ($self, $outputDirectory) = @_;      my ($self, $entityName) = @_;
1863      # Now we need to run through all the relations. First, we loop through the entities.      # Declare the return variable.
1864      my $metaData = $self->{_metaData};      my %retVal = ();
1865      my $entities = $metaData->{Entities};      # Find the entity's data structure.
1866      for my $entityName (keys %{$entities}) {      my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1867          my $entityStructure = $entities->{$entityName};      # Loop through its fields, adding each special field to the return hash.
1868          # Get the entity's relations.      my $fieldHash = $entityData->{Fields};
1869          my $relationList = $entityStructure->{Relations};      for my $fieldName (keys %{$fieldHash}) {
1870          # Loop through the relations, dumping them.          my $fieldData = $fieldHash->{$fieldName};
1871          for my $relationName (keys %{$relationList}) {          if (exists $fieldData->{special}) {
1872              my $relation = $relationList->{$relationName};              $retVal{$fieldName} = $fieldData->{special};
             $self->_DumpRelation($outputDirectory, $relationName, $relation);  
         }  
1873      }      }
     # Next, we loop through the relationships.  
     my $relationships = $metaData->{Relationships};  
     for my $relationshipName (keys %{$relationships}) {  
         my $relationshipStructure = $relationships->{$relationshipName};  
         # Dump this relationship's relation.  
         $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
1874      }      }
1875        # Return the result.
1876        return %retVal;
1877  }  }
1878    
1879  =head3 InsertObject  =head3 Delete
1880    
1881  C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>      my $stats = $erdb->Delete($entityName, $objectID, %options);
1882    
1883  Insert an object into the database. The object is defined by a type name and then a hash  Delete an entity instance from the database. The instance is deleted along with all entity and
1884  of field names to values. Field values in the primary relation are represented by scalars.  relationship instances dependent on it. The definition of I<dependence> is recursive.
 (Note that for relationships, the primary relation is the B<only> relation.)  
 Field values for the other relations comprising the entity are always list references. For  
 example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  
 C<ZP_00210270.1> and C<gi|46206278>.  
1885    
1886  C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1887    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1888    dependent relationship.
1889    
1890  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  =over 4
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
1891    
1892  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  =item entityName
1893    
1894  =over 4  Name of the entity type for the instance being deleted.
1895    
1896  =item newObjectType  =item objectID
1897    
1898  Type name of the object to insert.  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1899    then it is presumed to by a LIKE pattern.
1900    
1901  =item fieldHash  =item options
1902    
1903  Hash of field names to values.  A hash detailing the options for this delete operation.
1904    
1905  =item RETURN  =item RETURN
1906    
1907  Returns 1 if successful, 0 if an error occurred.  Returns a statistics object indicating how many records of each particular table were
1908    deleted.
1909    
1910  =back  =back
1911    
1912  =cut  The permissible options for this method are as follows.
1913    
1914  sub InsertObject {  =over 4
1915    
1916    =item testMode
1917    
1918    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1919    
1920    =item keepRoot
1921    
1922    If TRUE, then the entity instances will not be deleted, only the dependent records.
1923    
1924    =back
1925    
1926    =cut
1927    #: Return Type $%;
1928    sub Delete {
1929      # Get the parameters.      # Get the parameters.
1930      my ($self, $newObjectType, $fieldHash) = @_;      my ($self, $entityName, $objectID, %options) = @_;
1931      # Denote that so far we appear successful.      # Declare the return variable.
1932      my $retVal = 1;      my $retVal = Stats->new();
1933      # Get the database handle.      # Get the DBKernel object.
1934      my $dbh = $self->{_dbh};      my $db = $self->{_dbh};
1935      # Get the relation list.      # We're going to generate all the paths branching out from the starting entity. One of
1936      my $relationTable = $self->_GetRelationTable($newObjectType);      # the things we have to be careful about is preventing loops. We'll use a hash to
1937      # Loop through the relations. We'll build insert statements for each one. If a relation is      # determine if we've hit a loop.
1938      # secondary, we may end up generating multiple insert statements. If an error occurs, we      my %alreadyFound = ();
1939      # stop the loop.      # These next lists will serve as our result stack. We start by pushing object lists onto
1940      my @relationList = keys %{$relationTable};      # the stack, and then popping them off to do the deletes. This means the deletes will
1941      for (my $i = 0; $retVal && $i <= $#relationList; $i++) {      # start with the longer paths before getting to the shorter ones. That, in turn, makes
1942          my $relationName = $relationList[$i];      # sure we don't delete records that might be needed to forge relationships back to the
1943          my $relationDefinition = $relationTable->{$relationName};      # original item. We have two lists-- one for TO-relationships, and one for
1944          # Get the relation's fields. For each field we will collect a value in the corresponding      # FROM-relationships and entities.
1945          # position of the @valueList array. If one of the fields is missing, we will add it to the      my @fromPathList = ();
1946          # @missing list.      my @toPathList = ();
1947          my @fieldList = @{$relationDefinition->{Fields}};      # This final list is used to remember what work still needs to be done. We push paths
1948          my @fieldNameList = ();      # onto the list, then pop them off to extend the paths. We prime it with the starting
1949          my @valueList = ();      # point. Note that we will work hard to insure that the last item on a path in the
1950          my @missing = ();      # to-do list is always an entity.
1951          my $recordCount = 1;      my @todoList = ([$entityName]);
1952          for my $fieldDescriptor (@fieldList) {      while (@todoList) {
1953              # Get the field name and save it. Note we need to fix it up so the hyphens          # Get the current path.
1954              # are converted to underscores.          my $current = pop @todoList;
1955              my $fieldName = $fieldDescriptor->{name};          # Copy it into a list.
1956              push @fieldNameList, _FixName($fieldName);          my @stackedPath = @{$current};
1957              # Look for the named field in the incoming structure. Note that we are looking          # Pull off the last item on the path. It will always be an entity.
1958              # for the real field name, not the fixed-up one!          my $myEntityName = pop @stackedPath;
1959              if (exists $fieldHash->{$fieldName}) {          # Add it to the alreadyFound list.
1960                  # Here we found the field. Stash it in the value list.          $alreadyFound{$myEntityName} = 1;
1961                  my $value = $fieldHash->{$fieldName};          # Figure out if we need to delete this entity.
1962                  push @valueList, $value;          if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1963                  # If the value is a list, we may need to increment the record count.              # Get the entity data.
1964                  if (ref $value eq "ARRAY") {              my $entityData = $self->_GetStructure($myEntityName);
1965                      my $thisCount = @{$value};              # Loop through the entity's relations. A DELETE command will be needed for each of them.
1966                      if ($recordCount == 1) {              my $relations = $entityData->{Relations};
1967                          # Here we have our first list, so we save its count.              for my $relation (keys %{$relations}) {
1968                          $recordCount = $thisCount;                  my @augmentedList = (@stackedPath, $relation);
1969                      } elsif ($recordCount != $thisCount) {                  push @fromPathList, \@augmentedList;
                         # Here we have a second list, so its length has to match the  
                         # previous lists.  
                         Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);  
                         $retVal = 0;  
1970                      }                      }
1971                  }                  }
1972            # Now we need to look for relationships connected to this entity.
1973            my $relationshipList = $self->{_metaData}->{Relationships};
1974            for my $relationshipName (keys %{$relationshipList}) {
1975                my $relationship = $relationshipList->{$relationshipName};
1976                # Check the FROM field. We're only interested if it's us.
1977                if ($relationship->{from} eq $myEntityName) {
1978                    # Add the path to this relationship.
1979                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1980                    push @fromPathList, \@augmentedList;
1981                    # Check the arity. If it's MM we're done. If it's 1M
1982                    # and the target hasn't been seen yet, we want to
1983                    # stack the entity for future processing.
1984                    if ($relationship->{arity} eq '1M') {
1985                        my $toEntity = $relationship->{to};
1986                        if (! exists $alreadyFound{$toEntity}) {
1987                            # Here we have a new entity that's dependent on
1988                            # the current entity, so we need to stack it.
1989                            my @stackList = (@augmentedList, $toEntity);
1990                            push @fromPathList, \@stackList;
1991              } else {              } else {
1992                  # Here the field is not present. Flag it as missing.                          Trace("$toEntity ignored because it occurred previously.") if T(4);
                 push @missing, $fieldName;  
1993              }              }
1994          }          }
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
1995          }          }
1996          # Only proceed if there are no missing fields.              # Now check the TO field. In this case only the relationship needs
1997          if (@missing > 0) {              # deletion.
1998              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .              if ($relationship->{to} eq $myEntityName) {
1999                  join(' ', @missing)) if T(1);                  my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
2000          } else {                  push @toPathList, \@augmentedList;
             # Build the INSERT statement.  
             my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .  
                 ") VALUES (";  
             # Create a marker list of the proper size and put it in the statement.  
             my @markers = ();  
             while (@markers < @fieldNameList) { push @markers, '?'; }  
             $statement .= join(', ', @markers) . ")";  
             # We have the insert statement, so prepare it.  
             my $sth = $dbh->prepare_command($statement);  
             Trace("Insert statement prepared: $statement") if T(3);  
             # Now we loop through the values. If a value is scalar, we use it unmodified. If it's  
             # a list, we use the current element. The values are stored in the @parameterList array.  
             my $done = 0;  
             for (my $i = 0; $i < $recordCount; $i++) {  
                 # Clear the parameter list array.  
                 my @parameterList = ();  
                 # Loop through the values.  
                 for my $value (@valueList) {  
                     # Check to see if this is a scalar value.  
                     if (ref $value eq "ARRAY") {  
                         # Here we have a list value. Pull the current entry.  
                         push @parameterList, $value->[$i];  
                     } else {  
                         # Here we have a scalar value. Use it unmodified.  
                         push @parameterList, $value;  
2001                      }                      }
2002                  }                  }
                 # Execute the INSERT statement with the specified parameter list.  
                 $retVal = $sth->execute(@parameterList);  
                 if (!$retVal) {  
                     my $errorString = $sth->errstr();  
                     Trace("Insert error: $errorString.") if T(0);  
2003                  }                  }
2004        # Create the first qualifier for the WHERE clause. This selects the
2005        # keys of the primary entity records to be deleted. When we're deleting
2006        # from a dependent table, we construct a join path from the first qualifier
2007        # to the table containing the dependent records to delete.
2008        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
2009        # We need to make two passes. The first is through the to-list, and
2010        # the second through the from-list. The from-list is second because
2011        # the to-list may need to pass through some of the entities the
2012        # from-list would delete.
2013        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
2014        # Now it's time to do the deletes. We do it in two passes.
2015        for my $keyName ('to_link', 'from_link') {
2016            # Get the list for this key.
2017            my @pathList = @{$stackList{$keyName}};
2018            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
2019            # Loop through this list.
2020            while (my $path = pop @pathList) {
2021                # Get the table whose rows are to be deleted.
2022                my @pathTables = @{$path};
2023                # Start the DELETE statement. We need to call DBKernel because the
2024                # syntax of a DELETE-USING varies among DBMSs.
2025                my $target = $pathTables[$#pathTables];
2026                my $stmt = $db->SetUsing(@pathTables);
2027                # Now start the WHERE. The first thing is the ID field from the starting table. That
2028                # starting table will either be the entity relation or one of the entity's
2029                # sub-relations.
2030                $stmt .= " WHERE $pathTables[0].id $qualifier";
2031                # Now we run through the remaining entities in the path, connecting them up.
2032                for (my $i = 1; $i <= $#pathTables; $i += 2) {
2033                    # Connect the current relationship to the preceding entity.
2034                    my ($entity, $rel) = @pathTables[$i-1,$i];
2035                    # The style of connection depends on the direction of the relationship.
2036                    $stmt .= " AND $entity.id = $rel.$keyName";
2037                    if ($i + 1 <= $#pathTables) {
2038                        # Here there's a next entity, so connect that to the relationship's
2039                        # to-link.
2040                        my $entity2 = $pathTables[$i+1];
2041                        $stmt .= " AND $rel.to_link = $entity2.id";
2042                    }
2043                }
2044                # Now we have our desired DELETE statement.
2045                if ($options{testMode}) {
2046                    # Here the user wants to trace without executing.
2047                    Trace($stmt) if T(0);
2048                } else {
2049                    # Here we can delete. Note that the SQL method dies with a confession
2050                    # if an error occurs, so we just go ahead and do it.
2051                    Trace("Executing delete from $target using '$objectID'.") if T(3);
2052                    my $rv = $db->SQL($stmt, 0, $objectID);
2053                    # Accumulate the statistics for this delete. The only rows deleted
2054                    # are from the target table, so we use its name to record the
2055                    # statistic.
2056                    $retVal->Add($target, $rv);
2057              }              }
2058          }          }
2059      }      }
2060      # Return the success indicator.      # Return the result.
2061      return $retVal;      return $retVal;
2062  }  }
2063    
2064  =head3 LoadTable  =head3 Disconnect
2065    
2066  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>      $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID);
2067    
2068  Load data from a tab-delimited file into a specified table, optionally re-creating the table  Disconnect an entity instance from all the objects to which it is related. This
2069  first.  will delete each relationship instance that connects to the specified entity.
2070    
2071  =over 4  =over 4
2072    
2073  =item fileName  =item relationshipName
   
 Name of the file from which the table data should be loaded.  
   
 =item relationName  
2074    
2075  Name of the relation to be loaded. This is the same as the table name.  Name of the relationship whose instances are to be deleted.
2076    
2077  =item truncateFlag  =item originEntityName
2078    
2079  TRUE if the table should be dropped and re-created, else FALSE  Name of the entity that is to be disconnected.
2080    
2081  =item RETURN  =item originEntityID
2082    
2083  Returns a statistical object containing the number of records read and a list of  ID of the entity that is to be disconnected.
 the error messages.  
2084    
2085  =back  =back
2086    
2087  =cut  =cut
2088  sub LoadTable {  
2089    sub Disconnect {
2090      # Get the parameters.      # Get the parameters.
2091      my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
2092      # Create the statistical return object.      # Get the relationship descriptor.
2093      my $retVal = _GetLoadStats();      my $structure = $self->_GetStructure($relationshipName);
2094      # Trace the fact of the load.      # Insure we have a relationship.
2095      Trace("Loading table $relationName from $fileName") if T(2);      if (! exists $structure->{from}) {
2096            Confess("$relationshipName is not a relationship in the database.");
2097        } else {
2098      # Get the database handle.      # Get the database handle.
2099      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
2100      # Get the input file size.          # We'll set this value to 1 if we find our entity.
2101      my $fileSize = -s $fileName;          my $found = 0;
2102      # Get the relation data.          # Loop through the ends of the relationship.
2103      my $relation = $self->_FindRelation($relationName);          for my $dir ('from', 'to') {
2104      # Check the truncation flag.              if ($structure->{$dir} eq $originEntityName) {
2105      if ($truncateFlag) {                  $found = 1;
2106          Trace("Creating table $relationName") if T(2);                  # Here we want to delete all relationship instances on this side of the
2107          # Compute the row count estimate. We take the size of the load file,                  # entity instance.
2108          # divide it by the estimated row size, and then multiply by 1.5 to                  Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2109          # leave extra room. We postulate a minimum row count of 1000 to                  # We do this delete in batches to keep it from dragging down the
2110          # prevent problems with incoming empty load files.                  # server.
2111          my $rowSize = $self->EstimateRowSize($relationName);                  my $limitClause = ($FIG_Config::delete_limit ? "LIMIT $FIG_Config::delete_limit" : "");
2112          my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);                  my $done = 0;
2113          # Re-create the table without its index.                  while (! $done) {
2114          $self->CreateTable($relationName, 0, $estimate);                      # Do the delete.
2115          # If this is a pre-index DBMS, create the index here.                      my $rows = $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ? $limitClause", 0, $originEntityID);
2116          if ($dbh->{_preIndex}) {                      # See if we're done. We're done if no rows were found or the delete is unlimited.
2117              eval {                      $done = ($rows == 0 || ! $limitClause);
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
             }  
2118          }          }
2119      }      }
     # Load the table.  
     my $rv;  
     eval {  
         $rv = $dbh->load_table(file => $fileName, tbl => $relationName);  
     };  
     if (!defined $rv) {  
         $retVal->AddMessage($@) if ($@);  
         $retVal->AddMessage("Table load failed for $relationName using $fileName.");  
         Trace("Table load failed for $relationName.") if T(1);  
     } else {  
         # Here we successfully loaded the table.  
         $retVal->Add("tables");  
         my $size = -s $fileName;  
         Trace("$size bytes loaded into $relationName.") if T(2);  
         # If we're rebuilding, we need to create the table indexes.  
         if ($truncateFlag && ! $dbh->{_preIndex}) {  
             eval {  
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
2120              }              }
2121            # Insure we found the entity on at least one end.
2122            if (! $found) {
2123                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2124          }          }
2125      }      }
     # Analyze the table to improve performance.  
     $dbh->vacuum_it($relationName);  
     # Return the statistics.  
     return $retVal;  
2126  }  }
2127    
2128  =head3 GenerateEntity  =head3 DeleteRow
2129    
2130  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>      $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values);
2131    
2132  Generate the data for a new entity instance. This method creates a field hash suitable for  Delete a row from a relationship. In most cases, only the from-link and to-link are
2133  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  needed; however, for relationships with intersection data values can be specified
2134  of the fields are generated using information in the database schema.  for the other fields using a hash.
   
 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.  
2135    
2136  =over 4  =over 4
2137    
2138  =item id  =item relationshipName
2139    
2140  ID to assign to the new entity.  Name of the relationship from which the row is to be deleted.
2141    
2142  =item type  =item fromLink
2143    
2144  Type name for the new entity.  ID of the entity instance in the From direction.
2145    
2146    =item toLink
2147    
2148    ID of the entity instance in the To direction.
2149    
2150  =item values  =item values
2151    
2152  Hash containing additional values that might be needed by the data generation methods (optional).  Reference to a hash of other values to be used for filtering the delete.
2153    
2154  =back  =back
2155    
2156  =cut  =cut
2157    
2158  sub GenerateEntity {  sub DeleteRow {
2159      # Get the parameters.      # Get the parameters.
2160      my ($self, $id, $type, $values) = @_;      my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2161      # Create the return hash.      # Create a hash of all the filter information.
2162      my $this = { id => $id };      my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2163      # Get the metadata structure.      if (defined $values) {
2164      my $metadata = $self->{_metaData};          for my $key (keys %{$values}) {
2165      # Get this entity's list of fields.              $filter{$key} = $values->{$key};
     if (!exists $metadata->{Entities}->{$type}) {  
         Confess("Unrecognized entity type $type in GenerateEntity.");  
     } else {  
         my $entity = $metadata->{Entities}->{$type};  
         my $fields = $entity->{Fields};  
         # Generate data from the fields.  
         _GenerateFields($this, $fields, $type, $values);  
2166      }      }
2167      # Return the hash created.      }
2168      return $this;      # Build an SQL statement out of the hash.
2169        my @filters = ();
2170        my @parms = ();
2171        for my $key (keys %filter) {
2172            push @filters, _FixName($key) . " = ?";
2173            push @parms, $filter{$key};
2174        }
2175        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2176        my $command = "DELETE FROM $relationshipName WHERE " .
2177                      join(" AND ", @filters);
2178        # Execute it.
2179        my $dbh = $self->{_dbh};
2180        $dbh->SQL($command, undef, @parms);
2181  }  }
2182    
2183  =head3 GetEntity  =head3 DeleteLike
2184    
2185  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>      my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms);
2186    
2187  Return an object describing the entity instance with a specified ID.  Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2188    filter, only fields from the relationship itself can be used.
2189    
2190  =over 4  =over 4
2191    
2192  =item entityType  =item relName
2193    
2194  Entity type name.  Name of the relationship whose records are to be deleted.
2195    
2196  =item ID  =item filter
2197    
2198  ID of the desired entity.  A filter clause (L</Get>-style) for the delete query.
2199    
2200    =item parms
2201    
2202    Reference to a list of parameters for the filter clause.
2203    
2204  =item RETURN  =item RETURN
2205    
2206  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a count of the number of rows deleted.
 instance is found with the specified key.  
2207    
2208  =back  =back
2209    
2210  =cut  =cut
2211    
2212  sub GetEntity {  sub DeleteLike {
2213      # Get the parameters.      # Get the parameters.
2214      my ($self, $entityType, $ID) = @_;      my ($self, $objectName, $filter, $parms) = @_;
2215      # Create a query.      # Declare the return variable.
2216      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $retVal;
2217      # Get the first (and only) object.      # Insure the parms argument is an array reference if the caller left it off.
2218      my $retVal = $query->Fetch();      if (! defined($parms)) {
2219      # Return the result.          $parms = [];
2220      return $retVal;      }
2221  }      # Insure we have a relationship. The main reason for this is if we delete an entity
2222        # instance we have to yank out a bunch of other stuff with it.
2223  =head3 GetEntityValues      if ($self->IsEntity($objectName)) {
2224            Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2225  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>      } else {
2226            # Create the SQL command suffix to get the desierd records.
2227            my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2228            # Convert it to a DELETE command.
2229            my $command = "DELETE $suffix";
2230            # Execute the command.
2231            my $dbh = $self->{_dbh};
2232            my $result = $dbh->SQL($command, 0, @{$parms});
2233            # Check the results. Note we convert the "0D0" result to a real zero.
2234            # A failure causes an abnormal termination, so the caller isn't going to
2235            # worry about it.
2236            if (! defined $result) {
2237                Confess("Error deleting from $objectName: " . $dbh->errstr());
2238            } elsif ($result == 0) {
2239                $retVal = 0;
2240            } else {
2241                $retVal = $result;
2242            }
2243        }
2244        # Return the result count.
2245        return $retVal;
2246    }
2247    
2248    =head3 SortNeeded
2249    
2250        my $parms = $erdb->SortNeeded($relationName);
2251    
2252    Return the pipe command for the sort that should be applied to the specified
2253    relation when creating the load file.
2254    
2255    For example, if the load file should be sorted ascending by the first
2256    field, this method would return
2257    
2258        sort -k1 -t"\t"
2259    
2260    If the first field is numeric, the method would return
2261    
2262        sort -k1n -t"\t"
2263    
2264    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2265    keys using a sort.
2266    
2267    =over 4
2268    
2269    =item relationName
2270    
2271    Name of the relation to be examined.
2272    
2273    =item
2274    
2275    Returns the sort command to use for sorting the relation, suitable for piping.
2276    
2277    =back
2278    
2279    =cut
2280    #: Return Type $;
2281    sub SortNeeded {
2282        # Get the parameters.
2283        my ($self, $relationName) = @_;
2284        # Declare a descriptor to hold the names of the key fields.
2285        my @keyNames = ();
2286        # Get the relation structure.
2287        my $relationData = $self->_FindRelation($relationName);
2288        # Find out if the relation is a primary entity relation,
2289        # a relationship relation, or a secondary entity relation.
2290        my $entityTable = $self->{_metaData}->{Entities};
2291        my $relationshipTable = $self->{_metaData}->{Relationships};
2292        if (exists $entityTable->{$relationName}) {
2293            # Here we have a primary entity relation.
2294            push @keyNames, "id";
2295        } elsif (exists $relationshipTable->{$relationName}) {
2296            # Here we have a relationship. We sort using the FROM index.
2297            my $relationshipData = $relationshipTable->{$relationName};
2298            my $index = $relationData->{Indexes}->{idxFrom};
2299            push @keyNames, @{$index->{IndexFields}};
2300        } else {
2301            # Here we have a secondary entity relation, so we have a sort on the ID field.
2302            push @keyNames, "id";
2303        }
2304        # Now we parse the key names into sort parameters. First, we prime the return
2305        # string.
2306        my $retVal = "sort -t\"\t\" ";
2307        # Get the relation's field list.
2308        my @fields = @{$relationData->{Fields}};
2309        # Loop through the keys.
2310        for my $keyData (@keyNames) {
2311            # Get the key and the ordering.
2312            my ($keyName, $ordering);
2313            if ($keyData =~ /^([^ ]+) DESC/) {
2314                ($keyName, $ordering) = ($1, "descending");
2315            } else {
2316                ($keyName, $ordering) = ($keyData, "ascending");
2317            }
2318            # Find the key's position and type.
2319            my $fieldSpec;
2320            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2321                my $thisField = $fields[$i];
2322                if ($thisField->{name} eq $keyName) {
2323                    # Get the sort modifier for this field type. The modifier
2324                    # decides whether we're using a character, numeric, or
2325                    # floating-point sort.
2326                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2327                    # If the index is descending for this field, denote we want
2328                    # to reverse the sort order on this field.
2329                    if ($ordering eq 'descending') {
2330                        $modifier .= "r";
2331                    }
2332                    # Store the position and modifier into the field spec, which
2333                    # will stop the inner loop. Note that the field number is
2334                    # 1-based in the sort command, so we have to increment the
2335                    # index.
2336                    $fieldSpec = ($i + 1) . $modifier;
2337                }
2338            }
2339            # Add this field to the sort command.
2340            $retVal .= " -k$fieldSpec";
2341        }
2342        # Return the result.
2343        return $retVal;
2344    }
2345    
2346    =head3 GetList
2347    
2348        my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params);
2349    
2350    Return a list of object descriptors for the specified objects as determined by the
2351    specified filter clause.
2352    
2353    This method is essentially the same as L</Get> except it returns a list of objects rather
2354    than a query object that can be used to get the results one record at a time.
2355    
2356    =over 4
2357    
2358    =item objectNames
2359    
2360    List containing the names of the entity and relationship objects to be retrieved.
2361    
2362    =item filterClause
2363    
2364    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2365    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2366    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2367    in the filter clause should be added to the parameter list as additional parameters. The
2368    fields in a filter clause can come from primary entity relations, relationship relations,
2369    or secondary entity relations; however, all of the entities and relationships involved must
2370    be included in the list of object names.
2371    
2372    The filter clause can also specify a sort order. To do this, simply follow the filter string
2373    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2374    particular genus and sorts them by species name.
2375    
2376        "Genome(genus) = ? ORDER BY Genome(species)"
2377    
2378    The rules for field references in a sort order are the same as those for field references in the
2379    filter clause in general; however, odd things may happen if a sort field is from a secondary
2380    relation.
2381    
2382    =item params
2383    
2384    Reference to a list of parameter values to be substituted into the filter clause.
2385    
2386    =item RETURN
2387    
2388    Returns a list of B<ERDBObject>s that satisfy the query conditions.
2389    
2390    =back
2391    
2392    =cut
2393    #: Return Type @%
2394    sub GetList {
2395        # Get the parameters.
2396        my ($self, $objectNames, $filterClause, $params) = @_;
2397        # Declare the return variable.
2398        my @retVal = ();
2399        # Perform the query.
2400        my $query = $self->Get($objectNames, $filterClause, $params);
2401        # Loop through the results.
2402        while (my $object = $query->Fetch) {
2403            push @retVal, $object;
2404        }
2405        # Return the result.
2406        return @retVal;
2407    }
2408    
2409    =head3 GetCount
2410    
2411        my $count = $erdb->GetCount(\@objectNames, $filter, \@params);
2412    
2413    Return the number of rows found by a specified query. This method would
2414    normally be used to count the records in a single table. For example, in a
2415    genetics database
2416    
2417        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2418    
2419    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2420    to use it to return records based on a join. For example,
2421    
2422        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2423                                    ['homo %']);
2424    
2425    would return the number of features for genomes in the genus I<homo>. Note that
2426    only the rows from the first table are counted. If the above command were
2427    
2428        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2429                                    ['homo %']);
2430    
2431    it would return the number of genomes, not the number of genome/feature pairs.
2432    
2433    =over 4
2434    
2435    =item objectNames
2436    
2437    Reference to a list of the objects (entities and relationships) included in the
2438    query.
2439    
2440    =item filter
2441    
2442    A filter clause for restricting the query. The rules are the same as for the L</Get>
2443    method.
2444    
2445    =item params
2446    
2447    Reference to a list of the parameter values to be substituted for the parameter marks
2448    in the filter.
2449    
2450    =item RETURN
2451    
2452    Returns a count of the number of records in the first table that would satisfy
2453    the query.
2454    
2455    =back
2456    
2457    =cut
2458    
2459    sub GetCount {
2460        # Get the parameters.
2461        my ($self, $objectNames, $filter, $params) = @_;
2462        # Insure the params argument is an array reference if the caller left it off.
2463        if (! defined($params)) {
2464            $params = [];
2465        }
2466        # Declare the return variable.
2467        my $retVal;
2468        # Find out if we're counting an entity or a relationship.
2469        my $countedField;
2470        if ($self->IsEntity($objectNames->[0])) {
2471            $countedField = "id";
2472        } else {
2473            # For a relationship we count the to-link because it's usually more
2474            # numerous. Note we're automatically converting to the SQL form
2475            # of the field name (to_link vs. to-link).
2476            $countedField = "to_link";
2477        }
2478        # Create the SQL command suffix to get the desired records.
2479        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2480                                                                                $filter);
2481        # Prefix it with text telling it we want a record count.
2482        my $firstObject = $mappedNameListRef->[0];
2483        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2484        # Prepare and execute the command.
2485        my $sth = $self->_GetStatementHandle($command, $params);
2486        # Get the count value.
2487        ($retVal) = $sth->fetchrow_array();
2488        # Check for a problem.
2489        if (! defined($retVal)) {
2490            if ($sth->err) {
2491                # Here we had an SQL error.
2492                Confess("Error retrieving row count: " . $sth->errstr());
2493            } else {
2494                # Here we have no result.
2495                Confess("No result attempting to retrieve row count.");
2496            }
2497        }
2498        # Return the result.
2499        return $retVal;
2500    }
2501    
2502    =head3 ComputeObjectSentence
2503    
2504        my $sentence = $erdb->ComputeObjectSentence($objectName);
2505    
2506    Check an object name, and if it is a relationship convert it to a relationship sentence.
2507    
2508    =over 4
2509    
2510    =item objectName
2511    
2512    Name of the entity or relationship.
2513    
2514    =item RETURN
2515    
2516    Returns a string containing the entity name or a relationship sentence.
2517    
2518    =back
2519    
2520    =cut
2521    
2522    sub ComputeObjectSentence {
2523        # Get the parameters.
2524        my ($self, $objectName) = @_;
2525        # Set the default return value.
2526        my $retVal = $objectName;
2527        # Look for the object as a relationship.
2528        my $relTable = $self->{_metaData}->{Relationships};
2529        if (exists $relTable->{$objectName}) {
2530            # Get the relationship sentence.
2531            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2532        }
2533        # Return the result.
2534        return $retVal;
2535    }
2536    
2537    =head3 DumpRelations
2538    
2539        $erdb->DumpRelations($outputDirectory);
2540    
2541    Write the contents of all the relations to tab-delimited files in the specified directory.
2542    Each file will have the same name as the relation dumped, with an extension of DTX.
2543    
2544    =over 4
2545    
2546    =item outputDirectory
2547    
2548    Name of the directory into which the relation files should be dumped.
2549    
2550    =back
2551    
2552    =cut
2553    
2554    sub DumpRelations {
2555        # Get the parameters.
2556        my ($self, $outputDirectory) = @_;
2557        # Now we need to run through all the relations. First, we loop through the entities.
2558        my $metaData = $self->{_metaData};
2559        my $entities = $metaData->{Entities};
2560        for my $entityName (keys %{$entities}) {
2561            my $entityStructure = $entities->{$entityName};
2562            # Get the entity's relations.
2563            my $relationList = $entityStructure->{Relations};
2564            # Loop through the relations, dumping them.
2565            for my $relationName (keys %{$relationList}) {
2566                my $relation = $relationList->{$relationName};
2567                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2568            }
2569        }
2570        # Next, we loop through the relationships.
2571        my $relationships = $metaData->{Relationships};
2572        for my $relationshipName (keys %{$relationships}) {
2573            my $relationshipStructure = $relationships->{$relationshipName};
2574            # Dump this relationship's relation.
2575            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2576        }
2577    }
2578    
2579    =head3 InsertValue
2580    
2581        $erdb->InsertValue($entityID, $fieldName, $value);
2582    
2583    This method will insert a new value into the database. The value must be one
2584    associated with a secondary relation, since primary values cannot be inserted:
2585    they occur exactly once. Secondary values, on the other hand, can be missing
2586    or multiply-occurring.
2587    
2588    =over 4
2589    
2590    =item entityID
2591    
2592    ID of the object that is to receive the new value.
2593    
2594    =item fieldName
2595    
2596    Field name for the new value-- this includes the entity name, since
2597    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2598    
2599    =item value
2600    
2601    New value to be put in the field.
2602    
2603    =back
2604    
2605    =cut
2606    
2607    sub InsertValue {
2608        # Get the parameters.
2609        my ($self, $entityID, $fieldName, $value) = @_;
2610        # Parse the entity name and the real field name.
2611        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2612            my $entityName = $1;
2613            my $fieldTitle = $2;
2614            # Get its descriptor.
2615            if (!$self->IsEntity($entityName)) {
2616                Confess("$entityName is not a valid entity.");
2617            } else {
2618                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2619                # Find the relation containing this field.
2620                my $fieldHash = $entityData->{Fields};
2621                if (! exists $fieldHash->{$fieldTitle}) {
2622                    Confess("$fieldTitle not found in $entityName.");
2623                } else {
2624                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2625                    if ($relation eq $entityName) {
2626                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2627                    } else {
2628                        # Now we can create an INSERT statement.
2629                        my $dbh = $self->{_dbh};
2630                        my $fixedName = _FixName($fieldTitle);
2631                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2632                        # Execute the command.
2633                        $dbh->SQL($statement, 0, $entityID, $value);
2634                    }
2635                }
2636            }
2637        } else {
2638            Confess("$fieldName is not a valid field name.");
2639        }
2640    }
2641    
2642    =head3 InsertObject
2643    
2644        $erdb->InsertObject($objectType, \%fieldHash);
2645    
2646    Insert an object into the database. The object is defined by a type name and then a hash
2647    of field names to values. Field values in the primary relation are represented by scalars.
2648    (Note that for relationships, the primary relation is the B<only> relation.)
2649    Field values for the other relations comprising the entity are always list references. For
2650    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2651    C<ZP_00210270.1> and C<gi|46206278>.
2652    
2653        $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2654    
2655    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2656    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2657    
2658        $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2659    
2660    =over 4
2661    
2662    =item newObjectType
2663    
2664    Type name of the object to insert.
2665    
2666    =item fieldHash
2667    
2668    Hash of field names to values.
2669    
2670    =back
2671    
2672    =cut
2673    
2674    sub InsertObject {
2675        # Get the parameters.
2676        my ($self, $newObjectType, $fieldHash) = @_;
2677        # Denote that so far we appear successful.
2678        my $retVal = 1;
2679        # Get the database handle.
2680        my $dbh = $self->{_dbh};
2681        # Get the relation list.
2682        my $relationTable = $self->_GetRelationTable($newObjectType);
2683        # Loop through the relations. We'll build insert statements for each one. If a relation is
2684        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2685        # stop the loop.
2686        my @relationList = keys %{$relationTable};
2687        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2688            my $relationName = $relationList[$i];
2689            my $relationDefinition = $relationTable->{$relationName};
2690            # Get the relation's fields. For each field we will collect a value in the corresponding
2691            # position of the @valueList array. If one of the fields is missing, we will add it to the
2692            # @missing list.
2693            my @fieldList = @{$relationDefinition->{Fields}};
2694            my @fieldNameList = ();
2695            my @valueList = ();
2696            my @missing = ();
2697            my $recordCount = 1;
2698            for my $fieldDescriptor (@fieldList) {
2699                # Get the field name and save it. Note we need to fix it up so the hyphens
2700                # are converted to underscores.
2701                my $fieldName = $fieldDescriptor->{name};
2702                push @fieldNameList, _FixName($fieldName);
2703                # Look for the named field in the incoming structure. Note that we are looking
2704                # for the real field name, not the fixed-up one!
2705                if (exists $fieldHash->{$fieldName}) {
2706                    # Here we found the field. Stash it in the value list.
2707                    my $value = $fieldHash->{$fieldName};
2708                    push @valueList, $value;
2709                    # If the value is a list, we may need to increment the record count.
2710                    if (ref $value eq "ARRAY") {
2711                        my $thisCount = @{$value};
2712                        if ($recordCount == 1) {
2713                            # Here we have our first list, so we save its count.
2714                            $recordCount = $thisCount;
2715                        } elsif ($recordCount != $thisCount) {
2716                            # Here we have a second list, so its length has to match the
2717                            # previous lists.
2718                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2719                            $retVal = 0;
2720                        }
2721                    }
2722                } else {
2723                    # Here the field is not present. Flag it as missing.
2724                    push @missing, $fieldName;
2725                }
2726            }
2727            # If we are the primary relation, add the new-record flag.
2728            if ($relationName eq $newObjectType) {
2729                push @valueList, 1;
2730                push @fieldNameList, "new_record";
2731            }
2732            # Only proceed if there are no missing fields.
2733            if (@missing > 0) {
2734                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2735                    join(' ', @missing)) if T(1);
2736            } else {
2737                # Build the INSERT statement.
2738                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2739                    ") VALUES (";
2740                # Create a marker list of the proper size and put it in the statement.
2741                my @markers = ();
2742                while (@markers < @fieldNameList) { push @markers, '?'; }
2743                $statement .= join(', ', @markers) . ")";
2744                # We have the insert statement, so prepare it.
2745                my $sth = $dbh->prepare_command($statement);
2746                Trace("Insert statement prepared: $statement") if T(3);
2747                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2748                # a list, we use the current element. The values are stored in the @parameterList array.
2749                my $done = 0;
2750                for (my $i = 0; $i < $recordCount; $i++) {
2751                    # Clear the parameter list array.
2752                    my @parameterList = ();
2753                    # Loop through the values.
2754                    for my $value (@valueList) {
2755                        # Check to see if this is a scalar value.
2756                        if (ref $value eq "ARRAY") {
2757                            # Here we have a list value. Pull the current entry.
2758                            push @parameterList, $value->[$i];
2759                        } else {
2760                            # Here we have a scalar value. Use it unmodified.
2761                            push @parameterList, $value;
2762                        }
2763                    }
2764                    # Execute the INSERT statement with the specified parameter list.
2765                    $retVal = $sth->execute(@parameterList);
2766                    if (!$retVal) {
2767                        my $errorString = $sth->errstr();
2768                        Confess("Error inserting into $relationName: $errorString");
2769                    } else {
2770                        Trace("Insert successful using $parameterList[0].") if T(3);
2771                    }
2772                }
2773            }
2774        }
2775        # Return a 1 for backward compatability.
2776        return 1;
2777    }
2778    
2779    =head3 UpdateEntity
2780    
2781        $erdb->UpdateEntity($entityName, $id, \%fields);
2782    
2783    Update the values of an entity. This is an unprotected update, so it should only be
2784    done if the database resides on a database server.
2785    
2786    =over 4
2787    
2788    =item entityName
2789    
2790    Name of the entity to update. (This is the entity type.)
2791    
2792    =item id
2793    
2794    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2795    
2796    =item fields
2797    
2798    Reference to a hash mapping field names to their new values. All of the fields named
2799    must be in the entity's primary relation, and they cannot any of them be the ID field.
2800    
2801    =back
2802    
2803    =cut
2804    
2805    sub UpdateEntity {
2806        # Get the parameters.
2807        my ($self, $entityName, $id, $fields) = @_;
2808        # Get a list of the field names being updated.
2809        my @fieldList = keys %{$fields};
2810        # Verify that the fields exist.
2811        my $checker = $self->GetFieldTable($entityName);
2812        for my $field (@fieldList) {
2813            if ($field eq 'id') {
2814                Confess("Cannot update the ID field for entity $entityName.");
2815            } elsif ($checker->{$field}->{relation} ne $entityName) {
2816                Confess("Cannot find $field in primary relation of $entityName.");
2817            }
2818        }
2819        # Build the SQL statement.
2820        my @sets = ();
2821        my @valueList = ();
2822        for my $field (@fieldList) {
2823            push @sets, _FixName($field) . " = ?";
2824            push @valueList, $fields->{$field};
2825        }
2826        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2827        # Add the ID to the list of binding values.
2828        push @valueList, $id;
2829        # Call SQL to do the work.
2830        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2831        # Check for errors.
2832        if ($rows == 0) {
2833            Confess("Entity $id of type $entityName not found.");
2834        }
2835    }
2836    
2837    =head3 LoadTable
2838    
2839        my $results = $erdb->LoadTable($fileName, $relationName, %options);
2840    
2841    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2842    first.
2843    
2844    =over 4
2845    
2846    =item fileName
2847    
2848    Name of the file from which the table data should be loaded.
2849    
2850    =item relationName
2851    
2852    Name of the relation to be loaded. This is the same as the table name.
2853    
2854    =item options
2855    
2856    A hash of load options.
2857    
2858    =item RETURN
2859    
2860    Returns a statistical object containing a list of the error messages.
2861    
2862    =back
2863    
2864    The permissible options are as follows.
2865    
2866    =over 4
2867    
2868    =item truncate
2869    
2870    If TRUE, then the table will be erased before loading.
2871    
2872    =item mode
2873    
2874    Mode in which the load should operate, either C<low_priority> or C<concurrent>.
2875    This option is only applicable to a MySQL database.
2876    
2877    =item partial
2878    
2879    If TRUE, then it is assumed that this is a partial load, and the table will not
2880    be analyzed and compacted at the end.
2881    
2882    =back
2883    
2884    =cut
2885    sub LoadTable {
2886        # Get the parameters.
2887        my ($self, $fileName, $relationName, %options) = @_;
2888        # Create the statistical return object.
2889        my $retVal = _GetLoadStats();
2890        # Trace the fact of the load.
2891        Trace("Loading table $relationName from $fileName") if T(2);
2892        # Get the database handle.
2893        my $dbh = $self->{_dbh};
2894        # Get the input file size.
2895        my $fileSize = -s $fileName;
2896        # Get the relation data.
2897        my $relation = $self->_FindRelation($relationName);
2898        # Check the truncation flag.
2899        if ($options{truncate}) {
2900            Trace("Creating table $relationName") if T(2);
2901            # Compute the row count estimate. We take the size of the load file,
2902            # divide it by the estimated row size, and then multiply by 2 to
2903            # leave extra room. We postulate a minimum row count of 1000 to
2904            # prevent problems with incoming empty load files.
2905            my $rowSize = $self->EstimateRowSize($relationName);
2906            my $estimate = $fileSize * 8 / $rowSize;
2907            if ($estimate < 1000) {
2908                $estimate = 1000;
2909            }
2910            # Re-create the table without its index.
2911            $self->CreateTable($relationName, 0, $estimate);
2912            # If this is a pre-index DBMS, create the index here.
2913            if ($dbh->{_preIndex}) {
2914                eval {
2915                    $self->CreateIndex($relationName);
2916                };
2917                if ($@) {
2918                    $retVal->AddMessage($@);
2919                }
2920            }
2921        }
2922        # Load the table.
2923        my $rv;
2924        eval {
2925            $rv = $dbh->load_table(file => $fileName, tbl => $relationName, style => $options{mode});
2926        };
2927        if (!defined $rv) {
2928            $retVal->AddMessage($@) if ($@);
2929            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2930            Trace("Table load failed for $relationName.") if T(1);
2931        } else {
2932            # Here we successfully loaded the table.
2933            $retVal->Add("tables");
2934            my $size = -s $fileName;
2935            Trace("$size bytes loaded into $relationName.") if T(2);
2936            $retVal->Add("bytes", $size);
2937            # If we're rebuilding, we need to create the table indexes.
2938            if ($options{truncate}) {
2939                # Indexes are created here for PostGres. For PostGres, indexes are
2940                # best built at the end. For MySQL, the reverse is true.
2941                if (! $dbh->{_preIndex}) {
2942                    eval {
2943                        $self->CreateIndex($relationName);
2944                    };
2945                    if ($@) {
2946                        $retVal->AddMessage($@);
2947                    }
2948                }
2949                # The full-text index (if any) is always built last, even for MySQL.
2950                # First we need to see if this table has a full-text index. Only
2951                # primary relations are allowed that privilege.
2952                Trace("Checking for full-text index on $relationName.") if T(2);
2953                if ($self->_IsPrimary($relationName)) {
2954                    $self->CreateSearchIndex($relationName);
2955                }
2956            }
2957        }
2958        # Analyze the table to improve performance.
2959        if (! $options{partial}) {
2960            Trace("Analyzing and compacting $relationName.") if T(3);
2961            $dbh->vacuum_it($relationName);
2962        }
2963        Trace("$relationName load completed.") if T(3);
2964        # Return the statistics.
2965        return $retVal;
2966    }
2967    
2968    =head3 CreateSearchIndex
2969    
2970        $erdb->CreateSearchIndex($objectName);
2971    
2972    Check for a full-text search index on the specified entity or relationship object, and
2973    if one is required, rebuild it.
2974    
2975    =over 4
2976    
2977    =item objectName
2978    
2979    Name of the entity or relationship to be indexed.
2980    
2981    =back
2982    
2983    =cut
2984    
2985    sub CreateSearchIndex {
2986        # Get the parameters.
2987        my ($self, $objectName) = @_;
2988        # Get the relation's entity/relationship structure.
2989        my $structure = $self->_GetStructure($objectName);
2990        # Get the database handle.
2991        my $dbh = $self->{_dbh};
2992        Trace("Checking for search fields in $objectName.") if T(3);
2993        # Check for a searchable fields list.
2994        if (exists $structure->{searchFields}) {
2995            # Here we know that we need to create a full-text search index.
2996            # Get an SQL-formatted field name list.
2997            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2998            # Create the index. If it already exists, it will be dropped.
2999            $dbh->create_index(tbl => $objectName, idx => "search_idx",
3000                               flds => $fields, kind => 'fulltext');
3001            Trace("Index created for $fields in $objectName.") if T(2);
3002        }
3003    }
3004    
3005    =head3 DropRelation
3006    
3007        $erdb->DropRelation($relationName);
3008    
3009    Physically drop a relation from the database.
3010    
3011    =over 4
3012    
3013    =item relationName
3014    
3015    Name of the relation to drop. If it does not exist, this method will have
3016    no effect.
3017    
3018    =back
3019    
3020    =cut
3021    
3022    sub DropRelation {
3023        # Get the parameters.
3024        my ($self, $relationName) = @_;
3025        # Get the database handle.
3026        my $dbh = $self->{_dbh};
3027        # Drop the relation. The method used here has no effect if the relation
3028        # does not exist.
3029        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
3030        $dbh->drop_table(tbl => $relationName);
3031    }
3032    
3033    =head3 MatchSqlPattern
3034    
3035        my $matched = ERDB::MatchSqlPattern($value, $pattern);
3036    
3037    Determine whether or not a specified value matches an SQL pattern. An SQL
3038    pattern has two wild card characters: C<%> that matches multiple characters,
3039    and C<_> that matches a single character. These can be escaped using a
3040    backslash (C<\>). We pull this off by converting the SQL pattern to a
3041    PERL regular expression. As per SQL rules, the match is case-insensitive.
3042    
3043    =over 4
3044    
3045    =item value
3046    
3047    Value to be matched against the pattern. Note that an undefined or empty
3048    value will not match anything.
3049    
3050    =item pattern
3051    
3052    SQL pattern against which to match the value. An undefined or empty pattern will
3053    match everything.
3054    
3055    =item RETURN
3056    
3057    Returns TRUE if the value and pattern match, else FALSE.
3058    
3059    =back
3060    
3061    =cut
3062    
3063    sub MatchSqlPattern {
3064        # Get the parameters.
3065        my ($value, $pattern) = @_;
3066        # Declare the return variable.
3067        my $retVal;
3068        # Insure we have a pattern.
3069        if (! defined($pattern) || $pattern eq "") {
3070            $retVal = 1;
3071        } else {
3072            # Break the pattern into pieces around the wildcard characters. Because we
3073            # use parentheses in the split function's delimiter expression, we'll get
3074            # list elements for the delimiters as well as the rest of the string.
3075            my @pieces = split /([_%]|\\[_%])/, $pattern;
3076            # Check some fast special cases.
3077            if ($pattern eq '%') {
3078                # A null pattern matches everything.
3079                $retVal = 1;
3080            } elsif (@pieces == 1) {
3081                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
3082                $retVal = (lc($value) eq lc($pattern));
3083            } elsif (@pieces == 2 && $pieces[1] eq '%') {
3084                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
3085                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
3086            } else {
3087                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
3088                my $realPattern = "";
3089                for my $piece (@pieces) {
3090                    # Determine the type of piece.
3091                    if ($piece eq "") {
3092                        # Empty pieces are ignored.
3093                    } elsif ($piece eq "%") {
3094                        # Here we have a multi-character wildcard. Note that it can match
3095                        # zero or more characters.
3096                        $realPattern .= ".*"
3097                    } elsif ($piece eq "_") {
3098                        # Here we have a single-character wildcard.
3099                        $realPattern .= ".";
3100                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
3101                        # This is an escape sequence (which is a rare thing, actually).
3102                        $realPattern .= substr($piece, 1, 1);
3103                    } else {
3104                        # Here we have raw text.
3105                        $realPattern .= quotemeta($piece);
3106                    }
3107                }
3108                # Do the match.
3109                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
3110            }
3111        }
3112        # Return the result.
3113        return $retVal;
3114    }
3115    
3116    =head3 GetEntity
3117    
3118        my $entityObject = $erdb->GetEntity($entityType, $ID);
3119    
3120    Return an object describing the entity instance with a specified ID.
3121    
3122    =over 4
3123    
3124    =item entityType
3125    
3126    Entity type name.
3127    
3128    =item ID
3129    
3130    ID of the desired entity.
3131    
3132    =item RETURN
3133    
3134    Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
3135    instance is found with the specified key.
3136    
3137    =back
3138    
3139    =cut
3140    
3141    sub GetEntity {
3142        # Get the parameters.
3143        my ($self, $entityType, $ID) = @_;
3144        # Create a query.
3145        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3146        # Get the first (and only) object.
3147        my $retVal = $query->Fetch();
3148        # Return the result.
3149        return $retVal;
3150    }
3151    
3152    =head3 GetChoices
3153    
3154        my @values = $erdb->GetChoices($entityName, $fieldName);
3155    
3156    Return a list of all the values for the specified field that are represented in the
3157    specified entity.
3158    
3159    Note that if the field is not indexed, then this will be a very slow operation.
3160    
3161    =over 4
3162    
3163    =item entityName
3164    
3165    Name of an entity in the database.
3166    
3167    =item fieldName
3168    
3169    Name of a field belonging to the entity. This is a raw field name without
3170    the standard parenthesized notation used in most calls.
3171    
3172    =item RETURN
3173    
3174    Returns a list of the distinct values for the specified field in the database.
3175    
3176    =back
3177    
3178    =cut
3179    
3180    sub GetChoices {
3181        # Get the parameters.
3182        my ($self, $entityName, $fieldName) = @_;
3183        # Declare the return variable.
3184        my @retVal;
3185        # Get the entity data structure.
3186        my $entityData = $self->_GetStructure($entityName);
3187        # Get the field.
3188        my $fieldHash = $entityData->{Fields};
3189        if (! exists $fieldHash->{$fieldName}) {
3190            Confess("$fieldName not found in $entityName.");
3191        } else {
3192            # Get the name of the relation containing the field.
3193            my $relation = $fieldHash->{$fieldName}->{relation};
3194            # Fix up the field name.
3195            my $realName = _FixName($fieldName);
3196            # Get the database handle.
3197            my $dbh = $self->{_dbh};
3198            # Query the database.
3199            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
3200            # Clean the results. They are stored as a list of lists, and we just want the one list.
3201            @retVal = sort map { $_->[0] } @{$results};
3202        }
3203        # Return the result.
3204        return @retVal;
3205    }
3206    
3207    =head3 GetEntityValues
3208    
3209        my @values = $erdb->GetEntityValues($entityType, $ID, \@fields);
3210    
3211    Return a list of values from a specified entity instance. If the entity instance
3212    does not exist, an empty list is returned.
3213    
3214    =over 4
3215    
3216    =item entityType
3217    
3218    Entity type name.
3219    
3220    =item ID
3221    
3222    ID of the desired entity.
3223    
3224    =item fields
3225    
3226    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
3227    
3228    =item RETURN
3229    
3230    Returns a flattened list of the values of the specified fields for the specified entity.
3231    
3232    =back
3233    
3234    =cut
3235    
3236    sub GetEntityValues {
3237        # Get the parameters.
3238        my ($self, $entityType, $ID, $fields) = @_;
3239        # Get the specified entity.
3240        my $entity = $self->GetEntity($entityType, $ID);
3241        # Declare the return list.
3242        my @retVal = ();
3243        # If we found the entity, push the values into the return list.
3244        if ($entity) {
3245            push @retVal, $entity->Values($fields);
3246        }
3247        # Return the result.
3248        return @retVal;
3249    }
3250    
3251    =head3 GetAll
3252    
3253        my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
3254    
3255    Return a list of values taken from the objects returned by a query. The first three
3256    parameters correspond to the parameters of the L</Get> method. The final parameter is
3257    a list of the fields desired from each record found by the query. The field name
3258    syntax is the standard syntax used for fields in the B<ERDB> system--
3259    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
3260    or relationship and I<fieldName> is the name of the field.
3261    
3262    The list returned will be a list of lists. Each element of the list will contain
3263    the values returned for the fields specified in the fourth parameter. If one of the
3264    fields specified returns multiple values, they are flattened in with the rest. For
3265    example, the following call will return a list of the features in a particular
3266    spreadsheet cell, and each feature will be represented by a list containing the
3267    feature ID followed by all of its essentiality determinations.
3268    
3269        @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']);
3270    
3271    =over 4
3272    
3273    =item objectNames
3274    
3275    List containing the names of the entity and relationship objects to be retrieved.
3276    
3277    =item filterClause
3278    
3279    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
3280    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
3281    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
3282    parameter list as additional parameters. The fields in a filter clause can come from primary
3283    entity relations, relationship relations, or secondary entity relations; however, all of the
3284    entities and relationships involved must be included in the list of object names.
3285    
3286    =item parameterList
3287    
3288    List of the parameters to be substituted in for the parameters marks in the filter clause.
3289    
3290    =item fields
3291    
3292    List of the fields to be returned in each element of the list returned.
3293    
3294    =item count
3295    
3296    Maximum number of records to return. If omitted or 0, all available records will be returned.
3297    
3298    =item RETURN
3299    
3300    Returns a list of list references. Each element of the return list contains the values for the
3301    fields specified in the B<fields> parameter.
3302    
3303    =back
3304    
3305    =cut
3306    #: Return Type @@;
3307    sub GetAll {
3308        # Get the parameters.
3309        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3310        # Translate the parameters from a list reference to a list. If the parameter
3311        # list is a scalar we convert it into a singleton list.
3312        my @parmList = ();
3313        if (ref $parameterList eq "ARRAY") {
3314            Trace("GetAll parm list is an array.") if T(4);
3315            @parmList = @{$parameterList};
3316        } else {
3317            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3318            push @parmList, $parameterList;
3319        }
3320        # Insure the counter has a value.
3321        if (!defined $count) {
3322            $count = 0;
3323        }
3324        # Add the row limit to the filter clause.
3325        if ($count > 0) {
3326            $filterClause .= " LIMIT $count";
3327        }
3328        # Create the query.
3329        my $query = $self->Get($objectNames, $filterClause, \@parmList);
3330        # Set up a counter of the number of records read.
3331        my $fetched = 0;
3332        # Loop through the records returned, extracting the fields. Note that if the
3333        # counter is non-zero, we stop when the number of records read hits the count.
3334        my @retVal = ();
3335        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3336            my @rowData = $row->Values($fields);
3337            push @retVal, \@rowData;
3338            $fetched++;
3339        }
3340        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3341        # Return the resulting list.
3342        return @retVal;
3343    }
3344    
3345    =head3 Exists
3346    
3347        my $found = $sprout->Exists($entityName, $entityID);
3348    
3349    Return TRUE if an entity exists, else FALSE.
3350    
3351    =over 4
3352    
3353    =item entityName
3354    
3355    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3356    
3357    =item entityID
3358    
3359    ID of the entity instance whose existence is to be checked.
3360    
3361    =item RETURN
3362    
3363    Returns TRUE if the entity instance exists, else FALSE.
3364    
3365    =back
3366    
3367    =cut
3368    #: Return Type $;
3369    sub Exists {
3370        # Get the parameters.
3371        my ($self, $entityName, $entityID) = @_;
3372        # Check for the entity instance.
3373        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3374        my $testInstance = $self->GetEntity($entityName, $entityID);
3375        # Return an existence indicator.
3376        my $retVal = ($testInstance ? 1 : 0);
3377        return $retVal;
3378    }
3379    
3380    =head3 EstimateRowSize
3381    
3382        my $rowSize = $erdb->EstimateRowSize($relName);
3383    
3384    Estimate the row size of the specified relation. The estimated row size is computed by adding
3385    up the average length for each data type.
3386    
3387    =over 4
3388    
3389    =item relName
3390    
3391    Name of the relation whose estimated row size is desired.
3392    
3393    =item RETURN
3394    
3395    Returns an estimate of the row size for the specified relation.
3396    
3397    =back
3398    
3399    =cut
3400    #: Return Type $;
3401    sub EstimateRowSize {
3402        # Get the parameters.
3403        my ($self, $relName) = @_;
3404        # Declare the return variable.
3405        my $retVal = 0;
3406        # Find the relation descriptor.
3407        my $relation = $self->_FindRelation($relName);
3408        # Get the list of fields.
3409        for my $fieldData (@{$relation->{Fields}}) {
3410            # Get the field type and add its length.
3411            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3412            $retVal += $fieldLen;
3413        }
3414        # Return the result.
3415        return $retVal;
3416    }
3417    
3418    =head3 GetFieldTable
3419    
3420        my $fieldHash = $self->GetFieldTable($objectnName);
3421    
3422    Get the field structure for a specified entity or relationship.
3423    
3424    =over 4
3425    
3426    =item objectName
3427    
3428    Name of the desired entity or relationship.
3429    
3430    =item RETURN
3431    
3432    The table containing the field descriptors for the specified object.
3433    
3434    =back
3435    
3436    =cut
3437    
3438    sub GetFieldTable {
3439        # Get the parameters.
3440        my ($self, $objectName) = @_;
3441        # Get the descriptor from the metadata.
3442        my $objectData = $self->_GetStructure($objectName);
3443        # Return the object's field table.
3444        return $objectData->{Fields};
3445    }
3446    
3447    =head3 SplitKeywords
3448    
3449        my @keywords = ERDB::SplitKeywords($keywordString);
3450    
3451    This method returns a list of the positive keywords in the specified
3452    keyword string. All of the operators will have been stripped off,
3453    and if the keyword is preceded by a minus operator (C<->), it will
3454    not be in the list returned. The idea here is to get a list of the
3455    keywords the user wants to see. The list will be processed to remove
3456    duplicates.
3457    
3458    It is possible to create a string that confuses this method. For example
3459    
3460        frog toad -frog
3461    
3462    would return both C<frog> and C<toad>. If this is a problem we can deal
3463    with it later.
3464    
3465    =over 4
3466    
3467    =item keywordString
3468    
3469    The keyword string to be parsed.
3470    
3471    =item RETURN
3472    
3473    Returns a list of the words in the keyword string the user wants to
3474    see.
3475    
3476    =back
3477    
3478    =cut
3479    
3480    sub SplitKeywords {
3481        # Get the parameters.
3482        my ($keywordString) = @_;
3483        # Make a safety copy of the string. (This helps during debugging.)
3484        my $workString = $keywordString;
3485        # Convert operators we don't care about to spaces.
3486        $workString =~ tr/+"()<>/ /;
3487        # Split the rest of the string along space boundaries. Note that we
3488        # eliminate any words that are zero length or begin with a minus sign.
3489        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3490        # Use a hash to remove duplicates.
3491        my %words = map { $_ => 1 } @wordList;
3492        # Return the result.
3493        return sort keys %words;
3494    }
3495    
3496    =head3 ValidateFieldName
3497    
3498        my $okFlag = ERDB::ValidateFieldName($fieldName);
3499    
3500    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3501    be hyphenated words subject to certain restrictions.
3502    
3503    =over 4
3504    
3505    =item fieldName
3506    
3507    Field name to be validated.
3508    
3509    =item RETURN
3510    
3511    Returns TRUE if the field name is valid, else FALSE.
3512    
3513    =back
3514    
3515    =cut
3516    
3517    sub ValidateFieldName {
3518        # Get the parameters.
3519        my ($fieldName) = @_;
3520        # Declare the return variable. The field name is valid until we hear
3521        # differently.
3522        my $retVal = 1;
3523        # Compute the maximum name length.
3524        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3525        # Look for bad stuff in the name.
3526        if ($fieldName =~ /--/) {
3527            # Here we have a doubled minus sign.
3528            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3529            $retVal = 0;
3530        } elsif ($fieldName !~ /^[A-Za-z]/) {
3531            # Here the field name is missing the initial letter.
3532            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3533            $retVal = 0;
3534        } elsif (length($fieldName) > $maxLen) {
3535            # Here the field name is too long.
3536            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3537        } else {
3538            # Strip out the minus signs. Everything remaining must be a letter,
3539            # underscore, or digit.
3540            my $strippedName = $fieldName;
3541            $strippedName =~ s/-//g;
3542            if ($strippedName !~ /^(\w|\d)+$/) {
3543                Trace("Field name $fieldName contains illegal characters.") if T(1);
3544                $retVal = 0;
3545            }
3546        }
3547        # Return the result.
3548        return $retVal;
3549    }
3550    
3551    =head3 ReadMetaXML
3552    
3553        my $rawMetaData = ERDB::ReadDBD($fileName);
3554    
3555    This method reads a raw database definition XML file and returns it.
3556    Normally, the metadata used by the ERDB system has been processed and
3557    modified to make it easier to load and retrieve the data; however,
3558    this method can be used to get the data in its raw form.
3559    
3560    =over 4
3561    
3562    =item fileName
3563    
3564    Name of the XML file to read.
3565    
3566    =item RETURN
3567    
3568    Returns a hash reference containing the raw XML data from the specified file.
3569    
3570    =back
3571    
3572    =cut
3573    
3574    sub ReadMetaXML {
3575        # Get the parameters.
3576        my ($fileName) = @_;
3577        # Read the XML.
3578        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3579        Trace("XML metadata loaded from file $fileName.") if T(1);
3580        # Return the result.
3581        return $retVal;
3582    }
3583    
3584    =head3 GetEntityFieldHash
3585    
3586        my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName);
3587    
3588    Get the field hash of the named entity in the specified raw XML structure.
3589    The field hash may not exist, in which case we need to create it.
3590    
3591    =over 4
3592    
3593    =item structure
3594    
3595    Raw XML structure defininng the database. This is not the run-time XML used by
3596    an ERDB object, since that has all sorts of optimizations built-in.
3597    
3598    =item entityName
3599    
3600    Name of the entity whose field structure is desired.
3601    
3602    =item RETURN
3603    
3604    Returns the field hash used to define the entity's fields.
3605    
3606    =back
3607    
3608    =cut
3609    
3610    sub GetEntityFieldHash {
3611        # Get the parameters.
3612        my ($structure, $entityName) = @_;
3613        # Get the entity structure.
3614        my $entityData = $structure->{Entities}->{$entityName};
3615        # Look for a field structure.
3616        my $retVal = $entityData->{Fields};
3617        # If it doesn't exist, create it.
3618        if (! defined($retVal)) {
3619            $entityData->{Fields} = {};
3620            $retVal = $entityData->{Fields};
3621        }
3622        # Return the result.
3623        return $retVal;
3624    }
3625    
3626    =head3 WriteMetaXML
3627    
3628        ERDB::WriteMetaXML($structure, $fileName);
3629    
3630    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3631    used to update the database definition. It must be used with care, however, since it
3632    will only work on a raw structure, not on the processed structure created by an ERDB
3633    constructor.
3634    
3635    =over 4
3636    
3637    =item structure
3638    
3639    XML structure to be written to the file.
3640    
3641    =item fileName
3642    
3643    Name of the output file to which the updated XML should be stored.
3644    
3645    =back
3646    
3647    =cut
3648    
3649    sub WriteMetaXML {
3650        # Get the parameters.
3651        my ($structure, $fileName) = @_;
3652        # Compute the output.
3653        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3654        # Write it to the file.
3655        my $xmlOut = Open(undef, ">$fileName");
3656        print $xmlOut $fileString;
3657    }
3658    
3659    
3660    =head3 HTMLNote
3661    
3662    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3663    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3664    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3665    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3666    
3667  Return a list of values from a specified entity instance.      my $realHtml = ERDB::HTMLNote($dataString);
3668    
3669  =over 4  =over 4
3670    
3671  =item entityType  =item dataString
3672    
3673  Entity type name.  String to convert to HTML.
3674    
3675  =item ID  =item RETURN
3676    
3677  ID of the desired entity.  An HTML string derived from the input string.
3678    
3679  =item fields  =back
3680    
3681  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  =cut
3682    
3683    sub HTMLNote {
3684        # Get the parameter.
3685        my ($dataString) = @_;
3686        # HTML-escape the text.
3687        my $retVal = CGI::escapeHTML($dataString);
3688        # Substitute the bulletin board codes.
3689        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3690        $retVal =~ s!\[p\]!</p><p>!g;
3691        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3692        $retVal =~ s!\[/link\]!</a>!g;
3693        # Return the result.
3694        return $retVal;
3695    }
3696    
3697    =head3 WikiNote
3698    
3699    Convert a note or comment to Wiki text by replacing some bulletin-board codes with HTML. The codes
3700    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3701    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3702    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3703    
3704        my $wikiText = ERDB::WikiNote($dataString);
3705    
3706    =over 4
3707    
3708    =item dataString
3709    
3710    String to convert to Wiki text.
3711    
3712  =item RETURN  =item RETURN
3713    
3714  Returns a flattened list of the values of the specified fields for the specified entity.  An Wiki text string derived from the input string.
3715    
3716  =back  =back
3717    
3718  =cut  =cut
3719    
3720  sub GetEntityValues {  sub WikiNote {
3721        # Get the parameter.
3722        my ($dataString) = @_;
3723        # HTML-escape the text.
3724        my $retVal = CGI::escapeHTML($dataString);
3725        # Substitute the bulletin board codes.
3726        my $italic = WikiTools::ItalicCode();
3727        $retVal =~ s/\[\/?i\]/$italic/g;
3728        my $bold = WikiTools::BoldCode();
3729        $retVal =~ s/\[\/?b\]/$bold/g;
3730        # Paragraph breaks are the same no matter which Wiki you're using.
3731        $retVal =~ s!\[p\]!\n\n!g;
3732        # Now we do the links, which are complicated by the need to know two
3733        # things: the target URL and the text.
3734        while ($retVal =~ /\[link\s+([^\]]+)\]([^\[]+)\[\/link\]/g) {
3735            # Replace the matched string with the Wiki markup for links. Note that
3736            # $-[0] is the starting position of the match for the entire expression,
3737            # and $+[0] is past the ending position.
3738            substr $retVal, $-[0], $+[0] - $-[0], WikiTools::LinkMarkup($1, $2);
3739        }
3740        # Return the result.
3741        return $retVal;
3742    }
3743    
3744    =head3 BeginTran
3745    
3746        $erdb->BeginTran();
3747    
3748    Start a database transaction.
3749    
3750    =cut
3751    
3752    sub BeginTran {
3753        my ($self) = @_;
3754        $self->{_dbh}->begin_tran();
3755    
3756    }
3757    
3758    =head3 CommitTran
3759    
3760        $erdb->CommitTran();
3761    
3762    Commit an active database transaction.
3763    
3764    =cut
3765    
3766    sub CommitTran {
3767        my ($self) = @_;
3768        $self->{_dbh}->commit_tran();
3769    }
3770    
3771    =head3 RollbackTran
3772    
3773        $erdb->RollbackTran();
3774    
3775    Roll back an active database transaction.
3776    
3777    =cut
3778    
3779    sub RollbackTran {
3780        my ($self) = @_;
3781        $self->{_dbh}->roll_tran();
3782    }
3783    
3784    =head3 UpdateField
3785    
3786        my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms);
3787    
3788    Update all occurrences of a specific field value to a new value. The number of rows changed will be
3789    returned.
3790    
3791    =over 4
3792    
3793    =item fieldName
3794    
3795    Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3796    
3797    =item oldValue
3798    
3799    Value to be modified. All occurrences of this value in the named field will be replaced by the
3800    new value.
3801    
3802    =item newValue
3803    
3804    New value to be substituted for the old value when it's found.
3805    
3806    =item filter
3807    
3808    A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3809    
3810    =item parms
3811    
3812    Reference to a list of parameter values in the filter.
3813    
3814    =item RETURN
3815    
3816    Returns the number of rows modified.
3817    
3818    =back
3819    
3820    =cut
3821    
3822    sub UpdateField {
3823      # Get the parameters.      # Get the parameters.
3824      my ($self, $entityType, $ID, $fields) = @_;      my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3825      # Get the specified entity.      # Get the object and field names from the field name parameter.
3826      my $entity = $self->GetEntity($entityType, $ID);      $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3827      # Declare the return list.      my $objectName = $1;
3828        my $realFieldName = _FixName($2);
3829        # Add the old value to the filter. Note we allow the possibility that no
3830        # filter was specified.
3831        my $realFilter = "$fieldName = ?";
3832        if ($filter) {
3833            $realFilter .= " AND $filter";
3834        }
3835        # Format the query filter.
3836        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3837            $self->_SetupSQL([$objectName], $realFilter);
3838        # Create the query. Since there is only one object name, the mapped-name data is not
3839        # necessary. Neither is the FROM clause.
3840        $suffix =~ s/^FROM.+WHERE\s+//;
3841        # Create the update statement.
3842        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3843        # Get the database handle.
3844        my $dbh = $self->{_dbh};
3845        # Add the old and new values to the parameter list. Note we allow the possibility that
3846        # there are no user-supplied parameters.
3847        my @params = ($newValue, $oldValue);
3848        if (defined $parms) {
3849            push @params, @{$parms};
3850        }
3851        # Execute the update.
3852        my $retVal = $dbh->SQL($command, 0, @params);
3853        # Make the funky zero a real zero.
3854        if ($retVal == 0) {
3855            $retVal = 0;
3856        }
3857        # Return the result.
3858        return $retVal;
3859    }
3860    
3861    
3862    =head2 Data Mining Methods
3863    
3864    =head3 GetUsefulCrossValues
3865    
3866        my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship);
3867    
3868    Return a list of the useful attributes that would be returned by a B<Cross> call
3869    from an entity of the source entity type through the specified relationship. This
3870    means it will return the fields of the target entity type and the intersection data
3871    fields in the relationship. Only primary table fields are returned. In other words,
3872    the field names returned will be for fields where there is always one and only one
3873    value.
3874    
3875    =over 4
3876    
3877    =item sourceEntity
3878    
3879    Name of the entity from which the relationship crossing will start.
3880    
3881    =item relationship
3882    
3883    Name of the relationship being crossed.
3884    
3885    =item RETURN
3886    
3887    Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3888    
3889    =back
3890    
3891    =cut
3892    #: Return Type @;
3893    sub GetUsefulCrossValues {
3894        # Get the parameters.
3895        my ($self, $sourceEntity, $relationship) = @_;
3896        # Declare the return variable.
3897      my @retVal = ();      my @retVal = ();
3898      # If we found the entity, push the values into the return list.      # Determine the target entity for the relationship. This is whichever entity is not
3899      if ($entity) {      # the source entity. So, if the source entity is the FROM, we'll get the name of
3900          push @retVal, $entity->Values($fields);      # the TO, and vice versa.
3901        my $relStructure = $self->_GetStructure($relationship);
3902        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3903        my $targetEntity = $relStructure->{$targetEntityType};
3904        # Get the field table for the entity.
3905        my $entityFields = $self->GetFieldTable($targetEntity);
3906        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3907        # For the entity fields, the key aspect of the target structure is that the {relation} value
3908        # must match the entity name.
3909        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3910                            keys %{$entityFields};
3911        # Push the fields found onto the return variable.
3912        push @retVal, sort @fieldList;
3913        # Get the field table for the relationship.
3914        my $relationshipFields = $self->GetFieldTable($relationship);
3915        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3916        # This may end up being an empty set.
3917        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3918                            keys %{$relationshipFields};
3919        # Push these onto the return list.
3920        push @retVal, sort @fieldList2;
3921        # Return the result.
3922        return @retVal;
3923    }
3924    
3925    =head3 FindColumn
3926    
3927        my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier);
3928    
3929    Return the location a desired column in a data mining header line. The data
3930    mining header line is a tab-separated list of column names. The column
3931    identifier is either the numerical index of a column or the actual column
3932    name.
3933    
3934    =over 4
3935    
3936    =item headerLine
3937    
3938    The header line from a data mining command, which consists of a tab-separated
3939    list of column names.
3940    
3941    =item columnIdentifier
3942    
3943    Either the ordinal number of the desired column (1-based), or the name of the
3944    desired column.
3945    
3946    =item RETURN
3947    
3948    Returns the array index (0-based) of the desired column.
3949    
3950    =back
3951    
3952    =cut
3953    
3954    sub FindColumn {
3955