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revision 1.42, Wed Apr 19 03:34:15 2006 UTC revision 1.90, Fri Apr 27 22:19:49 2007 UTC
# Line 6  Line 6 
6      use Data::Dumper;      use Data::Dumper;
7      use XML::Simple;      use XML::Simple;
8      use DBQuery;      use DBQuery;
9      use DBObject;      use ERDBObject;
10      use Stats;      use Stats;
11      use Time::HiRes qw(gettimeofday);      use Time::HiRes qw(gettimeofday);
12      use Digest::MD5 qw(md5_base64);      use Digest::MD5 qw(md5_base64);
13      use FIG;      use CGI;
14    
15  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
16    
# Line 59  Line 59 
59  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
60  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
61    
62  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
63  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
64  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
65  to generate documentation for the database.  for the database.
66    
67    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
68    in which case it will be used to generate a text search index in which the user searches for words
69    in the field instead of a particular field value.
70    
71  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
72  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
73  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
74    
 To facilitate testing, the ERDB module supports automatic generation of test data. This process  
 is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
 fully implemented.  
   
75  =head2 XML Database Description  =head2 XML Database Description
76    
77  =head3 Data Types  =head3 Data Types
# Line 91  Line 91 
91    
92  32-bit signed integer  32-bit signed integer
93    
94    =item counter
95    
96    32-bit unsigned integer
97    
98  =item date  =item date
99    
100  64-bit unsigned integer, representing a PERL date/time value  64-bit unsigned integer, representing a PERL date/time value
# Line 110  Line 114 
114  compatability with certain database packages), but the only values supported are  compatability with certain database packages), but the only values supported are
115  0 and 1.  0 and 1.
116    
117    =item id-string
118    
119    variable-length string, maximum 25 characters
120    
121  =item key-string  =item key-string
122    
123  variable-length string, maximum 40 characters  variable-length string, maximum 40 characters
# Line 182  Line 190 
190    
191  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),  Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
192  and the first character should be a letter. Most underlying databases are case-insensitive  and the first character should be a letter. Most underlying databases are case-insensitive
193  with the respect to field names, so a best practice is to use lower-case letters only.  with the respect to field names, so a best practice is to use lower-case letters only. Finally,
194    the name C<search-relevance> has special meaning for full-text searches and should not be
195    used as a field name.
196    
197  =item type  =item type
198    
# Line 201  Line 211 
211  entity, the fields without a relation attribute are said to belong to the  entity, the fields without a relation attribute are said to belong to the
212  I<primary relation>. This relation has the same name as the entity itself.  I<primary relation>. This relation has the same name as the entity itself.
213    
214    =item searchable
215    
216    If specified, then the field is a candidate for full-text searching. A single full-text
217    index will be created for each relation with at least one searchable field in it.
218    For best results, this option should only be used for string or text fields.
219    
220    =item special
221    
222    This attribute allows the subclass to assign special meaning for certain fields.
223    The interpretation is up to the subclass itself. Currently, only entity fields
224    can have this attribute.
225    
226  =back  =back
227    
228  =head3 Indexes  =head3 Indexes
229    
230  An entity can have multiple alternate indexes associated with it. The fields must  An entity can have multiple alternate indexes associated with it. The fields in an
231  be from the primary relation. The alternate indexes assist in ordering results  index must all be from the same relation. The alternate indexes assist in searching
232  from a query. A relationship can have up to two indexes-- a I<to-index> and a  on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
233  I<from-index>. These order the results when crossing the relationship. For  I<from-index> that order the results when crossing the relationship. For
234  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the  example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
235  from-index would order the contigs of a ganome, and the to-index would order  from-index would order the contigs of a ganome, and the to-index would order
236  the genomes of a contig. A relationship's index must specify only fields in  the genomes of a contig. In addition, it can have zero or more alternate
237    indexes. A relationship's index must specify only fields in
238  the relationship.  the relationship.
239    
240  The indexes for an entity must be listed inside the B<Indexes> tag. The from-index  The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
241  of a relationship is specified using the B<FromIndex> tag; the to-index is specified  The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
242  using the B<ToIndex> tag.  specified using the B<ToIndex> tag.
243    
244  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>  Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245  tag containing the B<IndexField> tags. These specify, in order, the fields used in  tag containing the B<IndexField> tags. These specify, in order, the fields used in
# Line 234  Line 257 
257    
258  =back  =back
259    
260  The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.  The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
261    have a B<Unique> attribute. If specified, the index will be generated as a unique
262    index.
263    
264  =head3 Object and Field Names  =head3 Object and Field Names
265    
# Line 278  Line 303 
303    
304  A relationship is described by the C<Relationship> tag. Within a relationship,  A relationship is described by the C<Relationship> tag. Within a relationship,
305  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data  there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306  fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing  fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
307  the to-index.  the to-index, and an C<Indexes> tag containing the alternate indexes.
308    
309  The C<Relationship> tag has the following attributes.  The C<Relationship> tag has the following attributes.
310    
# Line 312  Line 337 
337    
338  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.  # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
339  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field  # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
340  # of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation  # of the specified type. "avgLen" is the average byte length for estimating
341  # string is specified in the field definition. "avgLen" is the average byte length for estimating  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
342  # record sizes.  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
343  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, dataGen => "StringGen('A')" },  # index
344                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, dataGen => "IntGen(0, 99999999)" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
345                    string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, dataGen => "StringGen(IntGen(10,250))" },                                 indexMod =>   0, notes => "single ASCII character"},
346                    text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, dataGen => "StringGen(IntGen(80,1000))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
347                    date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
348                    float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, dataGen => "FloatGen(0.0, 100.0)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
349                    boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, dataGen => "IntGen(0, 1)" },                                 indexMod =>   0, notes => "unsigned 32-bit integer"},
350                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
351                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
352                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
353                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
355                                   indexMod =>   0, notes => "signed, 64-bit integer"},
356                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
357                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
358                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
359                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
360                   'hash-string' =>                   'hash-string' =>
361                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, dataGen => "SringGen(22)" },                               { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
362                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
363                     'id-string' =>
364                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
365                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
366                   'key-string' =>                   'key-string' =>
367                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
368                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
369                   'name-string' =>                   'name-string' =>
370                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
371                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
372                   'medium-string' =>                   'medium-string' =>
373                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
374                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
375                  );                  );
376    
377  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 338  Line 380 
380                     'MM' => 'many-to-many'                     'MM' => 'many-to-many'
381                   );                   );
382    
383  # Table for interpreting string patterns.  # Options for XML input and output.
384    
385    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
386                                      Entities => 'Entity',
387                                      Fields => 'Field',
388                                      Indexes => 'Index',
389                                      IndexFields => 'IndexField'
390                                    },
391                      KeyAttr =>    { Relationship => 'name',
392                                      Entity => 'name',
393                                      Field => 'name'
394                                    },
395                      SuppressEmpty => 1,
396                     );
397    
398  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
399                       '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
400                       'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
401                       'V' => "aeiou",                    NormalizeSpace => 2,
402                       'K' => "bcdfghjklmnoprstvwxyz"                   );
403    my %XmlOutOpts = (
404                      RootName => 'Database',
405                      XMLDecl => 1,
406                     );                     );
407    
408    
409  =head2 Public Methods  =head2 Public Methods
410    
411  =head3 new  =head3 new
# Line 416  Line 475 
475      # Write the HTML heading stuff.      # Write the HTML heading stuff.
476      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";      print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
477      print HTMLOUT "</head>\n<body>\n";      print HTMLOUT "</head>\n<body>\n";
478        # Write the documentation.
479        print HTMLOUT $self->DisplayMetaData();
480        # Close the document.
481        print HTMLOUT "</body>\n</html>\n";
482        # Close the file.
483        close HTMLOUT;
484    }
485    
486    =head3 DisplayMetaData
487    
488    C<< my $html = $erdb->DisplayMetaData(); >>
489    
490    Return an HTML description of the database. This description can be used to help users create
491    the data to be loaded into the relations and form queries. The output is raw includable HTML
492    without any HEAD or BODY tags.
493    
494    =over 4
495    
496    =item filename
497    
498    The name of the output file.
499    
500    =back
501    
502    =cut
503    
504    sub DisplayMetaData {
505        # Get the parameters.
506        my ($self) = @_;
507        # Get the metadata and the title string.
508        my $metadata = $self->{_metaData};
509        # Get the title string.
510        my $title = $metadata->{Title};
511        # Get the entity and relationship lists.
512        my $entityList = $metadata->{Entities};
513        my $relationshipList = $metadata->{Relationships};
514        # Declare the return variable.
515        my $retVal = "";
516        # Open the output file.
517        Trace("Building MetaData table of contents.") if T(4);
518      # Here we do the table of contents. It starts as an unordered list of section names. Each      # Here we do the table of contents. It starts as an unordered list of section names. Each
519      # section contains an ordered list of entity or relationship subsections.      # section contains an ordered list of entity or relationship subsections.
520      print HTMLOUT "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";      $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
521      # Loop through the Entities, displaying a list item for each.      # Loop through the Entities, displaying a list item for each.
522      foreach my $key (sort keys %{$entityList}) {      foreach my $key (sort keys %{$entityList}) {
523          # Display this item.          # Display this item.
524          print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
525      }      }
526      # Close off the entity section and start the relationship section.      # Close off the entity section and start the relationship section.
527      print HTMLOUT "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";      $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
528      # Loop through the Relationships.      # Loop through the Relationships.
529      foreach my $key (sort keys %{$relationshipList}) {      foreach my $key (sort keys %{$relationshipList}) {
530          # Display this item.          # Display this item.
531          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});          my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
532          print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
533      }      }
534      # Close off the relationship section and list the join table section.      # Close off the relationship section and list the join table section.
535      print HTMLOUT "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";      $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
536      # Close off the table of contents itself.      # Close off the table of contents itself.
537      print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
538      # Now we start with the actual data. Denote we're starting the entity section.      # Now we start with the actual data. Denote we're starting the entity section.
539      print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
540      # Loop through the entities.      # Loop through the entities.
541      for my $key (sort keys %{$entityList}) {      for my $key (sort keys %{$entityList}) {
542          Trace("Building MetaData entry for $key entity.") if T(4);          Trace("Building MetaData entry for $key entity.") if T(4);
543          # Create the entity header. It contains a bookmark and the entity name.          # Create the entity header. It contains a bookmark and the entity name.
544          print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
545          # Get the entity data.          # Get the entity data.
546          my $entityData = $entityList->{$key};          my $entityData = $entityList->{$key};
547          # If there's descriptive text, display it.          # If there's descriptive text, display it.
548          if (my $notes = $entityData->{Notes}) {          if (my $notes = $entityData->{Notes}) {
549              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
550          }          }
551          # Now we want a list of the entity's relationships. First, we set up the relationship subsection.          # See if we need a list of the entity's relationships.
552          print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          my $relCount = keys %{$relationshipList};
553            if ($relCount > 0) {
554                # First, we set up the relationship subsection.
555                $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
556          # Loop through the relationships.          # Loop through the relationships.
557          for my $relationship (sort keys %{$relationshipList}) {          for my $relationship (sort keys %{$relationshipList}) {
558              # Get the relationship data.              # Get the relationship data.
# Line 460  Line 562 
562                  # Get the relationship sentence and append the arity.                  # Get the relationship sentence and append the arity.
563                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
564                  # Display the relationship data.                  # Display the relationship data.
565                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                      $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
566              }              }
567          }          }
568          # Close off the relationship list.          # Close off the relationship list.
569          print HTMLOUT "</ul>\n";              $retVal .= "</ul>\n";
570            }
571          # Get the entity's relations.          # Get the entity's relations.
572          my $relationList = $entityData->{Relations};          my $relationList = $entityData->{Relations};
573          # Create a header for the relation subsection.          # Create a header for the relation subsection.
574          print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
575          # Loop through the relations, displaying them.          # Loop through the relations, displaying them.
576          for my $relation (sort keys %{$relationList}) {          for my $relation (sort keys %{$relationList}) {
577              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});              my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
578              print HTMLOUT $htmlString;              $retVal .= $htmlString;
579          }          }
580      }      }
581      # Denote we're starting the relationship section.      # Denote we're starting the relationship section.
582      print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
583      # Loop through the relationships.      # Loop through the relationships.
584      for my $key (sort keys %{$relationshipList}) {      for my $key (sort keys %{$relationshipList}) {
585          Trace("Building MetaData entry for $key relationship.") if T(4);          Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 484  Line 587 
587          my $relationshipStructure = $relationshipList->{$key};          my $relationshipStructure = $relationshipList->{$key};
588          # Create the relationship header.          # Create the relationship header.
589          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);          my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
590          print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
591          # Get the entity names.          # Get the entity names.
592          my $fromEntity = $relationshipStructure->{from};          my $fromEntity = $relationshipStructure->{from};
593          my $toEntity = $relationshipStructure->{to};          my $toEntity = $relationshipStructure->{to};
# Line 494  Line 597 
597          # since both sentences will say the same thing.          # since both sentences will say the same thing.
598          my $arity = $relationshipStructure->{arity};          my $arity = $relationshipStructure->{arity};
599          if ($arity eq "11") {          if ($arity eq "11") {
600              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
601          } else {          } else {
602              print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
603              if ($arity eq "MM" && $fromEntity ne $toEntity) {              if ($arity eq "MM" && $fromEntity ne $toEntity) {
604                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
605              }              }
606          }          }
607          print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
608          # If there are notes on this relationship, display them.          # If there are notes on this relationship, display them.
609          if (my $notes = $relationshipStructure->{Notes}) {          if (my $notes = $relationshipStructure->{Notes}) {
610              print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
611          }          }
612          # Generate the relationship's relation table.          # Generate the relationship's relation table.
613          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});          my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
614          print HTMLOUT $htmlString;          $retVal .= $htmlString;
615      }      }
616      Trace("Building MetaData join table.") if T(4);      Trace("Building MetaData join table.") if T(4);
617      # Denote we're starting the join table.      # Denote we're starting the join table.
618      print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
619      # Create a table header.      # Create a table header.
620      print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
621      # Loop through the joins.      # Loop through the joins.
622      my $joinTable = $metadata->{Joins};      my $joinTable = $metadata->{Joins};
623      my @joinKeys = keys %{$joinTable};      my @joinKeys = keys %{$joinTable};
# Line 527  Line 630 
630          my $target = $self->ComputeObjectSentence($targetRelation);          my $target = $self->ComputeObjectSentence($targetRelation);
631          my $clause = $joinTable->{$joinKey};          my $clause = $joinTable->{$joinKey};
632          # Display them in a table row.          # Display them in a table row.
633          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";
634      }      }
635      # Close the table.      # Close the table.
636      print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
637      # Close the document.      Trace("Built MetaData HTML.") if T(3);
638      print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
639      # Close the file.      return $retVal;
     close HTMLOUT;  
     Trace("Built MetaData web page.") if T(3);  
640  }  }
641    
642  =head3 DumpMetaData  =head3 DumpMetaData
# Line 553  Line 654 
654      return Data::Dumper::Dumper($self->{_metaData});      return Data::Dumper::Dumper($self->{_metaData});
655  }  }
656    
657    =head3 CreatePPO
658    
659    C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
660    
661    Create a PPO XML file from an ERDB data definition XML file. At the
662    current time, the PPO XML file can be used to create a database with
663    similar functionality. Eventually, the PPO will be able to use the
664    created XML to access the live ERDB database.
665    
666    =over 4
667    
668    =item erdbXMLFile
669    
670    Name of the XML data definition file for the ERDB database. This
671    file must exist.
672    
673    =item ppoXMLFile
674    
675    Output file for the PPO XML definition. If this file exists, it
676    will be overwritten.
677    
678    =back
679    
680    =cut
681    
682    sub CreatePPO {
683        # Get the parameters.
684        my ($erdbXMLFile, $ppoXMLFile) = @_;
685        # First, we want to slurp in the ERDB XML file in its raw form.
686        my $xml = ReadMetaXML($erdbXMLFile);
687        # Create a variable to hold all of the objects in the PPO project.
688        my @objects = ();
689        # Get the relationship hash.
690        my $relationships = $xml->{Relationships};
691        # Loop through the entities.
692        my $entities = $xml->{Entities};
693        for my $entityName (keys %{$entities}) {
694            # Get the entity's data structures.
695            my $entityObject = $entities->{$entityName};
696            # We put the object's fields in here, according to their type.
697            my (@object_refs, @scalars, @indexes, @arrays);
698            # Create the ID field for the entity. We get the key type from the
699            # entity object and compute the corresponding SQL type.
700            my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
701            push @scalars, { label => 'id', type => $type };
702            # Loop through the entity fields.
703            for my $fieldName ( keys %{$entityObject->{Fields}} ) {
704                # Get the field object.
705                my $fieldObject = $entityObject->{Fields}->{$fieldName};
706                # Convert it to a scalar tag.
707                my $scalar = _CreatePPOField($fieldName, $fieldObject);
708                # If we have a relation, this field is stored in an array.
709                # otherwise, it is a scalar. The array tag has scalars
710                # stored as an XML array. In ERDB, there is only ever one,
711                # but PPO can have more.
712                my $relation = $fieldObject->{relation};
713                if ($relation) {
714                    push @arrays, { scalar => [$scalar] };
715                } else {
716                    push @scalars, $scalar;
717                }
718            }
719            # Loop through the relationships. If this entity is the to-entity
720            # on a relationship of 1M arity, then it is implemented as a PPO
721            # object reference.
722            for my $relationshipName (keys %{$relationships}) {
723                # Get the relationship data.
724                my $relationshipData = $relationships->{$relationshipName};
725                # If we have a from for this entity and an arity of 1M, we
726                # have an object reference.
727                if ($relationshipData->{to} eq $entityName &&
728                    $relationshipData->{arity} eq '1M') {
729                    # Build the object reference tag.
730                    push @object_refs, { label => $relationshipName,
731                                         type => $relationshipData->{from} };
732                }
733            }
734            # Create the indexes.
735            my $indexList = $entityObject->{Indexes};
736            push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
737            # Build the object XML tree.
738            my $object = { label => $entityName,
739                           object_ref => \@object_refs,
740                           scalar => \@scalars,
741                           index => \@indexes,
742                           array => \@arrays
743                          };
744            # Push the object onto the objects list.
745            push @objects, $object;
746        }
747        # Loop through the relationships, searching for MMs. The 1Ms were
748        # already handled by the entity search above.
749        for my $relationshipName (keys %{$relationships}) {
750            # Get this relationship's object.
751            my $relationshipObject = $relationships->{$relationshipName};
752            # Only proceed if it's many-to-many.
753            if ($relationshipObject->{arity} eq 'MM') {
754                # Create the tag lists for the relationship object.
755                my (@object_refs, @scalars, @indexes);
756                # The relationship will be created as an object with object
757                # references for its links to the participating entities.
758                my %links = ( from_link => $relationshipObject->{from},
759                              to_link => $relationshipObject->{to} );
760                for my $link (keys %links) {
761                    # Create an object_ref tag for this piece of the
762                    # relationship (from or to).
763                    my $object_ref = { label => $link,
764                                       type => $links{$link} };
765                    push @object_refs, $object_ref;
766                }
767                # Loop through the intersection data fields, creating scalar tags.
768                # There are no fancy array tags in a relationship.
769                for my $fieldName (keys %{$relationshipObject->{Fields}}) {
770                    my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
771                    push @scalars, _CreatePPOField($fieldName, $fieldObject);
772                }
773                # Finally, the indexes: currently we cannot support the to-index and
774                # from-index in PPO, so we just process the alternate indexes.
775                my $indexList = $relationshipObject->{Indexes};
776                push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
777                # Wrap up all the stuff about this relationship.
778                my $object = { label => $relationshipName,
779                               scalar => \@scalars,
780                               object_ref => \@object_refs,
781                               index => \@indexes
782                             };
783                # Push it into the object list.
784                push @objects, $object;
785            }
786        }
787        # Compute a title.
788        my $title;
789        if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
790            # Here we have a standard file name we can use for a title.
791            $title = $2;
792        } else {
793            # Here the file name is non-standard, so we carve up the
794            # database title.
795            $title = $xml->{Title}->{content};
796            $title =~ s/\s\.,//g;
797        }
798        # Wrap up the XML as a project.
799        my $ppoXML = { project => { label => $title,
800                                    object => \@objects }};
801        # Write out the results.
802        my $ppoString = XML::Simple::XMLout($ppoXML,
803                                            AttrIndent => 1,
804                                            KeepRoot => 1);
805        Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
806    }
807    
808    =head3 FindIndexForEntity
809    
810    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
811    
812    This method locates the entry in an entity's index list that begins with the
813    specified attribute name. If the entity has no index list, one will be
814    created. This method works on raw XML, not a live ERDB object.
815    
816    =over 4
817    
818    =item xml
819    
820    The raw XML structure defining the database.
821    
822    =item entityName
823    
824    The name of the relevant entity.
825    
826    =item attributeName
827    
828    The name of the attribute relevant to the search.
829    
830    =item RETURN
831    
832    The numerical index in the index list of the index entry for the specified entity and
833    attribute, or C<undef> if no such index exists.
834    
835    =back
836    
837    =cut
838    
839    sub FindIndexForEntity {
840        # Get the parameters.
841        my ($xml, $entityName, $attributeName) = @_;
842        # Declare the return variable.
843        my $retVal;
844        # Get the named entity.
845        my $entityData = $xml->{Entities}->{$entityName};
846        if (! $entityData) {
847            Confess("Entity $entityName not found in DBD structure.");
848        } else {
849            # Insure it has an index list.
850            if (! exists $entityData->{Indexes}) {
851                $entityData->{Indexes} = [];
852            } else {
853                # Search for the desired index.
854                my $indexList = $entityData->{Indexes};
855                my $n = scalar @{$indexList};
856                Trace("Searching $n indexes in index list for $entityName.") if T(2);
857                # We use an indexed FOR here because we're returning an
858                # index number instead of an object. We do THAT so we can
859                # delete the index from the list if needed.
860                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
861                    my $index = $indexList->[$i];
862                    my $fields = $index->{IndexFields};
863                    # Technically this IF should be safe (that is, we are guaranteed
864                    # the existence of a "$fields->[0]"), because when we load the XML
865                    # we have SuppressEmpty specified.
866                    if ($fields->[0]->{name} eq $attributeName) {
867                        $retVal = $i;
868                    }
869                }
870            }
871        }
872        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
873        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
874        # Return the result.
875        return $retVal;
876    }
877    
878  =head3 CreateTables  =head3 CreateTables
879    
880  C<< $erdb->CreateTables(); >>  C<< $erdb->CreateTables(); >>
# Line 572  Line 894 
894      # Loop through the relations.      # Loop through the relations.
895      for my $relationName (@relNames) {      for my $relationName (@relNames) {
896          # Create a table for this relation.          # Create a table for this relation.
897          $self->CreateTable($relationName);          $self->CreateTable($relationName, 1);
898          Trace("Relation $relationName created.") if T(2);          Trace("Relation $relationName created.") if T(2);
899      }      }
900  }  }
# Line 640  Line 962 
962      Trace("Creating table $relationName: $fieldThing") if T(2);      Trace("Creating table $relationName: $fieldThing") if T(2);
963      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
964      Trace("Relation $relationName created in database.") if T(2);      Trace("Relation $relationName created in database.") if T(2);
965      # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
966        # index will not be built until the table has been loaded.
967      if ($indexFlag) {      if ($indexFlag) {
968          $self->CreateIndex($relationName);          $self->CreateIndex($relationName);
969      }      }
# Line 736  Line 1059 
1059          my $fieldType = $fieldTypes->[$i]->{type};          my $fieldType = $fieldTypes->[$i]->{type};
1060          # If it's a hash string, digest it in place.          # If it's a hash string, digest it in place.
1061          if ($fieldType eq 'hash-string') {          if ($fieldType eq 'hash-string') {
1062              $fieldList->[$i] = md5_base64($fieldList->[$i]);              $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1063            }
1064          }          }
1065      }      }
1066    
1067    =head3 DigestKey
1068    
1069    C<< my $digested = $erdb->DigestKey($keyValue); >>
1070    
1071    Return the digested value of a symbolic key. The digested value can then be plugged into a
1072    key-based search into a table with key-type hash-string.
1073    
1074    Currently the digesting process is independent of the database structure, but that may not
1075    always be the case, so this is an instance method instead of a static method.
1076    
1077    =over 4
1078    
1079    =item keyValue
1080    
1081    Key value to digest.
1082    
1083    =item RETURN
1084    
1085    Digested value of the key.
1086    
1087    =back
1088    
1089    =cut
1090    
1091    sub DigestKey {
1092        # Get the parameters.
1093        my ($self, $keyValue) = @_;
1094        # Compute the digest.
1095        my $retVal = md5_base64($keyValue);
1096        # Return the result.
1097        return $retVal;
1098  }  }
1099    
1100  =head3 CreateIndex  =head3 CreateIndex
# Line 764  Line 1120 
1120      for my $indexName (keys %{$indexHash}) {      for my $indexName (keys %{$indexHash}) {
1121          my $indexData = $indexHash->{$indexName};          my $indexData = $indexHash->{$indexName};
1122          # Get the index's field list.          # Get the index's field list.
1123          my @fieldList = _FixNames(@{$indexData->{IndexFields}});          my @rawFields = @{$indexData->{IndexFields}};
1124            # Get a hash of the relation's field types.
1125            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1126            # We need to check for text fields so we can append a length limitation for them. To do
1127            # that, we need the relation's field list.
1128            my $relFields = $relationData->{Fields};
1129            for (my $i = 0; $i <= $#rawFields; $i++) {
1130                # Get the field type.
1131                my $field = $rawFields[$i];
1132                my $type = $types{$field};
1133                # Ask if it requires using prefix notation for the index.
1134                my $mod = $TypeTable{$type}->{indexMod};
1135                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1136                if ($mod) {
1137                    # Append the prefix length to the field name,
1138                    $rawFields[$i] .= "($mod)";
1139                }
1140            }
1141            my @fieldList = _FixNames(@rawFields);
1142          my $flds = join(', ', @fieldList);          my $flds = join(', ', @fieldList);
1143          # Get the index's uniqueness flag.          # Get the index's uniqueness flag.
1144          my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');          my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1145          # Create the index.          # Create the index.
1146          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,          my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1147                                      flds => $flds, unique => $unique);                                      flds => $flds, kind => $unique);
1148          if ($rv) {          if ($rv) {
1149              Trace("Index created: $indexName for $relationName ($flds)") if T(1);              Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1150          } else {          } else {
# Line 779  Line 1153 
1153      }      }
1154  }  }
1155    
1156    =head3 GetSecondaryFields
1157    
1158    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1159    
1160    This method will return a list of the name and type of each of the secondary
1161    fields for a specified entity. Secondary fields are stored in two-column tables
1162    in addition to the primary entity table. This enables the field to have no value
1163    or to have multiple values.
1164    
1165    =over 4
1166    
1167    =item entityName
1168    
1169    Name of the entity whose secondary fields are desired.
1170    
1171    =item RETURN
1172    
1173    Returns a hash mapping the field names to their field types.
1174    
1175    =back
1176    
1177    =cut
1178    
1179    sub GetSecondaryFields {
1180        # Get the parameters.
1181        my ($self, $entityName) = @_;
1182        # Declare the return variable.
1183        my %retVal = ();
1184        # Look for the entity.
1185        my $table = $self->GetFieldTable($entityName);
1186        # Loop through the fields, pulling out the secondaries.
1187        for my $field (sort keys %{$table}) {
1188            if ($table->{$field}->{relation} ne $entityName) {
1189                # Here we have a secondary field.
1190                $retVal{$field} = $table->{$field}->{type};
1191            }
1192        }
1193        # Return the result.
1194        return %retVal;
1195    }
1196    
1197    =head3 GetFieldRelationName
1198    
1199    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1200    
1201    Return the name of the relation containing a specified field.
1202    
1203    =over 4
1204    
1205    =item objectName
1206    
1207    Name of the entity or relationship containing the field.
1208    
1209    =item fieldName
1210    
1211    Name of the relevant field in that entity or relationship.
1212    
1213    =item RETURN
1214    
1215    Returns the name of the database relation containing the field, or C<undef> if
1216    the field does not exist.
1217    
1218    =back
1219    
1220    =cut
1221    
1222    sub GetFieldRelationName {
1223        # Get the parameters.
1224        my ($self, $objectName, $fieldName) = @_;
1225        # Declare the return variable.
1226        my $retVal;
1227        # Get the object field table.
1228        my $table = $self->GetFieldTable($objectName);
1229        # Only proceed if the field exists.
1230        if (exists $table->{$fieldName}) {
1231            # Determine the name of the relation that contains this field.
1232            $retVal = $table->{$fieldName}->{relation};
1233        }
1234        # Return the result.
1235        return $retVal;
1236    }
1237    
1238    =head3 DeleteValue
1239    
1240    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1241    
1242    Delete secondary field values from the database. This method can be used to delete all
1243    values of a specified field for a particular entity instance, or only a single value.
1244    
1245    Secondary fields are stored in two-column relations separate from an entity's primary
1246    table, and as a result a secondary field can legitimately have no value or multiple
1247    values. Therefore, it makes sense to talk about deleting secondary fields where it
1248    would not make sense for primary fields.
1249    
1250    =over 4
1251    
1252    =item entityName
1253    
1254    Name of the entity from which the fields are to be deleted.
1255    
1256    =item id
1257    
1258    ID of the entity instance to be processed. If the instance is not found, this
1259    method will have no effect. If C<undef> is specified, all values for all of
1260    the entity instances will be deleted.
1261    
1262    =item fieldName
1263    
1264    Name of the field whose values are to be deleted.
1265    
1266    =item fieldValue (optional)
1267    
1268    Value to be deleted. If not specified, then all values of the specified field
1269    will be deleted for the entity instance. If specified, then only the values which
1270    match this parameter will be deleted.
1271    
1272    =item RETURN
1273    
1274    Returns the number of rows deleted.
1275    
1276    =back
1277    
1278    =cut
1279    
1280    sub DeleteValue {
1281        # Get the parameters.
1282        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1283        # Declare the return value.
1284        my $retVal = 0;
1285        # We need to set up an SQL command to do the deletion. First, we
1286        # find the name of the field's relation.
1287        my $table = $self->GetFieldTable($entityName);
1288        my $field = $table->{$fieldName};
1289        my $relation = $field->{relation};
1290        # Make sure this is a secondary field.
1291        if ($relation eq $entityName) {
1292            Confess("Cannot delete values of $fieldName for $entityName.");
1293        } else {
1294            # Set up the SQL command to delete all values.
1295            my $sql = "DELETE FROM $relation";
1296            # Build the filter.
1297            my @filters = ();
1298            my @parms = ();
1299            # Check for a filter by ID.
1300            if (defined $id) {
1301                push @filters, "id = ?";
1302                push @parms, $id;
1303            }
1304            # Check for a filter by value.
1305            if (defined $fieldValue) {
1306                push @filters, "$fieldName = ?";
1307                push @parms, $fieldValue;
1308            }
1309            # Append the filters to the command.
1310            if (@filters) {
1311                $sql .= " WHERE " . join(" AND ", @filters);
1312            }
1313            # Execute the command.
1314            my $dbh = $self->{_dbh};
1315            $retVal = $dbh->SQL($sql, 0, @parms);
1316        }
1317        # Return the result.
1318        return $retVal;
1319    }
1320    
1321  =head3 LoadTables  =head3 LoadTables
1322    
1323  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>  C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
# Line 873  Line 1412 
1412      return sort keys %{$entityList};      return sort keys %{$entityList};
1413  }  }
1414    
1415    =head3 GetDataTypes
1416    
1417    C<< my %types = ERDB::GetDataTypes(); >>
1418    
1419    Return a table of ERDB data types. The table returned is a hash of hashes.
1420    The keys of the big hash are the datatypes. Each smaller hash has several
1421    values used to manage the data. The most interesting is the SQL type (key
1422    C<sqlType>) and the descriptive node (key C<notes>).
1423    
1424    Note that changing the values in the smaller hashes will seriously break
1425    things, so this data should be treated as read-only.
1426    
1427    =cut
1428    
1429    sub GetDataTypes {
1430        return %TypeTable;
1431    }
1432    
1433    
1434  =head3 IsEntity  =head3 IsEntity
1435    
1436  C<< my $flag = $erdb->IsEntity($entityName); >>  C<< my $flag = $erdb->IsEntity($entityName); >>
# Line 902  Line 1460 
1460    
1461  =head3 Get  =head3 Get
1462    
1463  C<< my $query = $erdb->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1464    
1465  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.
1466  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 910  Line 1468 
1468  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
1469  $genus.  $genus.
1470    
1471  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1472    
1473  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
1474  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 927  Line 1485 
1485  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
1486  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,
1487    
1488  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1489    
1490  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
1491  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 984  Line 1542 
1542    
1543  C<< "LIMIT 10" >>  C<< "LIMIT 10" >>
1544    
1545  =item param1, param2, ..., paramN  =item params
1546    
1547  Parameter values to be substituted into the filter clause.  Reference to a list of parameter values to be substituted into the filter clause.
1548    
1549  =item RETURN  =item RETURN
1550    
# Line 998  Line 1556 
1556    
1557  sub Get {  sub Get {
1558      # Get the parameters.      # Get the parameters.
1559      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1560      # Adjust the list of object names to account for multiple occurrences of the      # Process the SQL stuff.
1561      # same object. We start with a hash table keyed on object name that will      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1562      # return the object suffix. The first time an object is encountered it will          $self->_SetupSQL($objectNames, $filterClause);
1563      # not be found in the hash. The next time the hash will map the object name      # Create the query.
1564      # to 2, then 3, and so forth.      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1565      my %objectHash = ();          ".* $suffix";
1566      # This list will contain the object names as they are to appear in the      my $sth = $self->_GetStatementHandle($command, $params);
1567      # FROM list.      # Now we create the relation map, which enables DBQuery to determine the order, name
1568      my @fromList = ();      # and mapped name for each object in the query.
1569      # This list contains the suffixed object name for each object. It is exactly      my @relationMap = ();
1570      # parallel to the list in the $objectNames parameter.      for my $mappedName (@{$mappedNameListRef}) {
1571      my @mappedNameList = ();          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1572      # Finally, this hash translates from a mapped name to its original object name.      }
1573      my %mappedNameHash = ();      # Return the statement object.
1574      # Now we create the lists. Note that for every single name we push something into      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1575      # @fromList and @mappedNameList. This insures that those two arrays are exactly      return $retVal;
1576      # parallel to $objectNames.  }
1577      for my $objectName (@{$objectNames}) {  
1578          # Get the next suffix for this object.  
1579          my $suffix = $objectHash{$objectName};  
1580          if (! $suffix) {  =head3 Search
1581              # Here we are seeing the object for the first time. The object name  
1582              # is used as is.  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1583              push @mappedNameList, $objectName;  
1584              push @fromList, $objectName;  Perform a full text search with filtering. The search will be against a specified object
1585              $mappedNameHash{$objectName} = $objectName;  in the object name list. That object will get an extra field containing the search
1586              # Denote the next suffix will be 2.  relevance. Note that except for the search expression, the parameters of this method are
1587              $objectHash{$objectName} = 2;  the same as those for L</Get> and follow the same rules.
1588    
1589    =over 4
1590    
1591    =item searchExpression
1592    
1593    Boolean search expression for the text fields of the target object. The default mode for
1594    a Boolean search expression is OR, but we want the default to be AND, so we will
1595    add a C<+> operator to each word with no other operator before it.
1596    
1597    =item idx
1598    
1599    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1600    
1601    =item objectNames
1602    
1603    List containing the names of the entity and relationship objects to be retrieved.
1604    
1605    =item filterClause
1606    
1607    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1608    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1609    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1610    in the filter clause should be added to the parameter list as additional parameters. The
1611    fields in a filter clause can come from primary entity relations, relationship relations,
1612    or secondary entity relations; however, all of the entities and relationships involved must
1613    be included in the list of object names.
1614    
1615    =item params
1616    
1617    Reference to a list of parameter values to be substituted into the filter clause.
1618    
1619    =item RETURN
1620    
1621    Returns a query object for the specified search.
1622    
1623    =back
1624    
1625    =cut
1626    
1627    sub Search {
1628        # Get the parameters.
1629        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1630        # Declare the return variable.
1631        my $retVal;
1632        # Create a safety copy of the parameter list. Note we have to be careful to insure
1633        # a parameter list exists before we copy it.
1634        my @myParams = ();
1635        if (defined $params) {
1636            @myParams = @{$params};
1637        }
1638        # Get the first object's structure so we have access to the searchable fields.
1639        my $object1Name = $objectNames->[$idx];
1640        my $object1Structure = $self->_GetStructure($object1Name);
1641        # Get the field list.
1642        if (! exists $object1Structure->{searchFields}) {
1643            Confess("No searchable index for $object1Name.");
1644        } else {
1645            # Get the field list.
1646            my @fields = @{$object1Structure->{searchFields}};
1647            # Clean the search expression.
1648            my $actualKeywords = $self->CleanKeywords($searchExpression);
1649            # Prefix a "+" to each uncontrolled word. This converts the default
1650            # search mode from OR to AND.
1651            $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1652            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1653            # We need two match expressions, one for the filter clause and one in the
1654            # query itself. Both will use a parameter mark, so we need to push the
1655            # search expression onto the front of the parameter list twice.
1656            unshift @myParams, $actualKeywords, $actualKeywords;
1657            # Build the match expression.
1658            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1659            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1660            # Process the SQL stuff.
1661            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1662                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1663            # Create the query. Note that the match clause is inserted at the front of
1664            # the select fields.
1665            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1666                ".* $suffix";
1667            my $sth = $self->_GetStatementHandle($command, \@myParams);
1668            # Now we create the relation map, which enables DBQuery to determine the order, name
1669            # and mapped name for each object in the query.
1670            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1671            # Return the statement object.
1672            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1673        }
1674        return $retVal;
1675    }
1676    
1677    =head3 GetFlat
1678    
1679    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1680    
1681    This is a variation of L</GetAll> that asks for only a single field per record and
1682    returns a single flattened list.
1683    
1684    =over 4
1685    
1686    =item objectNames
1687    
1688    List containing the names of the entity and relationship objects to be retrieved.
1689    
1690    =item filterClause
1691    
1692    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1693    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1694    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1695    parameter list as additional parameters. The fields in a filter clause can come from primary
1696    entity relations, relationship relations, or secondary entity relations; however, all of the
1697    entities and relationships involved must be included in the list of object names.
1698    
1699    =item parameterList
1700    
1701    List of the parameters to be substituted in for the parameters marks in the filter clause.
1702    
1703    =item field
1704    
1705    Name of the field to be used to get the elements of the list returned.
1706    
1707    =item RETURN
1708    
1709    Returns a list of values.
1710    
1711    =back
1712    
1713    =cut
1714    #: Return Type @;
1715    sub GetFlat {
1716        # Get the parameters.
1717        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1718        # Construct the query.
1719        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1720        # Create the result list.
1721        my @retVal = ();
1722        # Loop through the records, adding the field values found to the result list.
1723        while (my $row = $query->Fetch()) {
1724            push @retVal, $row->Value($field);
1725        }
1726        # Return the list created.
1727        return @retVal;
1728    }
1729    
1730    =head3 SpecialFields
1731    
1732    C<< my %specials = $erdb->SpecialFields($entityName); >>
1733    
1734    Return a hash mapping special fields in the specified entity to the value of their
1735    C<special> attribute. This enables the subclass to get access to the special field
1736    attributes without needed to plumb the internal ERDB data structures.
1737    
1738    =over 4
1739    
1740    =item entityName
1741    
1742    Name of the entity whose special fields are desired.
1743    
1744    =item RETURN
1745    
1746    Returns a hash. The keys of the hash are the special field names, and the values
1747    are the values from each special field's C<special> attribute.
1748    
1749    =back
1750    
1751    =cut
1752    
1753    sub SpecialFields {
1754        # Get the parameters.
1755        my ($self, $entityName) = @_;
1756        # Declare the return variable.
1757        my %retVal = ();
1758        # Find the entity's data structure.
1759        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1760        # Loop through its fields, adding each special field to the return hash.
1761        my $fieldHash = $entityData->{Fields};
1762        for my $fieldName (keys %{$fieldHash}) {
1763            my $fieldData = $fieldHash->{$fieldName};
1764            if (exists $fieldData->{special}) {
1765                $retVal{$fieldName} = $fieldData->{special};
1766            }
1767        }
1768        # Return the result.
1769        return %retVal;
1770    }
1771    
1772    =head3 Delete
1773    
1774    C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1775    
1776    Delete an entity instance from the database. The instance is deleted along with all entity and
1777    relationship instances dependent on it. The definition of I<dependence> is recursive.
1778    
1779    An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1780    relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1781    dependent relationship.
1782    
1783    =over 4
1784    
1785    =item entityName
1786    
1787    Name of the entity type for the instance being deleted.
1788    
1789    =item objectID
1790    
1791    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1792    then it is presumed to by a LIKE pattern.
1793    
1794    =item options
1795    
1796    A hash detailing the options for this delete operation.
1797    
1798    =item RETURN
1799    
1800    Returns a statistics object indicating how many records of each particular table were
1801    deleted.
1802    
1803    =back
1804    
1805    The permissible options for this method are as follows.
1806    
1807    =over 4
1808    
1809    =item testMode
1810    
1811    If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1812    
1813    =item keepRoot
1814    
1815    If TRUE, then the entity instances will not be deleted, only the dependent records.
1816    
1817    =back
1818    
1819    =cut
1820    #: Return Type $%;
1821    sub Delete {
1822        # Get the parameters.
1823        my ($self, $entityName, $objectID, %options) = @_;
1824        # Declare the return variable.
1825        my $retVal = Stats->new();
1826        # Get the DBKernel object.
1827        my $db = $self->{_dbh};
1828        # We're going to generate all the paths branching out from the starting entity. One of
1829        # the things we have to be careful about is preventing loops. We'll use a hash to
1830        # determine if we've hit a loop.
1831        my %alreadyFound = ();
1832        # These next lists will serve as our result stack. We start by pushing object lists onto
1833        # the stack, and then popping them off to do the deletes. This means the deletes will
1834        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1835        # sure we don't delete records that might be needed to forge relationships back to the
1836        # original item. We have two lists-- one for TO-relationships, and one for
1837        # FROM-relationships and entities.
1838        my @fromPathList = ();
1839        my @toPathList = ();
1840        # This final list is used to remember what work still needs to be done. We push paths
1841        # onto the list, then pop them off to extend the paths. We prime it with the starting
1842        # point. Note that we will work hard to insure that the last item on a path in the
1843        # to-do list is always an entity.
1844        my @todoList = ([$entityName]);
1845        while (@todoList) {
1846            # Get the current path.
1847            my $current = pop @todoList;
1848            # Copy it into a list.
1849            my @stackedPath = @{$current};
1850            # Pull off the last item on the path. It will always be an entity.
1851            my $myEntityName = pop @stackedPath;
1852            # Add it to the alreadyFound list.
1853            $alreadyFound{$myEntityName} = 1;
1854            # Figure out if we need to delete this entity.
1855            if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1856                # Get the entity data.
1857                my $entityData = $self->_GetStructure($myEntityName);
1858                # Loop through the entity's relations. A DELETE command will be needed for each of them.
1859                my $relations = $entityData->{Relations};
1860                for my $relation (keys %{$relations}) {
1861                    my @augmentedList = (@stackedPath, $relation);
1862                    push @fromPathList, \@augmentedList;
1863                }
1864            }
1865            # Now we need to look for relationships connected to this entity.
1866            my $relationshipList = $self->{_metaData}->{Relationships};
1867            for my $relationshipName (keys %{$relationshipList}) {
1868                my $relationship = $relationshipList->{$relationshipName};
1869                # Check the FROM field. We're only interested if it's us.
1870                if ($relationship->{from} eq $myEntityName) {
1871                    # Add the path to this relationship.
1872                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1873                    push @fromPathList, \@augmentedList;
1874                    # Check the arity. If it's MM we're done. If it's 1M
1875                    # and the target hasn't been seen yet, we want to
1876                    # stack the entity for future processing.
1877                    if ($relationship->{arity} eq '1M') {
1878                        my $toEntity = $relationship->{to};
1879                        if (! exists $alreadyFound{$toEntity}) {
1880                            # Here we have a new entity that's dependent on
1881                            # the current entity, so we need to stack it.
1882                            my @stackList = (@augmentedList, $toEntity);
1883                            push @fromPathList, \@stackList;
1884                        } else {
1885                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1886                        }
1887                    }
1888                }
1889                # Now check the TO field. In this case only the relationship needs
1890                # deletion.
1891                if ($relationship->{to} eq $myEntityName) {
1892                    my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1893                    push @toPathList, \@augmentedList;
1894                }
1895            }
1896        }
1897        # Create the first qualifier for the WHERE clause. This selects the
1898        # keys of the primary entity records to be deleted. When we're deleting
1899        # from a dependent table, we construct a join path from the first qualifier
1900        # to the table containing the dependent records to delete.
1901        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1902        # We need to make two passes. The first is through the to-list, and
1903        # the second through the from-list. The from-list is second because
1904        # the to-list may need to pass through some of the entities the
1905        # from-list would delete.
1906        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1907        # Now it's time to do the deletes. We do it in two passes.
1908        for my $keyName ('to_link', 'from_link') {
1909            # Get the list for this key.
1910            my @pathList = @{$stackList{$keyName}};
1911            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1912            # Loop through this list.
1913            while (my $path = pop @pathList) {
1914                # Get the table whose rows are to be deleted.
1915                my @pathTables = @{$path};
1916                # Start the DELETE statement. We need to call DBKernel because the
1917                # syntax of a DELETE-USING varies among DBMSs.
1918                my $target = $pathTables[$#pathTables];
1919                my $stmt = $db->SetUsing(@pathTables);
1920                # Now start the WHERE. The first thing is the ID field from the starting table. That
1921                # starting table will either be the entity relation or one of the entity's
1922                # sub-relations.
1923                $stmt .= " WHERE $pathTables[0].id $qualifier";
1924                # Now we run through the remaining entities in the path, connecting them up.
1925                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1926                    # Connect the current relationship to the preceding entity.
1927                    my ($entity, $rel) = @pathTables[$i-1,$i];
1928                    # The style of connection depends on the direction of the relationship.
1929                    $stmt .= " AND $entity.id = $rel.$keyName";
1930                    if ($i + 1 <= $#pathTables) {
1931                        # Here there's a next entity, so connect that to the relationship's
1932                        # to-link.
1933                        my $entity2 = $pathTables[$i+1];
1934                        $stmt .= " AND $rel.to_link = $entity2.id";
1935                    }
1936                }
1937                # Now we have our desired DELETE statement.
1938                if ($options{testMode}) {
1939                    # Here the user wants to trace without executing.
1940                    Trace($stmt) if T(0);
1941                } else {
1942                    # Here we can delete. Note that the SQL method dies with a confession
1943                    # if an error occurs, so we just go ahead and do it.
1944                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1945                    my $rv = $db->SQL($stmt, 0, $objectID);
1946                    # Accumulate the statistics for this delete. The only rows deleted
1947                    # are from the target table, so we use its name to record the
1948                    # statistic.
1949                    $retVal->Add($target, $rv);
1950                }
1951            }
1952        }
1953        # Return the result.
1954        return $retVal;
1955    }
1956    
1957    =head3 Disconnect
1958    
1959    C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1960    
1961    Disconnect an entity instance from all the objects to which it is related. This
1962    will delete each relationship instance that connects to the specified entity.
1963    
1964    =over 4
1965    
1966    =item relationshipName
1967    
1968    Name of the relationship whose instances are to be deleted.
1969    
1970    =item originEntityName
1971    
1972    Name of the entity that is to be disconnected.
1973    
1974    =item originEntityID
1975    
1976    ID of the entity that is to be disconnected.
1977    
1978    =back
1979    
1980    =cut
1981    
1982    sub Disconnect {
1983        # Get the parameters.
1984        my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1985        # Get the relationship descriptor.
1986        my $structure = $self->_GetStructure($relationshipName);
1987        # Insure we have a relationship.
1988        if (! exists $structure->{from}) {
1989            Confess("$relationshipName is not a relationship in the database.");
1990        } else {
1991            # Get the database handle.
1992            my $dbh = $self->{_dbh};
1993            # We'll set this value to 1 if we find our entity.
1994            my $found = 0;
1995            # Loop through the ends of the relationship.
1996            for my $dir ('from', 'to') {
1997                if ($structure->{$dir} eq $originEntityName) {
1998                    # Delete all relationship instances on this side of the entity instance.
1999                    Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2000                    $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2001                    $found = 1;
2002                }
2003            }
2004            # Insure we found the entity on at least one end.
2005            if (! $found) {
2006                Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2007            }
2008        }
2009    }
2010    
2011    =head3 DeleteRow
2012    
2013    C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
2014    
2015    Delete a row from a relationship. In most cases, only the from-link and to-link are
2016    needed; however, for relationships with intersection data values can be specified
2017    for the other fields using a hash.
2018    
2019    =over 4
2020    
2021    =item relationshipName
2022    
2023    Name of the relationship from which the row is to be deleted.
2024    
2025    =item fromLink
2026    
2027    ID of the entity instance in the From direction.
2028    
2029    =item toLink
2030    
2031    ID of the entity instance in the To direction.
2032    
2033    =item values
2034    
2035    Reference to a hash of other values to be used for filtering the delete.
2036    
2037    =back
2038    
2039    =cut
2040    
2041    sub DeleteRow {
2042        # Get the parameters.
2043        my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2044        # Create a hash of all the filter information.
2045        my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2046        if (defined $values) {
2047            for my $key (keys %{$values}) {
2048                $filter{$key} = $values->{$key};
2049            }
2050        }
2051        # Build an SQL statement out of the hash.
2052        my @filters = ();
2053        my @parms = ();
2054        for my $key (keys %filter) {
2055            push @filters, _FixName($key) . " = ?";
2056            push @parms, $filter{$key};
2057        }
2058        Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2059        my $command = "DELETE FROM $relationshipName WHERE " .
2060                      join(" AND ", @filters);
2061        # Execute it.
2062        my $dbh = $self->{_dbh};
2063        $dbh->SQL($command, undef, @parms);
2064    }
2065    
2066    =head3 SortNeeded
2067    
2068    C<< my $parms = $erdb->SortNeeded($relationName); >>
2069    
2070    Return the pipe command for the sort that should be applied to the specified
2071    relation when creating the load file.
2072    
2073    For example, if the load file should be sorted ascending by the first
2074    field, this method would return
2075    
2076        sort -k1 -t"\t"
2077    
2078    If the first field is numeric, the method would return
2079    
2080        sort -k1n -t"\t"
2081    
2082    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2083    keys using a sort.
2084    
2085    =over 4
2086    
2087    =item relationName
2088    
2089    Name of the relation to be examined.
2090    
2091    =item
2092    
2093    Returns the sort command to use for sorting the relation, suitable for piping.
2094    
2095    =back
2096    
2097    =cut
2098    #: Return Type $;
2099    sub SortNeeded {
2100        # Get the parameters.
2101        my ($self, $relationName) = @_;
2102        # Declare a descriptor to hold the names of the key fields.
2103        my @keyNames = ();
2104        # Get the relation structure.
2105        my $relationData = $self->_FindRelation($relationName);
2106        # Find out if the relation is a primary entity relation,
2107        # a relationship relation, or a secondary entity relation.
2108        my $entityTable = $self->{_metaData}->{Entities};
2109        my $relationshipTable = $self->{_metaData}->{Relationships};
2110        if (exists $entityTable->{$relationName}) {
2111            # Here we have a primary entity relation.
2112            push @keyNames, "id";
2113        } elsif (exists $relationshipTable->{$relationName}) {
2114            # Here we have a relationship. We sort using the FROM index.
2115            my $relationshipData = $relationshipTable->{$relationName};
2116            my $index = $relationData->{Indexes}->{idxFrom};
2117            push @keyNames, @{$index->{IndexFields}};
2118        } else {
2119            # Here we have a secondary entity relation, so we have a sort on the ID field.
2120            push @keyNames, "id";
2121        }
2122        # Now we parse the key names into sort parameters. First, we prime the return
2123        # string.
2124        my $retVal = "sort -t\"\t\" ";
2125        # Get the relation's field list.
2126        my @fields = @{$relationData->{Fields}};
2127        # Loop through the keys.
2128        for my $keyData (@keyNames) {
2129            # Get the key and the ordering.
2130            my ($keyName, $ordering);
2131            if ($keyData =~ /^([^ ]+) DESC/) {
2132                ($keyName, $ordering) = ($1, "descending");
2133            } else {
2134                ($keyName, $ordering) = ($keyData, "ascending");
2135            }
2136            # Find the key's position and type.
2137            my $fieldSpec;
2138            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2139                my $thisField = $fields[$i];
2140                if ($thisField->{name} eq $keyName) {
2141                    # Get the sort modifier for this field type. The modifier
2142                    # decides whether we're using a character, numeric, or
2143                    # floating-point sort.
2144                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
2145                    # If the index is descending for this field, denote we want
2146                    # to reverse the sort order on this field.
2147                    if ($ordering eq 'descending') {
2148                        $modifier .= "r";
2149                    }
2150                    # Store the position and modifier into the field spec, which
2151                    # will stop the inner loop. Note that the field number is
2152                    # 1-based in the sort command, so we have to increment the
2153                    # index.
2154                    $fieldSpec = ($i + 1) . $modifier;
2155                }
2156            }
2157            # Add this field to the sort command.
2158            $retVal .= " -k$fieldSpec";
2159        }
2160        # Return the result.
2161        return $retVal;
2162    }
2163    
2164    =head3 GetList
2165    
2166    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2167    
2168    Return a list of object descriptors for the specified objects as determined by the
2169    specified filter clause.
2170    
2171    This method is essentially the same as L</Get> except it returns a list of objects rather
2172    than a query object that can be used to get the results one record at a time.
2173    
2174    =over 4
2175    
2176    =item objectNames
2177    
2178    List containing the names of the entity and relationship objects to be retrieved.
2179    
2180    =item filterClause
2181    
2182    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2183    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2184    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2185    in the filter clause should be added to the parameter list as additional parameters. The
2186    fields in a filter clause can come from primary entity relations, relationship relations,
2187    or secondary entity relations; however, all of the entities and relationships involved must
2188    be included in the list of object names.
2189    
2190    The filter clause can also specify a sort order. To do this, simply follow the filter string
2191    with an ORDER BY clause. For example, the following filter string gets all genomes for a
2192    particular genus and sorts them by species name.
2193    
2194    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2195    
2196    The rules for field references in a sort order are the same as those for field references in the
2197    filter clause in general; however, odd things may happen if a sort field is from a secondary
2198    relation.
2199    
2200    =item params
2201    
2202    Reference to a list of parameter values to be substituted into the filter clause.
2203    
2204    =item RETURN
2205    
2206    Returns a list of B<ERDBObject>s that satisfy the query conditions.
2207    
2208    =back
2209    
2210    =cut
2211    #: Return Type @%
2212    sub GetList {
2213        # Get the parameters.
2214        my ($self, $objectNames, $filterClause, $params) = @_;
2215        # Declare the return variable.
2216        my @retVal = ();
2217        # Perform the query.
2218        my $query = $self->Get($objectNames, $filterClause, $params);
2219        # Loop through the results.
2220        while (my $object = $query->Fetch) {
2221            push @retVal, $object;
2222        }
2223        # Return the result.
2224        return @retVal;
2225    }
2226    
2227    =head3 GetCount
2228    
2229    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2230    
2231    Return the number of rows found by a specified query. This method would
2232    normally be used to count the records in a single table. For example, in a
2233    genetics database
2234    
2235        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2236    
2237    would return the number of genomes for the genus I<homo>. It is conceivable, however,
2238    to use it to return records based on a join. For example,
2239    
2240        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2241                                    ['homo %']);
2242    
2243    would return the number of features for genomes in the genus I<homo>. Note that
2244    only the rows from the first table are counted. If the above command were
2245    
2246        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2247                                    ['homo %']);
2248    
2249    it would return the number of genomes, not the number of genome/feature pairs.
2250    
2251    =over 4
2252    
2253    =item objectNames
2254    
2255    Reference to a list of the objects (entities and relationships) included in the
2256    query.
2257    
2258    =item filter
2259    
2260    A filter clause for restricting the query. The rules are the same as for the L</Get>
2261    method.
2262    
2263    =item params
2264    
2265    Reference to a list of the parameter values to be substituted for the parameter marks
2266    in the filter.
2267    
2268    =item RETURN
2269    
2270    Returns a count of the number of records in the first table that would satisfy
2271    the query.
2272    
2273    =back
2274    
2275    =cut
2276    
2277    sub GetCount {
2278        # Get the parameters.
2279        my ($self, $objectNames, $filter, $params) = @_;
2280        # Insure the params argument is an array reference if the caller left it off.
2281        if (! defined($params)) {
2282            $params = [];
2283        }
2284        # Declare the return variable.
2285        my $retVal;
2286        # Find out if we're counting an entity or a relationship.
2287        my $countedField;
2288        if ($self->IsEntity($objectNames->[0])) {
2289            $countedField = "id";
2290        } else {
2291            # For a relationship we count the to-link because it's usually more
2292            # numerous. Note we're automatically converting to the SQL form
2293            # of the field name (to_link vs. to-link).
2294            $countedField = "to_link";
2295        }
2296        # Create the SQL command suffix to get the desired records.
2297        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2298                                                                                $filter);
2299        # Prefix it with text telling it we want a record count.
2300        my $firstObject = $mappedNameListRef->[0];
2301        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2302        # Prepare and execute the command.
2303        my $sth = $self->_GetStatementHandle($command, $params);
2304        # Get the count value.
2305        ($retVal) = $sth->fetchrow_array();
2306        # Check for a problem.
2307        if (! defined($retVal)) {
2308            if ($sth->err) {
2309                # Here we had an SQL error.
2310                Confess("Error retrieving row count: " . $sth->errstr());
2311            } else {
2312                # Here we have no result.
2313                Confess("No result attempting to retrieve row count.");
2314            }
2315        }
2316        # Return the result.
2317        return $retVal;
2318    }
2319    
2320    =head3 ComputeObjectSentence
2321    
2322    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2323    
2324    Check an object name, and if it is a relationship convert it to a relationship sentence.
2325    
2326    =over 4
2327    
2328    =item objectName
2329    
2330    Name of the entity or relationship.
2331    
2332    =item RETURN
2333    
2334    Returns a string containing the entity name or a relationship sentence.
2335    
2336    =back
2337    
2338    =cut
2339    
2340    sub ComputeObjectSentence {
2341        # Get the parameters.
2342        my ($self, $objectName) = @_;
2343        # Set the default return value.
2344        my $retVal = $objectName;
2345        # Look for the object as a relationship.
2346        my $relTable = $self->{_metaData}->{Relationships};
2347        if (exists $relTable->{$objectName}) {
2348            # Get the relationship sentence.
2349            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2350        }
2351        # Return the result.
2352        return $retVal;
2353    }
2354    
2355    =head3 DumpRelations
2356    
2357    C<< $erdb->DumpRelations($outputDirectory); >>
2358    
2359    Write the contents of all the relations to tab-delimited files in the specified directory.
2360    Each file will have the same name as the relation dumped, with an extension of DTX.
2361    
2362    =over 4
2363    
2364    =item outputDirectory
2365    
2366    Name of the directory into which the relation files should be dumped.
2367    
2368    =back
2369    
2370    =cut
2371    
2372    sub DumpRelations {
2373        # Get the parameters.
2374        my ($self, $outputDirectory) = @_;
2375        # Now we need to run through all the relations. First, we loop through the entities.
2376        my $metaData = $self->{_metaData};
2377        my $entities = $metaData->{Entities};
2378        for my $entityName (keys %{$entities}) {
2379            my $entityStructure = $entities->{$entityName};
2380            # Get the entity's relations.
2381            my $relationList = $entityStructure->{Relations};
2382            # Loop through the relations, dumping them.
2383            for my $relationName (keys %{$relationList}) {
2384                my $relation = $relationList->{$relationName};
2385                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2386            }
2387        }
2388        # Next, we loop through the relationships.
2389        my $relationships = $metaData->{Relationships};
2390        for my $relationshipName (keys %{$relationships}) {
2391            my $relationshipStructure = $relationships->{$relationshipName};
2392            # Dump this relationship's relation.
2393            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2394        }
2395    }
2396    
2397    =head3 InsertValue
2398    
2399    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2400    
2401    This method will insert a new value into the database. The value must be one
2402    associated with a secondary relation, since primary values cannot be inserted:
2403    they occur exactly once. Secondary values, on the other hand, can be missing
2404    or multiply-occurring.
2405    
2406    =over 4
2407    
2408    =item entityID
2409    
2410    ID of the object that is to receive the new value.
2411    
2412    =item fieldName
2413    
2414    Field name for the new value-- this includes the entity name, since
2415    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2416    
2417    =item value
2418    
2419    New value to be put in the field.
2420    
2421    =back
2422    
2423    =cut
2424    
2425    sub InsertValue {
2426        # Get the parameters.
2427        my ($self, $entityID, $fieldName, $value) = @_;
2428        # Parse the entity name and the real field name.
2429        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2430            my $entityName = $1;
2431            my $fieldTitle = $2;
2432            # Get its descriptor.
2433            if (!$self->IsEntity($entityName)) {
2434                Confess("$entityName is not a valid entity.");
2435            } else {
2436                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2437                # Find the relation containing this field.
2438                my $fieldHash = $entityData->{Fields};
2439                if (! exists $fieldHash->{$fieldTitle}) {
2440                    Confess("$fieldTitle not found in $entityName.");
2441                } else {
2442                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2443                    if ($relation eq $entityName) {
2444                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2445                    } else {
2446                        # Now we can create an INSERT statement.
2447                        my $dbh = $self->{_dbh};
2448                        my $fixedName = _FixName($fieldTitle);
2449                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2450                        # Execute the command.
2451                        $dbh->SQL($statement, 0, $entityID, $value);
2452                    }
2453                }
2454            }
2455        } else {
2456            Confess("$fieldName is not a valid field name.");
2457        }
2458    }
2459    
2460    =head3 InsertObject
2461    
2462    C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2463    
2464    Insert an object into the database. The object is defined by a type name and then a hash
2465    of field names to values. Field values in the primary relation are represented by scalars.
2466    (Note that for relationships, the primary relation is the B<only> relation.)
2467    Field values for the other relations comprising the entity are always list references. For
2468    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2469    C<ZP_00210270.1> and C<gi|46206278>.
2470    
2471    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2472    
2473    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2474    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2475    
2476    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2477    
2478    =over 4
2479    
2480    =item newObjectType
2481    
2482    Type name of the object to insert.
2483    
2484    =item fieldHash
2485    
2486    Hash of field names to values.
2487    
2488    =back
2489    
2490    =cut
2491    
2492    sub InsertObject {
2493        # Get the parameters.
2494        my ($self, $newObjectType, $fieldHash) = @_;
2495        # Denote that so far we appear successful.
2496        my $retVal = 1;
2497        # Get the database handle.
2498        my $dbh = $self->{_dbh};
2499        # Get the relation list.
2500        my $relationTable = $self->_GetRelationTable($newObjectType);
2501        # Loop through the relations. We'll build insert statements for each one. If a relation is
2502        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2503        # stop the loop.
2504        my @relationList = keys %{$relationTable};
2505        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2506            my $relationName = $relationList[$i];
2507            my $relationDefinition = $relationTable->{$relationName};
2508            # Get the relation's fields. For each field we will collect a value in the corresponding
2509            # position of the @valueList array. If one of the fields is missing, we will add it to the
2510            # @missing list.
2511            my @fieldList = @{$relationDefinition->{Fields}};
2512            my @fieldNameList = ();
2513            my @valueList = ();
2514            my @missing = ();
2515            my $recordCount = 1;
2516            for my $fieldDescriptor (@fieldList) {
2517                # Get the field name and save it. Note we need to fix it up so the hyphens
2518                # are converted to underscores.
2519                my $fieldName = $fieldDescriptor->{name};
2520                push @fieldNameList, _FixName($fieldName);
2521                # Look for the named field in the incoming structure. Note that we are looking
2522                # for the real field name, not the fixed-up one!
2523                if (exists $fieldHash->{$fieldName}) {
2524                    # Here we found the field. Stash it in the value list.
2525                    my $value = $fieldHash->{$fieldName};
2526                    push @valueList, $value;
2527                    # If the value is a list, we may need to increment the record count.
2528                    if (ref $value eq "ARRAY") {
2529                        my $thisCount = @{$value};
2530                        if ($recordCount == 1) {
2531                            # Here we have our first list, so we save its count.
2532                            $recordCount = $thisCount;
2533                        } elsif ($recordCount != $thisCount) {
2534                            # Here we have a second list, so its length has to match the
2535                            # previous lists.
2536                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2537                            $retVal = 0;
2538                        }
2539                    }
2540          } else {          } else {
2541              # Here we've seen the object before. We construct a new name using                  # Here the field is not present. Flag it as missing.
2542              # the suffix from the hash and update the hash.                  push @missing, $fieldName;
2543              my $mappedName = "$objectName$suffix";              }
2544              $objectHash{$objectName} = $suffix + 1;          }
2545              # The FROM list has the object name followed by the mapped name. This          # If we are the primary relation, add the new-record flag.
2546              # tells SQL it's still the same table, but we're using a different name          if ($relationName eq $newObjectType) {
2547              # for it to avoid confusion.              push @valueList, 1;
2548              push @fromList, "$objectName $mappedName";              push @fieldNameList, "new_record";
2549              # The mapped-name list contains the real mapped name.          }
2550              push @mappedNameList, $mappedName;          # Only proceed if there are no missing fields.
2551              # Finally, enable us to get back from the mapped name to the object name.          if (@missing > 0) {
2552              $mappedNameHash{$mappedName} = $objectName;              Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2553                    join(' ', @missing)) if T(1);
2554            } else {
2555                # Build the INSERT statement.
2556                my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2557                    ") VALUES (";
2558                # Create a marker list of the proper size and put it in the statement.
2559                my @markers = ();
2560                while (@markers < @fieldNameList) { push @markers, '?'; }
2561                $statement .= join(', ', @markers) . ")";
2562                # We have the insert statement, so prepare it.
2563                my $sth = $dbh->prepare_command($statement);
2564                Trace("Insert statement prepared: $statement") if T(3);
2565                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2566                # a list, we use the current element. The values are stored in the @parameterList array.
2567                my $done = 0;
2568                for (my $i = 0; $i < $recordCount; $i++) {
2569                    # Clear the parameter list array.
2570                    my @parameterList = ();
2571                    # Loop through the values.
2572                    for my $value (@valueList) {
2573                        # Check to see if this is a scalar value.
2574                        if (ref $value eq "ARRAY") {
2575                            # Here we have a list value. Pull the current entry.
2576                            push @parameterList, $value->[$i];
2577                        } else {
2578                            # Here we have a scalar value. Use it unmodified.
2579                            push @parameterList, $value;
2580                        }
2581                    }
2582                    # Execute the INSERT statement with the specified parameter list.
2583                    $retVal = $sth->execute(@parameterList);
2584                    if (!$retVal) {
2585                        my $errorString = $sth->errstr();
2586                        Confess("Error inserting into $relationName: $errorString");
2587                    } else {
2588                        Trace("Insert successful using $parameterList[0].") if T(3);
2589                    }
2590                }
2591            }
2592        }
2593        # Return a 1 for backward compatability.
2594        return 1;
2595    }
2596    
2597    =head3 UpdateEntity
2598    
2599    C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2600    
2601    Update the values of an entity. This is an unprotected update, so it should only be
2602    done if the database resides on a database server.
2603    
2604    =over 4
2605    
2606    =item entityName
2607    
2608    Name of the entity to update. (This is the entity type.)
2609    
2610    =item id
2611    
2612    ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2613    
2614    =item fields
2615    
2616    Reference to a hash mapping field names to their new values. All of the fields named
2617    must be in the entity's primary relation, and they cannot any of them be the ID field.
2618    
2619    =back
2620    
2621    =cut
2622    
2623    sub UpdateEntity {
2624        # Get the parameters.
2625        my ($self, $entityName, $id, $fields) = @_;
2626        # Get a list of the field names being updated.
2627        my @fieldList = keys %{$fields};
2628        # Verify that the fields exist.
2629        my $checker = $self->GetFieldTable($entityName);
2630        for my $field (@fieldList) {
2631            if ($field eq 'id') {
2632                Confess("Cannot update the ID field for entity $entityName.");
2633            } elsif ($checker->{$field}->{relation} ne $entityName) {
2634                Confess("Cannot find $field in primary relation of $entityName.");
2635            }
2636        }
2637        # Build the SQL statement.
2638        my @sets = ();
2639        my @valueList = ();
2640        for my $field (@fieldList) {
2641            push @sets, _FixName($field) . " = ?";
2642            push @valueList, $fields->{$field};
2643        }
2644        my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2645        # Add the ID to the list of binding values.
2646        push @valueList, $id;
2647        # Call SQL to do the work.
2648        my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2649        # Check for errors.
2650        if ($rows == 0) {
2651            Confess("Entity $id of type $entityName not found.");
2652        }
2653    }
2654    
2655    =head3 LoadTable
2656    
2657    C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2658    
2659    Load data from a tab-delimited file into a specified table, optionally re-creating the table
2660    first.
2661    
2662    =over 4
2663    
2664    =item fileName
2665    
2666    Name of the file from which the table data should be loaded.
2667    
2668    =item relationName
2669    
2670    Name of the relation to be loaded. This is the same as the table name.
2671    
2672    =item truncateFlag
2673    
2674    TRUE if the table should be dropped and re-created, else FALSE
2675    
2676    =item RETURN
2677    
2678    Returns a statistical object containing a list of the error messages.
2679    
2680    =back
2681    
2682    =cut
2683    sub LoadTable {
2684        # Get the parameters.
2685        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2686        # Create the statistical return object.
2687        my $retVal = _GetLoadStats();
2688        # Trace the fact of the load.
2689        Trace("Loading table $relationName from $fileName") if T(2);
2690        # Get the database handle.
2691        my $dbh = $self->{_dbh};
2692        # Get the input file size.
2693        my $fileSize = -s $fileName;
2694        # Get the relation data.
2695        my $relation = $self->_FindRelation($relationName);
2696        # Check the truncation flag.
2697        if ($truncateFlag) {
2698            Trace("Creating table $relationName") if T(2);
2699            # Compute the row count estimate. We take the size of the load file,
2700            # divide it by the estimated row size, and then multiply by 1.5 to
2701            # leave extra room. We postulate a minimum row count of 1000 to
2702            # prevent problems with incoming empty load files.
2703            my $rowSize = $self->EstimateRowSize($relationName);
2704            my $estimate = $fileSize * 1.5 / $rowSize;
2705            if ($estimate < 1000) {
2706                $estimate = 1000;
2707            }
2708            # Re-create the table without its index.
2709            $self->CreateTable($relationName, 0, $estimate);
2710            # If this is a pre-index DBMS, create the index here.
2711            if ($dbh->{_preIndex}) {
2712                eval {
2713                    $self->CreateIndex($relationName);
2714                };
2715                if ($@) {
2716                    $retVal->AddMessage($@);
2717                }
2718            }
2719        }
2720        # Load the table.
2721        my $rv;
2722        eval {
2723            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2724        };
2725        if (!defined $rv) {
2726            $retVal->AddMessage($@) if ($@);
2727            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2728            Trace("Table load failed for $relationName.") if T(1);
2729        } else {
2730            # Here we successfully loaded the table.
2731            $retVal->Add("tables");
2732            my $size = -s $fileName;
2733            Trace("$size bytes loaded into $relationName.") if T(2);
2734            # If we're rebuilding, we need to create the table indexes.
2735            if ($truncateFlag) {
2736                # Indexes are created here for PostGres. For PostGres, indexes are
2737                # best built at the end. For MySQL, the reverse is true.
2738                if (! $dbh->{_preIndex}) {
2739                    eval {
2740                        $self->CreateIndex($relationName);
2741                    };
2742                    if ($@) {
2743                        $retVal->AddMessage($@);
2744                    }
2745                }
2746                # The full-text index (if any) is always built last, even for MySQL.
2747                # First we need to see if this table has a full-text index. Only
2748                # primary relations are allowed that privilege.
2749                Trace("Checking for full-text index on $relationName.") if T(2);
2750                if ($self->_IsPrimary($relationName)) {
2751                    $self->CreateSearchIndex($relationName);
2752                }
2753            }
2754        }
2755        # Analyze the table to improve performance.
2756        Trace("Analyzing and compacting $relationName.") if T(3);
2757        $dbh->vacuum_it($relationName);
2758        Trace("$relationName load completed.") if T(3);
2759        # Return the statistics.
2760        return $retVal;
2761    }
2762    
2763    =head3 CreateSearchIndex
2764    
2765    C<< $erdb->CreateSearchIndex($objectName); >>
2766    
2767    Check for a full-text search index on the specified entity or relationship object, and
2768    if one is required, rebuild it.
2769    
2770    =over 4
2771    
2772    =item objectName
2773    
2774    Name of the entity or relationship to be indexed.
2775    
2776    =back
2777    
2778    =cut
2779    
2780    sub CreateSearchIndex {
2781        # Get the parameters.
2782        my ($self, $objectName) = @_;
2783        # Get the relation's entity/relationship structure.
2784        my $structure = $self->_GetStructure($objectName);
2785        # Get the database handle.
2786        my $dbh = $self->{_dbh};
2787        Trace("Checking for search fields in $objectName.") if T(3);
2788        # Check for a searchable fields list.
2789        if (exists $structure->{searchFields}) {
2790            # Here we know that we need to create a full-text search index.
2791            # Get an SQL-formatted field name list.
2792            my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2793            # Create the index. If it already exists, it will be dropped.
2794            $dbh->create_index(tbl => $objectName, idx => "search_idx",
2795                               flds => $fields, kind => 'fulltext');
2796            Trace("Index created for $fields in $objectName.") if T(2);
2797        }
2798    }
2799    
2800    =head3 DropRelation
2801    
2802    C<< $erdb->DropRelation($relationName); >>
2803    
2804    Physically drop a relation from the database.
2805    
2806    =over 4
2807    
2808    =item relationName
2809    
2810    Name of the relation to drop. If it does not exist, this method will have
2811    no effect.
2812    
2813    =back
2814    
2815    =cut
2816    
2817    sub DropRelation {
2818        # Get the parameters.
2819        my ($self, $relationName) = @_;
2820        # Get the database handle.
2821        my $dbh = $self->{_dbh};
2822        # Drop the relation. The method used here has no effect if the relation
2823        # does not exist.
2824        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2825        $dbh->drop_table(tbl => $relationName);
2826    }
2827    
2828    =head3 MatchSqlPattern
2829    
2830    C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2831    
2832    Determine whether or not a specified value matches an SQL pattern. An SQL
2833    pattern has two wild card characters: C<%> that matches multiple characters,
2834    and C<_> that matches a single character. These can be escaped using a
2835    backslash (C<\>). We pull this off by converting the SQL pattern to a
2836    PERL regular expression. As per SQL rules, the match is case-insensitive.
2837    
2838    =over 4
2839    
2840    =item value
2841    
2842    Value to be matched against the pattern. Note that an undefined or empty
2843    value will not match anything.
2844    
2845    =item pattern
2846    
2847    SQL pattern against which to match the value. An undefined or empty pattern will
2848    match everything.
2849    
2850    =item RETURN
2851    
2852    Returns TRUE if the value and pattern match, else FALSE.
2853    
2854    =back
2855    
2856    =cut
2857    
2858    sub MatchSqlPattern {
2859        # Get the parameters.
2860        my ($value, $pattern) = @_;
2861        # Declare the return variable.
2862        my $retVal;
2863        # Insure we have a pattern.
2864        if (! defined($pattern) || $pattern eq "") {
2865            $retVal = 1;
2866        } else {
2867            # Break the pattern into pieces around the wildcard characters. Because we
2868            # use parentheses in the split function's delimiter expression, we'll get
2869            # list elements for the delimiters as well as the rest of the string.
2870            my @pieces = split /([_%]|\\[_%])/, $pattern;
2871            # Check some fast special cases.
2872            if ($pattern eq '%') {
2873                # A null pattern matches everything.
2874                $retVal = 1;
2875            } elsif (@pieces == 1) {
2876                # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2877                $retVal = (lc($value) eq lc($pattern));
2878            } elsif (@pieces == 2 && $pieces[1] eq '%') {
2879                # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2880                $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2881            } else {
2882                # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2883                my $realPattern = "";
2884                for my $piece (@pieces) {
2885                    # Determine the type of piece.
2886                    if ($piece eq "") {
2887                        # Empty pieces are ignored.
2888                    } elsif ($piece eq "%") {
2889                        # Here we have a multi-character wildcard. Note that it can match
2890                        # zero or more characters.
2891                        $realPattern .= ".*"
2892                    } elsif ($piece eq "_") {
2893                        # Here we have a single-character wildcard.
2894                        $realPattern .= ".";
2895                    } elsif ($piece eq "\\%" || $piece eq "\\_") {
2896                        # This is an escape sequence (which is a rare thing, actually).
2897                        $realPattern .= substr($piece, 1, 1);
2898                    } else {
2899                        # Here we have raw text.
2900                        $realPattern .= quotemeta($piece);
2901                    }
2902                }
2903                # Do the match.
2904                $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2905          }          }
2906      }      }
2907      # Construct the SELECT statement. The general pattern is      # Return the result.
2908      #      return $retVal;
2909      # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN  }
2910      #  
2911      my $dbh = $self->{_dbh};  =head3 GetEntity
2912      my $command = "SELECT DISTINCT " . join('.*, ', @mappedNameList) . ".* FROM " .  
2913                  join(', ', @fromList);  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2914      # Check for a filter clause.  
2915      if ($filterClause) {  Return an object describing the entity instance with a specified ID.
2916          # Here we have one, so we convert its field names and add it to the query. First,  
2917          # We create a copy of the filter string we can work with.  =over 4
2918          my $filterString = $filterClause;  
2919          # Next, we sort the object names by length. This helps protect us from finding  =item entityType
2920          # object names inside other object names when we're doing our search and replace.  
2921          my @sortedNames = sort { length($b) - length($a) } @mappedNameList;  Entity type name.
2922          # We will also keep a list of conditions to add to the WHERE clause in order to link  
2923          # entities and relationships as well as primary relations to secondary ones.  =item ID
2924          my @joinWhere = ();  
2925          # The final preparatory step is to create a hash table of relation names. The  ID of the desired entity.
2926          # table begins with the relation names already in the SELECT command. We may  
2927          # need to add relations later if there is filtering on a field in a secondary  =item RETURN
2928          # relation. The secondary relations are the ones that contain multiply-  
2929          # occurring or optional fields.  Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2930          my %fromNames = map { $_ => 1 } @sortedNames;  instance is found with the specified key.
2931          # We are ready to begin. We loop through the object names, replacing each  
2932          # object name's field references by the corresponding SQL field reference.  =back
2933          # Along the way, if we find a secondary relation, we will need to add it  
2934          # to the FROM clause.  =cut
2935          for my $mappedName (@sortedNames) {  
2936              # Get the length of the object name plus 2. This is the value we add to the  sub GetEntity {
2937              # size of the field name to determine the size of the field reference as a      # Get the parameters.
2938              # whole.      my ($self, $entityType, $ID) = @_;
2939              my $nameLength = 2 + length $mappedName;      # Create a query.
2940              # Get the real object name for this mapped name.      my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2941              my $objectName = $mappedNameHash{$mappedName};      # Get the first (and only) object.
2942              Trace("Processing $mappedName for object $objectName.") if T(4);      my $retVal = $query->Fetch();
2943              # Get the object's field list.      # Return the result.
2944              my $fieldList = $self->GetFieldTable($objectName);      return $retVal;
2945              # Find the field references for this object.  }
2946              while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {  
2947                  # At this point, $1 contains the field name, and the current position  =head3 GetChoices
2948                  # is set immediately after the final parenthesis. We pull out the name of  
2949                  # the field and the position and length of the field reference as a whole.  C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2950                  my $fieldName = $1;  
2951                  my $len = $nameLength + length $fieldName;  Return a list of all the values for the specified field that are represented in the
2952                  my $pos = pos($filterString) - $len;  specified entity.
2953                  # Insure the field exists.  
2954                  if (!exists $fieldList->{$fieldName}) {  Note that if the field is not indexed, then this will be a very slow operation.
2955                      Confess("Field $fieldName not found for object $objectName.");  
2956    =over 4
2957    
2958    =item entityName
2959    
2960    Name of an entity in the database.
2961    
2962    =item fieldName
2963    
2964    Name of a field belonging to the entity. This is a raw field name without
2965    the standard parenthesized notation used in most calls.
2966    
2967    =item RETURN
2968    
2969    Returns a list of the distinct values for the specified field in the database.
2970    
2971    =back
2972    
2973    =cut
2974    
2975    sub GetChoices {
2976        # Get the parameters.
2977        my ($self, $entityName, $fieldName) = @_;
2978        # Declare the return variable.
2979        my @retVal;
2980        # Get the entity data structure.
2981        my $entityData = $self->_GetStructure($entityName);
2982        # Get the field.
2983        my $fieldHash = $entityData->{Fields};
2984        if (! exists $fieldHash->{$fieldName}) {
2985            Confess("$fieldName not found in $entityName.");
2986                  } else {                  } else {
2987                      Trace("Processing $fieldName at position $pos.") if T(4);          # Get the name of the relation containing the field.
2988                      # Get the field's relation.          my $relation = $fieldHash->{$fieldName}->{relation};
2989                      my $relationName = $fieldList->{$fieldName}->{relation};          # Fix up the field name.
2990                      # Now we have a secondary relation. We need to insure it matches the          my $realName = _FixName($fieldName);
2991                      # mapped name of the primary relation. First we peel off the suffix          # Get the database handle.
2992                      # from the mapped name.          my $dbh = $self->{_dbh};
2993                      my $mappingSuffix = substr $mappedName, length($objectName);          # Query the database.
2994                      # Put the mapping suffix onto the relation name to get the          my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2995                      # mapped relation name.          # Clean the results. They are stored as a list of lists, and we just want the one list.
2996                      my $mappedRelationName = "$relationName$mappingSuffix";          @retVal = sort map { $_->[0] } @{$results};
2997                      # Insure the relation is in the FROM clause.      }
2998                      if (!exists $fromNames{$mappedRelationName}) {      # Return the result.
2999                          # Add the relation to the FROM clause.      return @retVal;
3000                          if ($mappedRelationName eq $relationName) {  }
3001                              # The name is un-mapped, so we add it without  
3002                              # any frills.  =head3 GetEntityValues
3003                              $command .= ", $relationName";  
3004                              push @joinWhere, "$objectName.id = $relationName.id";  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
3005    
3006    Return a list of values from a specified entity instance. If the entity instance
3007    does not exist, an empty list is returned.
3008    
3009    =over 4
3010    
3011    =item entityType
3012    
3013    Entity type name.
3014    
3015    =item ID
3016    
3017    ID of the desired entity.
3018    
3019    =item fields
3020    
3021    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
3022    
3023    =item RETURN
3024    
3025    Returns a flattened list of the values of the specified fields for the specified entity.
3026    
3027    =back
3028    
3029    =cut
3030    
3031    sub GetEntityValues {
3032        # Get the parameters.
3033        my ($self, $entityType, $ID, $fields) = @_;
3034        # Get the specified entity.
3035        my $entity = $self->GetEntity($entityType, $ID);
3036        # Declare the return list.
3037        my @retVal = ();
3038        # If we found the entity, push the values into the return list.
3039        if ($entity) {
3040            push @retVal, $entity->Values($fields);
3041        }
3042        # Return the result.
3043        return @retVal;
3044    }
3045    
3046    =head3 GetAll
3047    
3048    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
3049    
3050    Return a list of values taken from the objects returned by a query. The first three
3051    parameters correspond to the parameters of the L</Get> method. The final parameter is
3052    a list of the fields desired from each record found by the query. The field name
3053    syntax is the standard syntax used for fields in the B<ERDB> system--
3054    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
3055    or relationship and I<fieldName> is the name of the field.
3056    
3057    The list returned will be a list of lists. Each element of the list will contain
3058    the values returned for the fields specified in the fourth parameter. If one of the
3059    fields specified returns multiple values, they are flattened in with the rest. For
3060    example, the following call will return a list of the features in a particular
3061    spreadsheet cell, and each feature will be represented by a list containing the
3062    feature ID followed by all of its aliases.
3063    
3064    C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
3065    
3066    =over 4
3067    
3068    =item objectNames
3069    
3070    List containing the names of the entity and relationship objects to be retrieved.
3071    
3072    =item filterClause
3073    
3074    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
3075    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
3076    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
3077    parameter list as additional parameters. The fields in a filter clause can come from primary
3078    entity relations, relationship relations, or secondary entity relations; however, all of the
3079    entities and relationships involved must be included in the list of object names.
3080    
3081    =item parameterList
3082    
3083    List of the parameters to be substituted in for the parameters marks in the filter clause.
3084    
3085    =item fields
3086    
3087    List of the fields to be returned in each element of the list returned.
3088    
3089    =item count
3090    
3091    Maximum number of records to return. If omitted or 0, all available records will be returned.
3092    
3093    =item RETURN
3094    
3095    Returns a list of list references. Each element of the return list contains the values for the
3096    fields specified in the B<fields> parameter.
3097    
3098    =back
3099    
3100    =cut
3101    #: Return Type @@;
3102    sub GetAll {
3103        # Get the parameters.
3104        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3105        # Translate the parameters from a list reference to a list. If the parameter
3106        # list is a scalar we convert it into a singleton list.
3107        my @parmList = ();
3108        if (ref $parameterList eq "ARRAY") {
3109            Trace("GetAll parm list is an array.") if T(4);
3110            @parmList = @{$parameterList};
3111                          } else {                          } else {
3112                              # Here we have a mapping situation.          Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3113                              $command .= ", $relationName $mappedRelationName";          push @parmList, $parameterList;
3114                              push @joinWhere, "$mappedRelationName.id = $mappedName.id";      }
3115        # Insure the counter has a value.
3116        if (!defined $count) {
3117            $count = 0;
3118        }
3119        # Add the row limit to the filter clause.
3120        if ($count > 0) {
3121            $filterClause .= " LIMIT $count";
3122        }
3123        # Create the query.
3124        my $query = $self->Get($objectNames, $filterClause, \@parmList);
3125        # Set up a counter of the number of records read.
3126        my $fetched = 0;
3127        # Loop through the records returned, extracting the fields. Note that if the
3128        # counter is non-zero, we stop when the number of records read hits the count.
3129        my @retVal = ();
3130        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3131            my @rowData = $row->Values($fields);
3132            push @retVal, \@rowData;
3133            $fetched++;
3134        }
3135        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3136        # Return the resulting list.
3137        return @retVal;
3138                          }                          }
3139                          # Denote we have this relation available for future fields.  
3140                          $fromNames{$mappedRelationName} = 1;  =head3 Exists
3141    
3142    C<< my $found = $sprout->Exists($entityName, $entityID); >>
3143    
3144    Return TRUE if an entity exists, else FALSE.
3145    
3146    =over 4
3147    
3148    =item entityName
3149    
3150    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3151    
3152    =item entityID
3153    
3154    ID of the entity instance whose existence is to be checked.
3155    
3156    =item RETURN
3157    
3158    Returns TRUE if the entity instance exists, else FALSE.
3159    
3160    =back
3161    
3162    =cut
3163    #: Return Type $;
3164    sub Exists {
3165        # Get the parameters.
3166        my ($self, $entityName, $entityID) = @_;
3167        # Check for the entity instance.
3168        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3169        my $testInstance = $self->GetEntity($entityName, $entityID);
3170        # Return an existence indicator.
3171        my $retVal = ($testInstance ? 1 : 0);
3172        return $retVal;
3173                      }                      }
3174                      # Form an SQL field reference from the relation name and the field name.  
3175                      my $sqlReference = "$mappedRelationName." . _FixName($fieldName);  =head3 EstimateRowSize
3176                      # Put it into the filter string in place of the old value.  
3177                      substr($filterString, $pos, $len) = $sqlReference;  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3178                      # Reposition the search.  
3179                      pos $filterString = $pos + length $sqlReference;  Estimate the row size of the specified relation. The estimated row size is computed by adding
3180    up the average length for each data type.
3181    
3182    =over 4
3183    
3184    =item relName
3185    
3186    Name of the relation whose estimated row size is desired.
3187    
3188    =item RETURN
3189    
3190    Returns an estimate of the row size for the specified relation.
3191    
3192    =back
3193    
3194    =cut
3195    #: Return Type $;
3196    sub EstimateRowSize {
3197        # Get the parameters.
3198        my ($self, $relName) = @_;
3199        # Declare the return variable.
3200        my $retVal = 0;
3201        # Find the relation descriptor.
3202        my $relation = $self->_FindRelation($relName);
3203        # Get the list of fields.
3204        for my $fieldData (@{$relation->{Fields}}) {
3205            # Get the field type and add its length.
3206            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3207            $retVal += $fieldLen;
3208                  }                  }
3209        # Return the result.
3210        return $retVal;
3211              }              }
3212    
3213    =head3 GetFieldTable
3214    
3215    C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3216    
3217    Get the field structure for a specified entity or relationship.
3218    
3219    =over 4
3220    
3221    =item objectName
3222    
3223    Name of the desired entity or relationship.
3224    
3225    =item RETURN
3226    
3227    The table containing the field descriptors for the specified object.
3228    
3229    =back
3230    
3231    =cut
3232    
3233    sub GetFieldTable {
3234        # Get the parameters.
3235        my ($self, $objectName) = @_;
3236        # Get the descriptor from the metadata.
3237        my $objectData = $self->_GetStructure($objectName);
3238        # Return the object's field table.
3239        return $objectData->{Fields};
3240          }          }
3241          # The next step is to join the objects together. We only need to do this if there  
3242          # is more than one object in the object list. We start with the first object and  =head3 SplitKeywords
3243          # run through the objects after it. Note also that we make a safety copy of the  
3244          # list before running through it.  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3245          my @mappedObjectList = @mappedNameList;  
3246          my $lastMappedObject = shift @mappedObjectList;  This method returns a list of the positive keywords in the specified
3247          # Get the join table.  keyword string. All of the operators will have been stripped off,
3248          my $joinTable = $self->{_metaData}->{Joins};  and if the keyword is preceded by a minus operator (C<->), it will
3249          # Loop through the object list.  not be in the list returned. The idea here is to get a list of the
3250          for my $thisMappedObject (@mappedObjectList) {  keywords the user wants to see. The list will be processed to remove
3251              # Look for a join using the real object names.  duplicates.
3252              my $lastObject = $mappedNameHash{$lastMappedObject};  
3253              my $thisObject = $mappedNameHash{$thisMappedObject};  It is possible to create a string that confuses this method. For example
3254              my $joinKey = "$lastObject/$thisObject";  
3255              if (!exists $joinTable->{$joinKey}) {      frog toad -frog
3256                  # Here there's no join, so we throw an error.  
3257                  Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");  would return both C<frog> and C<toad>. If this is a problem we can deal
3258    with it later.
3259    
3260    =over 4
3261    
3262    =item keywordString
3263    
3264    The keyword string to be parsed.
3265    
3266    =item RETURN
3267    
3268    Returns a list of the words in the keyword string the user wants to
3269    see.
3270    
3271    =back
3272    
3273    =cut
3274    
3275    sub SplitKeywords {
3276        # Get the parameters.
3277        my ($keywordString) = @_;
3278        # Make a safety copy of the string. (This helps during debugging.)
3279        my $workString = $keywordString;
3280        # Convert operators we don't care about to spaces.
3281        $workString =~ tr/+"()<>/ /;
3282        # Split the rest of the string along space boundaries. Note that we
3283        # eliminate any words that are zero length or begin with a minus sign.
3284        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3285        # Use a hash to remove duplicates.
3286        my %words = map { $_ => 1 } @wordList;
3287        # Return the result.
3288        return sort keys %words;
3289    }
3290    
3291    =head3 ValidateFieldName
3292    
3293    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3294    
3295    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3296    be hyphenated words subject to certain restrictions.
3297    
3298    =over 4
3299    
3300    =item fieldName
3301    
3302    Field name to be validated.
3303    
3304    =item RETURN
3305    
3306    Returns TRUE if the field name is valid, else FALSE.
3307    
3308    =back
3309    
3310    =cut
3311    
3312    sub ValidateFieldName {
3313        # Get the parameters.
3314        my ($fieldName) = @_;
3315        # Declare the return variable. The field name is valid until we hear
3316        # differently.
3317        my $retVal = 1;
3318        # Compute the maximum name length.
3319        my $maxLen = $TypeTable{'name-string'}->{maxLen};
3320        # Look for bad stuff in the name.
3321        if ($fieldName =~ /--/) {
3322            # Here we have a doubled minus sign.
3323            Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3324            $retVal = 0;
3325        } elsif ($fieldName !~ /^[A-Za-z]/) {
3326            # Here the field name is missing the initial letter.
3327            Trace("Field name $fieldName does not begin with a letter.") if T(1);
3328            $retVal = 0;
3329        } elsif (length($fieldName) > $maxLen) {
3330            # Here the field name is too long.
3331            Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3332              } else {              } else {
3333                  # Get the join clause.          # Strip out the minus signs. Everything remaining must be a letter,
3334                  my $unMappedJoin = $joinTable->{$joinKey};          # underscore, or digit.
3335                  # Fix the names.          my $strippedName = $fieldName;
3336                  $unMappedJoin =~ s/$lastObject/$lastMappedObject/;          $strippedName =~ s/-//g;
3337                  $unMappedJoin =~ s/$thisObject/$thisMappedObject/;          if ($strippedName !~ /^(\w|\d)+$/) {
3338                  push @joinWhere, $unMappedJoin;              Trace("Field name $fieldName contains illegal characters.") if T(1);
3339                  # Save this object as the last object for the next iteration.              $retVal = 0;
                 $lastMappedObject = $thisMappedObject;  
3340              }              }
3341          }          }
3342          # Now we need to handle the whole ORDER BY / LIMIT thing. The important part      # Return the result.
3343          # here is we want the filter clause to be empty if there's no WHERE filter.      return $retVal;
         # 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 = $1;  
3344          }          }
3345          # Add the filter and the join clauses (if any) to the SELECT command.  
3346          if ($filterString) {  =head3 ReadMetaXML
3347              Trace("Filter string is \"$filterString\".") if T(4);  
3348              push @joinWhere, "($filterString)";  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3349    
3350    This method reads a raw database definition XML file and returns it.
3351    Normally, the metadata used by the ERDB system has been processed and
3352    modified to make it easier to load and retrieve the data; however,
3353    this method can be used to get the data in its raw form.
3354    
3355    =over 4
3356    
3357    =item fileName
3358    
3359    Name of the XML file to read.
3360    
3361    =item RETURN
3362    
3363    Returns a hash reference containing the raw XML data from the specified file.
3364    
3365    =back
3366    
3367    =cut
3368    
3369    sub ReadMetaXML {
3370        # Get the parameters.
3371        my ($fileName) = @_;
3372        # Read the XML.
3373        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3374        Trace("XML metadata loaded from file $fileName.") if T(1);
3375        # Return the result.
3376        return $retVal;
3377          }          }
3378          if (@joinWhere) {  
3379              $command .= " WHERE " . join(' AND ', @joinWhere);  =head3 GetEntityFieldHash
3380    
3381    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3382    
3383    Get the field hash of the named entity in the specified raw XML structure.
3384    The field hash may not exist, in which case we need to create it.
3385    
3386    =over 4
3387    
3388    =item structure
3389    
3390    Raw XML structure defininng the database. This is not the run-time XML used by
3391    an ERDB object, since that has all sorts of optimizations built-in.
3392    
3393    =item entityName
3394    
3395    Name of the entity whose field structure is desired.
3396    
3397    =item RETURN
3398    
3399    Returns the field hash used to define the entity's fields.
3400    
3401    =back
3402    
3403    =cut
3404    
3405    sub GetEntityFieldHash {
3406        # Get the parameters.
3407        my ($structure, $entityName) = @_;
3408        # Get the entity structure.
3409        my $entityData = $structure->{Entities}->{$entityName};
3410        # Look for a field structure.
3411        my $retVal = $entityData->{Fields};
3412        # If it doesn't exist, create it.
3413        if (! defined($retVal)) {
3414            $entityData->{Fields} = {};
3415            $retVal = $entityData->{Fields};
3416          }          }
3417          # Add the sort or limit clause (if any) to the SELECT command.      # Return the result.
3418          if ($orderClause) {      return $retVal;
3419              $command .= " $orderClause";  }
3420    
3421    =head3 WriteMetaXML
3422    
3423    C<< ERDB::WriteMetaXML($structure, $fileName); >>
3424    
3425    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3426    used to update the database definition. It must be used with care, however, since it
3427    will only work on a raw structure, not on the processed structure created by an ERDB
3428    constructor.
3429    
3430    =over 4
3431    
3432    =item structure
3433    
3434    XML structure to be written to the file.
3435    
3436    =item fileName
3437    
3438    Name of the output file to which the updated XML should be stored.
3439    
3440    =back
3441    
3442    =cut
3443    
3444    sub WriteMetaXML {
3445        # Get the parameters.
3446        my ($structure, $fileName) = @_;
3447        # Compute the output.
3448        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3449        # Write it to the file.
3450        my $xmlOut = Open(undef, ">$fileName");
3451        print $xmlOut $fileString;
3452    }
3453    
3454    
3455    =head3 HTMLNote
3456    
3457    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3458    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3459    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3460    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3461    
3462    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3463    
3464    =over 4
3465    
3466    =item dataString
3467    
3468    String to convert to HTML.
3469    
3470    =item RETURN
3471    
3472    An HTML string derived from the input string.
3473    
3474    =back
3475    
3476    =cut
3477    
3478    sub HTMLNote {
3479        # Get the parameter.
3480        my ($dataString) = @_;
3481        # HTML-escape the text.
3482        my $retVal = CGI::escapeHTML($dataString);
3483        # Substitute the bulletin board codes.
3484        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3485        $retVal =~ s!\[p\]!</p><p>!g;
3486        $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3487        $retVal =~ s!\[/link\]!</a>!g;
3488        # Return the result.
3489        return $retVal;
3490          }          }
3491    
3492    =head3 BeginTran
3493    
3494    C<< $erdb->BeginTran(); >>
3495    
3496    Start a database transaction.
3497    
3498    =cut
3499    
3500    sub BeginTran {
3501        my ($self) = @_;
3502        $self->{_dbh}->begin_tran();
3503    
3504      }      }
3505      Trace("SQL query: $command") if T(SQL => 3);  
3506      Trace("PARMS: '" . (join "', '", @params) . "'") if (T(SQL => 4) && (@params > 0));  =head3 CommitTran
3507      my $sth = $dbh->prepare_command($command);  
3508      # Execute it with the parameters bound in.  C<< $erdb->CommitTran(); >>
3509      $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
3510      # Now we create the relation map, which enables DBQuery to determine the order, name  Commit an active database transaction.
3511      # and mapped name for each object in the query.  
3512      my @relationMap = ();  =cut
3513      for my $mappedName (@mappedNameList) {  
3514          push @relationMap, [$mappedName, $mappedNameHash{$mappedName}];  sub CommitTran {
3515        my ($self) = @_;
3516        $self->{_dbh}->commit_tran();
3517      }      }
3518      # Return the statement object.  
3519      my $retVal = DBQuery::_new($self, $sth, \@relationMap);  =head3 RollbackTran
3520      return $retVal;  
3521    C<< $erdb->RollbackTran(); >>
3522    
3523    Roll back an active database transaction.
3524    
3525    =cut
3526    
3527    sub RollbackTran {
3528        my ($self) = @_;
3529        $self->{_dbh}->roll_tran();
3530  }  }
3531    
3532  =head3 Delete  =head3 UpdateField
3533    
3534  C<< my $stats = $erdb->Delete($entityName, $objectID); >>  C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>
3535    
3536  Delete an entity instance from the database. The instance is deleted along with all entity and  Update all occurrences of a specific field value to a new value. The number of rows changed will be
3537  relationship instances dependent on it. The idea of dependence here is recursive. An object 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.  
3538    
3539  =over 4  =over 4
3540    
3541  =item entityName  =item fieldName
3542    
3543  Name of the entity type for the instance being deleted.  Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3544    
3545  =item objectID  =item oldValue
3546    
3547  ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),  Value to be modified. All occurrences of this value in the named field will be replaced by the
3548  then it is presumed to by a LIKE pattern.  new value.
3549    
3550    =item newValue
3551    
3552    New value to be substituted for the old value when it's found.
3553    
3554    =item filter
3555    
3556  =item testFlag  A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3557    
3558  If TRUE, the delete statements will be traced without being executed.  =item parms
3559    
3560    Reference to a list of parameter values in the filter.
3561    
3562  =item RETURN  =item RETURN
3563    
3564  Returns a statistics object indicating how many records of each particular table were  Returns the number of rows modified.
 deleted.  
3565    
3566  =back  =back
3567    
3568  =cut  =cut
3569  #: Return Type $%;  
3570  sub Delete {  sub UpdateField {
3571      # Get the parameters.      # Get the parameters.
3572      my ($self, $entityName, $objectID, $testFlag) = @_;      my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3573      # Declare the return variable.      # Get the object and field names from the field name parameter.
3574      my $retVal = Stats->new();      $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3575      # Get the DBKernel object.      my $objectName = $1;
3576      my $db = $self->{_dbh};      my $realFieldName = _FixName($2);
3577      # We're going to generate all the paths branching out from the starting entity. One of      # Add the old value to the filter. Note we allow the possibility that no
3578      # the things we have to be careful about is preventing loops. We'll use a hash to      # filter was specified.
3579      # determine if we've hit a loop.      my $realFilter = "$fieldName = ?";
3580      my %alreadyFound = ();      if ($filter) {
3581      # These next lists will serve as our result stack. We start by pushing object lists onto          $realFilter .= " AND $filter";
     # the stack, and then popping them off to do the deletes. This means the deletes will  
     # start with the longer paths before getting to the shorter ones. That, in turn, makes  
     # sure we don't delete records that might be needed to forge relationships back to the  
     # original item. We have two lists-- one for TO-relationships, and one for  
     # FROM-relationships and entities.  
     my @fromPathList = ();  
     my @toPathList = ();  
     # This final hash is used to remember what work still needs to be done. We push paths  
     # onto the list, then pop them off to extend the paths. We prime it with the starting  
     # point. Note that we will work hard to insure that the last item on a path in the  
     # TODO list is always an entity.  
     my @todoList = ([$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, $rv);  
             }  
3582          }          }
3583        # Format the query filter.
3584        my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3585            $self->_SetupSQL([$objectName], $realFilter);
3586        # Create the query. Since there is only one object name, the mapped-name data is not
3587        # necessary. Neither is the FROM clause.
3588        $suffix =~ s/^FROM.+WHERE\s+//;
3589        # Create the update statement.
3590        my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3591        # Get the database handle.
3592        my $dbh = $self->{_dbh};
3593        # Add the old and new values to the parameter list. Note we allow the possibility that
3594        # there are no user-supplied parameters.
3595        my @params = ($newValue, $oldValue);
3596        if (defined $parms) {
3597            push @params, @{$parms};
3598        }
3599        # Execute the update.
3600        my $retVal = $dbh->SQL($command, 0, @params);
3601        # Make the funky zero a real zero.
3602        if ($retVal == 0) {
3603            $retVal = 0;
3604      }      }
3605      # Return the result.      # Return the result.
3606      return $retVal;      return $retVal;
3607  }  }
3608    
 =head3 GetList  
   
 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  
   
 Return a list of object descriptors for the specified objects as determined by the  
 specified filter clause.  
   
 This method is essentially the same as L</Get> except it returns a list of objects rather  
 than a query object that can be used to get the results one record at a time.  
   
 =over 4  
3609    
3610  =item objectNames  =head2 Data Mining Methods
3611    
3612  List containing the names of the entity and relationship objects to be retrieved.  =head3 GetUsefulCrossValues
3613    
3614  =item filterClause  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3615    
3616  WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  Return a list of the useful attributes that would be returned by a B<Cross> call
3617  be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be  from an entity of the source entity type through the specified relationship. This
3618  specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified  means it will return the fields of the target entity type and the intersection data
3619  in the filter clause should be added to the parameter list as additional parameters. The  fields in the relationship. Only primary table fields are returned. In other words,
3620  fields in a filter clause can come from primary entity relations, relationship relations,  the field names returned will be for fields where there is always one and only one
3621  or secondary entity relations; however, all of the entities and relationships involved must  value.
 be included in the list of object names.  
3622    
3623  The filter clause can also specify a sort order. To do this, simply follow the filter string  =over 4
 with an ORDER BY clause. For example, the following filter string gets all genomes for a  
 particular genus and sorts them by species name.  
3624    
3625  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  =item sourceEntity
3626    
3627  The rules for field references in a sort order are the same as those for field references in the  Name of the entity from which the relationship crossing will start.
 filter clause in general; however, odd things may happen if a sort field is from a secondary  
 relation.  
3628    
3629  =item param1, param2, ..., paramN  =item relationship
3630    
3631  Parameter values to be substituted into the filter clause.  Name of the relationship being crossed.
3632    
3633  =item RETURN  =item RETURN
3634    
3635  Returns a list of B<DBObject>s that satisfy the query conditions.  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3636    
3637  =back  =back
3638    
3639  =cut  =cut
3640  #: Return Type @%  #: Return Type @;
3641  sub GetList {  sub GetUsefulCrossValues {
3642      # Get the parameters.      # Get the parameters.
3643      my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $sourceEntity, $relationship) = @_;
3644      # Declare the return variable.      # Declare the return variable.
3645      my @retVal = ();      my @retVal = ();
3646      # Perform the query.      # Determine the target entity for the relationship. This is whichever entity is not
3647      my $query = $self->Get($objectNames, $filterClause, @params);      # the source entity. So, if the source entity is the FROM, we'll get the name of
3648      # Loop through the results.      # the TO, and vice versa.
3649      while (my $object = $query->Fetch) {      my $relStructure = $self->_GetStructure($relationship);
3650          push @retVal, $object;      my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3651      }      my $targetEntity = $relStructure->{$targetEntityType};
3652        # Get the field table for the entity.
3653        my $entityFields = $self->GetFieldTable($targetEntity);
3654        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3655        # For the entity fields, the key aspect of the target structure is that the {relation} value
3656        # must match the entity name.
3657        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3658                            keys %{$entityFields};
3659        # Push the fields found onto the return variable.
3660        push @retVal, sort @fieldList;
3661        # Get the field table for the relationship.
3662        my $relationshipFields = $self->GetFieldTable($relationship);
3663        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3664        # This may end up being an empty set.
3665        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3666                            keys %{$relationshipFields};
3667        # Push these onto the return list.
3668        push @retVal, sort @fieldList2;
3669      # Return the result.      # Return the result.
3670      return @retVal;      return @retVal;
3671  }  }
3672    
3673  =head3 ComputeObjectSentence  =head3 FindColumn
3674    
3675  C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>  C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3676    
3677  Check an object name, and if it is a relationship convert it to a relationship sentence.  Return the location a desired column in a data mining header line. The data
3678    mining header line is a tab-separated list of column names. The column
3679    identifier is either the numerical index of a column or the actual column
3680    name.
3681    
3682  =over 4  =over 4
3683    
3684  =item objectName  =item headerLine
3685    
3686  Name of the entity or relationship.  The header line from a data mining command, which consists of a tab-separated
3687    list of column names.
3688    
3689    =item columnIdentifier
3690    
3691    Either the ordinal number of the desired column (1-based), or the name of the
3692    desired column.
3693    
3694  =item RETURN  =item RETURN
3695    
3696  Returns a string containing the entity name or a relationship sentence.  Returns the array index (0-based) of the desired column.
3697    
3698  =back  =back
3699    
3700  =cut  =cut
3701    
3702  sub ComputeObjectSentence {  sub FindColumn {
3703      # Get the parameters.      # Get the parameters.
3704      my ($self, $objectName) = @_;      my ($headerLine, $columnIdentifier) = @_;
3705      # Set the default return value.      # Declare the return variable.
3706      my $retVal = $objectName;      my $retVal;
3707      # Look for the object as a relationship.      # Split the header line into column names.
3708      my $relTable = $self->{_metaData}->{Relationships};      my @headers = ParseColumns($headerLine);
3709      if (exists $relTable->{$objectName}) {      # Determine whether we have a number or a name.
3710          # Get the relationship sentence.      if ($columnIdentifier =~ /^\d+$/) {
3711          $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          # Here we have a number. Subtract 1 and validate the result.
3712            $retVal = $columnIdentifier - 1;
3713            if ($retVal < 0 || $retVal > $#headers) {
3714                Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3715      }      }
3716      # Return the result.      } else {
3717      return $retVal;          # Here we have a name. We need to find it in the list.
3718            for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3719                if ($headers[$i] eq $columnIdentifier) {
3720                    $retVal = $i;
3721  }  }
   
 =head3 DumpRelations  
   
 C<< $erdb->DumpRelations($outputDirectory); >>  
   
 Write the contents of all the relations to tab-delimited files in the specified directory.  
 Each file will have the same name as the relation dumped, with an extension of DTX.  
   
 =over 4  
   
 =item outputDirectory  
   
 Name of the directory into which the relation files should be dumped.  
   
 =back  
   
 =cut  
   
 sub DumpRelations {  
     # Get the parameters.  
     my ($self, $outputDirectory) = @_;  
     # Now we need to run through all the relations. First, we loop through the entities.  
     my $metaData = $self->{_metaData};  
     my $entities = $metaData->{Entities};  
     for my $entityName (keys %{$entities}) {  
         my $entityStructure = $entities->{$entityName};  
         # Get the entity's relations.  
         my $relationList = $entityStructure->{Relations};  
         # Loop through the relations, dumping them.  
         for my $relationName (keys %{$relationList}) {  
             my $relation = $relationList->{$relationName};  
             $self->_DumpRelation($outputDirectory, $relationName, $relation);  
3722          }          }
3723            if (! defined($retVal)) {
3724                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3725      }      }
     # 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});  
3726      }      }
3727        # Return the result.
3728        return $retVal;
3729  }  }
3730    
3731  =head3 InsertObject  =head3 ParseColumns
   
 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>  
3732    
3733  Insert an object into the database. The object is defined by a type name and then a hash  C<< my @columns = ERDB::ParseColumns($line); >>
 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']}); >>  
3734    
3735  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  Convert the specified data line to a list of columns.
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
   
 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  
3736    
3737  =over 4  =over 4
3738    
3739  =item newObjectType  =item line
   
 Type name of the object to insert.  
   
 =item fieldHash  
3740    
3741  Hash of field names to values.  A data mining input, consisting of a tab-separated list of columns terminated by a
3742    new-line.
3743    
3744  =item RETURN  =item RETURN
3745    
3746  Returns 1 if successful, 0 if an error occurred.  Returns a list consisting of the column values.
3747    
3748  =back  =back
3749    
3750  =cut  =cut
3751    
3752  sub InsertObject {  sub ParseColumns {
3753      # Get the parameters.      # Get the parameters.
3754      my ($self, $newObjectType, $fieldHash) = @_;      my ($line) = @_;
3755      # Denote that so far we appear successful.      # Chop off the line-end.
3756      my $retVal = 1;      chomp $line;
3757      # Get the database handle.      # Split it into a list.
3758      my $dbh = $self->{_dbh};      my @retVal = split(/\t/, $line);
3759      # Get the relation list.      # Return the result.
3760      my $relationTable = $self->_GetRelationTable($newObjectType);      return @retVal;
     # 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;  
3761  }  }
3762    
3763  =head3 LoadTable  =head2 Virtual Methods
   
 C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>  
   
 Load data from a tab-delimited file into a specified table, optionally re-creating the table  
 first.  
   
 =over 4  
3764    
3765  =item fileName  =head3 _CreatePPOIndex
   
 Name of the file from which the table data should be loaded.  
3766    
3767  =item relationName  C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3768    
3769  Name of the relation to be loaded. This is the same as the table name.  Convert the XML for an ERDB index to the XML structure for a PPO
3770    index.
3771    
3772  =item truncateFlag  =over 4
3773    
3774  TRUE if the table should be dropped and re-created, else FALSE  ERDB XML structure for an index.
3775    
3776  =item RETURN  =item RETURN
3777    
3778  Returns a statistical object containing a list of the error messages.  PPO XML structure for the same index.
3779    
3780  =back  =back
3781    
3782  =cut  =cut
3783  sub LoadTable {  
3784      # Get the parameters.  sub _CreatePPOIndex {
3785      my ($self, $fileName, $relationName, $truncateFlag) = @_;      # Get the parameters.
3786      # Create the statistical return object.      my ($indexObject) = @_;
3787      my $retVal = _GetLoadStats();      # The incoming index contains a list of the index fields in the IndexFields
3788      # Trace the fact of the load.      # member. We loop through it to create the index tags.
3789      Trace("Loading table $relationName from $fileName") if T(2);      my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3790      # Get the database handle.      # Wrap the fields in attribute tags.
3791      my $dbh = $self->{_dbh};      my $retVal = { attribute => \@fields };
3792      # Get the input file size.      # Return the result.
     my $fileSize = -s $fileName;  
     # Get the relation data.  
     my $relation = $self->_FindRelation($relationName);  
     # Check the truncation flag.  
     if ($truncateFlag) {  
         Trace("Creating table $relationName") if T(2);  
         # Compute the row count estimate. We take the size of the load file,  
         # divide it by the estimated row size, and then multiply by 1.5 to  
         # leave extra room. We postulate a minimum row count of 1000 to  
         # prevent problems with incoming empty load files.  
         my $rowSize = $self->EstimateRowSize($relationName);  
         my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);  
         # Re-create the table without its index.  
         $self->CreateTable($relationName, 0, $estimate);  
         # If this is a pre-index DBMS, create the index here.  
         if ($dbh->{_preIndex}) {  
             eval {  
                 $self->CreateIndex($relationName);  
             };  
             if ($@) {  
                 $retVal->AddMessage($@);  
             }  
         }  
     }  
     # 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 ($@) {  
                 $retVal->AddMessage($@);  
             }  
         }  
     }  
     # Analyze the table to improve performance.  
     $dbh->vacuum_it($relationName);  
     # Return the statistics.  
3793      return $retVal;      return $retVal;
3794  }  }
3795    
3796  =head3 GenerateEntity  =head3 _CreatePPOField
3797    
3798  C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>  C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3799    
3800  Generate the data for a new entity instance. This method creates a field hash suitable for  Convert the ERDB XML structure for a field to a PPO scalar XML structure.
 passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  
 of the fields are generated using information in the database schema.  
   
 Each data type has a default algorithm for generating random test data. This can be overridden  
 by including a B<DataGen> element in the field. If this happens, the content of the element is  
 executed as a PERL program in the context of this module. The element may make use of a C<$this>  
 variable which contains the field hash as it has been built up to the current point. If any  
 fields are dependent on other fields, the C<pass> attribute can be used to control the order  
 in which the fields are generated. A field with a high data pass number will be generated after  
 a field with a lower one. If any external values are needed, they should be passed in via the  
 optional third parameter, which will be available to the data generation script under the name  
 C<$value>. Several useful utility methods are provided for generating random values, including  
 L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated  
 in the form of a timestamp number rather than a string.  
3801    
3802  =over 4  =over 4
3803    
3804  =item id  =item fieldName
3805    
3806  ID to assign to the new entity.  Name of the scalar field.
3807    
3808  =item type  =item fieldObject
3809    
3810  Type name for the new entity.  ERDB XML structure describing the field.
3811    
3812  =item values  =item RETURN
3813    
3814  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a PPO XML structure for the same field.
3815    
3816  =back  =back
3817    
3818  =cut  =cut
3819    
3820  sub GenerateEntity {  sub _CreatePPOField {
3821      # Get the parameters.      # Get the parameters.
3822      my ($self, $id, $type, $values) = @_;      my ($fieldName, $fieldObject) = @_;
3823      # Create the return hash.      # Get the field type.
3824      my $this = { id => $id };      my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3825      # Get the metadata structure.      # Fix up the field name.
3826      my $metadata = $self->{_metaData};      $fieldName = _FixName($fieldName);
3827      # Get this entity's list of fields.      # Build the scalar tag.
3828      if (!exists $metadata->{Entities}->{$type}) {      my $retVal = { label => $fieldName, type => $type };
3829          Confess("Unrecognized entity type $type in GenerateEntity.");      # Return the result.
3830      } else {      return $retVal;
         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;  
3831  }  }
3832    
3833  =head3 GetEntity  =head3 CleanKeywords
3834    
3835  C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3836    
3837  Return an object describing the entity instance with a specified ID.  Clean up a search expression or keyword list. This is a virtual method that may
3838    be overridden by the subclass. The base-class method removes extra spaces
3839    and converts everything to lower case.
3840    
3841  =over 4  =over 4
3842    
3843  =item entityType  =item searchExpression
   
 Entity type name.  
   
 =item ID  
3844    
3845  ID of the desired entity.  Search expression or keyword list to clean. Note that a search expression may
3846    contain boolean operators which need to be preserved. This includes leading
3847    minus signs.
3848    
3849  =item RETURN  =item RETURN
3850    
3851  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Cleaned expression or keyword list.
 instance is found with the specified key.  
3852    
3853  =back  =back
3854    
3855  =cut  =cut
3856    
3857  sub GetEntity {  sub CleanKeywords {
3858      # Get the parameters.      # Get the parameters.
3859      my ($self, $entityType, $ID) = @_;      my ($self, $searchExpression) = @_;
3860      # Create a query.      # Lower-case the expression and copy it into the return variable. Note that we insure we
3861      my $query = $self->Get([$entityType], "$entityType(id) = ?", $ID);      # don't accidentally end up with an undefined value.
3862      # Get the first (and only) object.      my $retVal = lc($searchExpression || "");
3863      my $retVal = $query->Fetch();      # Remove extra spaces.
3864        $retVal =~ s/\s+/ /g;
3865        $retVal =~ s/(^\s+)|(\s+$)//g;
3866      # Return the result.      # Return the result.
3867      return $retVal;      return $retVal;
3868  }  }
3869    
3870  =head3 GetEntityValues  =head3 GetSourceObject
3871    
3872  C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>  C<< my $source = $erdb->GetSourceObject($entityName); >>
3873    
3874  Return a list of values from a specified entity instance.  Return the object to be used in loading special attributes of the specified entity. The
3875    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3876    XML
3877    
3878  =over 4  =head2 Internal Utility Methods
3879    
3880  =item entityType  =head3 _RelationMap
3881    
3882  Entity type name.  C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3883    
3884  =item ID  Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3885    to determine how to interpret the results of the query.
3886    
3887  ID of the desired entity.  =over 4
3888    
3889  =item fields  =item mappedNameHashRef
3890    
3891  List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  Reference to a hash that maps modified object names to real object names.
3892    
3893    =item mappedNameListRef
3894    
3895    Reference to a list of modified object names in the order they appear in the
3896    SELECT list.
3897    
3898  =item RETURN  =item RETURN
3899    
3900  Returns a flattened list of the values of the specified fields for the specified entity.  Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3901    query followed by the actual name of that object. This enables the B<ERDBObject> to
3902    determine the order of the tables in the query and which object name belongs to each
3903    mapped object name. Most of the time these two values are the same; however, if a
3904    relation occurs twice in the query, the relation name in the field list and WHERE
3905    clause will use a mapped name (generally the actual relation name with a numeric
3906    suffix) that does not match the actual relation name.
3907    
3908  =back  =back
3909    
3910  =cut  =cut
3911    
3912  sub GetEntityValues {  sub _RelationMap {
3913      # Get the parameters.      # Get the parameters.
3914      my ($self, $entityType, $ID, $fields) = @_;      my ($mappedNameHashRef, $mappedNameListRef) = @_;
3915      # Get the specified entity.      # Declare the return variable.
     my $entity = $self->GetEntity($entityType, $ID);  
     # Declare the return list.  
3916      my @retVal = ();      my @retVal = ();
3917      # If we found the entity, push the values into the return list.      # Build the map.
3918      if ($entity) {      for my $mappedName (@{$mappedNameListRef}) {
3919          push @retVal, $entity->Values($fields);          push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3920      }      }
3921      # Return the result.      # Return it.
3922      return @retVal;      return @retVal;
3923  }  }
3924    
 =head3 GetAll  
   
 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
3925    
3926  Return a list of values taken from the objects returned by a query. The first three  =head3 _SetupSQL
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
3927    
3928  The list returned will be a list of lists. Each element of the list will contain  Process a list of object names and a filter clause so that they can be used to
3929  the values returned for the fields specified in the fourth parameter. If one of the  build an SQL statement. This method takes in a reference to a list of object names
3930  fields specified returns multiple values, they are flattened in with the rest. For  and a filter clause. It will return a corrected filter clause, a list of mapped
3931  example, the following call will return a list of the features in a particular  names and the mapped name hash.
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
3932    
3933  C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  This is an instance method.
3934    
3935  =over 4  =over 4
3936    
3937  =item objectNames  =item objectNames
3938    
3939  List containing the names of the entity and relationship objects to be retrieved.  Reference to a list of the object names to be included in the query.
3940    
3941  =item filterClause  =item filterClause
3942    
3943  WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  A string containing the WHERE clause for the query (without the C<WHERE>) and also
3944  be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  optionally the C<ORDER BY> and C<LIMIT> clauses.
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item fields  
   
 List of the fields to be returned in each element of the list returned.  
3945    
3946  =item count  =item matchClause
3947    
3948  Maximum number of records to return. If omitted or 0, all available records will be returned.  An optional full-text search clause. If specified, it will be inserted at the
3949    front of the WHERE clause. It should already be SQL-formatted; that is, the
3950    field names should be in the form I<table>C<.>I<fieldName>.
3951    
3952  =item RETURN  =item RETURN
3953    
3954  Returns a list of list references. Each element of the return list contains the values for the  Returns a three-element list. The first element is the SQL statement suffix, beginning
3955  fields specified in the B<fields> parameter.  with the FROM clause. The second element is a reference to a list of the names to be
3956    used in retrieving the fields. The third element is a hash mapping the names to the
3957    objects they represent.
3958    
3959  =back  =back
3960    
3961  =cut  =cut
3962  #: Return Type @@;  
3963  sub GetAll {  sub _SetupSQL {
3964      # Get the parameters.      my ($self, $objectNames, $filterClause, $matchClause) = @_;
3965      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Adjust the list of object names to account for multiple occurrences of the
3966      # Translate the parameters from a list reference to a list. If the parameter      # same object. We start with a hash table keyed on object name that will
3967      # list is a scalar we convert it into a singleton list.      # return the object suffix. The first time an object is encountered it will
3968      my @parmList = ();      # not be found in the hash. The next time the hash will map the object name
3969      if (ref $parameterList eq "ARRAY") {      # to 2, then 3, and so forth.
3970          @parmList = @{$parameterList};      my %objectHash = ();
3971        # This list will contain the object names as they are to appear in the
3972        # FROM list.
3973        my @fromList = ();
3974        # This list contains the suffixed object name for each object. It is exactly
3975        # parallel to the list in the $objectNames parameter.
3976        my @mappedNameList = ();
3977        # Finally, this hash translates from a mapped name to its original object name.
3978        my %mappedNameHash = ();
3979        # Now we create the lists. Note that for every single name we push something into
3980        # @fromList and @mappedNameList. This insures that those two arrays are exactly
3981        # parallel to $objectNames.
3982        for my $objectName (@{$objectNames}) {
3983            # Get the next suffix for this object.
3984            my $suffix = $objectHash{$objectName};
3985            if (! $suffix) {
3986                # Here we are seeing the object for the first time. The object name
3987                # is used as is.
3988                push @mappedNameList, $objectName;
3989                push @fromList, $objectName;
3990                $mappedNameHash{$objectName} = $objectName;
3991                # Denote the next suffix will be 2.
3992                $objectHash{$objectName} = 2;
3993      } else {      } else {
3994          push @parmList, $parameterList;              # Here we've seen the object before. We construct a new name using
3995                # the suffix from the hash and update the hash.
3996                my $mappedName = "$objectName$suffix";
3997                $objectHash{$objectName} = $suffix + 1;
3998                # The FROM list has the object name followed by the mapped name. This
3999                # tells SQL it's still the same table, but we're using a different name
4000                # for it to avoid confusion.
4001                push @fromList, "$objectName $mappedName";
4002                # The mapped-name list contains the real mapped name.
4003                push @mappedNameList, $mappedName;
4004                # Finally, enable us to get back from the mapped name to the object name.
4005                $mappedNameHash{$mappedName} = $objectName;
4006      }      }
     # Insure the counter has a value.  
     if (!defined $count) {  
         $count = 0;  
4007      }      }
4008      # Add the row limit to the filter clause.      # Begin the SELECT suffix. It starts with
4009      if ($count > 0) {      #
4010          $filterClause .= " LIMIT $count";      # FROM name1, name2, ... nameN
4011        #
4012        my $suffix = "FROM " . join(', ', @fromList);
4013        # Now for the WHERE. First, we need a place for the filter string.
4014        my $filterString = "";
4015        # We will also keep a list of conditions to add to the WHERE clause in order to link
4016        # entities and relationships as well as primary relations to secondary ones.
4017        my @joinWhere = ();
4018        # Check for a filter clause.
4019        if ($filterClause) {
4020            # Here we have one, so we convert its field names and add it to the query. First,
4021            # We create a copy of the filter string we can work with.
4022            $filterString = $filterClause;
4023            # Next, we sort the object names by length. This helps protect us from finding
4024            # object names inside other object names when we're doing our search and replace.
4025            my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
4026            # The final preparatory step is to create a hash table of relation names. The
4027            # table begins with the relation names already in the SELECT command. We may
4028            # need to add relations later if there is filtering on a field in a secondary
4029            # relation. The secondary relations are the ones that contain multiply-
4030            # occurring or optional fields.
4031            my %fromNames = map { $_ => 1 } @sortedNames;
4032            # We are ready to begin. We loop through the object names, replacing each
4033            # object name's field references by the corresponding SQL field reference.
4034            # Along the way, if we find a secondary relation, we will need to add it
4035            # to the FROM clause.
4036            for my $mappedName (@sortedNames) {
4037                # Get the length of the object name plus 2. This is the value we add to the
4038                # size of the field name to determine the size of the field reference as a
4039                # whole.
4040                my $nameLength = 2 + length $mappedName;
4041                # Get the real object name for this mapped name.
4042                my $objectName = $mappedNameHash{$mappedName};
4043                Trace("Processing $mappedName for object $objectName.") if T(4);
4044                # Get the object's field list.
4045                my $fieldList = $self->GetFieldTable($objectName);
4046                # Find the field references for this object.
4047                while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
4048                    # At this point, $1 contains the field name, and the current position
4049                    # is set immediately after the final parenthesis. We pull out the name of
4050                    # the field and the position and length of the field reference as a whole.
4051                    my $fieldName = $1;
4052                    my $len = $nameLength + length $fieldName;
4053                    my $pos = pos($filterString) - $len;
4054                    # Insure the field exists.
4055                    if (!exists $fieldList->{$fieldName}) {
4056                        Confess("Field $fieldName not found for object $objectName.");
4057                    } else {
4058                        Trace("Processing $fieldName at position $pos.") if T(4);
4059                        # Get the field's relation.
4060                        my $relationName = $fieldList->{$fieldName}->{relation};
4061                        # Now we have a secondary relation. We need to insure it matches the
4062                        # mapped name of the primary relation. First we peel off the suffix
4063                        # from the mapped name.
4064                        my $mappingSuffix = substr $mappedName, length($objectName);
4065                        # Put the mapping suffix onto the relation name to get the
4066                        # mapped relation name.
4067                        my $m