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revision 1.41, Wed Mar 29 20:51:37 2006 UTC revision 1.86, Mon Feb 12 19:23:32 2007 UTC
# Line 9  Line 9 
9      use DBObject;      use DBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13      use FIG;      use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 58  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
 To facilitate testing, the ERDB module supports automatic generation of test data. This process  
 is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
 fully implemented.  
   
76  =head2 XML Database Description  =head2 XML Database Description
77    
78  =head3 Data Types  =head3 Data Types
# Line 90  Line 92 
92    
93  32-bit signed integer  32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99  =item date  =item date
100    
101  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 109  Line 115 
115  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
116  0 and 1.  0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122  =item key-string  =item key-string
123    
124  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 125  Line 135 
135    
136  variable-length string, maximum 255 characters  variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142  =back  =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151  =head3 Global Tags  =head3 Global Tags
152    
153  The entire database definition must be inside a B<Database> tag. The display name of  The entire database definition must be inside a B<Database> tag. The display name of
# Line 170  Line 191 
191    
192  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
194  with the respect to field names, so a best practice is to use lower-case letters only.  with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198  =item type  =item type
199    
# Line 189  Line 212 
212  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
213  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227  =back  =back
228    
229  =head3 Indexes  =head3 Indexes
230    
231  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields 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 =>   1, 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                  );                  );
377    
378  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 324  Line 381 
381                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
382                   );                   );
383    
384  # Table for interpreting string patterns.  # Options for XML input and output.
385    
386    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
387                                      Entities => 'Entity',
388                                      Fields => 'Field',
389                                      Indexes => 'Index',
390                                      IndexFields => 'IndexField'
391                                    },
392                      KeyAttr =>    { Relationship => 'name',
393                                      Entity => 'name',
394                                      Field => 'name'
395                                    },
396                      SuppressEmpty => 1,
397                     );
398    
399  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
400                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
401                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
402                       'V' => "aeiou",                    NormalizeSpace => 2,
                      'K' => "bcdfghjklmnoprstvwxyz"  
403                     );                     );
404    my %XmlOutOpts = (
405                      RootName => 'Database',
406                      XMLDecl => 1,
407                     );
408    
409    
410  =head2 Public Methods  =head2 Public Methods
411    
# Line 402  Line 476 
476      # Write the HTML heading stuff.      # Write the HTML heading stuff.
477      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
478      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
479        # Write the documentation.
480        print HTMLOUT $self->DisplayMetaData();
481        # Close the document.
482        print HTMLOUT "</body>\n</html>\n";
483        # Close the file.
484        close HTMLOUT;
485    }
486    
487    =head3 DisplayMetaData
488    
489    C<< my $html = $erdb->DisplayMetaData(); >>
490    
491    Return an HTML description of the database. This description can be used to help users create
492    the data to be loaded into the relations and form queries. The output is raw includable HTML
493    without any HEAD or BODY tags.
494    
495    =over 4
496    
497    =item filename
498    
499    The name of the output file.
500    
501    =back
502    
503    =cut
504    
505    sub DisplayMetaData {
506        # Get the parameters.
507        my ($self) = @_;
508        # Get the metadata and the title string.
509        my $metadata = $self->{_metaData};
510        # Get the title string.
511        my $title = $metadata->{Title};
512        # Get the entity and relationship lists.
513        my $entityList = $metadata->{Entities};
514        my $relationshipList = $metadata->{Relationships};
515        # Declare the return variable.
516        my $retVal = "";
517        # Open the output file.
518        Trace("Building MetaData table of contents.") if T(4);
519      # 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
520      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
521      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";
522      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
523      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
524          # Display this item.          # Display this item.
525          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
526      }      }
527      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
528      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";
529      # Loop through the Relationships.      # Loop through the Relationships.
530      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
531          # Display this item.          # Display this item.
532          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
533          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
534      }      }
535      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
536      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";
537      # Close off the table of contents itself.      # Close off the table of contents itself.
538      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
539      # 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.
540      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
541      # Loop through the entities.      # Loop through the entities.
542      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
543          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
544          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
545          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
546          # Get the entity data.          # Get the entity data.
547          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
548          # If there's descriptive text, display it.          # If there's descriptive text, display it.
549          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
550              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
551          }          }
552          # 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.
553          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
554            if ($relCount > 0) {
555                # First, we set up the relationship subsection.
556                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
557          # Loop through the relationships.          # Loop through the relationships.
558          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
559              # Get the relationship data.              # Get the relationship data.
# Line 446  Line 563 
563                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
564                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
565                  # Display the relationship data.                  # Display the relationship data.
566                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
567              }              }
568          }          }
569          # Close off the relationship list.          # Close off the relationship list.
570          print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
571            }
572          # Get the entity's relations.          # Get the entity's relations.
573          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
574          # Create a header for the relation subsection.          # Create a header for the relation subsection.
575          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
576          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
577          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
578              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
579              print HTMLOUT $htmlString;              $retVal .= $htmlString;
580          }          }
581      }      }
582      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
583      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
584      # Loop through the relationships.      # Loop through the relationships.
585      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
586          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 470  Line 588 
588          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
589          # Create the relationship header.          # Create the relationship header.
590          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
591          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
592          # Get the entity names.          # Get the entity names.
593          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
594          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 480  Line 598 
598          # since both sentences will say the same thing.          # since both sentences will say the same thing.
599          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
600          if ($arity eq "11") {          if ($arity eq "11") {
601              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
602          } else {          } else {
603              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
604              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
605                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
606              }              }
607          }          }
608          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
609          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
610          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
611              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
612          }          }
613          # Generate the relationship's relation table.          # Generate the relationship's relation table.
614          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
615          print HTMLOUT $htmlString;          $retVal .= $htmlString;
616      }      }
617      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
618      # Denote we're starting the join table.      # Denote we're starting the join table.
619      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
620      # Create a table header.      # Create a table header.
621      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
622      # Loop through the joins.      # Loop through the joins.
623      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
624      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 513  Line 631 
631          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
632          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
633          # Display them in a table row.          # Display them in a table row.
634          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";
635      }      }
636      # Close the table.      # Close the table.
637      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
638      # Close the document.      Trace("Built MetaData HTML.") if T(3);
639      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
640      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
641  }  }
642    
643  =head3 DumpMetaData  =head3 DumpMetaData
# Line 539  Line 655 
655      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
656  }  }
657    
658    =head3 FindIndexForEntity
659    
660    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
661    
662    This method locates the entry in an entity's index list that begins with the
663    specified attribute name. If the entity has no index list, one will be
664    created. This method works on raw XML, not a live ERDB object.
665    
666    =over 4
667    
668    =item xml
669    
670    The raw XML structure defining the database.
671    
672    =item entityName
673    
674    The name of the relevant entity.
675    
676    =item attributeName
677    
678    The name of the attribute relevant to the search.
679    
680    =item RETURN
681    
682    The numerical index in the index list of the index entry for the specified entity and
683    attribute, or C<undef> if no such index exists.
684    
685    =back
686    
687    =cut
688    
689    sub FindIndexForEntity {
690        # Get the parameters.
691        my ($xml, $entityName, $attributeName) = @_;
692        # Declare the return variable.
693        my $retVal;
694        # Get the named entity.
695        my $entityData = $xml->{Entities}->{$entityName};
696        if (! $entityData) {
697            Confess("Entity $entityName not found in DBD structure.");
698        } else {
699            # Insure it has an index list.
700            if (! exists $entityData->{Indexes}) {
701                $entityData->{Indexes} = [];
702            } else {
703                # Search for the desired index.
704                my $indexList = $entityData->{Indexes};
705                my $n = scalar @{$indexList};
706                Trace("Searching $n indexes in index list for $entityName.") if T(2);
707                # We use an indexed FOR here because we're returning an
708                # index number instead of an object. We do THAT so we can
709                # delete the index from the list if needed.
710                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
711                    my $index = $indexList->[$i];
712                    my $fields = $index->{IndexFields};
713                    # Technically this IF should be safe (that is, we are guaranteed
714                    # the existence of a "$fields->[0]"), because when we load the XML
715                    # we have SuppressEmpty specified.
716                    if ($fields->[0]->{name} eq $attributeName) {
717                        $retVal = $i;
718                    }
719                }
720            }
721        }
722        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
723        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
724        # Return the result.
725        return $retVal;
726    }
727    
728  =head3 CreateTables  =head3 CreateTables
729    
730  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 626  Line 812 
812      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
813      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
814      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
815      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
816        # index will not be built until the table has been loaded.
817      if ($indexFlag) {      if ($indexFlag) {
818          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
819      }      }
# Line 687  Line 874 
874      return $retVal;      return $retVal;
875  }  }
876    
877    =head3 DigestFields
878    
879    C<< $erdb->DigestFields($relName, $fieldList); >>
880    
881    Digest the strings in the field list that correspond to data type C<hash-string> in the
882    specified relation.
883    
884    =over 4
885    
886    =item relName
887    
888    Name of the relation to which the fields belong.
889    
890    =item fieldList
891    
892    List of field contents to be loaded into the relation.
893    
894    =back
895    
896    =cut
897    #: Return Type ;
898    sub DigestFields {
899        # Get the parameters.
900        my ($self, $relName, $fieldList) = @_;
901        # Get the relation definition.
902        my $relData = $self->_FindRelation($relName);
903        # Get the list of field descriptors.
904        my $fieldTypes = $relData->{Fields};
905        my $fieldCount = scalar @{$fieldTypes};
906        # Loop through the two lists.
907        for (my $i = 0; $i < $fieldCount; $i++) {
908            # Get the type of the current field.
909            my $fieldType = $fieldTypes->[$i]->{type};
910            # If it's a hash string, digest it in place.
911            if ($fieldType eq 'hash-string') {
912                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
913            }
914        }
915    }
916    
917    =head3 DigestKey
918    
919    C<< my $digested = $erdb->DigestKey($keyValue); >>
920    
921    Return the digested value of a symbolic key. The digested value can then be plugged into a
922    key-based search into a table with key-type hash-string.
923    
924    Currently the digesting process is independent of the database structure, but that may not
925    always be the case, so this is an instance method instead of a static method.
926    
927    =over 4
928    
929    =item keyValue
930    
931    Key value to digest.
932    
933    =item RETURN
934    
935    Digested value of the key.
936    
937    =back
938    
939    =cut
940    
941    sub DigestKey {
942        # Get the parameters.
943        my ($self, $keyValue) = @_;
944        # Compute the digest.
945        my $retVal = md5_base64($keyValue);
946        # Return the result.
947        return $retVal;
948    }
949    
950  =head3 CreateIndex  =head3 CreateIndex
951    
952  C<< $erdb->CreateIndex($relationName); >>  C<< $erdb->CreateIndex($relationName); >>
# Line 710  Line 970 
970      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
971          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
972          # Get the index's field list.          # Get the index's field list.
973          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
974            # Get a hash of the relation's field types.
975            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
976            # We need to check for text fields so we can append a length limitation for them. To do
977            # that, we need the relation's field list.
978            my $relFields = $relationData->{Fields};
979            for (my $i = 0; $i <= $#rawFields; $i++) {
980                # Get the field type.
981                my $field = $rawFields[$i];
982                my $type = $types{$field};
983                # Ask if it requires using prefix notation for the index.
984                my $mod = $TypeTable{$type}->{indexMod};
985                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
986                if ($mod) {
987                    # Append the prefix length to the field name,
988                    $rawFields[$i] .= "($mod)";
989                }
990            }
991            my @fieldList = _FixNames(@rawFields);
992          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
993          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
994          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
995          # Create the index.          # Create the index.
996          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
997                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
998          if ($rv) {          if ($rv) {
999              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1000          } else {          } else {
# Line 725  Line 1003 
1003      }      }
1004  }  }
1005    
1006    =head3 GetSecondaryFields
1007    
1008    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1009    
1010    This method will return a list of the name and type of each of the secondary
1011    fields for a specified entity. Secondary fields are stored in two-column tables
1012    in addition to the primary entity table. This enables the field to have no value
1013    or to have multiple values.
1014    
1015    =over 4
1016    
1017    =item entityName
1018    
1019    Name of the entity whose secondary fields are desired.
1020    
1021    =item RETURN
1022    
1023    Returns a hash mapping the field names to their field types.
1024    
1025    =back
1026    
1027    =cut
1028    
1029    sub GetSecondaryFields {
1030        # Get the parameters.
1031        my ($self, $entityName) = @_;
1032        # Declare the return variable.
1033        my %retVal = ();
1034        # Look for the entity.
1035        my $table = $self->GetFieldTable($entityName);
1036        # Loop through the fields, pulling out the secondaries.
1037        for my $field (sort keys %{$table}) {
1038            if ($table->{$field}->{relation} ne $entityName) {
1039                # Here we have a secondary field.
1040                $retVal{$field} = $table->{$field}->{type};
1041            }
1042        }
1043        # Return the result.
1044        return %retVal;
1045    }
1046    
1047    =head3 GetFieldRelationName
1048    
1049    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1050    
1051    Return the name of the relation containing a specified field.
1052    
1053    =over 4
1054    
1055    =item objectName
1056    
1057    Name of the entity or relationship containing the field.
1058    
1059    =item fieldName
1060    
1061    Name of the relevant field in that entity or relationship.
1062    
1063    =item RETURN
1064    
1065    Returns the name of the database relation containing the field, or C<undef> if
1066    the field does not exist.
1067    
1068    =back
1069    
1070    =cut
1071    
1072    sub GetFieldRelationName {
1073        # Get the parameters.
1074        my ($self, $objectName, $fieldName) = @_;
1075        # Declare the return variable.
1076        my $retVal;
1077        # Get the object field table.
1078        my $table = $self->GetFieldTable($objectName);
1079        # Only proceed if the field exists.
1080        if (exists $table->{$fieldName}) {
1081            # Determine the name of the relation that contains this field.
1082            $retVal = $table->{$fieldName}->{relation};
1083        }
1084        # Return the result.
1085        return $retVal;
1086    }
1087    
1088    =head3 DeleteValue
1089    
1090    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1091    
1092    Delete secondary field values from the database. This method can be used to delete all
1093    values of a specified field for a particular entity instance, or only a single value.
1094    
1095    Secondary fields are stored in two-column relations separate from an entity's primary
1096    table, and as a result a secondary field can legitimately have no value or multiple
1097    values. Therefore, it makes sense to talk about deleting secondary fields where it
1098    would not make sense for primary fields.
1099    
1100    =over 4
1101    
1102    =item entityName
1103    
1104    Name of the entity from which the fields are to be deleted.
1105    
1106    =item id
1107    
1108    ID of the entity instance to be processed. If the instance is not found, this
1109    method will have no effect. If C<undef> is specified, all values for all of
1110    the entity instances will be deleted.
1111    
1112    =item fieldName
1113    
1114    Name of the field whose values are to be deleted.
1115    
1116    =item fieldValue (optional)
1117    
1118    Value to be deleted. If not specified, then all values of the specified field
1119    will be deleted for the entity instance. If specified, then only the values which
1120    match this parameter will be deleted.
1121    
1122    =item RETURN
1123    
1124    Returns the number of rows deleted.
1125    
1126    =back
1127    
1128    =cut
1129    
1130    sub DeleteValue {
1131        # Get the parameters.
1132        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1133        # Declare the return value.
1134        my $retVal = 0;
1135        # We need to set up an SQL command to do the deletion. First, we
1136        # find the name of the field's relation.
1137        my $table = $self->GetFieldTable($entityName);
1138        my $field = $table->{$fieldName};
1139        my $relation = $field->{relation};
1140        # Make sure this is a secondary field.
1141        if ($relation eq $entityName) {
1142            Confess("Cannot delete values of $fieldName for $entityName.");
1143        } else {
1144            # Set up the SQL command to delete all values.
1145            my $sql = "DELETE FROM $relation";
1146            # Build the filter.
1147            my @filters = ();
1148            my @parms = ();
1149            # Check for a filter by ID.
1150            if (defined $id) {
1151                push @filters, "id = ?";
1152                push @parms, $id;
1153            }
1154            # Check for a filter by value.
1155            if (defined $fieldValue) {
1156                push @filters, "$fieldName = ?";
1157                push @parms, $fieldValue;
1158            }
1159            # Append the filters to the command.
1160            if (@filters) {
1161                $sql .= " WHERE " . join(" AND ", @filters);
1162            }
1163            # Execute the command.
1164            my $dbh = $self->{_dbh};
1165            $retVal = $dbh->SQL($sql, 0, @parms);
1166        }
1167        # Return the result.
1168        return $retVal;
1169    }
1170    
1171  =head3 LoadTables  =head3 LoadTables
1172    
1173  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
# Line 819  Line 1262 
1262      return sort keys %{$entityList};      return sort keys %{$entityList};
1263  }  }
1264    
1265    =head3 GetDataTypes
1266    
1267    C<< my %types = ERDB::GetDataTypes(); >>
1268    
1269    Return a table of ERDB data types. The table returned is a hash of hashes.
1270    The keys of the big hash are the datatypes. Each smaller hash has several
1271    values used to manage the data. The most interesting is the SQL type (key
1272    C<sqlType>) and the descriptive node (key C<notes>).
1273    
1274    Note that changing the values in the smaller hashes will seriously break
1275    things, so this data should be treated as read-only.
1276    
1277    =cut
1278    
1279    sub GetDataTypes {
1280        return %TypeTable;
1281    }
1282    
1283    
1284  =head3 IsEntity  =head3 IsEntity
1285    
1286  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
# Line 848  Line 1310 
1310    
1311  =head3 Get  =head3 Get
1312    
1313  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1314    
1315  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.
1316  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
# Line 856  Line 1318 
1318  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
1319  $genus.  $genus.
1320    
1321  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1322    
1323  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
1324  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
# Line 873  Line 1335 
1335  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
1336  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,
1337    
1338  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1339    
1340  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
1341  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.
# Line 930  Line 1392 
1392    
1393  C<< "LIMIT 10" >>  C<< "LIMIT 10" >>
1394    
1395  =item param1, param2, ..., paramN  =item params
1396    
1397  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1398    
1399  =item RETURN  =item RETURN
1400    
# Line 944  Line 1406 
1406    
1407  sub Get {  sub Get {
1408      # Get the parameters.      # Get the parameters.
1409      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1410      # Adjust the list of object names to account for multiple occurrences of the      # Process the SQL stuff.
1411      # same object. We start with a hash table keyed on object name that will      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1412      # return the object suffix. The first time an object is encountered it will          $self->_SetupSQL($objectNames, $filterClause);
1413      # not be found in the hash. The next time the hash will map the object name      # Create the query.
1414      # to 2, then 3, and so forth.      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1415      my %objectHash = ();          ".* $suffix";
1416      # This list will contain the object names as they are to appear in the      my $sth = $self->_GetStatementHandle($command, $params);
1417      # FROM list.      # Now we create the relation map, which enables DBQuery to determine the order, name
1418      my @fromList = ();      # and mapped name for each object in the query.
1419      # This list contains the suffixed object name for each object. It is exactly      my @relationMap = ();
1420      # parallel to the list in the $objectNames parameter.      for my $mappedName (@{$mappedNameListRef}) {
1421      my @mappedNameList = ();          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1422      # Finally, this hash translates from a mapped name to its original object name.      }
1423      my %mappedNameHash = ();      # Return the statement object.
1424      # Now we create the lists. Note that for every single name we push something into      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1425      # @fromList and @mappedNameList. This insures that those two arrays are exactly      return $retVal;
1426      # parallel to $objectNames.  }
1427      for my $objectName (@{$objectNames}) {  
1428          # Get the next suffix for this object.  
1429          my $suffix = $objectHash{$objectName};  
1430          if (! $suffix) {  =head3 Search
1431              # Here we are seeing the object for the first time. The object name  
1432              # is used as is.  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1433              push @mappedNameList, $objectName;  
1434              push @fromList, $objectName;  Perform a full text search with filtering. The search will be against a specified object
1435              $mappedNameHash{$objectName} = $objectName;  in the object name list. That object will get an extra field containing the search
1436              # Denote the next suffix will be 2.  relevance. Note that except for the search expression, the parameters of this method are
1437              $objectHash{$objectName} = 2;  the same as those for L</Get> and follow the same rules.
1438    
1439    =over 4
1440    
1441    =item searchExpression
1442    
1443    Boolean search expression for the text fields of the target object. The default mode for
1444    a Boolean search expression is OR, but we want the default to be AND, so we will
1445    add a C<+> operator to each word with no other operator before it.
1446    
1447    =item idx
1448    
1449    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1450    
1451    =item objectNames
1452    
1453    List containing the names of the entity and relationship objects to be retrieved.
1454    
1455    =item filterClause
1456    
1457    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1458    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1459    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1460    in the filter clause should be added to the parameter list as additional parameters. The
1461    fields in a filter clause can come from primary entity relations, relationship relations,
1462    or secondary entity relations; however, all of the entities and relationships involved must
1463    be included in the list of object names.
1464    
1465    =item params
1466    
1467    Reference to a list of parameter values to be substituted into the filter clause.
1468    
1469    =item RETURN
1470    
1471    Returns a query object for the specified search.
1472    
1473    =back
1474    
1475    =cut
1476    
1477    sub Search {
1478        # Get the parameters.
1479        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1480        # Declare the return variable.
1481        my $retVal;
1482        # Create a safety copy of the parameter list. Note we have to be careful to insure
1483        # a parameter list exists before we copy it.
1484        my @myParams = ();
1485        if (defined $params) {
1486            @myParams = @{$params};
1487        }
1488        # Get the first object's structure so we have access to the searchable fields.
1489        my $object1Name = $objectNames->[$idx];
1490        my $object1Structure = $self->_GetStructure($object1Name);
1491        # Get the field list.
1492        if (! exists $object1Structure->{searchFields}) {
1493            Confess("No searchable index for $object1Name.");
1494        } else {
1495            # Get the field list.
1496            my @fields = @{$object1Structure->{searchFields}};
1497            # Clean the search expression.
1498            my $actualKeywords = $self->CleanKeywords($searchExpression);
1499            # Prefix a "+" to each uncontrolled word. This converts the default
1500            # search mode from OR to AND.
1501            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1502            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1503            # We need two match expressions, one for the filter clause and one in the
1504            # query itself. Both will use a parameter mark, so we need to push the
1505            # search expression onto the front of the parameter list twice.
1506            unshift @myParams, $actualKeywords, $actualKeywords;
1507            # Build the match expression.
1508            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1509            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1510            # Process the SQL stuff.
1511            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1512                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1513            # Create the query. Note that the match clause is inserted at the front of
1514            # the select fields.
1515            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1516                ".* $suffix";
1517            my $sth = $self->_GetStatementHandle($command, \@myParams);
1518            # Now we create the relation map, which enables DBQuery to determine the order, name
1519            # and mapped name for each object in the query.
1520            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1521            # Return the statement object.
1522            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1523        }
1524        return $retVal;
1525    }
1526    
1527    =head3 GetFlat
1528    
1529    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1530    
1531    This is a variation of L</GetAll> that asks for only a single field per record and
1532    returns a single flattened list.
1533    
1534    =over 4
1535    
1536    =item objectNames
1537    
1538    List containing the names of the entity and relationship objects to be retrieved.
1539    
1540    =item filterClause
1541    
1542    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1543    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1544    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1545    parameter list as additional parameters. The fields in a filter clause can come from primary
1546    entity relations, relationship relations, or secondary entity relations; however, all of the
1547    entities and relationships involved must be included in the list of object names.
1548    
1549    =item parameterList
1550    
1551    List of the parameters to be substituted in for the parameters marks in the filter clause.
1552    
1553    =item field
1554    
1555    Name of the field to be used to get the elements of the list returned.
1556    
1557    =item RETURN
1558    
1559    Returns a list of values.
1560    
1561    =back
1562    
1563    =cut
1564    #: Return Type @;
1565    sub GetFlat {
1566        # Get the parameters.
1567        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1568        # Construct the query.
1569        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1570        # Create the result list.
1571        my @retVal = ();
1572        # Loop through the records, adding the field values found to the result list.
1573        while (my $row = $query->Fetch()) {
1574            push @retVal, $row->Value($field);
1575        }
1576        # Return the list created.
1577        return @retVal;
1578    }
1579    
1580    =head3 SpecialFields
1581    
1582    C<< my %specials = $erdb->SpecialFields($entityName); >>
1583    
1584    Return a hash mapping special fields in the specified entity to the value of their
1585    C<special> attribute. This enables the subclass to get access to the special field
1586    attributes without needed to plumb the internal ERDB data structures.
1587    
1588    =over 4
1589    
1590    =item entityName
1591    
1592    Name of the entity whose special fields are desired.
1593    
1594    =item RETURN
1595    
1596    Returns a hash. The keys of the hash are the special field names, and the values
1597    are the values from each special field's C<special> attribute.
1598    
1599    =back
1600    
1601    =cut
1602    
1603    sub SpecialFields {
1604        # Get the parameters.
1605        my ($self, $entityName) = @_;
1606        # Declare the return variable.
1607        my %retVal = ();
1608        # Find the entity's data structure.
1609        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1610        # Loop through its fields, adding each special field to the return hash.
1611        my $fieldHash = $entityData->{Fields};
1612        for my $fieldName (keys %{$fieldHash}) {
1613            my $fieldData = $fieldHash->{$fieldName};
1614            if (exists $fieldData->{special}) {
1615                $retVal{$fieldName} = $fieldData->{special};
1616            }
1617        }
1618        # Return the result.
1619        return %retVal;
1620    }
1621    
1622    =head3 Delete
1623    
1624    C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1625    
1626    Delete an entity instance from the database. The instance is deleted along with all entity and
1627    relationship instances dependent on it. The definition of I<dependence> is recursive.
1628    
1629    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1630    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1631    dependent relationship.
1632    
1633    =over 4
1634    
1635    =item entityName
1636    
1637    Name of the entity type for the instance being deleted.
1638    
1639    =item objectID
1640    
1641    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1642    then it is presumed to by a LIKE pattern.
1643    
1644    =item options
1645    
1646    A hash detailing the options for this delete operation.
1647    
1648    =item RETURN
1649    
1650    Returns a statistics object indicating how many records of each particular table were
1651    deleted.
1652    
1653    =back
1654    
1655    The permissible options for this method are as follows.
1656    
1657    =over 4
1658    
1659    =item testMode
1660    
1661    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1662    
1663    =item keepRoot
1664    
1665    If TRUE, then the entity instances will not be deleted, only the dependent records.
1666    
1667    =back
1668    
1669    =cut
1670    #: Return Type $%;
1671    sub Delete {
1672        # Get the parameters.
1673        my ($self, $entityName, $objectID, %options) = @_;
1674        # Declare the return variable.
1675        my $retVal = Stats->new();
1676        # Get the DBKernel object.
1677        my $db = $self->{_dbh};
1678        # We're going to generate all the paths branching out from the starting entity. One of
1679        # the things we have to be careful about is preventing loops. We'll use a hash to
1680        # determine if we've hit a loop.
1681        my %alreadyFound = ();
1682        # These next lists will serve as our result stack. We start by pushing object lists onto
1683        # the stack, and then popping them off to do the deletes. This means the deletes will
1684        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1685        # sure we don't delete records that might be needed to forge relationships back to the
1686        # original item. We have two lists-- one for TO-relationships, and one for
1687        # FROM-relationships and entities.
1688        my @fromPathList = ();
1689        my @toPathList = ();
1690        # This final list is used to remember what work still needs to be done. We push paths
1691        # onto the list, then pop them off to extend the paths. We prime it with the starting
1692        # point. Note that we will work hard to insure that the last item on a path in the
1693        # to-do list is always an entity.
1694        my @todoList = ([$entityName]);
1695        while (@todoList) {
1696            # Get the current path.
1697            my $current = pop @todoList;
1698            # Copy it into a list.
1699            my @stackedPath = @{$current};
1700            # Pull off the last item on the path. It will always be an entity.
1701            my $myEntityName = pop @stackedPath;
1702            # Add it to the alreadyFound list.
1703            $alreadyFound{$myEntityName} = 1;
1704            # Figure out if we need to delete this entity.
1705            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1706                # Get the entity data.
1707                my $entityData = $self->_GetStructure($myEntityName);
1708                # Loop through the entity's relations. A DELETE command will be needed for each of them.
1709                my $relations = $entityData->{Relations};
1710                for my $relation (keys %{$relations}) {
1711                    my @augmentedList = (@stackedPath, $relation);
1712                    push @fromPathList, \@augmentedList;
1713                }
1714            }
1715            # Now we need to look for relationships connected to this entity.
1716            my $relationshipList = $self->{_metaData}->{Relationships};
1717            for my $relationshipName (keys %{$relationshipList}) {
1718                my $relationship = $relationshipList->{$relationshipName};
1719                # Check the FROM field. We're only interested if it's us.
1720                if ($relationship->{from} eq $myEntityName) {
1721                    # Add the path to this relationship.
1722                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1723                    push @fromPathList, \@augmentedList;
1724                    # Check the arity. If it's MM we're done. If it's 1M
1725                    # and the target hasn't been seen yet, we want to
1726                    # stack the entity for future processing.
1727                    if ($relationship->{arity} eq '1M') {
1728                        my $toEntity = $relationship->{to};
1729                        if (! exists $alreadyFound{$toEntity}) {
1730                            # Here we have a new entity that's dependent on
1731                            # the current entity, so we need to stack it.
1732                            my @stackList = (@augmentedList, $toEntity);
1733                            push @fromPathList, \@stackList;
1734                        } else {
1735                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1736                        }
1737                    }
1738                }
1739                # Now check the TO field. In this case only the relationship needs
1740                # deletion.
1741                if ($relationship->{to} eq $myEntityName) {
1742                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1743                    push @toPathList, \@augmentedList;
1744                }
1745            }
1746        }
1747        # Create the first qualifier for the WHERE clause. This selects the
1748        # keys of the primary entity records to be deleted. When we're deleting
1749        # from a dependent table, we construct a join path from the first qualifier
1750        # to the table containing the dependent records to delete.
1751        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1752        # We need to make two passes. The first is through the to-list, and
1753        # the second through the from-list. The from-list is second because
1754        # the to-list may need to pass through some of the entities the
1755        # from-list would delete.
1756        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1757        # Now it's time to do the deletes. We do it in two passes.
1758        for my $keyName ('to_link', 'from_link') {
1759            # Get the list for this key.
1760            my @pathList = @{$stackList{$keyName}};
1761            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1762            # Loop through this list.
1763            while (my $path = pop @pathList) {
1764                # Get the table whose rows are to be deleted.
1765                my @pathTables = @{$path};
1766                # Start the DELETE statement. We need to call DBKernel because the
1767                # syntax of a DELETE-USING varies among DBMSs.
1768                my $target = $pathTables[$#pathTables];
1769                my $stmt = $db->SetUsing(@pathTables);
1770                # Now start the WHERE. The first thing is the ID field from the starting table. That
1771                # starting table will either be the entity relation or one of the entity's
1772                # sub-relations.
1773                $stmt .= " WHERE $pathTables[0].id $qualifier";
1774                # Now we run through the remaining entities in the path, connecting them up.
1775                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1776                    # Connect the current relationship to the preceding entity.
1777                    my ($entity, $rel) = @pathTables[$i-1,$i];
1778                    # The style of connection depends on the direction of the relationship.
1779                    $stmt .= " AND $entity.id = $rel.$keyName";
1780                    if ($i + 1 <= $#pathTables) {
1781                        # Here there's a next entity, so connect that to the relationship's
1782                        # to-link.
1783                        my $entity2 = $pathTables[$i+1];
1784                        $stmt .= " AND $rel.to_link = $entity2.id";
1785                    }
1786                }
1787                # Now we have our desired DELETE statement.
1788                if ($options{testMode}) {
1789                    # Here the user wants to trace without executing.
1790                    Trace($stmt) if T(0);
1791                } else {
1792                    # Here we can delete. Note that the SQL method dies with a confession
1793                    # if an error occurs, so we just go ahead and do it.
1794                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1795                    my $rv = $db->SQL($stmt, 0, $objectID);
1796                    # Accumulate the statistics for this delete. The only rows deleted
1797                    # are from the target table, so we use its name to record the
1798                    # statistic.
1799                    $retVal->Add($target, $rv);
1800                }
1801            }
1802        }
1803        # Return the result.
1804        return $retVal;
1805    }
1806    
1807    =head3 Disconnect
1808    
1809    C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1810    
1811    Disconnect an entity instance from all the objects to which it is related. This
1812    will delete each relationship instance that connects to the specified entity.
1813    
1814    =over 4
1815    
1816    =item relationshipName
1817    
1818    Name of the relationship whose instances are to be deleted.
1819    
1820    =item originEntityName
1821    
1822    Name of the entity that is to be disconnected.
1823    
1824    =item originEntityID
1825    
1826    ID of the entity that is to be disconnected.
1827    
1828    =back
1829    
1830    =cut
1831    
1832    sub Disconnect {
1833        # Get the parameters.
1834        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1835        # Get the relationship descriptor.
1836        my $structure = $self->_GetStructure($relationshipName);
1837        # Insure we have a relationship.
1838        if (! exists $structure->{from}) {
1839            Confess("$relationshipName is not a relationship in the database.");
1840        } else {
1841            # Get the database handle.
1842            my $dbh = $self->{_dbh};
1843            # We'll set this value to 1 if we find our entity.
1844            my $found = 0;
1845            # Loop through the ends of the relationship.
1846            for my $dir ('from', 'to') {
1847                if ($structure->{$dir} eq $originEntityName) {
1848                    # Delete all relationship instances on this side of the entity instance.
1849                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
1850                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1851                    $found = 1;
1852                }
1853            }
1854            # Insure we found the entity on at least one end.
1855            if (! $found) {
1856                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1857            }
1858        }
1859    }
1860    
1861    =head3 DeleteRow
1862    
1863    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1864    
1865    Delete a row from a relationship. In most cases, only the from-link and to-link are
1866    needed; however, for relationships with intersection data values can be specified
1867    for the other fields using a hash.
1868    
1869    =over 4
1870    
1871    =item relationshipName
1872    
1873    Name of the relationship from which the row is to be deleted.
1874    
1875    =item fromLink
1876    
1877    ID of the entity instance in the From direction.
1878    
1879    =item toLink
1880    
1881    ID of the entity instance in the To direction.
1882    
1883    =item values
1884    
1885    Reference to a hash of other values to be used for filtering the delete.
1886    
1887    =back
1888    
1889    =cut
1890    
1891    sub DeleteRow {
1892        # Get the parameters.
1893        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1894        # Create a hash of all the filter information.
1895        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1896        if (defined $values) {
1897            for my $key (keys %{$values}) {
1898                $filter{$key} = $values->{$key};
1899            }
1900        }
1901        # Build an SQL statement out of the hash.
1902        my @filters = ();
1903        my @parms = ();
1904        for my $key (keys %filter) {
1905            push @filters, _FixName($key) . " = ?";
1906            push @parms, $filter{$key};
1907        }
1908        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1909        my $command = "DELETE FROM $relationshipName WHERE " .
1910                      join(" AND ", @filters);
1911        # Execute it.
1912        my $dbh = $self->{_dbh};
1913        $dbh->SQL($command, undef, @parms);
1914    }
1915    
1916    =head3 SortNeeded
1917    
1918    C<< my $parms = $erdb->SortNeeded($relationName); >>
1919    
1920    Return the pipe command for the sort that should be applied to the specified
1921    relation when creating the load file.
1922    
1923    For example, if the load file should be sorted ascending by the first
1924    field, this method would return
1925    
1926        sort -k1 -t"\t"
1927    
1928    If the first field is numeric, the method would return
1929    
1930        sort -k1n -t"\t"
1931    
1932    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1933    keys using a sort.
1934    
1935    =over 4
1936    
1937    =item relationName
1938    
1939    Name of the relation to be examined.
1940    
1941    =item
1942    
1943    Returns the sort command to use for sorting the relation, suitable for piping.
1944    
1945    =back
1946    
1947    =cut
1948    #: Return Type $;
1949    sub SortNeeded {
1950        # Get the parameters.
1951        my ($self, $relationName) = @_;
1952        # Declare a descriptor to hold the names of the key fields.
1953        my @keyNames = ();
1954        # Get the relation structure.
1955        my $relationData = $self->_FindRelation($relationName);
1956        # Find out if the relation is a primary entity relation,
1957        # a relationship relation, or a secondary entity relation.
1958        my $entityTable = $self->{_metaData}->{Entities};
1959        my $relationshipTable = $self->{_metaData}->{Relationships};
1960        if (exists $entityTable->{$relationName}) {
1961            # Here we have a primary entity relation.
1962            push @keyNames, "id";
1963        } elsif (exists $relationshipTable->{$relationName}) {
1964            # Here we have a relationship. We sort using the FROM index.
1965            my $relationshipData = $relationshipTable->{$relationName};
1966            my $index = $relationData->{Indexes}->{idxFrom};
1967            push @keyNames, @{$index->{IndexFields}};
1968        } else {
1969            # Here we have a secondary entity relation, so we have a sort on the ID field.
1970            push @keyNames, "id";
1971        }
1972        # Now we parse the key names into sort parameters. First, we prime the return
1973        # string.
1974        my $retVal = "sort -t\"\t\" ";
1975        # Get the relation's field list.
1976        my @fields = @{$relationData->{Fields}};
1977        # Loop through the keys.
1978        for my $keyData (@keyNames) {
1979            # Get the key and the ordering.
1980            my ($keyName, $ordering);
1981            if ($keyData =~ /^([^ ]+) DESC/) {
1982                ($keyName, $ordering) = ($1, "descending");
1983            } else {
1984                ($keyName, $ordering) = ($keyData, "ascending");
1985            }
1986            # Find the key's position and type.
1987            my $fieldSpec;
1988            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1989                my $thisField = $fields[$i];
1990                if ($thisField->{name} eq $keyName) {
1991                    # Get the sort modifier for this field type. The modifier
1992                    # decides whether we're using a character, numeric, or
1993                    # floating-point sort.
1994                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1995                    # If the index is descending for this field, denote we want
1996                    # to reverse the sort order on this field.
1997                    if ($ordering eq 'descending') {
1998                        $modifier .= "r";
1999                    }
2000                    # Store the position and modifier into the field spec, which
2001                    # will stop the inner loop. Note that the field number is
2002                    # 1-based in the sort command, so we have to increment the
2003                    # index.
2004                    $fieldSpec = ($i + 1) . $modifier;
2005                }
2006            }
2007            # Add this field to the sort command.
2008            $retVal .= " -k$fieldSpec";
2009        }
2010        # Return the result.
2011        return $retVal;
2012    }
2013    
2014    =head3 GetList
2015    
2016    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2017    
2018    Return a list of object descriptors for the specified objects as determined by the
2019    specified filter clause.
2020    
2021    This method is essentially the same as L</Get> except it returns a list of objects rather
2022    than a query object that can be used to get the results one record at a time.
2023    
2024    =over 4
2025    
2026    =item objectNames
2027    
2028    List containing the names of the entity and relationship objects to be retrieved.
2029    
2030    =item filterClause
2031    
2032    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2033    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2034    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2035    in the filter clause should be added to the parameter list as additional parameters. The
2036    fields in a filter clause can come from primary entity relations, relationship relations,
2037    or secondary entity relations; however, all of the entities and relationships involved must
2038    be included in the list of object names.
2039    
2040    The filter clause can also specify a sort order. To do this, simply follow the filter string
2041    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2042    particular genus and sorts them by species name.
2043    
2044    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2045    
2046    The rules for field references in a sort order are the same as those for field references in the
2047    filter clause in general; however, odd things may happen if a sort field is from a secondary
2048    relation.
2049    
2050    =item params
2051    
2052    Reference to a list of parameter values to be substituted into the filter clause.
2053    
2054    =item RETURN
2055    
2056    Returns a list of B<DBObject>s that satisfy the query conditions.
2057    
2058    =back
2059    
2060    =cut
2061    #: Return Type @%
2062    sub GetList {
2063        # Get the parameters.
2064        my ($self, $objectNames, $filterClause, $params) = @_;
2065        # Declare the return variable.
2066        my @retVal = ();
2067        # Perform the query.
2068        my $query = $self->Get($objectNames, $filterClause, $params);
2069        # Loop through the results.
2070        while (my $object = $query->Fetch) {
2071            push @retVal, $object;
2072        }
2073        # Return the result.
2074        return @retVal;
2075    }
2076    
2077    =head3 GetCount
2078    
2079    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2080    
2081    Return the number of rows found by a specified query. This method would
2082    normally be used to count the records in a single table. For example, in a
2083    genetics database
2084    
2085        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2086    
2087    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2088    to use it to return records based on a join. For example,
2089    
2090        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2091                                    ['homo %']);
2092    
2093    would return the number of features for genomes in the genus I<homo>. Note that
2094    only the rows from the first table are counted. If the above command were
2095    
2096        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2097                                    ['homo %']);
2098    
2099    it would return the number of genomes, not the number of genome/feature pairs.
2100    
2101    =over 4
2102    
2103    =item objectNames
2104    
2105    Reference to a list of the objects (entities and relationships) included in the
2106    query.
2107    
2108    =item filter
2109    
2110    A filter clause for restricting the query. The rules are the same as for the L</Get>
2111    method.
2112    
2113    =item params
2114    
2115    Reference to a list of the parameter values to be substituted for the parameter marks
2116    in the filter.
2117    
2118    =item RETURN
2119    
2120    Returns a count of the number of records in the first table that would satisfy
2121    the query.
2122    
2123    =back
2124    
2125    =cut
2126    
2127    sub GetCount {
2128        # Get the parameters.
2129        my ($self, $objectNames, $filter, $params) = @_;
2130        # Insure the params argument is an array reference if the caller left it off.
2131        if (! defined($params)) {
2132            $params = [];
2133        }
2134        # Declare the return variable.
2135        my $retVal;
2136        # Find out if we're counting an entity or a relationship.
2137        my $countedField;
2138        if ($self->IsEntity($objectNames->[0])) {
2139            $countedField = "id";
2140        } else {
2141            # For a relationship we count the to-link because it's usually more
2142            # numerous. Note we're automatically converting to the SQL form
2143            # of the field name (to_link vs. to-link).
2144            $countedField = "to_link";
2145        }
2146        # Create the SQL command suffix to get the desired records.
2147        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2148                                                                                $filter);
2149        # Prefix it with text telling it we want a record count.
2150        my $firstObject = $mappedNameListRef->[0];
2151        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2152        # Prepare and execute the command.
2153        my $sth = $self->_GetStatementHandle($command, $params);
2154        # Get the count value.
2155        ($retVal) = $sth->fetchrow_array();
2156        # Check for a problem.
2157        if (! defined($retVal)) {
2158            if ($sth->err) {
2159                # Here we had an SQL error.
2160                Confess("Error retrieving row count: " . $sth->errstr());
2161            } else {
2162                # Here we have no result.
2163                Confess("No result attempting to retrieve row count.");
2164            }
2165        }
2166        # Return the result.
2167        return $retVal;
2168    }
2169    
2170    =head3 ComputeObjectSentence
2171    
2172    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2173    
2174    Check an object name, and if it is a relationship convert it to a relationship sentence.
2175    
2176    =over 4
2177    
2178    =item objectName
2179    
2180    Name of the entity or relationship.
2181    
2182    =item RETURN
2183    
2184    Returns a string containing the entity name or a relationship sentence.
2185    
2186    =back
2187    
2188    =cut
2189    
2190    sub ComputeObjectSentence {
2191        # Get the parameters.
2192        my ($self, $objectName) = @_;
2193        # Set the default return value.
2194        my $retVal = $objectName;
2195        # Look for the object as a relationship.
2196        my $relTable = $self->{_metaData}->{Relationships};
2197        if (exists $relTable->{$objectName}) {
2198            # Get the relationship sentence.
2199            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2200        }
2201        # Return the result.
2202        return $retVal;
2203    }
2204    
2205    =head3 DumpRelations
2206    
2207    C<< $erdb->DumpRelations($outputDirectory); >>
2208    
2209    Write the contents of all the relations to tab-delimited files in the specified directory.
2210    Each file will have the same name as the relation dumped, with an extension of DTX.
2211    
2212    =over 4
2213    
2214    =item outputDirectory
2215    
2216    Name of the directory into which the relation files should be dumped.
2217    
2218    =back
2219    
2220    =cut
2221    
2222    sub DumpRelations {
2223        # Get the parameters.
2224        my ($self, $outputDirectory) = @_;
2225        # Now we need to run through all the relations. First, we loop through the entities.
2226        my $metaData = $self->{_metaData};
2227        my $entities = $metaData->{Entities};
2228        for my $entityName (keys %{$entities}) {
2229            my $entityStructure = $entities->{$entityName};
2230            # Get the entity's relations.
2231            my $relationList = $entityStructure->{Relations};
2232            # Loop through the relations, dumping them.
2233            for my $relationName (keys %{$relationList}) {
2234                my $relation = $relationList->{$relationName};
2235                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2236            }
2237        }
2238        # Next, we loop through the relationships.
2239        my $relationships = $metaData->{Relationships};
2240        for my $relationshipName (keys %{$relationships}) {
2241            my $relationshipStructure = $relationships->{$relationshipName};
2242            # Dump this relationship's relation.
2243            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2244        }
2245    }
2246    
2247    =head3 InsertValue
2248    
2249    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2250    
2251    This method will insert a new value into the database. The value must be one
2252    associated with a secondary relation, since primary values cannot be inserted:
2253    they occur exactly once. Secondary values, on the other hand, can be missing
2254    or multiply-occurring.
2255    
2256    =over 4
2257    
2258    =item entityID
2259    
2260    ID of the object that is to receive the new value.
2261    
2262    =item fieldName
2263    
2264    Field name for the new value-- this includes the entity name, since
2265    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2266    
2267    =item value
2268    
2269    New value to be put in the field.
2270    
2271    =back
2272    
2273    =cut
2274    
2275    sub InsertValue {
2276        # Get the parameters.
2277        my ($self, $entityID, $fieldName, $value) = @_;
2278        # Parse the entity name and the real field name.
2279        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2280            my $entityName = $1;
2281            my $fieldTitle = $2;
2282            # Get its descriptor.
2283            if (!$self->IsEntity($entityName)) {
2284                Confess("$entityName is not a valid entity.");
2285          } else {          } else {
2286              # Here we've seen the object before. We construct a new name using              my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2287              # the suffix from the hash and update the hash.              # Find the relation containing this field.
2288              my $mappedName = "$objectName$suffix";              my $fieldHash = $entityData->{Fields};
2289              $objectHash{$objectName} = $suffix + 1;              if (! exists $fieldHash->{$fieldTitle}) {
2290              # The FROM list has the object name followed by the mapped name. This                  Confess("$fieldTitle not found in $entityName.");
2291              # tells SQL it's still the same table, but we're using a different name              } else {
2292              # for it to avoid confusion.                  my $relation = $fieldHash->{$fieldTitle}->{relation};
2293              push @fromList, "$objectName $mappedName";                  if ($relation eq $entityName) {
2294              # The mapped-name list contains the real mapped name.                      Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2295              push @mappedNameList, $mappedName;                  } else {
2296              # Finally, enable us to get back from the mapped name to the object name.                      # Now we can create an INSERT statement.
2297              $mappedNameHash{$mappedName} = $objectName;                      my $dbh = $self->{_dbh};
2298                        my $fixedName = _FixName($fieldTitle);
2299                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2300                        # Execute the command.
2301                        $dbh->SQL($statement, 0, $entityID, $value);
2302          }          }
2303      }      }
2304      # Construct the SELECT statement. The general pattern is          }
2305      #      } else {
2306      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          Confess("$fieldName is not a valid field name.");
2307      #      }
2308    }
2309    
2310    =head3 InsertObject
2311    
2312    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2313    
2314    Insert an object into the database. The object is defined by a type name and then a hash
2315    of field names to values. Field values in the primary relation are represented by scalars.
2316    (Note that for relationships, the primary relation is the B<only> relation.)
2317    Field values for the other relations comprising the entity are always list references. For
2318    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2319    C<ZP_00210270.1> and C<gi|46206278>.
2320    
2321    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2322    
2323    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2324    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2325    
2326    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2327    
2328    =over 4
2329    
2330    =item newObjectType
2331    
2332    Type name of the object to insert.
2333    
2334    =item fieldHash
2335    
2336    Hash of field names to values.
2337    
2338    =back
2339    
2340    =cut
2341    
2342    sub InsertObject {
2343        # Get the parameters.
2344        my ($self, $newObjectType, $fieldHash) = @_;
2345        # Denote that so far we appear successful.
2346        my $retVal = 1;
2347        # Get the database handle.
2348      my $dbh = $self->{_dbh};      my $dbh = $self->{_dbh};
2349      my $command = "SELECT DISTINCT " . join('.*, ', @mappedNameList) . ".* FROM " .      # Get the relation list.
2350                  join(', ', @fromList);      my $relationTable = $self->_GetRelationTable($newObjectType);
2351      # Check for a filter clause.      # Loop through the relations. We'll build insert statements for each one. If a relation is
2352      if ($filterClause) {      # secondary, we may end up generating multiple insert statements. If an error occurs, we
2353          # Here we have one, so we convert its field names and add it to the query. First,      # stop the loop.
2354          # We create a copy of the filter string we can work with.      my @relationList = keys %{$relationTable};
2355          my $filterString = $filterClause;      for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2356          # Next, we sort the object names by length. This helps protect us from finding          my $relationName = $relationList[$i];
2357          # object names inside other object names when we're doing our search and replace.          my $relationDefinition = $relationTable->{$relationName};
2358          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;          # Get the relation's fields. For each field we will collect a value in the corresponding
2359          # We will also keep a list of conditions to add to the WHERE clause in order to link          # position of the @valueList array. If one of the fields is missing, we will add it to the
2360          # entities and relationships as well as primary relations to secondary ones.          # @missing list.
2361          my @joinWhere = ();          my @fieldList = @{$relationDefinition->{Fields}};
2362          # The final preparatory step is to create a hash table of relation names. The          my @fieldNameList = ();
2363          # table begins with the relation names already in the SELECT command. We may          my @valueList = ();
2364          # need to add relations later if there is filtering on a field in a secondary          my @missing = ();
2365          # relation. The secondary relations are the ones that contain multiply-          my $recordCount = 1;
2366          # occurring or optional fields.          for my $fieldDescriptor (@fieldList) {
2367          my %fromNames = map { $_ => 1 } @sortedNames;              # Get the field name and save it. Note we need to fix it up so the hyphens
2368          # We are ready to begin. We loop through the object names, replacing each              # are converted to underscores.
2369          # object name's field references by the corresponding SQL field reference.              my $fieldName = $fieldDescriptor->{name};
2370          # Along the way, if we find a secondary relation, we will need to add it              push @fieldNameList, _FixName($fieldName);
2371          # to the FROM clause.              # Look for the named field in the incoming structure. Note that we are looking
2372          for my $mappedName (@sortedNames) {              # for the real field name, not the fixed-up one!
2373              # Get the length of the object name plus 2. This is the value we add to the              if (exists $fieldHash->{$fieldName}) {
2374              # size of the field name to determine the size of the field reference as a                  # Here we found the field. Stash it in the value list.
2375              # whole.                  my $value = $fieldHash->{$fieldName};
2376              my $nameLength = 2 + length $mappedName;                  push @valueList, $value;
2377              # Get the real object name for this mapped name.                  # If the value is a list, we may need to increment the record count.
2378              my $objectName = $mappedNameHash{$mappedName};                  if (ref $value eq "ARRAY") {
2379              Trace("Processing $mappedName for object $objectName.") if T(4);                      my $thisCount = @{$value};
2380              # Get the object's field list.                      if ($recordCount == 1) {
2381              my $fieldList = $self->GetFieldTable($objectName);                          # Here we have our first list, so we save its count.
2382              # Find the field references for this object.                          $recordCount = $thisCount;
2383              while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {                      } elsif ($recordCount != $thisCount) {
2384                  # At this point, $1 contains the field name, and the current position                          # Here we have a second list, so its length has to match the
2385                  # is set immediately after the final parenthesis. We pull out the name of                          # previous lists.
2386                  # the field and the position and length of the field reference as a whole.                          Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2387                  my $fieldName = $1;                          $retVal = 0;
2388                  my $len = $nameLength + length $fieldName;                      }
2389                  my $pos = pos($filterString) - $len;                  }
                 # Insure the field exists.  
                 if (!exists $fieldList->{$fieldName}) {  
                     Confess("Field $fieldName not found for object $objectName.");  
2390                  } else {                  } else {
2391                      Trace("Processing $fieldName at position $pos.") if T(4);                  # Here the field is not present. Flag it as missing.
2392                      # Get the field's relation.                  push @missing, $fieldName;
2393                      my $relationName = $fieldList->{$fieldName}->{relation};              }
2394                      # Now we have a secondary relation. We need to insure it matches the          }
2395                      # mapped name of the primary relation. First we peel off the suffix          # If we are the primary relation, add the new-record flag.
2396                      # from the mapped name.          if ($relationName eq $newObjectType) {
2397                      my $mappingSuffix = substr $mappedName, length($objectName);              push @valueList, 1;
2398                      # Put the mapping suffix onto the relation name to get the              push @fieldNameList, "new_record";
2399                      # mapped relation name.          }
2400                      my $mappedRelationName = "$relationName$mappingSuffix";          # Only proceed if there are no missing fields.
2401                      # Insure the relation is in the FROM clause.          if (@missing > 0) {
2402                      if (!exists $fromNames{$mappedRelationName}) {              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2403                          # Add the relation to the FROM clause.                  join(' ', @missing)) if T(1);
2404                          if ($mappedRelationName eq $relationName) {          } else {
2405                              # The name is un-mapped, so we add it without              # Build the INSERT statement.
2406                              # any frills.              my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2407                              $command .= ", $relationName";                  ") VALUES (";
2408                              push @joinWhere, "$objectName.id = $relationName.id";              # Create a marker list of the proper size and put it in the statement.
2409                my @markers = ();
2410                while (@markers < @fieldNameList) { push @markers, '?'; }
2411                $statement .= join(', ', @markers) . ")";
2412                # We have the insert statement, so prepare it.
2413                my $sth = $dbh->prepare_command($statement);
2414                Trace("Insert statement prepared: $statement") if T(3);
2415                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2416                # a list, we use the current element. The values are stored in the @parameterList array.
2417                my $done = 0;
2418                for (my $i = 0; $i < $recordCount; $i++) {
2419                    # Clear the parameter list array.
2420                    my @parameterList = ();
2421                    # Loop through the values.
2422                    for my $value (@valueList) {
2423                        # Check to see if this is a scalar value.
2424                        if (ref $value eq "ARRAY") {
2425                            # Here we have a list value. Pull the current entry.
2426                            push @parameterList, $value->[$i];
2427                        } else {
2428                            # Here we have a scalar value. Use it unmodified.
2429                            push @parameterList, $value;
2430                        }
2431                    }
2432                    # Execute the INSERT statement with the specified parameter list.
2433                    $retVal = $sth->execute(@parameterList);
2434                    if (!$retVal) {
2435                        my $errorString = $sth->errstr();
2436                        Confess("Error inserting into $relationName: $errorString");
2437                    } else {
2438                        Trace("Insert successful using $parameterList[0].") if T(3);
2439                    }
2440                }
2441            }
2442        }
2443        # Return a 1 for backward compatability.
2444        return 1;
2445    }
2446    
2447    =head3 UpdateEntity
2448    
2449    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2450    
2451    Update the values of an entity. This is an unprotected update, so it should only be
2452    done if the database resides on a database server.
2453    
2454    =over 4
2455    
2456    =item entityName
2457    
2458    Name of the entity to update. (This is the entity type.)
2459    
2460    =item id
2461    
2462    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2463    
2464    =item fields
2465    
2466    Reference to a hash mapping field names to their new values. All of the fields named
2467    must be in the entity's primary relation, and they cannot any of them be the ID field.
2468    
2469    =back
2470    
2471    =cut
2472    
2473    sub UpdateEntity {
2474        # Get the parameters.
2475        my ($self, $entityName, $id, $fields) = @_;
2476        # Get a list of the field names being updated.
2477        my @fieldList = keys %{$fields};
2478        # Verify that the fields exist.
2479        my $checker = $self->GetFieldTable($entityName);
2480        for my $field (@fieldList) {
2481            if ($field eq 'id') {
2482                Confess("Cannot update the ID field for entity $entityName.");
2483            } elsif ($checker->{$field}->{relation} ne $entityName) {
2484                Confess("Cannot find $field in primary relation of $entityName.");
2485            }
2486        }
2487        # Build the SQL statement.
2488        my @sets = ();
2489        my @valueList = ();
2490        for my $field (@fieldList) {
2491            push @sets, _FixName($field) . " = ?";
2492            push @valueList, $fields->{$field};
2493        }
2494        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2495        # Add the ID to the list of binding values.
2496        push @valueList, $id;
2497        # Call SQL to do the work.
2498        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2499        # Check for errors.
2500        if ($rows == 0) {
2501            Confess("Entity $id of type $entityName not found.");
2502        }
2503    }
2504    
2505    =head3 LoadTable
2506    
2507    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2508    
2509    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2510    first.
2511    
2512    =over 4
2513    
2514    =item fileName
2515    
2516    Name of the file from which the table data should be loaded.
2517    
2518    =item relationName
2519    
2520    Name of the relation to be loaded. This is the same as the table name.
2521    
2522    =item truncateFlag
2523    
2524    TRUE if the table should be dropped and re-created, else FALSE
2525    
2526    =item RETURN
2527    
2528    Returns a statistical object containing a list of the error messages.
2529    
2530    =back
2531    
2532    =cut
2533    sub LoadTable {
2534        # Get the parameters.
2535        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2536        # Create the statistical return object.
2537        my $retVal = _GetLoadStats();
2538        # Trace the fact of the load.
2539        Trace("Loading table $relationName from $fileName") if T(2);
2540        # Get the database handle.
2541        my $dbh = $self->{_dbh};
2542        # Get the input file size.
2543        my $fileSize = -s $fileName;
2544        # Get the relation data.
2545        my $relation = $self->_FindRelation($relationName);
2546        # Check the truncation flag.
2547        if ($truncateFlag) {
2548            Trace("Creating table $relationName") if T(2);
2549            # Compute the row count estimate. We take the size of the load file,
2550            # divide it by the estimated row size, and then multiply by 1.5 to
2551            # leave extra room. We postulate a minimum row count of 1000 to
2552            # prevent problems with incoming empty load files.
2553            my $rowSize = $self->EstimateRowSize($relationName);
2554            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2555            # Re-create the table without its index.
2556            $self->CreateTable($relationName, 0, $estimate);
2557            # If this is a pre-index DBMS, create the index here.
2558            if ($dbh->{_preIndex}) {
2559                eval {
2560                    $self->CreateIndex($relationName);
2561                };
2562                if ($@) {
2563                    $retVal->AddMessage($@);
2564                }
2565            }
2566        }
2567        # Load the table.
2568        my $rv;
2569        eval {
2570            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2571        };
2572        if (!defined $rv) {
2573            $retVal->AddMessage($@) if ($@);
2574            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2575            Trace("Table load failed for $relationName.") if T(1);
2576                          } else {                          } else {
2577                              # Here we have a mapping situation.          # Here we successfully loaded the table.
2578                              $command .= ", $relationName $mappedRelationName";          $retVal->Add("tables");
2579                              push @joinWhere, "$mappedRelationName.id = $mappedName.id";          my $size = -s $fileName;
2580            Trace("$size bytes loaded into $relationName.") if T(2);
2581            # If we're rebuilding, we need to create the table indexes.
2582            if ($truncateFlag) {
2583                # Indexes are created here for PostGres. For PostGres, indexes are
2584                # best built at the end. For MySQL, the reverse is true.
2585                if (! $dbh->{_preIndex}) {
2586                    eval {
2587                        $self->CreateIndex($relationName);
2588                    };
2589                    if ($@) {
2590                        $retVal->AddMessage($@);
2591                          }                          }
                         # Denote we have this relation available for future fields.  
                         $fromNames{$mappedRelationName} = 1;  
2592                      }                      }
2593                      # Form an SQL field reference from the relation name and the field name.              # The full-text index (if any) is always built last, even for MySQL.
2594                      my $sqlReference = "$mappedRelationName." . _FixName($fieldName);              # First we need to see if this table has a full-text index. Only
2595                      # Put it into the filter string in place of the old value.              # primary relations are allowed that privilege.
2596                      substr($filterString, $pos, $len) = $sqlReference;              Trace("Checking for full-text index on $relationName.") if T(2);
2597                      # Reposition the search.              if ($self->_IsPrimary($relationName)) {
2598                      pos $filterString = $pos + length $sqlReference;                  $self->CreateSearchIndex($relationName);
2599                  }                  }
2600              }              }
2601          }          }
2602          # The next step is to join the objects together. We only need to do this if there      # Analyze the table to improve performance.
2603          # is more than one object in the object list. We start with the first object and      Trace("Analyzing and compacting $relationName.") if T(3);
2604          # run through the objects after it. Note also that we make a safety copy of the      $dbh->vacuum_it($relationName);
2605          # list before running through it.      Trace("$relationName load completed.") if T(3);
2606          my @mappedObjectList = @mappedNameList;      # Return the statistics.
2607          my $lastMappedObject = shift @mappedObjectList;      return $retVal;
         # Get the join table.  
         my $joinTable = $self->{_metaData}->{Joins};  
         # Loop through the object list.  
         for my $thisMappedObject (@mappedObjectList) {  
             # Look for a join using the real object names.  
             my $lastObject = $mappedNameHash{$lastMappedObject};  
             my $thisObject = $mappedNameHash{$thisMappedObject};  
             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 $lastMappedObject to $thisMappedObject.");  
             } else {  
                 # Get the join clause.  
                 my $unMappedJoin = $joinTable->{$joinKey};  
                 # Fix the names.  
                 $unMappedJoin =~ s/$lastObject/$lastMappedObject/;  
                 $unMappedJoin =~ s/$thisObject/$thisMappedObject/;  
                 push @joinWhere, $unMappedJoin;  
                 # Save this object as the last object for the next iteration.  
                 $lastMappedObject = $thisMappedObject;  
2608              }              }
2609    
2610    =head3 CreateSearchIndex
2611    
2612    C<< $erdb->CreateSearchIndex($objectName); >>
2613    
2614    Check for a full-text search index on the specified entity or relationship object, and
2615    if one is required, rebuild it.
2616    
2617    =over 4
2618    
2619    =item objectName
2620    
2621    Name of the entity or relationship to be indexed.
2622    
2623    =back
2624    
2625    =cut
2626    
2627    sub CreateSearchIndex {
2628        # Get the parameters.
2629        my ($self, $objectName) = @_;
2630        # Get the relation's entity/relationship structure.
2631        my $structure = $self->_GetStructure($objectName);
2632        # Get the database handle.
2633        my $dbh = $self->{_dbh};
2634        Trace("Checking for search fields in $objectName.") if T(3);
2635        # Check for a searchable fields list.
2636        if (exists $structure->{searchFields}) {
2637            # Here we know that we need to create a full-text search index.
2638            # Get an SQL-formatted field name list.
2639            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2640            # Create the index. If it already exists, it will be dropped.
2641            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2642                               flds => $fields, kind => 'fulltext');
2643            Trace("Index created for $fields in $objectName.") if T(2);
2644          }          }
         # Now we need to handle the whole ORDER BY / LIMIT thing. The important part  
         # here is we want the filter clause to be empty if there's no WHERE filter.  
         # We'll put the ORDER BY / LIMIT clauses in the following variable.  
         my $orderClause = "";  
         # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy  
         # operator so that we find the first occurrence of either verb.  
         if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {  
             # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.  
             my $pos = pos $filterString;  
             $orderClause = $2 . substr($filterString, $pos);  
             $filterString = $1;  
2645          }          }
2646          # Add the filter and the join clauses (if any) to the SELECT command.  
2647          if ($filterString) {  =head3 DropRelation
2648              Trace("Filter string is \"$filterString\".") if T(4);  
2649              push @joinWhere, "($filterString)";  C<< $erdb->DropRelation($relationName); >>
2650    
2651    Physically drop a relation from the database.
2652    
2653    =over 4
2654    
2655    =item relationName
2656    
2657    Name of the relation to drop. If it does not exist, this method will have
2658    no effect.
2659    
2660    =back
2661    
2662    =cut
2663    
2664    sub DropRelation {
2665        # Get the parameters.
2666        my ($self, $relationName) = @_;
2667        # Get the database handle.
2668        my $dbh = $self->{_dbh};
2669        # Drop the relation. The method used here has no effect if the relation
2670        # does not exist.
2671        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2672        $dbh->drop_table(tbl => $relationName);
2673          }          }
2674          if (@joinWhere) {  
2675              $command .= " WHERE " . join(' AND ', @joinWhere);  =head3 MatchSqlPattern
2676    
2677    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2678    
2679    Determine whether or not a specified value matches an SQL pattern. An SQL
2680    pattern has two wild card characters: C<%> that matches multiple characters,
2681    and C<_> that matches a single character. These can be escaped using a
2682    backslash (C<\>). We pull this off by converting the SQL pattern to a
2683    PERL regular expression. As per SQL rules, the match is case-insensitive.
2684    
2685    =over 4
2686    
2687    =item value
2688    
2689    Value to be matched against the pattern. Note that an undefined or empty
2690    value will not match anything.
2691    
2692    =item pattern
2693    
2694    SQL pattern against which to match the value. An undefined or empty pattern will
2695    match everything.
2696    
2697    =item RETURN
2698    
2699    Returns TRUE if the value and pattern match, else FALSE.
2700    
2701    =back
2702    
2703    =cut
2704    
2705    sub MatchSqlPattern {
2706        # Get the parameters.
2707        my ($value, $pattern) = @_;
2708        # Declare the return variable.
2709        my $retVal;
2710        # Insure we have a pattern.
2711        if (! defined($pattern) || $pattern eq "") {
2712            $retVal = 1;
2713        } else {
2714            # Break the pattern into pieces around the wildcard characters. Because we
2715            # use parentheses in the split function's delimiter expression, we'll get
2716            # list elements for the delimiters as well as the rest of the string.
2717            my @pieces = split /([_%]|\\[_%])/, $pattern;
2718            # Check some fast special cases.
2719            if ($pattern eq '%') {
2720                # A null pattern matches everything.
2721                $retVal = 1;
2722            } elsif (@pieces == 1) {
2723                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2724                $retVal = (lc($value) eq lc($pattern));
2725            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2726                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2727                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2728            } else {
2729                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2730                my $realPattern = "";
2731                for my $piece (@pieces) {
2732                    # Determine the type of piece.
2733                    if ($piece eq "") {
2734                        # Empty pieces are ignored.
2735                    } elsif ($piece eq "%") {
2736                        # Here we have a multi-character wildcard. Note that it can match
2737                        # zero or more characters.
2738                        $realPattern .= ".*"
2739                    } elsif ($piece eq "_") {
2740                        # Here we have a single-character wildcard.
2741                        $realPattern .= ".";
2742                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2743                        # This is an escape sequence (which is a rare thing, actually).
2744                        $realPattern .= substr($piece, 1, 1);
2745                    } else {
2746                        # Here we have raw text.
2747                        $realPattern .= quotemeta($piece);
2748          }          }
         # Add the sort or limit clause (if any) to the SELECT command.  
         if ($orderClause) {  
             $command .= " $orderClause";  
2749          }          }
2750                # Do the match.
2751                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2752      }      }
     Trace("SQL query: $command") if T(SQL => 3);  
     Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));  
     my $sth = $dbh->prepare_command($command);  
     # Execute it with the parameters bound in.  
     $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
     # Now we create the relation map, which enables DBQuery to determine the order, name  
     # and mapped name for each object in the query.  
     my @relationMap = ();  
     for my $mappedName (@mappedNameList) {  
         push @relationMap, [$mappedName, $mappedNameHash{$mappedName}];  
2753      }      }
2754      # Return the statement object.      # Return the result.
2755      my $retVal = DBQuery::_new($self, $sth, \@relationMap);      return $retVal;
2756    }
2757    
2758    =head3 GetEntity
2759    
2760    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2761    
2762    Return an object describing the entity instance with a specified ID.
2763    
2764    =over 4
2765    
2766    =item entityType
2767    
2768    Entity type name.
2769    
2770    =item ID
2771    
2772    ID of the desired entity.
2773    
2774    =item RETURN
2775    
2776    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2777    instance is found with the specified key.
2778    
2779    =back
2780    
2781    =cut
2782    
2783    sub GetEntity {
2784        # Get the parameters.
2785        my ($self, $entityType, $ID) = @_;
2786        # Create a query.
2787        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2788        # Get the first (and only) object.
2789        my $retVal = $query->Fetch();
2790        # Return the result.
2791      return $retVal;      return $retVal;
2792  }  }
2793    
2794  =head3 Delete  =head3 GetChoices
2795    
2796    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2797    
2798    Return a list of all the values for the specified field that are represented in the
2799    specified entity.
2800    
2801    Note that if the field is not indexed, then this will be a very slow operation.
2802    
2803    =over 4
2804    
2805    =item entityName
2806    
2807    Name of an entity in the database.
2808    
2809    =item fieldName
2810    
2811    Name of a field belonging to the entity. This is a raw field name without
2812    the standard parenthesized notation used in most calls.
2813    
2814    =item RETURN
2815    
2816    Returns a list of the distinct values for the specified field in the database.
2817    
2818    =back
2819    
2820    =cut
2821    
2822    sub GetChoices {
2823        # Get the parameters.
2824        my ($self, $entityName, $fieldName) = @_;
2825        # Declare the return variable.
2826        my @retVal;
2827        # Get the entity data structure.
2828        my $entityData = $self->_GetStructure($entityName);
2829        # Get the field.
2830        my $fieldHash = $entityData->{Fields};
2831        if (! exists $fieldHash->{$fieldName}) {
2832            Confess("$fieldName not found in $entityName.");
2833        } else {
2834            # Get the name of the relation containing the field.
2835            my $relation = $fieldHash->{$fieldName}->{relation};
2836            # Fix up the field name.
2837            my $realName = _FixName($fieldName);
2838            # Get the database handle.
2839            my $dbh = $self->{_dbh};
2840            # Query the database.
2841            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2842            # Clean the results. They are stored as a list of lists, and we just want the one list.
2843            @retVal = sort map { $_->[0] } @{$results};
2844        }
2845        # Return the result.
2846        return @retVal;
2847    }
2848    
2849    =head3 GetEntityValues
2850    
2851  C<< my $stats = $erdb->Delete($entityName, $objectID); >>  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2852    
2853  Delete an entity instance from the database. The instance is deleted along with all entity and  Return a list of values from a specified entity instance. If the entity instance
2854  relationship instances dependent on it. The idea of dependence here is recursive. An object is  does not exist, an empty list is returned.
 always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many  
 relationship connected to a dependent entity or the "to" entity connected to a 1-to-many  
 dependent relationship.  
2855    
2856  =over 4  =over 4
2857    
2858  =item entityName  =item entityType
2859    
2860  Name of the entity type for the instance being deleted.  Entity type name.
2861    
2862  =item objectID  =item ID
2863    
2864  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  ID of the desired entity.
 then it is presumed to by a LIKE pattern.  
2865    
2866  =item testFlag  =item fields
2867    
2868  If TRUE, the delete statements will be traced without being executed.  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2869    
2870  =item RETURN  =item RETURN
2871    
2872  Returns a statistics object indicating how many records of each particular table were  Returns a flattened list of the values of the specified fields for the specified entity.
 deleted.  
2873    
2874  =back  =back
2875    
2876  =cut  =cut
2877  #: Return Type $%;  
2878  sub Delete {  sub GetEntityValues {
2879      # Get the parameters.      # Get the parameters.
2880      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $entityType, $ID, $fields) = @_;
2881      # Declare the return variable.      # Get the specified entity.
2882      my $retVal = Stats->new();      my $entity = $self->GetEntity($entityType, $ID);
2883      # Get the DBKernel object.      # Declare the return list.
2884      my $db = $self->{_dbh};      my @retVal = ();
2885      # We're going to generate all the paths branching out from the starting entity. One of      # If we found the entity, push the values into the return list.
2886      # the things we have to be careful about is preventing loops. We'll use a hash to      if ($entity) {
2887      # determine if we've hit a loop.          push @retVal, $entity->Values($fields);
     my %alreadyFound = ();  
     # These next lists will serve as our result stack. We start by pushing object lists onto  
     # the stack, and then popping them off to do the deletes. This means the deletes will  
     # start with the longer paths before getting to the shorter ones. That, in turn, makes  
     # sure we don't delete records that might be needed to forge relationships back to the  
     # original item. We have two lists-- one for TO-relationships, and one for  
     # FROM-relationships and entities.  
     my @fromPathList = ();  
     my @toPathList = ();  
     # This final hash is used to remember what work still needs to be done. We push paths  
     # onto the list, then pop them off to extend the paths. We prime it with the starting  
     # point. Note that we will work hard to insure that the last item on a path in the  
     # TODO list is always an entity.  
     my @todoList = ([$entityName]);  
     while (@todoList) {  
         # Get the current path.  
         my $current = pop @todoList;  
         # Copy it into a list.  
         my @stackedPath = @{$current};  
         # Pull off the last item on the path. It will always be an entity.  
         my $entityName = pop @stackedPath;  
         # Add it to the alreadyFound list.  
         $alreadyFound{$entityName} = 1;  
         # Get the entity data.  
         my $entityData = $self->_GetStructure($entityName);  
         # The first task is to loop through the entity's relation. A DELETE command will  
         # be needed for each of them.  
         my $relations = $entityData->{Relations};  
         for my $relation (keys %{$relations}) {  
             my @augmentedList = (@stackedPath, $relation);  
             push @fromPathList, \@augmentedList;  
         }  
         # Now we need to look for relationships connected to this entity.  
         my $relationshipList = $self->{_metaData}->{Relationships};  
         for my $relationshipName (keys %{$relationshipList}) {  
             my $relationship = $relationshipList->{$relationshipName};  
             # Check the FROM field. We're only interested if it's us.  
             if ($relationship->{from} eq $entityName) {  
                 # Add the path to this relationship.  
                 my @augmentedList = (@stackedPath, $entityName, $relationshipName);  
                 push @fromPathList, \@augmentedList;  
                 # Check the arity. If it's MM we're done. If it's 1M  
                 # and the target hasn't been seen yet, we want to  
                 # stack the entity for future processing.  
                 if ($relationship->{arity} eq '1M') {  
                     my $toEntity = $relationship->{to};  
                     if (! exists $alreadyFound{$toEntity}) {  
                         # Here we have a new entity that's dependent on  
                         # the current entity, so we need to stack it.  
                         my @stackList = (@augmentedList, $toEntity);  
                         push @fromPathList, \@stackList;  
                     } else {  
                         Trace("$toEntity ignored because it occurred previously.") if T(4);  
                     }  
                 }  
             }  
             # Now check the TO field. In this case only the relationship needs  
             # deletion.  
             if ($relationship->{to} eq $entityName) {  
                 my @augmentedList = (@stackedPath, $entityName, $relationshipName);  
                 push @toPathList, \@augmentedList;  
             }  
         }  
     }  
     # Create the first qualifier for the WHERE clause. This selects the  
     # keys of the primary entity records to be deleted. When we're deleting  
     # from a dependent table, we construct a join page from the first qualifier  
     # to the table containing the dependent records to delete.  
     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");  
     # We need to make two passes. The first is through the to-list, and  
     # the second through the from-list. The from-list is second because  
     # the to-list may need to pass through some of the entities the  
     # from-list would delete.  
     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );  
     # Now it's time to do the deletes. We do it in two passes.  
     for my $keyName ('to_link', 'from_link') {  
         # Get the list for this key.  
         my @pathList = @{$stackList{$keyName}};  
         Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);  
         # Loop through this list.  
         while (my $path = pop @pathList) {  
             # Get the table whose rows are to be deleted.  
             my @pathTables = @{$path};  
             # Start the DELETE statement. We need to call DBKernel because the  
             # syntax of a DELETE-USING varies among DBMSs.  
             my $target = $pathTables[$#pathTables];  
             my $stmt = $db->SetUsing(@pathTables);  
             # Now start the WHERE. The first thing is the ID field from the starting table. That  
             # starting table will either be the entity relation or one of the entity's  
             # sub-relations.  
             $stmt .= " WHERE $pathTables[0].id $qualifier";  
             # Now we run through the remaining entities in the path, connecting them up.  
             for (my $i = 1; $i <= $#pathTables; $i += 2) {  
                 # Connect the current relationship to the preceding entity.  
                 my ($entity, $rel) = @pathTables[$i-1,$i];  
                 # The style of connection depends on the direction of the relationship.  
                 $stmt .= " AND $entity.id = $rel.$keyName";  
                 if ($i + 1 <= $#pathTables) {  
                     # Here there's a next entity, so connect that to the relationship's  
                     # to-link.  
                     my $entity2 = $pathTables[$i+1];  
                     $stmt .= " AND $rel.to_link = $entity2.id";  
                 }  
             }  
             # Now we have our desired DELETE statement.  
             if ($testFlag) {  
                 # Here the user wants to trace without executing.  
                 Trace($stmt) if T(0);  
             } else {  
                 # Here we can delete. Note that the SQL method dies with a confessing  
                 # if an error occurs, so we just go ahead and do it.  
                 Trace("Executing delete from $target using '$objectID'.") if T(3);  
                 my $rv = $db->SQL($stmt, 0, $objectID);  
                 # Accumulate the statistics for this delete. The only rows deleted  
                 # are from the target table, so we use its name to record the  
                 # statistic.  
                 $retVal->Add($target, $rv);  
             }  
         }  
2888      }      }
2889      # Return the result.      # Return the result.
2890      return $retVal;      return @retVal;
2891  }  }
2892    
2893  =head3 GetList  =head3 GetAll
2894    
2895  C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2896    
2897  Return a list of object descriptors for the specified objects as determined by the  Return a list of values taken from the objects returned by a query. The first three
2898  specified filter clause.  parameters correspond to the parameters of the L</Get> method. The final parameter is
2899    a list of the fields desired from each record found by the query. The field name
2900    syntax is the standard syntax used for fields in the B<ERDB> system--
2901    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2902    or relationship and I<fieldName> is the name of the field.
2903    
2904  This method is essentially the same as L</Get> except it returns a list of objects rather  The list returned will be a list of lists. Each element of the list will contain
2905  than a query object that can be used to get the results one record at a time.  the values returned for the fields specified in the fourth parameter. If one of the
2906    fields specified returns multiple values, they are flattened in with the rest. For
2907    example, the following call will return a list of the features in a particular
2908    spreadsheet cell, and each feature will be represented by a list containing the
2909    feature ID followed by all of its aliases.
2910    
2911    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2912    
2913  =over 4  =over 4
2914    
# Line 1328  Line 2918 
2918    
2919  =item filterClause  =item filterClause
2920    
2921  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2922  be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2923  specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2924  in the filter clause should be added to the parameter list as additional parameters. The  parameter list as additional parameters. The fields in a filter clause can come from primary
2925  fields in a filter clause can come from primary entity relations, relationship relations,  entity relations, relationship relations, or secondary entity relations; however, all of the
2926  or secondary entity relations; however, all of the entities and relationships involved must  entities and relationships involved must be included in the list of object names.
 be included in the list of object names.  
2927    
2928  The filter clause can also specify a sort order. To do this, simply follow the filter string  =item parameterList
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
2929    
2930  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  List of the parameters to be substituted in for the parameters marks in the filter clause.
2931    
2932  The rules for field references in a sort order are the same as those for field references in the  =item fields
2933  filter clause in general; however, odd things may happen if a sort field is from a secondary  
2934  relation.  List of the fields to be returned in each element of the list returned.
2935    
2936  =item param1, param2, ..., paramN  =item count
2937    
2938  Parameter values to be substituted into the filter clause.  Maximum number of records to return. If omitted or 0, all available records will be returned.
2939    
2940  =item RETURN  =item RETURN
2941    
2942  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of list references. Each element of the return list contains the values for the
2943    fields specified in the B<fields> parameter.
2944    
2945  =back  =back
2946    
2947  =cut  =cut
2948  #: Return Type @%  #: Return Type @@;
2949  sub GetList {  sub GetAll {
2950      # Get the parameters.      # Get the parameters.
2951      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2952      # Declare the return variable.      # Translate the parameters from a list reference to a list. If the parameter
2953        # list is a scalar we convert it into a singleton list.
2954        my @parmList = ();
2955        if (ref $parameterList eq "ARRAY") {
2956            Trace("GetAll parm list is an array.") if T(4);
2957            @parmList = @{$parameterList};
2958        } else {
2959            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2960            push @parmList, $parameterList;
2961        }
2962        # Insure the counter has a value.
2963        if (!defined $count) {
2964            $count = 0;
2965        }
2966        # Add the row limit to the filter clause.
2967        if ($count > 0) {
2968            $filterClause .= " LIMIT $count";
2969        }
2970        # Create the query.
2971        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2972        # Set up a counter of the number of records read.
2973        my $fetched = 0;
2974        # Loop through the records returned, extracting the fields. Note that if the
2975        # counter is non-zero, we stop when the number of records read hits the count.
2976      my @retVal = ();      my @retVal = ();
2977      # Perform the query.      while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2978      my $query = $self->Get($objectNames, $filterClause, @params);          my @rowData = $row->Values($fields);
2979      # Loop through the results.          push @retVal, \@rowData;
2980      while (my $object = $query->Fetch) {          $fetched++;
         push @retVal, $object;  
2981      }      }
2982      # Return the result.      Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2983        # Return the resulting list.
2984      return @retVal;      return @retVal;
2985  }  }
2986    
2987  =head3 ComputeObjectSentence  =head3 Exists
2988    
2989  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $found = $sprout->Exists($entityName, $entityID); >>
2990    
2991  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return TRUE if an entity exists, else FALSE.
2992    
2993  =over 4  =over 4
2994    
2995  =item objectName  =item entityName
2996    
2997  Name of the entity or relationship.  Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2998    
2999  =item RETURN  =item entityID
3000    
3001  Returns a string containing the entity name or a relationship sentence.  ID of the entity instance whose existence is to be checked.
3002    
3003  =back  =item RETURN
3004    
3005  =cut  Returns TRUE if the entity instance exists, else FALSE.
3006    
3007  sub ComputeObjectSentence {  =back
3008      # Get the parameters.  
3009      my ($self, $objectName) = @_;  =cut
3010      # Set the default return value.  #: Return Type $;
3011      my $retVal = $objectName;  sub Exists {
3012      # Look for the object as a relationship.      # Get the parameters.
3013      my $relTable = $self->{_metaData}->{Relationships};      my ($self, $entityName, $entityID) = @_;
3014      if (exists $relTable->{$objectName}) {      # Check for the entity instance.
3015          # Get the relationship sentence.      Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3016          $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});      my $testInstance = $self->GetEntity($entityName, $entityID);
3017      }      # Return an existence indicator.
3018      # Return the result.      my $retVal = ($testInstance ? 1 : 0);
3019      return $retVal;      return $retVal;
3020  }  }
3021    
3022  =head3 DumpRelations  =head3 EstimateRowSize
3023    
3024  C<< $erdb->DumpRelations($outputDirectory); >>  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3025    
3026  Write the contents of all the relations to tab-delimited files in the specified directory.  Estimate the row size of the specified relation. The estimated row size is computed by adding
3027  Each file will have the same name as the relation dumped, with an extension of DTX.  up the average length for each data type.
3028    
3029  =over 4  =over 4
3030    
3031  =item outputDirectory  =item relName
3032    
3033  Name of the directory into which the relation files should be dumped.  Name of the relation whose estimated row size is desired.
3034    
3035    =item RETURN
3036    
3037    Returns an estimate of the row size for the specified relation.
3038    
3039  =back  =back
3040    
3041  =cut  =cut
3042    #: Return Type $;
3043  sub DumpRelations {  sub EstimateRowSize {
3044      # Get the parameters.      # Get the parameters.
3045      my ($self, $outputDirectory) = @_;      my ($self, $relName) = @_;
3046      # Now we need to run through all the relations. First, we loop through the entities.      # Declare the return variable.
3047      my $metaData = $self->{_metaData};      my $retVal = 0;
3048      my $entities = $metaData->{Entities};      # Find the relation descriptor.
3049      for my $entityName (keys %{$entities}) {      my $relation = $self->_FindRelation($relName);
3050          my $entityStructure = $entities->{$entityName};      # Get the list of fields.
3051          # Get the entity's relations.      for my $fieldData (@{$relation->{Fields}}) {
3052          my $relationList = $entityStructure->{Relations};          # Get the field type and add its length.
3053          # Loop through the relations, dumping them.          my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3054          for my $relationName (keys %{$relationList}) {          $retVal += $fieldLen;
             my $relation = $relationList->{$relationName};  
             $self->_DumpRelation($outputDirectory, $relationName, $relation);  
         }  
     }  
     # 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});  
3055      }      }
3056        # Return the result.
3057        return $retVal;
3058  }  }
3059    
3060  =head3 InsertObject  =head3 GetFieldTable
   
 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  
   
 Insert an object into the database. The object is defined by a type name and then a hash  
 of field names to values. Field values in the primary relation are represented by scalars.  
 (Note that for relationships, the primary relation is the B<only> relation.)  
 Field values for the other relations comprising the entity are always list references. For  
 example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  
 C<ZP_00210270.1> and C<gi|46206278>.  
   
 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  
3061    
3062  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
3063    
3064  C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  Get the field structure for a specified entity or relationship.
3065    
3066  =over 4  =over 4
3067    
3068  =item newObjectType  =item objectName
   
 Type name of the object to insert.  
   
 =item fieldHash  
3069    
3070  Hash of field names to values.  Name of the desired entity or relationship.
3071    
3072  =item RETURN  =item RETURN
3073    
3074  Returns 1 if successful, 0 if an error occurred.  The table containing the field descriptors for the specified object.
3075    
3076  =back  =back
3077    
3078  =cut  =cut
3079    
3080  sub InsertObject {  sub GetFieldTable {
3081      # Get the parameters.      # Get the parameters.
3082      my ($self, $newObjectType, $fieldHash) = @_;      my ($self, $objectName) = @_;
3083      # Denote that so far we appear successful.      # Get the descriptor from the metadata.
3084      my $retVal = 1;      my $objectData = $self->_GetStructure($objectName);
3085      # Get the database handle.      # Return the object's field table.
3086      my $dbh = $self->{_dbh};      return $objectData->{Fields};
     # Get the relation list.  
     my $relationTable = $self->_GetRelationTable($newObjectType);  
     # Loop through the relations. We'll build insert statements for each one. If a relation is  
     # secondary, we may end up generating multiple insert statements. If an error occurs, we  
     # stop the loop.  
     my @relationList = keys %{$relationTable};  
     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {  
         my $relationName = $relationList[$i];  
         my $relationDefinition = $relationTable->{$relationName};  
         # Get the relation's fields. For each field we will collect a value in the corresponding  
         # position of the @valueList array. If one of the fields is missing, we will add it to the  
         # @missing list.  
         my @fieldList = @{$relationDefinition->{Fields}};  
         my @fieldNameList = ();  
         my @valueList = ();  
         my @missing = ();  
         my $recordCount = 1;  
         for my $fieldDescriptor (@fieldList) {  
             # Get the field name and save it. Note we need to fix it up so the hyphens  
             # are converted to underscores.  
             my $fieldName = $fieldDescriptor->{name};  
             push @fieldNameList, _FixName($fieldName);  
             # Look for the named field in the incoming structure. Note that we are looking  
             # for the real field name, not the fixed-up one!  
             if (exists $fieldHash->{$fieldName}) {  
                 # Here we found the field. Stash it in the value list.  
                 my $value = $fieldHash->{$fieldName};  
                 push @valueList, $value;  
                 # If the value is a list, we may need to increment the record count.  
                 if (ref $value eq "ARRAY") {  
                     my $thisCount = @{$value};  
                     if ($recordCount == 1) {  
                         # Here we have our first list, so we save its count.  
                         $recordCount = $thisCount;  
                     } elsif ($recordCount != $thisCount) {  
                         # Here we have a second list, so its length has to match the  
                         # previous lists.  
                         Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);  
                         $retVal = 0;  
                     }  
                 }  
             } else {  
                 # Here the field is not present. Flag it as missing.  
                 push @missing, $fieldName;  
             }  
         }  
         # If we are the primary relation, add the new-record flag.  
         if ($relationName eq $newObjectType) {  
             push @valueList, 1;  
             push @fieldNameList, "new_record";  
         }  
         # Only proceed if there are no missing fields.  
         if (@missing > 0) {  
             Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .  
                 join(' ', @missing)) if T(1);  
         } else {  
             # 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;  
                     }  
                 }  
                 # 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);  
                 }  
             }  
         }  
     }  
     # Return the success indicator.  
     return $retVal;  
3087  }  }
3088    
3089  =head3 LoadTable  =head3 SplitKeywords
   
 C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  
3090    
3091  Load data from a tab-delimited file into a specified table, optionally re-creating the table  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
 first.  
3092    
3093  =over 4  This method returns a list of the positive keywords in the specified
3094    keyword string. All of the operators will have been stripped off,
3095    and if the keyword is preceded by a minus operator (C<->), it will
3096    not be in the list returned. The idea here is to get a list of the
3097    keywords the user wants to see. The list will be processed to remove
3098    duplicates.
3099    
3100  =item fileName  It is possible to create a string that confuses this method. For example
3101    
3102  Name of the file from which the table data should be loaded.      frog toad -frog
3103    
3104  =item relationName  would return both C<frog> and C<toad>. If this is a problem we can deal
3105    with it later.
3106    
3107  Name of the relation to be loaded. This is the same as the table name.  =over 4
3108    
3109  =item truncateFlag  =item keywordString
3110    
3111  TRUE if the table should be dropped and re-created, else FALSE  The keyword string to be parsed.
3112    
3113  =item RETURN  =item RETURN
3114    
3115  Returns a statistical object containing a list of the error messages.  Returns a list of the words in the keyword string the user wants to
3116    see.
3117  =back  
3118    =back
3119  =cut  
3120  sub LoadTable {  =cut
3121      # Get the parameters.  
3122      my ($self, $fileName, $relationName, $truncateFlag) = @_;  sub SplitKeywords {
3123      # Create the statistical return object.      # Get the parameters.
3124      my $retVal = _GetLoadStats();      my ($keywordString) = @_;
3125      # Trace the fact of the load.      # Make a safety copy of the string. (This helps during debugging.)
3126      Trace("Loading table $relationName from $fileName") if T(2);      my $workString = $keywordString;
3127      # Get the database handle.      # Convert operators we don't care about to spaces.
3128      my $dbh = $self->{_dbh};      $workString =~ tr/+"()<>/ /;
3129      # Get the input file size.      # Split the rest of the string along space boundaries. Note that we
3130      my $fileSize = -s $fileName;      # eliminate any words that are zero length or begin with a minus sign.
3131      # Get the relation data.      my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3132      my $relation = $self->_FindRelation($relationName);      # Use a hash to remove duplicates.
3133      # Check the truncation flag.      my %words = map { $_ => 1 } @wordList;
3134      if ($truncateFlag) {      # Return the result.
3135          Trace("Creating table $relationName") if T(2);      return sort keys %words;
         # Compute the row count estimate. We take the size of the load file,  
         # divide it by the estimated row size, and then multiply by 1.5 to  
         # leave extra room. We postulate a minimum row count of 1000 to  
         # prevent problems with incoming empty load files.  
         my $rowSize = $self->EstimateRowSize($relationName);  
         my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);  
         # Re-create the table without its index.  
         $self->CreateTable($relationName, 0, $estimate);  
         # If this is a pre-index DBMS, create the index here.  
         if ($dbh->{_preIndex}) {  
             eval {  
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
             }  
         }  
     }  
     # 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 ($@) {  
                 $retVal->AddMessage($@);  
3136              }              }
3137    
3138    =head3 ValidateFieldName
3139    
3140    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3141    
3142    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3143    be hyphenated words subject to certain restrictions.
3144    
3145    =over 4
3146    
3147    =item fieldName
3148    
3149    Field name to be validated.
3150    
3151    =item RETURN
3152    
3153    Returns TRUE if the field name is valid, else FALSE.
3154    
3155    =back
3156    
3157    =cut
3158    
3159    sub ValidateFieldName {
3160        # Get the parameters.
3161        my ($fieldName) = @_;
3162        # Declare the return variable. The field name is valid until we hear
3163        # differently.
3164        my $retVal = 1;
3165        # Compute the maximum name length.
3166        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3167        # Look for bad stuff in the name.
3168        if ($fieldName =~ /--/) {
3169            # Here we have a doubled minus sign.
3170            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3171            $retVal = 0;
3172        } elsif ($fieldName !~ /^[A-Za-z]/) {
3173            # Here the field name is missing the initial letter.
3174            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3175            $retVal = 0;
3176        } elsif (length($fieldName) > $maxLen) {
3177            # Here the field name is too long.
3178            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3179        } else {
3180            # Strip out the minus signs. Everything remaining must be a letter,
3181            # underscore, or digit.
3182            my $strippedName = $fieldName;
3183            $strippedName =~ s/-//g;
3184            if ($strippedName !~ /^(\w|\d)+$/) {
3185                Trace("Field name $fieldName contains illegal characters.") if T(1);
3186                $retVal = 0;
3187          }          }
3188      }      }
3189      # Analyze the table to improve performance.      # Return the result.
     $dbh->vacuum_it($relationName);  
     # Return the statistics.  
3190      return $retVal;      return $retVal;
3191  }  }
3192    
3193  =head3 GenerateEntity  =head3 ReadMetaXML
3194    
3195  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3196    
3197  Generate the data for a new entity instance. This method creates a field hash suitable for  This method reads a raw database definition XML file and returns it.
3198  passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  Normally, the metadata used by the ERDB system has been processed and
3199  of the fields are generated using information in the database schema.  modified to make it easier to load and retrieve the data; however,
3200    this method can be used to get the data in its raw form.
 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.  
3201    
3202  =over 4  =over 4
3203    
3204  =item id  =item fileName
   
 ID to assign to the new entity.  
   
 =item type  
3205    
3206  Type name for the new entity.  Name of the XML file to read.
3207    
3208  =item values  =item RETURN
3209    
3210  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a hash reference containing the raw XML data from the specified file.
3211    
3212  =back  =back
3213    
3214  =cut  =cut
3215    
3216  sub GenerateEntity {  sub ReadMetaXML {
3217      # Get the parameters.      # Get the parameters.
3218      my ($self, $id, $type, $values) = @_;      my ($fileName) = @_;
3219      # Create the return hash.      # Read the XML.
3220      my $this = { id => $id };      my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3221      # Get the metadata structure.      Trace("XML metadata loaded from file $fileName.") if T(1);
3222      my $metadata = $self->{_metaData};      # Return the result.
3223      # Get this entity's list of fields.      return $retVal;
     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);  
     }  
     # Return the hash created.  
     return $this;  
3224  }  }
3225    
3226  =head3 GetEntity  =head3 GetEntityFieldHash
3227    
3228  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>  C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3229    
3230  Return an object describing the entity instance with a specified ID.  Get the field hash of the named entity in the specified raw XML structure.
3231    The field hash may not exist, in which case we need to create it.
3232    
3233  =over 4  =over 4
3234    
3235  =item entityType  =item structure
3236    
3237  Entity type name.  Raw XML structure defininng the database. This is not the run-time XML used by
3238    an ERDB object, since that has all sorts of optimizations built-in.
3239    
3240  =item ID  =item entityName
3241    
3242  ID of the desired entity.  Name of the entity whose field structure is desired.
3243    
3244  =item RETURN  =item RETURN
3245    
3246  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns the field hash used to define the entity's fields.
 instance is found with the specified key.  
3247    
3248  =back  =back
3249    
3250  =cut  =cut
3251    
3252  sub GetEntity {  sub GetEntityFieldHash {
3253      # Get the parameters.      # Get the parameters.
3254      my ($self, $entityType, $ID) = @_;      my ($structure, $entityName) = @_;
3255      # Create a query.      # Get the entity structure.
3256      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      my $entityData = $structure->{Entities}->{$entityName};
3257      # Get the first (and only) object.      # Look for a field structure.
3258      my $retVal = $query->Fetch();      my $retVal = $entityData->{Fields};
3259        # If it doesn't exist, create it.
3260        if (! defined($retVal)) {
3261            $entityData->{Fields} = {};
3262            $retVal = $entityData->{Fields};
3263        }
3264      # Return the result.      # Return the result.
3265      return $retVal;      return $retVal;
3266  }  }
3267    
3268  =head3 GetEntityValues  =head3 WriteMetaXML
3269    
3270  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< ERDB::WriteMetaXML($structure, $fileName); >>
3271    
3272  Return a list of values from a specified entity instance.  Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3273    used to update the database definition. It must be used with care, however, since it
3274    will only work on a raw structure, not on the processed structure created by an ERDB
3275    constructor.
3276    
3277  =over 4  =over 4
3278    
3279  =item entityType  =item structure
3280    
3281  Entity type name.  XML structure to be written to the file.
3282    
3283  =item ID  =item fileName
3284    
3285  ID of the desired entity.  Name of the output file to which the updated XML should be stored.
3286    
3287  =item fields  =back
3288    
3289  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  =cut
3290    
3291    sub WriteMetaXML {
3292        # Get the parameters.
3293        my ($structure, $fileName) = @_;
3294        # Compute the output.
3295        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3296        # Write it to the file.
3297        my $xmlOut = Open(undef, ">$fileName");
3298        print $xmlOut $fileString;
3299    }
3300    
3301    
3302    =head3 HTMLNote
3303    
3304    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3305    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3306    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3307    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3308    
3309    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3310    
3311    =over 4
3312    
3313    =item dataString
3314    
3315    String to convert to HTML.
3316    
3317  =item RETURN  =item RETURN
3318    
3319  Returns a flattened list of the values of the specified fields for the specified entity.  An HTML string derived from the input string.
3320    
3321  =back  =back
3322    
3323  =cut  =cut
3324    
3325  sub GetEntityValues {  sub HTMLNote {
3326      # Get the parameters.      # Get the parameter.
3327      my ($self, $entityType, $ID, $fields) = @_;      my ($dataString) = @_;
3328      # Get the specified entity.      # HTML-escape the text.
3329      my $entity = $self->GetEntity($entityType, $ID);      my $retVal = CGI::escapeHTML($dataString);
3330      # Declare the return list.      # Substitute the bulletin board codes.
3331      my @retVal = ();      $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3332      # If we found the entity, push the values into the return list.      $retVal =~ s!\[p\]!</p><p>!g;
3333      if ($entity) {      $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3334          push @retVal, $entity->Values($fields);      $retVal =~ s!\[/link\]!</a>!g;
     }  
3335      # Return the result.      # Return the result.
3336      return @retVal;      return $retVal;
3337  }  }
3338    
 =head3 GetAll  
3339    
3340  C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  =head2 Data Mining Methods
3341    
3342  Return a list of values taken from the objects returned by a query. The first three  =head3 GetUsefulCrossValues
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
3343    
3344  The list returned will be a list of lists. Each element of the list will contain  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
 the values returned for the fields specified in the fourth parameter. If one of the  
 fields specified returns multiple values, they are flattened in with the rest. For  
 example, the following call will return a list of the features in a particular  
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
3345    
3346  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  Return a list of the useful attributes that would be returned by a B<Cross> call
3347    from an entity of the source entity type through the specified relationship. This
3348    means it will return the fields of the target entity type and the intersection data
3349    fields in the relationship. Only primary table fields are returned. In other words,
3350    the field names returned will be for fields where there is always one and only one
3351    value.
3352    
3353  =over 4  =over 4
3354    
3355  =item objectNames  =item sourceEntity
3356    
3357  List containing the names of the entity and relationship objects to be retrieved.  Name of the entity from which the relationship crossing will start.
3358    
3359  =item filterClause  =item relationship
3360    
3361  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  Name of the relationship being crossed.
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
3362    
3363  =item parameterList  =item RETURN
3364    
3365  List of the parameters to be substituted in for the parameters marks in the filter clause.  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3366    
3367  =item fields  =back
3368    
3369  List of the fields to be returned in each element of the list returned.  =cut
3370    #: Return Type @;
3371    sub GetUsefulCrossValues {
3372        # Get the parameters.
3373        my ($self, $sourceEntity, $relationship) = @_;
3374        # Declare the return variable.
3375        my @retVal = ();
3376        # Determine the target entity for the relationship. This is whichever entity is not
3377        # the source entity. So, if the source entity is the FROM, we'll get the name of
3378        # the TO, and vice versa.
3379        my $relStructure = $self->_GetStructure($relationship);
3380        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3381        my $targetEntity = $relStructure->{$targetEntityType};
3382        # Get the field table for the entity.
3383        my $entityFields = $self->GetFieldTable($targetEntity);
3384        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3385        # For the entity fields, the key aspect of the target structure is that the {relation} value
3386        # must match the entity name.
3387        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3388                            keys %{$entityFields};
3389        # Push the fields found onto the return variable.
3390        push @retVal, sort @fieldList;
3391        # Get the field table for the relationship.
3392        my $relationshipFields = $self->GetFieldTable($relationship);
3393        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3394        # This may end up being an empty set.
3395        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3396                            keys %{$relationshipFields};
3397        # Push these onto the return list.
3398        push @retVal, sort @fieldList2;
3399        # Return the result.
3400        return @retVal;
3401    }
3402    
3403  =item count  =head3 FindColumn
3404    
3405  Maximum number of records to return. If omitted or 0, all available records will be returned.  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3406    
3407    Return the location a desired column in a data mining header line. The data
3408    mining header line is a tab-separated list of column names. The column
3409    identifier is either the numerical index of a column or the actual column
3410    name.
3411    
3412    =over 4
3413    
3414    =item headerLine
3415    
3416    The header line from a data mining command, which consists of a tab-separated
3417    list of column names.
3418    
3419    =item columnIdentifier
3420    
3421    Either the ordinal number of the desired column (1-based), or the name of the
3422    desired column.
3423    
3424  =item RETURN  =item RETURN
3425    
3426  Returns a list of list references. Each element of the return list contains the values for the  Returns the array index (0-based) of the desired column.
 fields specified in the B<fields> parameter.  
3427    
3428  =back  =back
3429    
3430  =cut  =cut
3431  #: Return Type @@;  
3432  sub GetAll {  sub FindColumn {
3433      # Get the parameters.      # Get the parameters.
3434      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      my ($headerLine, $columnIdentifier) = @_;
3435      # Translate the parameters from a list reference to a list. If the parameter      # Declare the return variable.
3436      # list is a scalar we convert it into a singleton list.      my $retVal;
3437      my @parmList = ();      # Split the header line into column names.
3438      if (ref $parameterList eq "ARRAY") {      my @headers = ParseColumns($headerLine);
3439          @parmList = @{$parameterList};      # Determine whether we have a number or a name.
3440        if ($columnIdentifier =~ /^\d+$/) {
3441            # Here we have a number. Subtract 1 and validate the result.
3442            $retVal = $columnIdentifier - 1;
3443            if ($retVal < 0 || $retVal > $#headers) {
3444                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3445            }
3446      } else {      } else {
3447          push @parmList, $parameterList;          # Here we have a name. We need to find it in the list.
3448            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3449                if ($headers[$i] eq $columnIdentifier) {
3450                    $retVal = $i;
3451      }      }
     # Insure the counter has a value.  
     if (!defined $count) {  
         $count = 0;  
3452      }      }
3453      # Add the row limit to the filter clause.          if (! defined($retVal)) {
3454      if ($count > 0) {              Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
         $filterClause .= " LIMIT $count";  
3455      }      }
     # Create the query.  
     my $query = $self->Get($objectNames, $filterClause, @parmList);  
     # Set up a counter of the number of records read.  
     my $fetched = 0;  
     # Loop through the records returned, extracting the fields. Note that if the  
     # counter is non-zero, we stop when the number of records read hits the count.  
     my @retVal = ();  
     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
         my @rowData = $row->Values($fields);  
         push @retVal, \@rowData;  
         $fetched++;  
3456      }      }
3457      # Return the resulting list.      # Return the result.
3458      return @retVal;      return $retVal;
3459  }  }
3460    
3461  =head3 EstimateRowSize  =head3 ParseColumns
3462    
3463  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3464    
3465  Estimate the row size of the specified relation. The estimated row size is computed by adding  Convert the specified data line to a list of columns.
 up the average length for each data type.  
3466    
3467  =over 4  =over 4
3468    
3469  =item relName  =item line
3470    
3471  Name of the relation whose estimated row size is desired.  A data mining input, consisting of a tab-separated list of columns terminated by a
3472    new-line.
3473    
3474  =item RETURN  =item RETURN
3475    
3476  Returns an estimate of the row size for the specified relation.  Returns a list consisting of the column values.
3477    
3478  =back  =back
3479    
3480  =cut  =cut
3481  #: Return Type $;  
3482  sub EstimateRowSize {  sub ParseColumns {
3483      # Get the parameters.      # Get the parameters.
3484      my ($self, $relName) = @_;      my ($line) = @_;
3485      # Declare the return variable.      # Chop off the line-end.
3486      my $retVal = 0;      chomp $line;
3487      # Find the relation descriptor.      # Split it into a list.
3488      my $relation = $self->_FindRelation($relName);      my @retVal = split(/\t/, $line);
     # Get the list of fields.  
     for my $fieldData (@{$relation->{Fields}}) {  
         # Get the field type and add its length.  
         my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};  
         $retVal += $fieldLen;  
     }  
3489      # Return the result.      # Return the result.
3490      return $retVal;      return @retVal;
3491  }  }
3492    
3493  =head3 GetFieldTable  =head2 Virtual Methods
3494    
3495  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>  =head3 CleanKeywords
3496    
3497  Get the field structure for a specified entity or relationship.  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3498    
3499    Clean up a search expression or keyword list. This is a virtual method that may
3500    be overridden by the subclass. The base-class method removes extra spaces
3501    and converts everything to lower case.
3502    
3503  =over 4  =over 4
3504    
3505  =item objectName  =item searchExpression
3506    
3507  Name of the desired entity or relationship.  Search expression or keyword list to clean. Note that a search expression may
3508    contain boolean operators which need to be preserved. This includes leading
3509    minus signs.
3510    
3511  =item RETURN  =item RETURN
3512    
3513  The table containing the field descriptors for the specified object.  Cleaned expression or keyword list.
3514    
3515  =back  =back
3516    
3517  =cut  =cut
3518    
3519  sub GetFieldTable {  sub CleanKeywords {
3520      # Get the parameters.      # Get the parameters.
3521      my ($self, $objectName) = @_;      my ($self, $searchExpression) = @_;
3522      # Get the descriptor from the metadata.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3523      my $objectData = $self->_GetStructure($objectName);      # don't accidentally end up with an undefined value.
3524      # Return the object's field table.      my $retVal = lc($searchExpression || "");
3525      return $objectData->{Fields};      # Remove extra spaces.
3526        $retVal =~ s/\s+/ /g;
3527        $retVal =~ s/(^\s+)|(\s+$)//g;
3528        # Return the result.
3529        return $retVal;
3530  }  }
3531    
3532  =head3 GetUsefulCrossValues  =head3 GetSourceObject
3533    
3534  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>  C<< my $source = $erdb->GetSourceObject($entityName); >>
3535    
3536  Return a list of the useful attributes that would be returned by a B<Cross> call  Return the object to be used in loading special attributes of the specified entity. The
3537  from an entity of the source entity type through the specified relationship. This  algorithm for loading special attributes is stored in the C<DataGen> elements of the
3538  means it will return the fields of the target entity type and the intersection data  XML
3539  fields in the relationship. Only primary table fields are returned. In other words,  
3540  the field names returned will be for fields where there is always one and only one  =head2 Internal Utility Methods
3541  value.  
3542    =head3 _RelationMap
3543    
3544    C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3545    
3546    Create the relation map for an SQL query. The relation map is used by B<DBObject>
3547    to determine how to interpret the results of the query.
3548    
3549  =over 4  =over 4
3550    
3551  =item sourceEntity  =item mappedNameHashRef
3552    
3553  Name of the entity from which the relationship crossing will start.  Reference to a hash that maps modified object names to real object names.
3554    
3555  =item relationship  =item mappedNameListRef
3556    
3557  Name of the relationship being crossed.  Reference to a list of modified object names in the order they appear in the
3558    SELECT list.
3559    
3560  =item RETURN  =item RETURN
3561    
3562  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3563    query followed by the actual name of that object. This enables the B<DBObject> to
3564    determine the order of the tables in the query and which object name belongs to each
3565    mapped object name. Most of the time these two values are the same; however, if a
3566    relation occurs twice in the query, the relation name in the field list and WHERE
3567    clause will use a mapped name (generally the actual relation name with a numeric
3568    suffix) that does not match the actual relation name.
3569    
3570  =back  =back
3571    
3572  =cut  =cut
3573  #: Return Type @;  
3574  sub GetUsefulCrossValues {  sub _RelationMap {
3575      # Get the parameters.      # Get the parameters.
3576      my ($self, $sourceEntity, $relationship) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
3577      # Declare the return variable.      # Declare the return variable.
3578      my @retVal = ();      my @retVal = ();
3579      # Determine the target entity for the relationship. This is whichever entity is not      # Build the map.
3580      # the source entity. So, if the source entity is the FROM, we'll get the name of      for my $mappedName (@{$mappedNameListRef}) {
3581      # the TO, and vice versa.          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3582      my $relStructure = $self->_GetStructure($relationship);      }
3583      my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");      # Return it.
     my $targetEntity = $relStructure->{$targetEntityType};  
     # Get the field table for the entity.  
     my $entityFields = $self->GetFieldTable($targetEntity);  
     # The field table is a hash. The hash key is the field name. The hash value is a structure.  
     # For the entity fields, the key aspect of the target structure is that the {relation} value  
     # must match the entity name.  
     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }  
                         keys %{$entityFields};  
     # Push the fields found onto the return variable.  
     push @retVal, sort @fieldList;  
     # Get the field table for the relationship.  
     my $relationshipFields = $self->GetFieldTable($relationship);  
     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".  
     # This may end up being an empty set.  
     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }  
                         keys %{$relationshipFields};  
     # Push these onto the return list.  
     push @retVal, sort @fieldList2;  
     # Return the result.  
3584      return @retVal;      return @retVal;
3585  }  }
3586    
 =head2 Internal Utility Methods  
3587    
3588  =head3 GetLoadStats  =head3 _SetupSQL
3589    
3590  Return a blank statistics object for use by the load methods.  Process a list of object names and a filter clause so that they can be used to
3591    build an SQL statement. This method takes in a reference to a list of object names
3592    and a filter clause. It will return a corrected filter clause, a list of mapped
3593    names and the mapped name hash.
3594    
3595  This is a static method.  This is an instance method.
3596    
3597    =over 4
3598    
3599    =item objectNames
3600    
3601    Reference to a list of the object names to be included in the query.
3602    
3603    =item filterClause
3604    
3605    A string containing the WHERE clause for the query (without the C<WHERE>) and also
3606    optionally the C<ORDER BY> and C<LIMIT> clauses.
3607    
3608    =item matchClause
3609    
3610    An optional full-text search clause. If specified, it will be inserted at the
3611    front of the WHERE clause. It should already be SQL-formatted; that is, the
3612    field names should be in the form I<table>C<.>I<fieldName>.
3613    
3614    =item RETURN
3615    
3616    Returns a three-element list. The first element is the SQL statement suffix, beginning
3617    with the FROM clause. The second element is a reference to a list of the names to be
3618    used in retrieving the fields. The third element is a hash mapping the names to the
3619    objects they represent.
3620    
3621    =back
3622    
3623  =cut  =cut
3624    
3625  sub _GetLoadStats{  sub _SetupSQL {
3626      return Stats->new();      my ($self, $objectNames, $filterClause, $matchClause) = @_;
3627        # Adjust the list of object names to account for multiple occurrences of the
3628        # same object. We start with a hash table keyed on object name that will
3629        # return the object suffix. The first time an object is encountered it will
3630        # not be found in the hash. The next time the hash will map the object name
3631        # to 2, then 3, and so forth.
3632        my %objectHash = ();
3633        # This list will contain the object names as they are to appear in the
3634        # FROM list.
3635        my @fromList = ();
3636        # This list contains the suffixed object name for each object. It is exactly
3637        # parallel to the list in the $objectNames parameter.
3638        my @mappedNameList = ();
3639        # Finally, this hash translates from a mapped name to its original object name.
3640        my %mappedNameHash = ();
3641        # Now we create the lists. Note that for every single name we push something into
3642        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3643        # parallel to $objectNames.
3644        for my $objectName (@{$objectNames}) {
3645            # Get the next suffix for this object.
3646            my $suffix = $objectHash{$objectName};
3647            if (! $suffix) {
3648                # Here we are seeing the object for the first time. The object name
3649                # is used as is.
3650                push @mappedNameList, $objectName;
3651                push @fromList, $objectName;
3652                $mappedNameHash{$objectName} = $objectName;
3653                # Denote the next suffix will be 2.
3654                $objectHash{$objectName} = 2;
3655            } else {
3656                # Here we've seen the object before. We construct a new name using
3657                # the suffix from the hash and update the hash.
3658                my $mappedName = "$objectName$suffix";
3659                $objectHash{$objectName} = $suffix + 1;
3660                # The FROM list has the object name followed by the mapped name. This
3661                # tells SQL it's still the same table, but we're using a different name
3662                # for it to avoid confusion.
3663                push @fromList, "$objectName $mappedName";
3664                # The mapped-name list contains the real mapped name.
3665                push @mappedNameList, $mappedName;
3666                # Finally, enable us to get back from the mapped name to the object name.
3667                $mappedNameHash{$mappedName} = $objectName;
3668            }
3669        }
3670        # Begin the SELECT suffix. It starts with
3671        #
3672        # FROM name1, name2, ... nameN
3673        #
3674        my $suffix = "FROM " . join(', ', @fromList);
3675        # Now for the WHERE. First, we need a place for the filter string.
3676        my $filterString = "";
3677        # We will also keep a list of conditions to add to the WHERE clause in order to link
3678        # entities and relationships as well as primary relations to secondary ones.
3679        my @joinWhere = ();
3680        # Check for a filter clause.
3681        if ($filterClause) {
3682            # Here we have one, so we convert its field names and add it to the query. First,
3683            # We create a copy of the filter string we can work with.
3684            $filterString = $filterClause;
3685            # Next, we sort the object names by length. This helps protect us from finding
3686            # object names inside other object names when we're doing our search and replace.
3687            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3688            # The final preparatory step is to create a hash table of relation names. The
3689            # table begins with the relation names already in the SELECT command. We may
3690            # need to add relations later if there is filtering on a field in a secondary
3691            # relation. The secondary relations are the ones that contain multiply-
3692            # occurring or optional fields.
3693            my %fromNames = map { $_ => 1 } @sortedNames;
3694            # We are ready to begin. We loop through the object names, replacing each
3695            # object name's field references by the corresponding SQL field reference.
3696            # Along the way, if we find a secondary relation, we will need to add it
3697            # to the FROM clause.
3698            for my $mappedName (@sortedNames) {
3699                # Get the length of the object name plus 2. This is the value we add to the
3700                # size of the field name to determine the size of the field reference as a
3701                # whole.
3702                my $nameLength = 2 + length $mappedName;
3703                # Get the real object name for this mapped name.
3704                my $objectName = $mappedNameHash{$mappedName};
3705                Trace("Processing $mappedName for object $objectName.") if T(4);
3706                # Get the object's field list.
3707                my $fieldList = $self->GetFieldTable($objectName);
3708                # Find the field references for this object.
3709                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3710                    # At this point, $1 contains the field name, and the current position
3711                    # is set immediately after the final parenthesis. We pull out the name of
3712                    # the field and the position and length of the field reference as a whole.
3713                    my $fieldName = $1;
3714                    my $len = $nameLength + length $fieldName;
3715                    my $pos = pos($filterString) - $len;
3716                    # Insure the field exists.
3717                    if (!exists $fieldList->{$fieldName}) {
3718                        Confess("Field $fieldName not found for object $objectName.");
3719                    } else {
3720                        Trace("Processing $fieldName at position $pos.") if T(4);
3721                        # Get the field's relation.
3722                        my $relationName = $fieldList->{$fieldName}->{relation};
3723                        # Now we have a secondary relation. We need to insure it matches the
3724                        # mapped name of the primary relation. First we peel off the suffix
3725                        # from the mapped name.
3726                        my $mappingSuffix = substr $mappedName, length($objectName);
3727                        # Put the mapping suffix onto the relation name to get the
3728                        # mapped relation name.
3729                        my $mappedRelationName = "$relationName$mappingSuffix";
3730                        # Insure the relation is in the FROM clause.
3731                        if (!exists $fromNames{$mappedRelationName}) {
3732                            # Add the relation to the FROM clause.
3733                            if ($mappedRelationName eq $relationName) {
3734                                # The name is un-mapped, so we add it without
3735                                # any frills.
3736                                $suffix .= ", $relationName";
3737                                push @joinWhere, "$objectName.id = $relationName.id";
3738                            } else {
3739                                # Here we have a mapping situation.
3740                                $suffix .= ", $relationName $mappedRelationName";
3741                                push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3742                            }
3743                            # Denote we have this relation available for future fields.
3744                            $fromNames{$mappedRelationName} = 1;
3745                        }
3746                        # Form an SQL field reference from the relation name and the field name.
3747                        my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3748                        # Put it into the filter string in place of the old value.
3749                        substr($filterString, $pos, $len) = $sqlReference;
3750                        # Reposition the search.
3751                        pos $filterString = $pos + length $sqlReference;
3752                    }
3753                }
3754            }
3755        }
3756        # The next step is to join the objects together. We only need to do this if there
3757        # is more than one object in the object list. We start with the first object and
3758        # run through the objects after it. Note also that we make a safety copy of the
3759        # list before running through it, because we shift off the first object before
3760        # processing the rest.
3761        my @mappedObjectList = @mappedNameList;
3762        my $lastMappedObject = shift @mappedObjectList;
3763        # Get the join table.
3764        my $joinTable = $self->{_metaData}->{Joins};
3765        # Loop through the object list.
3766        for my $thisMappedObject (@mappedObjectList) {
3767            # Look for a join using the real object names.
3768            my $lastObject = $mappedNameHash{$lastMappedObject};
3769            my $thisObject = $mappedNameHash{$thisMappedObject};
3770            my $joinKey = "$lastObject/$thisObject";
3771            if (!exists $joinTable->{$joinKey}) {
3772                # Here there's no join, so we throw an error.
3773                Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3774            } else {
3775                # Get the join clause.
3776                my $unMappedJoin = $joinTable->{$joinKey};
3777                # Fix the names.
3778                $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3779                $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3780                push @joinWhere, $unMappedJoin;
3781                # Save this object as the last object for the next iteration.
3782                $lastMappedObject = $thisMappedObject;
3783            }
3784        }
3785        # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3786        # here is we want the filter clause to be empty if there's no WHERE filter.
3787        # We'll put the ORDER BY / LIMIT clauses in the following variable.
3788        my $orderClause = "";
3789        # This is only necessary if we have a filter string in which the ORDER BY