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revision 1.5, Tue Apr 5 05:17:01 2005 UTC revision 1.75, Thu Nov 9 21:21:49 2006 UTC
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1  package ERDB;  package ERDB;
2    
3          use strict;          use strict;
         use Carp;  
4          use Tracer;          use Tracer;
5          use DBKernel;      use DBrtns;
6          use Data::Dumper;          use Data::Dumper;
7          use XML::Simple;          use XML::Simple;
8          use DBQuery;          use DBQuery;
9          use DBObject;          use DBObject;
10          use Stats;          use Stats;
11          use Time::HiRes qw(gettimeofday);          use Time::HiRes qw(gettimeofday);
12        use Digest::MD5 qw(md5_base64);
13        use FIG;
14        use CGI;
15    
16  =head1 Entity-Relationship Database Package  =head1 Entity-Relationship Database Package
17    
# Line 33  Line 35 
35  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).  relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36  The B<FEATURE> entity also contains an optional virulence number. This is implemented  The B<FEATURE> entity also contains an optional virulence number. This is implemented
37  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number  as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in the  (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39  C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence number.  the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40  If the virulence of I<ABC> is not known, there will not be any rows for it in C<FeatureVirulence>.  number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41    C<FeatureVirulence>.
42    
43  Entities are connected by binary relationships implemented using single relations possessing the  Entities are connected by binary relationships implemented using single relations possessing the
44  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),  same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
# Line 57  Line 60 
60  B<start-position>, which indicates where in the contig that the sequence begins. This attribute  B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.  is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62    
63  The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to  The database itself is described by an XML file. In addition to all the data required to define
64  all the data required to define the entities, relationships, and attributes, the schema provides  the entities, relationships, and attributes, the schema provides space for notes describing
65  space for notes describing the data and what it means. These notes are used by L</ShowMetaData>  the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66  to generate documentation for the database.  for the database.
67    
68    Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69    in which case it will be used to generate a text search index in which the user searches for words
70    in the field instead of a particular field value.
71    
72  Finally, every entity and relationship object has a flag indicating if it is new or old. The object  Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it  is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74  was inserted by the L</InsertObject> method.  was inserted by the L</InsertObject> method.
75    
76  To facilitate testing, the ERDB module supports automatic generation of test data. This process  =head2 XML Database Description
77  is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet  
78  fully implemented.  =head3 Data Types
79    
80    The ERDB system supports the following data types. Note that there are numerous string
81    types depending on the maximum length. Some database packages limit the total number of
82    characters you have in an index key; to insure the database works in all environments,
83    the type of string should be the shortest one possible that supports all the known values.
84    
85    =over 4
86    
87    =item char
88    
89    single ASCII character
90    
91    =item int
92    
93    32-bit signed integer
94    
95    =item counter
96    
97    32-bit unsigned integer
98    
99    =item date
100    
101    64-bit unsigned integer, representing a PERL date/time value
102    
103    =item text
104    
105    long string; Text fields cannot be used in indexes or sorting and do not support the
106    normal syntax of filter clauses, but can be up to a billion character in length
107    
108    =item float
109    
110    double-precision floating-point number
111    
112    =item boolean
113    
114    single-bit numeric value; The value is stored as a 16-bit signed integer (for
115    compatability with certain database packages), but the only values supported are
116    0 and 1.
117    
118    =item id-string
119    
120    variable-length string, maximum 25 characters
121    
122    =item key-string
123    
124    variable-length string, maximum 40 characters
125    
126    =item name-string
127    
128    variable-length string, maximum 80 characters
129    
130    =item medium-string
131    
132    variable-length string, maximum 160 characters
133    
134    =item string
135    
136    variable-length string, maximum 255 characters
137    
138    =item hash-string
139    
140    variable-length string, maximum 22 characters
141    
142    =back
143    
144    The hash-string data type has a special meaning. The actual key passed into the loader will
145    be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146    MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147    digest. Therefore, it is presumed the keys will be unique. When the database is actually
148    in use, the hashed keys will be presented rather than the original values. For this reason,
149    they should not be used for entities where the key is meaningful.
150    
151    =head3 Global Tags
152    
153    The entire database definition must be inside a B<Database> tag. The display name of
154    the database is given by the text associated with the B<Title> tag. The display name
155    is only used in the automated documentation. It has no other effect. The entities and
156    relationships are listed inside the B<Entities> and B<Relationships> tags,
157    respectively. None of these tags have attributes.
158    
159        <Database>
160            <Title>... display title here...</Title>
161            <Entities>
162                ... entity definitions here ...
163            </Entities>
164            <Relationships>
165                ... relationship definitions here...
166            </Relationships>
167        </Database>
168    
169    Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170    The text inside the B<Notes> tag contains comments that will appear when the database
171    documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172    italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173    
174    =head3 Fields
175    
176    Both entities and relationships have fields described by B<Field> tags. A B<Field>
177    tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178    object mus be inside B<Fields> tags.
179    
180        <Entity ... >
181            <Fields>
182                ... Field tags ...
183            </Fields>
184        </Entity>
185    
186    The attributes for the B<Field> tag are as follows.
187    
188    =over 4
189    
190    =item name
191    
192    Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193    and the first character should be a letter. Most underlying databases are case-insensitive
194    with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195    the name C<search-relevance> has special meaning for full-text searches and should not be
196    used as a field name.
197    
198    =item type
199    
200    Data type of the field. The legal data types are given above.
201    
202    =item relation
203    
204    Name of the relation containing the field. This should only be specified for entity
205    fields. The ERDB system does not support optional fields or multi-occurring fields
206    in the primary relation of an entity. Instead, they are put into secondary relations.
207    So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208    grouping used to select a subset of the genomes. A given genome may not be in any
209    groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210    value. The relation name specified must be a valid table name. By convention, it is
211    usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212    entity, the fields without a relation attribute are said to belong to the
213    I<primary relation>. This relation has the same name as the entity itself.
214    
215    =item searchable
216    
217    If specified, then the field is a candidate for full-text searching. A single full-text
218    index will be created for each relation with at least one searchable field in it.
219    For best results, this option should only be used for string or text fields.
220    
221    =item special
222    
223    This attribute allows the subclass to assign special meaning for certain fields.
224    The interpretation is up to the subclass itself. Currently, only entity fields
225    can have this attribute.
226    
227    =back
228    
229    =head3 Indexes
230    
231    An entity can have multiple alternate indexes associated with it. The fields must
232    all be from the same relation. The alternate indexes assist in ordering results
233    from a query. A relationship can have up to two indexes-- a I<to-index> and a
234    I<from-index>. These order the results when crossing the relationship. For
235    example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236    from-index would order the contigs of a ganome, and the to-index would order
237    the genomes of a contig. A relationship's index must specify only fields in
238    the relationship.
239    
240    The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
241    of a relationship is specified using the B<FromIndex> tag; the to-index is specified
242    using the B<ToIndex> tag.
243    
244    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
246    the index. The attributes of an B<IndexField> tag are as follows.
247    
248    =over 4
249    
250    =item name
251    
252    Name of the field.
253    
254    =item order
255    
256    Sort order of the field-- C<ascending> or C<descending>.
257    
258    =back
259    
260    The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
261    
262    =head3 Object and Field Names
263    
264    By convention entity and relationship names use capital casing (e.g. C<Genome> or
265    C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
266    with respect to relation names, converting them internally to all-upper case or
267    all-lower case.
268    
269    If syntax or parsing errors occur when you try to load or use an ERDB database, the
270    most likely reason is that one of your objects has an SQL reserved word as its name.
271    The list of SQL reserved words keeps increasing; however, most are unlikely to show
272    up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
273    C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
274    C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
275    
276    Every entity has a field called C<id> that acts as its primary key. Every relationship
277    has fields called C<from-link> and C<to-link> that contain copies of the relevant
278    entity IDs. These are essentially ERDB's reserved words, and should not be used
279    for user-defined field names.
280    
281    =head3 Entities
282    
283    An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
284    B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
285    containing one or more fields. The attributes of the B<Entity> tag are as follows.
286    
287    =over 4
288    
289    =item name
290    
291    Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
292    or C<GroupBlock>) and should be a noun or noun phrase.
293    
294    =item keyType
295    
296    Data type of the primary key. The primary key is always named C<id>.
297    
298    =back
299    
300    =head3 Relationships
301    
302    A relationship is described by the C<Relationship> tag. Within a relationship,
303    there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
304    fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
305    the to-index.
306    
307    The C<Relationship> tag has the following attributes.
308    
309    =over 4
310    
311    =item name
312    
313    Name of the relationship. The relationship name, by convention, uses capital casing
314    (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
315    phrase, designed to fit between the from-entity and the to-entity (e.g.
316    Block C<ContainsRegionIn> Genome).
317    
318    =item from
319    
320    Name of the entity from which the relationship starts.
321    
322    =item to
323    
324    Name of the entity to which the relationship proceeds.
325    
326    =item arity
327    
328    Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
329    
330    =back
331    
332  =cut  =cut
333    
# Line 76  Line 335 
335    
336  # 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.
337  # "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
338  # 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
339   #string is specified in the field definition.  # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
340  my %TypeTable = ( char =>        { sqlType => 'CHAR(1)',                        maxLen => 1,                    dataGen => "StringGen('A')" },  # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
341                                    int =>         { sqlType => 'INTEGER',                        maxLen => 20,                   dataGen => "IntGen(0, 99999999)" },  # index
342                                    string =>  { sqlType => 'VARCHAR(255)',               maxLen => 255,                  dataGen => "StringGen(IntGen(10,250))" },  my %TypeTable = ( char =>    { sqlType => 'CHAR(1)',            maxLen => 1,            avgLen =>   1, sort => "",
343                                    text =>        { sqlType => 'TEXT',                           maxLen => 1000000000,   dataGen => "StringGen(IntGen(80,1000))" },                                 indexMod =>   0, notes => "single ASCII character"},
344                                    date =>        { sqlType => 'BIGINT',                         maxLen => 80,                   dataGen => "DateGen(-7, 7, IntGen(0,1400))" },                    int =>     { sqlType => 'INTEGER',            maxLen => 20,           avgLen =>   4, sort => "n",
345                                    float =>       { sqlType => 'DOUBLE PRECISION',       maxLen => 40,                   dataGen => "FloatGen(0.0, 100.0)" },                                 indexMod =>   0, notes => "signed 32-bit integer"},
346                                    boolean => { sqlType => 'SMALLINT',                   maxLen => 1,                    dataGen => "IntGen(0, 1)" },                    counter => { sqlType => 'INTEGER UNSIGNED',   maxLen => 20,           avgLen =>   4, sort => "n",
347                                   indexMod =>   0, notes => "unsigned 32-bit integer"},
348                      string =>  { sqlType => 'VARCHAR(255)',       maxLen => 255,          avgLen => 100, sort => "",
349                                   indexMod =>   0, notes => "character string, 0 to 255 characters"},
350                      text =>    { sqlType => 'TEXT',               maxLen => 1000000000,   avgLen => 500, sort => "",
351                                   indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
352                      date =>    { sqlType => 'BIGINT',             maxLen => 80,           avgLen =>   8, sort => "n",
353                                   indexMod =>   0, notes => "signed, 64-bit integer"},
354                      float =>   { sqlType => 'DOUBLE PRECISION',   maxLen => 40,           avgLen =>   8, sort => "g",
355                                   indexMod =>   0, notes => "64-bit double precision floating-point number"},
356                      boolean => { sqlType => 'SMALLINT',           maxLen => 1,            avgLen =>   1, sort => "n",
357                                   indexMod =>   0, notes => "boolean value: 0 if false, 1 if true"},
358                     'hash-string' =>
359                                 { sqlType => 'VARCHAR(22)',        maxLen => 22,           avgLen =>  22, sort => "",
360                                   indexMod =>   0, notes => "string stored in digested form, used for certain types of key fields"},
361                     'id-string' =>
362                                 { sqlType => 'VARCHAR(25)',        maxLen => 25,           avgLen =>  25, sort => "",
363                                   indexMod =>   0, notes => "character string, 0 to 25 characters"},
364                               'key-string' =>                               'key-string' =>
365                                                           { sqlType => 'VARCHAR(40)',            maxLen => 40,                   dataGen => "StringGen(IntGen(10,40))" },                               { sqlType => 'VARCHAR(40)',        maxLen => 40,           avgLen =>  10, sort => "",
366                                   indexMod =>   0, notes => "character string, 0 to 40 characters"},
367                                   'name-string' =>                                   'name-string' =>
368                                                           { sqlType => 'VARCHAR(80)',            maxLen => 80,                   dataGen => "StringGen(IntGen(10,80))" },                               { sqlType => 'VARCHAR(80)',        maxLen => 80,           avgLen =>  40, sort => "",
369                                   indexMod =>   0, notes => "character string, 0 to 80 characters"},
370                                   'medium-string' =>                                   'medium-string' =>
371                                                           { sqlType => 'VARCHAR(160)',           maxLen => 160,                  dataGen => "StringGen(IntGen(10,160))" },                               { sqlType => 'VARCHAR(160)',       maxLen => 160,          avgLen =>  40, sort => "",
372                                   indexMod =>   0, notes => "character string, 0 to 160 characters"},
373                                  );                                  );
374    
375  # Table translating arities into natural language.  # Table translating arities into natural language.
# Line 99  Line 378 
378                                     'MM' => 'many-to-many'                                     'MM' => 'many-to-many'
379                                   );                                   );
380    
381  # Table for interpreting string patterns.  # Options for XML input and output.
382    
383    my %XmlOptions = (GroupTags =>  { Relationships => 'Relationship',
384                                      Entities => 'Entity',
385                                      Fields => 'Field',
386                                      Indexes => 'Index',
387                                      IndexFields => 'IndexField'
388                                    },
389                      KeyAttr =>    { Relationship => 'name',
390                                      Entity => 'name',
391                                      Field => 'name'
392                                    },
393                      SuppressEmpty => 1,
394                     );
395    
396  my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",  my %XmlInOpts  = (
397                                           '9' => "0123456789",                    ForceArray => ['Field', 'Index', 'IndexField'],
398                                           'X' => "abcdefghijklmnopqrstuvwxyz0123456789",                    ForceContent => 1,
399                                           'V' => "aeiou",                    NormalizeSpace => 2,
                                          'K' => "bcdfghjklmnoprstvwxyz"  
400                                     );                                     );
401    my %XmlOutOpts = (
402                      RootName => 'Database',
403                      XMLDecl => 1,
404                     );
405    
406    
407  =head2 Public Methods  =head2 Public Methods
408    
# Line 140  Line 436 
436                                   _metaData => $metaData                                   _metaData => $metaData
437                             };                             };
438          # Bless and return it.          # Bless and return it.
439          bless $self;      bless $self, $class;
440          return $self;          return $self;
441  }  }
442    
443  =head3 ShowMetaData  =head3 ShowMetaData
444    
445  C<< $database->ShowMetaData($fileName); >>  C<< $erdb->ShowMetaData($fileName); >>
446    
447  This method outputs a description of the database. This description can be used to help users create  This method outputs a description of the database. This description can be used to help users create
448  the data to be loaded into the relations.  the data to be loaded into the relations.
# Line 177  Line 473 
473          # Write the HTML heading stuff.          # Write the HTML heading stuff.
474          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";          print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
475          print HTMLOUT "</head>\n<body>\n";          print HTMLOUT "</head>\n<body>\n";
476        # Write the documentation.
477        print HTMLOUT $self->DisplayMetaData();
478        # Close the document.
479        print HTMLOUT "</body>\n</html>\n";
480        # Close the file.
481        close HTMLOUT;
482    }
483    
484    =head3 DisplayMetaData
485    
486    C<< my $html = $erdb->DisplayMetaData(); >>
487    
488    Return an HTML description of the database. This description can be used to help users create
489    the data to be loaded into the relations and form queries. The output is raw includable HTML
490    without any HEAD or BODY tags.
491    
492    =over 4
493    
494    =item filename
495    
496    The name of the output file.
497    
498    =back
499    
500    =cut
501    
502    sub DisplayMetaData {
503        # Get the parameters.
504        my ($self) = @_;
505        # Get the metadata and the title string.
506        my $metadata = $self->{_metaData};
507        # Get the title string.
508        my $title = $metadata->{Title};
509        # Get the entity and relationship lists.
510        my $entityList = $metadata->{Entities};
511        my $relationshipList = $metadata->{Relationships};
512        # Declare the return variable.
513        my $retVal = "";
514        # Open the output file.
515        Trace("Building MetaData table of contents.") if T(4);
516          # 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
517          # section contains an ordered list of entity or relationship subsections.          # section contains an ordered list of entity or relationship subsections.
518          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";
519          # Loop through the Entities, displaying a list item for each.          # Loop through the Entities, displaying a list item for each.
520          foreach my $key (sort keys %{$entityList}) {          foreach my $key (sort keys %{$entityList}) {
521                  # Display this item.                  # Display this item.
522                  print HTMLOUT "<li><a href=\"#$key\">$key</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
523          }          }
524          # Close off the entity section and start the relationship section.          # Close off the entity section and start the relationship section.
525          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";
526          # Loop through the Relationships.          # Loop through the Relationships.
527          foreach my $key (sort keys %{$relationshipList}) {          foreach my $key (sort keys %{$relationshipList}) {
528                  # Display this item.                  # Display this item.
529                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});                  my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
530                  print HTMLOUT "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";          $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
531          }          }
532          # Close off the relationship section and list the join table section.          # Close off the relationship section and list the join table section.
533          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";
534          # Close off the table of contents itself.          # Close off the table of contents itself.
535          print HTMLOUT "</ul>\n";      $retVal .=  "</ul>\n";
536          # 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.
537          print HTMLOUT "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";      $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
538          # Loop through the entities.          # Loop through the entities.
539          for my $key (sort keys %{$entityList}) {          for my $key (sort keys %{$entityList}) {
540                  Trace("Building MetaData entry for $key entity.") if T(4);                  Trace("Building MetaData entry for $key entity.") if T(4);
541                  # Create the entity header. It contains a bookmark and the entity name.                  # Create the entity header. It contains a bookmark and the entity name.
542                  print HTMLOUT "<a name=\"$key\"></a><h3>$key</h3>\n";          $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
543                  # Get the entity data.                  # Get the entity data.
544                  my $entityData = $entityList->{$key};                  my $entityData = $entityList->{$key};
545                  # If there's descriptive text, display it.                  # If there's descriptive text, display it.
546                  if (my $notes = $entityData->{Notes}) {                  if (my $notes = $entityData->{Notes}) {
547                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
548                  }                  }
549                  # Now we want a list of the entity's relationships. First, we set up the relationship subsection.                  # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
550                  print HTMLOUT "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";          $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
551                  # Loop through the relationships.                  # Loop through the relationships.
552                  for my $relationship (sort keys %{$relationshipList}) {                  for my $relationship (sort keys %{$relationshipList}) {
553                          # Get the relationship data.                          # Get the relationship data.
# Line 221  Line 557 
557                                  # Get the relationship sentence and append the arity.                                  # Get the relationship sentence and append the arity.
558                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);                                  my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
559                                  # Display the relationship data.                                  # Display the relationship data.
560                                  print HTMLOUT "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";                  $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
561                          }                          }
562                  }                  }
563                  # Close off the relationship list.                  # Close off the relationship list.
564                  print HTMLOUT "</ul>\n";          $retVal .= "</ul>\n";
565                  # Get the entity's relations.                  # Get the entity's relations.
566                  my $relationList = $entityData->{Relations};                  my $relationList = $entityData->{Relations};
567                  # Create a header for the relation subsection.                  # Create a header for the relation subsection.
568                  print HTMLOUT "<h4>Relations for <b>$key</b></h4>\n";          $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
569                  # Loop through the relations, displaying them.                  # Loop through the relations, displaying them.
570                  for my $relation (sort keys %{$relationList}) {                  for my $relation (sort keys %{$relationList}) {
571                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});                          my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
572                          print HTMLOUT $htmlString;              $retVal .= $htmlString;
573                  }                  }
574          }          }
575          # Denote we're starting the relationship section.          # Denote we're starting the relationship section.
576          print HTMLOUT "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";      $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
577          # Loop through the relationships.          # Loop through the relationships.
578          for my $key (sort keys %{$relationshipList}) {          for my $key (sort keys %{$relationshipList}) {
579                  Trace("Building MetaData entry for $key relationship.") if T(4);                  Trace("Building MetaData entry for $key relationship.") if T(4);
# Line 245  Line 581 
581                  my $relationshipStructure = $relationshipList->{$key};                  my $relationshipStructure = $relationshipList->{$key};
582                  # Create the relationship header.                  # Create the relationship header.
583                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);                  my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
584                  print HTMLOUT "<h3><a name=\"$key\"></a>$headerText</h3>\n";          $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
585                  # Get the entity names.                  # Get the entity names.
586                  my $fromEntity = $relationshipStructure->{from};                  my $fromEntity = $relationshipStructure->{from};
587                  my $toEntity = $relationshipStructure->{to};                  my $toEntity = $relationshipStructure->{to};
# Line 255  Line 591 
591                  # since both sentences will say the same thing.                  # since both sentences will say the same thing.
592                  my $arity = $relationshipStructure->{arity};                  my $arity = $relationshipStructure->{arity};
593                  if ($arity eq "11") {                  if ($arity eq "11") {
594                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
595                  } else {                  } else {
596                          print HTMLOUT "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";              $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
597                          if ($arity eq "MM" && $fromEntity ne $toEntity) {                          if ($arity eq "MM" && $fromEntity ne $toEntity) {
598                                  print HTMLOUT "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";                  $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
599                          }                          }
600                  }                  }
601                  print HTMLOUT "</p>\n";          $retVal .= "</p>\n";
602                  # If there are notes on this relationship, display them.                  # If there are notes on this relationship, display them.
603                  if (my $notes = $relationshipStructure->{Notes}) {                  if (my $notes = $relationshipStructure->{Notes}) {
604                          print HTMLOUT "<p>" . _HTMLNote($notes->{content}) . "</p>\n";              $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
605                  }                  }
606                  # Generate the relationship's relation table.                  # Generate the relationship's relation table.
607                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});                  my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
608                  print HTMLOUT $htmlString;          $retVal .= $htmlString;
609          }          }
610          Trace("Building MetaData join table.") if T(4);          Trace("Building MetaData join table.") if T(4);
611          # Denote we're starting the join table.          # Denote we're starting the join table.
612          print HTMLOUT "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";      $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
613          # Create a table header.          # Create a table header.
614          print HTMLOUT _OpenTable("Join Table", "Source", "Target", "Join Condition");      $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
615          # Loop through the joins.          # Loop through the joins.
616          my $joinTable = $metadata->{Joins};          my $joinTable = $metadata->{Joins};
617          for my $joinKey (sort keys %{$joinTable}) {      my @joinKeys = keys %{$joinTable};
618        for my $joinKey (sort @joinKeys) {
619                  # Separate out the source, the target, and the join clause.                  # Separate out the source, the target, and the join clause.
620                  $joinKey =~ m!([^/]*)/(.*)$!;          $joinKey =~ m!^([^/]+)/(.+)$!;
621                  my ($source, $target, $clause) = ($self->ComputeObjectSentence($1),          my ($sourceRelation, $targetRelation) = ($1, $2);
622                                                                                    $self->ComputeObjectSentence($2),          Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
623                                                                                    $joinTable->{$joinKey});          my $source = $self->ComputeObjectSentence($sourceRelation);
624            my $target = $self->ComputeObjectSentence($targetRelation);
625            my $clause = $joinTable->{$joinKey};
626                  # Display them in a table row.                  # Display them in a table row.
627                  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";
628          }          }
629          # Close the table.          # Close the table.
630          print HTMLOUT _CloseTable();      $retVal .= _CloseTable();
631          # Close the document.      Trace("Built MetaData HTML.") if T(3);
632          print HTMLOUT "</body>\n</html>\n";      # Return the HTML.
633          # Close the file.      return $retVal;
         close HTMLOUT;  
         Trace("Built MetaData web page.") if T(3);  
634  }  }
635    
636  =head3 DumpMetaData  =head3 DumpMetaData
637    
638  C<< $database->DumpMetaData(); >>  C<< $erdb->DumpMetaData(); >>
639    
640  Return a dump of the metadata structure.  Return a dump of the metadata structure.
641    
# Line 311  Line 648 
648          return Data::Dumper::Dumper($self->{_metaData});          return Data::Dumper::Dumper($self->{_metaData});
649  }  }
650    
651    =head3 FindIndexForEntity
652    
653    C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
654    
655    This method locates the entry in an entity's index list that begins with the
656    specified attribute name. If the entity has no index list, one will be
657    created. This method works on raw XML, not a live ERDB object.
658    
659    =over 4
660    
661    =item xml
662    
663    The raw XML structure defining the database.
664    
665    =item entityName
666    
667    The name of the relevant entity.
668    
669    =item attributeName
670    
671    The name of the attribute relevant to the search.
672    
673    =item RETURN
674    
675    The numerical index in the index list of the index entry for the specified entity and
676    attribute, or C<undef> if no such index exists.
677    
678    =back
679    
680    =cut
681    
682    sub FindIndexForEntity {
683        # Get the parameters.
684        my ($xml, $entityName, $attributeName) = @_;
685        # Declare the return variable.
686        my $retVal;
687        # Get the named entity.
688        my $entityData = $xml->{Entities}->{$entityName};
689        if (! $entityData) {
690            Confess("Entity $entityName not found in DBD structure.");
691        } else {
692            # Insure it has an index list.
693            if (! exists $entityData->{Indexes}) {
694                $entityData->{Indexes} = [];
695            } else {
696                # Search for the desired index.
697                my $indexList = $entityData->{Indexes};
698                my $n = scalar @{$indexList};
699                Trace("Searching $n indexes in index list for $entityName.") if T(2);
700                # We use an indexed FOR here because we're returning an
701                # index number instead of an object. We do THAT so we can
702                # delete the index from the list if needed.
703                for (my $i = 0; $i < $n && !defined($retVal); $i++) {
704                    my $index = $indexList->[$i];
705                    my $fields = $index->{IndexFields};
706                    # Technically this IF should be safe (that is, we are guaranteed
707                    # the existence of a "$fields->[0]"), because when we load the XML
708                    # we have SuppressEmpty specified.
709                    if ($fields->[0]->{name} eq $attributeName) {
710                        $retVal = $i;
711                    }
712                }
713            }
714        }
715        Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
716        Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
717        # Return the result.
718        return $retVal;
719    }
720    
721  =head3 CreateTables  =head3 CreateTables
722    
723  C<< $datanase->CreateTables(); >>  C<< $erdb->CreateTables(); >>
724    
725  This method creates the tables for the database from the metadata structure loaded by the  This method creates the tables for the database from the metadata structure loaded by the
726  constructor. It is expected this function will only be used on rare occasions, when the  constructor. It is expected this function will only be used on rare occasions, when the
# Line 325  Line 732 
732  sub CreateTables {  sub CreateTables {
733          # Get the parameters.          # Get the parameters.
734          my ($self) = @_;          my ($self) = @_;
735          my $metadata = $self->{_metaData};      # Get the relation names.
736          my $dbh = $self->{_dbh};      my @relNames = $self->GetTableNames();
737          # Loop through the entities.      # Loop through the relations.
738          while (my ($entityName, $entityData) = each %{$metadata->{Entities}}) {      for my $relationName (@relNames) {
                 # Tell the user what we're doing.  
                 Trace("Creating relations for entity $entityName.") if T(1);  
                 # Loop through the entity's relations.  
                 for my $relationName (keys %{$entityData->{Relations}}) {  
739                          # Create a table for this relation.                          # Create a table for this relation.
740                          $self->CreateTable($relationName);                          $self->CreateTable($relationName);
741                          Trace("Relation $relationName created.") if T(1);          Trace("Relation $relationName created.") if T(2);
                 }  
         }  
         # Loop through the relationships.  
         my $relationshipTable = $metadata->{Relationships};  
         for my $relationshipName (keys %{$metadata->{Relationships}}) {  
                 # Create a table for this relationship.  
                 Trace("Creating relationship $relationshipName.") if T(1);  
                 $self->CreateTable($relationshipName);  
742          }          }
743  }  }
744    
745  =head3 CreateTable  =head3 CreateTable
746    
747  C<< $database->CreateTable($tableName, $indexFlag); >>  C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
748    
749  Create the table for a relation and optionally create its indexes.  Create the table for a relation and optionally create its indexes.
750    
# Line 359  Line 754 
754    
755  Name of the relation (which will also be the table name).  Name of the relation (which will also be the table name).
756    
757  =item $indexFlag  =item indexFlag
758    
759  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,  TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
760  L</CreateIndexes> must be called later to bring the indexes into existence.  L</CreateIndexes> must be called later to bring the indexes into existence.
761    
762    =item estimatedRows (optional)
763    
764    If specified, the estimated maximum number of rows for the relation. This
765    information allows the creation of tables using storage engines that are
766    faster but require size estimates, such as MyISAM.
767    
768  =back  =back
769    
770  =cut  =cut
771    
772  sub CreateTable {  sub CreateTable {
773          # Get the parameters.          # Get the parameters.
774          my ($self, $relationName, $indexFlag) = @_;      my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
775          # Get the database handle.          # Get the database handle.
776          my $dbh = $self->{_dbh};          my $dbh = $self->{_dbh};
777          # Get the relation data and determine whether or not the relation is primary.          # Get the relation data and determine whether or not the relation is primary.
# Line 394  Line 795 
795          # Insure the table is not already there.          # Insure the table is not already there.
796          $dbh->drop_table(tbl => $relationName);          $dbh->drop_table(tbl => $relationName);
797          Trace("Table $relationName dropped.") if T(2);          Trace("Table $relationName dropped.") if T(2);
798        # If there are estimated rows, create an estimate so we can take advantage of
799        # faster DB technologies.
800        my $estimation = undef;
801        if ($estimatedRows) {
802            $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
803        }
804          # Create the table.          # Create the table.
805          Trace("Creating table $relationName: $fieldThing") if T(2);          Trace("Creating table $relationName: $fieldThing") if T(2);
806          $dbh->create_table(tbl => $relationName, flds => $fieldThing);      $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
807          Trace("Relation $relationName created in database.") if T(2);          Trace("Relation $relationName created in database.") if T(2);
808          # If we want to build the indexes, we do it here.      # If we want to build the indexes, we do it here. Note that the full-text search
809        # index will not be built until the table has been loaded.
810          if ($indexFlag) {          if ($indexFlag) {
811                  $self->CreateIndex($relationName);                  $self->CreateIndex($relationName);
812          }          }
813  }  }
814    
815  =head3 CreateIndex  =head3 VerifyFields
   
 C<< $database->CreateIndex($relationName); >>  
   
 Create the indexes for a relation. If a table is being loaded from a large source file (as  
 is the case in L</LoadTable>), it is best to create the indexes after the load. If that is  
 the case, then L</CreateTable> should be called with the index flag set to FALSE, and this  
 method used after the load to create the indexes for the table.  
   
 =cut  
   
 sub CreateIndex {  
         # Get the parameters.  
         my ($self, $relationName) = @_;  
         # Get the relation's descriptor.  
         my $relationData = $self->_FindRelation($relationName);  
         # Get the database handle.  
         my $dbh = $self->{_dbh};  
         # Now we need to create this relation's indexes. We do this by looping through its index table.  
         while (my ($indexName, $indexData) = each %{$relationData->{Indexes}}) {  
                 # Get the index's field list.  
                 my @fieldList = _FixNames(@{$indexData->{IndexFields}});  
                 my $flds = join(', ', @fieldList);  
                 # Get the index's uniqueness flag.  
                 my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');  
                 # Create the index.  
                 $dbh->create_index(idx => $indexName, tbl => $relationName, flds => $flds, unique => $unique);  
                 Trace("Index created: $indexName for $relationName ($flds)") if T(1);  
         }  
 }  
   
 =head3 LoadTables  
   
 C<< my $stats = $database->LoadTables($directoryName, $rebuild); >>  
816    
817  This method will load the database tables from a directory. The tables must already have been created  C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
 in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;  
 all of the relations to be loaded must have a file in the directory with the same name as the relation  
 (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each  
 line of the file will be loaded as a row of the target relation table. The field values should be in  
 the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is  
 erased before the new data is loaded in.  
818    
819  A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and  Run through the list of proposed field values, insuring that all the character fields are
820  tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must  below the maximum length. If any fields are too long, they will be truncated in place.
 be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.  
821    
822  =over 4  =over 4
823    
824  =item directoryName  =item relName
825    
826  Name of the directory containing the relation files to be loaded.  Name of the relation for which the specified fields are destined.
827    
828  =item rebuild  =item fieldList
829    
830  TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the  Reference to a list, in order, of the fields to be put into the relation.
 only way to erase existing data in the tables, since the TRUNCATE command is not supported  
 by all of the DB engines we use.  
831    
832  =item RETURN  =item RETURN
833    
834  Returns a statistical object describing the number of records read and a list of the error messages.  Returns the number of fields truncated.
835    
836  =back  =back
837    
838  =cut  =cut
839    
840  sub LoadTables {  sub VerifyFields {
841          # Get the parameters.          # Get the parameters.
842          my ($self, $directoryName, $rebuild) = @_;      my ($self, $relName, $fieldList) = @_;
843          # Start the timer.      # Initialize the return value.
844          my $startTime = gettimeofday;      my $retVal = 0;
845          # Clean any trailing slash from the directory name.      # Get the relation definition.
846          $directoryName =~ s!/\\$!!;      my $relData = $self->_FindRelation($relName);
847          # Declare the return variable.      # Get the list of field descriptors.
848          my $retVal = Stats->new();      my $fieldTypes = $relData->{Fields};
849          # Get the metadata structure.      my $fieldCount = scalar @{$fieldTypes};
850          my $metaData = $self->{_metaData};      # Loop through the two lists.
851          # Loop through the entities.      for (my $i = 0; $i < $fieldCount; $i++) {
852          for my $entity (values %{$metaData->{Entities}}) {          # Get the type of the current field.
853                  # Loop through the entity's relations.          my $fieldType = $fieldTypes->[$i]->{type};
854                  for my $relationName (keys %{$entity->{Relations}}) {          # If it's a character field, verify the length.
855                          # Try to load this relation.          if ($fieldType =~ /string/) {
856                          my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);              my $maxLen = $TypeTable{$fieldType}->{maxLen};
857                          # Accumulate the statistics.              my $oldString = $fieldList->[$i];
858                          $retVal->Accumulate($result);              if (length($oldString) > $maxLen) {
859                    # Here it's too big, so we truncate it.
860                    Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
861                    $fieldList->[$i] = substr $oldString, 0, $maxLen;
862                    $retVal++;
863                  }                  }
864          }          }
         # Loop through the relationships.  
         for my $relationshipName (keys %{$metaData->{Relationships}}) {  
                 # Try to load this relationship's relation.  
                 my $result = $self->_LoadRelation($directoryName, $relationshipName, $rebuild);  
                 # Accumulate the statistics.  
                 $retVal->Accumulate($result);  
865          }          }
866          # Add the duration of the load to the statistical object.      # Return the truncation count.
         $retVal->Add('duration', gettimeofday - $startTime);  
         # Return the accumulated statistics.  
867          return $retVal;          return $retVal;
868  }  }
869    
870  =head3 GetTableNames  =head3 DigestFields
871    
872  C<< my @names = $database->GetTableNames; >>  C<< $erdb->DigestFields($relName, $fieldList); >>
873    
874  Return a list of the relations required to implement this database.  Digest the strings in the field list that correspond to data type C<hash-string> in the
875    specified relation.
876    
877  =cut  =over 4
878    
879  sub GetTableNames {  =item relName
880    
881    Name of the relation to which the fields belong.
882    
883    =item fieldList
884    
885    List of field contents to be loaded into the relation.
886    
887    =back
888    
889    =cut
890    #: Return Type ;
891    sub DigestFields {
892        # Get the parameters.
893        my ($self, $relName, $fieldList) = @_;
894        # Get the relation definition.
895        my $relData = $self->_FindRelation($relName);
896        # Get the list of field descriptors.
897        my $fieldTypes = $relData->{Fields};
898        my $fieldCount = scalar @{$fieldTypes};
899        # Loop through the two lists.
900        for (my $i = 0; $i < $fieldCount; $i++) {
901            # Get the type of the current field.
902            my $fieldType = $fieldTypes->[$i]->{type};
903            # If it's a hash string, digest it in place.
904            if ($fieldType eq 'hash-string') {
905                $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
906            }
907        }
908    }
909    
910    =head3 DigestKey
911    
912    C<< my $digested = $erdb->DigestKey($keyValue); >>
913    
914    Return the digested value of a symbolic key. The digested value can then be plugged into a
915    key-based search into a table with key-type hash-string.
916    
917    Currently the digesting process is independent of the database structure, but that may not
918    always be the case, so this is an instance method instead of a static method.
919    
920    =over 4
921    
922    =item keyValue
923    
924    Key value to digest.
925    
926    =item RETURN
927    
928    Digested value of the key.
929    
930    =back
931    
932    =cut
933    
934    sub DigestKey {
935        # Get the parameters.
936        my ($self, $keyValue) = @_;
937        # Compute the digest.
938        my $retVal = md5_base64($keyValue);
939        # Return the result.
940        return $retVal;
941    }
942    
943    =head3 CreateIndex
944    
945    C<< $erdb->CreateIndex($relationName); >>
946    
947    Create the indexes for a relation. If a table is being loaded from a large source file (as
948    is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
949    If that is the case, then L</CreateTable> should be called with the index flag set to
950    FALSE, and this method used after the load to create the indexes for the table.
951    
952    =cut
953    
954    sub CreateIndex {
955        # Get the parameters.
956        my ($self, $relationName) = @_;
957        # Get the relation's descriptor.
958        my $relationData = $self->_FindRelation($relationName);
959        # Get the database handle.
960        my $dbh = $self->{_dbh};
961        # Now we need to create this relation's indexes. We do this by looping through its index table.
962        my $indexHash = $relationData->{Indexes};
963        for my $indexName (keys %{$indexHash}) {
964            my $indexData = $indexHash->{$indexName};
965            # Get the index's field list.
966            my @rawFields = @{$indexData->{IndexFields}};
967            # Get a hash of the relation's field types.
968            my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
969            # We need to check for text fields. We need a append a length limitation for them. To do
970            # that, we need the relation's field list.
971            my $relFields = $relationData->{Fields};
972            for (my $i = 0; $i <= $#rawFields; $i++) {
973                # Get the field type.
974                my $field = $rawFields[$i];
975                my $type = $types{$field};
976                # Ask if it requires using prefix notation for the index.
977                my $mod = $TypeTable{$type}->{indexMod};
978                Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
979                if ($mod) {
980                    # Append the prefix length to the field name,
981                    $rawFields[$i] .= "($mod)";
982                }
983            }
984            my @fieldList = _FixNames(@rawFields);
985            my $flds = join(', ', @fieldList);
986            # Get the index's uniqueness flag.
987            my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
988            # Create the index.
989            my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
990                                        flds => $flds, kind => $unique);
991            if ($rv) {
992                Trace("Index created: $indexName for $relationName ($flds)") if T(1);
993            } else {
994                Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
995            }
996        }
997    }
998    
999    =head3 GetSecondaryFields
1000    
1001    C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1002    
1003    This method will return a list of the name and type of each of the secondary
1004    fields for a specified entity. Secondary fields are stored in two-column tables
1005    in addition to the primary entity table. This enables the field to have no value
1006    or to have multiple values.
1007    
1008    =over 4
1009    
1010    =item entityName
1011    
1012    Name of the entity whose secondary fields are desired.
1013    
1014    =item RETURN
1015    
1016    Returns a hash mapping the field names to their field types.
1017    
1018    =back
1019    
1020    =cut
1021    
1022    sub GetSecondaryFields {
1023        # Get the parameters.
1024        my ($self, $entityName) = @_;
1025        # Declare the return variable.
1026        my %retVal = ();
1027        # Look for the entity.
1028        my $table = $self->GetFieldTable($entityName);
1029        # Loop through the fields, pulling out the secondaries.
1030        for my $field (sort keys %{$table}) {
1031            if ($table->{$field}->{relation} ne $entityName) {
1032                # Here we have a secondary field.
1033                $retVal{$field} = $table->{$field}->{type};
1034            }
1035        }
1036        # Return the result.
1037        return %retVal;
1038    }
1039    
1040    =head3 GetFieldRelationName
1041    
1042    C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1043    
1044    Return the name of the relation containing a specified field.
1045    
1046    =over 4
1047    
1048    =item objectName
1049    
1050    Name of the entity or relationship containing the field.
1051    
1052    =item fieldName
1053    
1054    Name of the relevant field in that entity or relationship.
1055    
1056    =item RETURN
1057    
1058    Returns the name of the database relation containing the field, or C<undef> if
1059    the field does not exist.
1060    
1061    =back
1062    
1063    =cut
1064    
1065    sub GetFieldRelationName {
1066        # Get the parameters.
1067        my ($self, $objectName, $fieldName) = @_;
1068        # Declare the return variable.
1069        my $retVal;
1070        # Get the object field table.
1071        my $table = $self->GetFieldTable($objectName);
1072        # Only proceed if the field exists.
1073        if (exists $table->{$fieldName}) {
1074            # Determine the name of the relation that contains this field.
1075            $retVal = $table->{$fieldName}->{relation};
1076        }
1077        # Return the result.
1078        return $retVal;
1079    }
1080    
1081    =head3 DeleteValue
1082    
1083    C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1084    
1085    Delete secondary field values from the database. This method can be used to delete all
1086    values of a specified field for a particular entity instance, or only a single value.
1087    
1088    Secondary fields are stored in two-column relations separate from an entity's primary
1089    table, and as a result a secondary field can legitimately have no value or multiple
1090    values. Therefore, it makes sense to talk about deleting secondary fields where it
1091    would not make sense for primary fields.
1092    
1093    =over 4
1094    
1095    =item entityName
1096    
1097    Name of the entity from which the fields are to be deleted.
1098    
1099    =item id
1100    
1101    ID of the entity instance to be processed. If the instance is not found, this
1102    method will have no effect.
1103    
1104    =item fieldName
1105    
1106    Name of the field whose values are to be deleted.
1107    
1108    =item fieldValue (optional)
1109    
1110    Value to be deleted. If not specified, then all values of the specified field
1111    will be deleted for the entity instance. If specified, then only the values which
1112    match this parameter will be deleted.
1113    
1114    =item RETURN
1115    
1116    Returns the number of rows deleted.
1117    
1118    =back
1119    
1120    =cut
1121    
1122    sub DeleteValue {
1123        # Get the parameters.
1124        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1125        # Declare the return value.
1126        my $retVal = 0;
1127        # We need to set up an SQL command to do the deletion. First, we
1128        # find the name of the field's relation.
1129        my $table = $self->GetFieldTable($entityName);
1130        my $field = $table->{$fieldName};
1131        my $relation = $field->{relation};
1132        # Make sure this is a secondary field.
1133        if ($relation eq $entityName) {
1134            Confess("Cannot delete values of $fieldName for $entityName.");
1135        } else {
1136            # Set up the SQL command to delete all values.
1137            my $sql = "DELETE FROM $relation WHERE id = ?";
1138            my @parms = $id;
1139            # If a value has been specified, append it to the statement.
1140            if (defined $fieldValue) {
1141                $sql .= " AND $fieldName = ?";
1142                push @parms, $fieldValue;
1143            }
1144            # Execute the command.
1145            my $dbh = $self->{_dbh};
1146            $retVal = $dbh->SQL($sql, 0, @parms);
1147        }
1148        # Return the result.
1149        return $retVal;
1150    }
1151    
1152    =head3 LoadTables
1153    
1154    C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1155    
1156    This method will load the database tables from a directory. The tables must already have been created
1157    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1158    all of the relations to be loaded must have a file in the directory with the same name as the relation
1159    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1160    line of the file will be loaded as a row of the target relation table. The field values should be in
1161    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1162    erased before the new data is loaded in.
1163    
1164    A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1165    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1166    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1167    
1168    =over 4
1169    
1170    =item directoryName
1171    
1172    Name of the directory containing the relation files to be loaded.
1173    
1174    =item rebuild
1175    
1176    TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1177    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1178    by all of the DB engines we use.
1179    
1180    =item RETURN
1181    
1182    Returns a statistical object describing the number of records read and a list of the error messages.
1183    
1184    =back
1185    
1186    =cut
1187    
1188    sub LoadTables {
1189        # Get the parameters.
1190        my ($self, $directoryName, $rebuild) = @_;
1191        # Start the timer.
1192        my $startTime = gettimeofday;
1193        # Clean any trailing slash from the directory name.
1194        $directoryName =~ s!/\\$!!;
1195        # Declare the return variable.
1196        my $retVal = Stats->new();
1197        # Get the relation names.
1198        my @relNames = $self->GetTableNames();
1199        for my $relationName (@relNames) {
1200            # Try to load this relation.
1201            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1202            # Accumulate the statistics.
1203            $retVal->Accumulate($result);
1204        }
1205        # Add the duration of the load to the statistical object.
1206        $retVal->Add('duration', gettimeofday - $startTime);
1207        # Return the accumulated statistics.
1208        return $retVal;
1209    }
1210    
1211    
1212    =head3 GetTableNames
1213    
1214    C<< my @names = $erdb->GetTableNames; >>
1215    
1216    Return a list of the relations required to implement this database.
1217    
1218    =cut
1219    
1220    sub GetTableNames {
1221          # Get the parameters.          # Get the parameters.
1222          my ($self) = @_;          my ($self) = @_;
1223          # Get the relation list from the metadata.          # Get the relation list from the metadata.
# Line 524  Line 1228 
1228    
1229  =head3 GetEntityTypes  =head3 GetEntityTypes
1230    
1231  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
1232    
1233  Return a list of the entity type names.  Return a list of the entity type names.
1234    
# Line 539  Line 1243 
1243          return sort keys %{$entityList};          return sort keys %{$entityList};
1244  }  }
1245    
1246    =head3 GetDataTypes
1247    
1248    C<< my %types = ERDB::GetDataTypes(); >>
1249    
1250    Return a table of ERDB data types. The table returned is a hash of hashes.
1251    The keys of the big hash are the datatypes. Each smaller hash has several
1252    values used to manage the data. The most interesting is the SQL type (key
1253    C<sqlType>) and the descriptive node (key C<notes>).
1254    
1255    Note that changing the values in the smaller hashes will seriously break
1256    things, so this data should be treated as read-only.
1257    
1258    =cut
1259    
1260    sub GetDataTypes {
1261        return %TypeTable;
1262    }
1263    
1264    
1265    =head3 IsEntity
1266    
1267    C<< my $flag = $erdb->IsEntity($entityName); >>
1268    
1269    Return TRUE if the parameter is an entity name, else FALSE.
1270    
1271    =over 4
1272    
1273    =item entityName
1274    
1275    Object name to be tested.
1276    
1277    =item RETURN
1278    
1279    Returns TRUE if the specified string is an entity name, else FALSE.
1280    
1281    =back
1282    
1283    =cut
1284    
1285    sub IsEntity {
1286        # Get the parameters.
1287        my ($self, $entityName) = @_;
1288        # Test to see if it's an entity.
1289        return exists $self->{_metaData}->{Entities}->{$entityName};
1290    }
1291    
1292  =head3 Get  =head3 Get
1293    
1294  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1295    
1296  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.
1297  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 549  Line 1299 
1299  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
1300  $genus.  $genus.
1301    
1302  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1303    
1304  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
1305  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1306    
1307  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1308    
1309  however, this version of the call would generate a syntax error if there were any quote  however, this version of the call would generate a syntax error if there were any quote
1310  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 566  Line 1316 
1316  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
1317  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,
1318    
1319  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1320    
1321  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
1322  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.
1323  In particular, you can't specify any entity or relationship more than once, and if a  In particular, if a relationship is recursive, the path is determined by the order in which
1324  relationship is recursive, the path is determined by the order in which the entity  the entity and the relationship appear. For example, consider a recursive relationship
1325  and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
 which relates B<People> objects to other B<People> objects. If the join path is  
1326  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1327  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1328    
1329    If an entity or relationship is mentioned twice, the name for the second occurrence will
1330    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1331    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1332    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1333    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1334    
1335  =over 4  =over 4
1336    
1337  =item objectNames  =item objectNames
# Line 599  Line 1354 
1354    
1355  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1356    
1357    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1358    be processed. The idea is to make it less likely to find the verb by accident.
1359    
1360  The rules for field references in a sort order are the same as those for field references in the  The rules for field references in a sort order are the same as those for field references in the
1361  filter clause in general; however, odd things may happen if a sort field is from a secondary  filter clause in general; however, odd things may happen if a sort field is from a secondary
1362  relation.  relation.
1363    
1364  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1365    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1366    a positive number. So, for example
1367    
1368    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1369    
1370  Parameter values to be substituted into the filter clause.  will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1371    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1372    use
1373    
1374    C<< "LIMIT 10" >>
1375    
1376    =item params
1377    
1378    Reference to a list of parameter values to be substituted into the filter clause.
1379    
1380  =item RETURN  =item RETURN
1381    
# Line 617  Line 1387 
1387    
1388  sub Get {  sub Get {
1389          # Get the parameters.          # Get the parameters.
1390          my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1391          # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1392          #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1393          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1394          #      # Create the query.
1395          my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1396          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1397                                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1398          # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1399          if ($filterClause) {      # and mapped name for each object in the query.
1400                  # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1401                  # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1402                  my $filterString = $filterClause;          push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
                 # Next, we sort the object names by length. This helps protect us from finding  
                 # object names inside other object names when we're doing our search and replace.  
                 my @sortedNames = sort { length($b) - length($a) } @{$objectNames};  
                 # We will also keep a list of conditions to add to the WHERE clause in order to link  
                 # entities and relationships as well as primary relations to secondary ones.  
                 my @joinWhere = ();  
                 # The final preparatory step is to create a hash table of relation names. The  
                 # table begins with the relation names already in the SELECT command.  
                 my %fromNames = ();  
                 for my $objectName (@sortedNames) {  
                         $fromNames{$objectName} = 1;  
1403                  }                  }
1404                  # We are ready to begin. We loop through the object names, replacing each      # Return the statement object.
1405                  # object name's field references by the corresponding SQL field reference.      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1406                  # Along the way, if we find a secondary relation, we will need to add it      return $retVal;
1407                  # to the FROM clause.  }
1408                  for my $objectName (@sortedNames) {  
1409                          # Get the length of the object name plus 2. This is the value we add to the  =head3 Search
1410                          # size of the field name to determine the size of the field reference as a  
1411                          # whole.  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1412                          my $nameLength = 2 + length $objectName;  
1413                          # Get the object's field list.  Perform a full text search with filtering. The search will be against a specified object
1414                          my $fieldList = $self->_GetFieldTable($objectName);  in the object name list. That object will get an extra field containing the search
1415                          # Find the field references for this object.  relevance. Note that except for the search expression, the parameters of this method are
1416                          while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  the same as those for L</Get> and follow the same rules.
1417                                  # At this point, $1 contains the field name, and the current position  
1418                                  # is set immediately after the final parenthesis. We pull out the name of  =over 4
1419                                  # the field and the position and length of the field reference as a whole.  
1420                                  my $fieldName = $1;  =item searchExpression
1421                                  my $len = $nameLength + length $fieldName;  
1422                                  my $pos = pos($filterString) - $len;  Boolean search expression for the text fields of the target object. The default mode for
1423                                  # Insure the field exists.  a Boolean search expression is OR, but we want the default to be AND, so we will
1424                                  if (!exists $fieldList->{$fieldName}) {  add a C<+> operator to each word with no other operator before it.
1425                                          Confess("Field $fieldName not found for object $objectName.");  
1426    =item idx
1427    
1428    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1429    
1430    =item objectNames
1431    
1432    List containing the names of the entity and relationship objects to be retrieved.
1433    
1434    =item filterClause
1435    
1436    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1437    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1438    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1439    in the filter clause should be added to the parameter list as additional parameters. The
1440    fields in a filter clause can come from primary entity relations, relationship relations,
1441    or secondary entity relations; however, all of the entities and relationships involved must
1442    be included in the list of object names.
1443    
1444    =item params
1445    
1446    Reference to a list of parameter values to be substituted into the filter clause.
1447    
1448    =item RETURN
1449    
1450    Returns a query object for the specified search.
1451    
1452    =back
1453    
1454    =cut
1455    
1456    sub Search {
1457        # Get the parameters.
1458        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1459        # Declare the return variable.
1460        my $retVal;
1461        # Create a safety copy of the parameter list. Note we have to be careful to insure
1462        # a parameter list exists before we copy it.
1463        my @myParams = ();
1464        if (defined $params) {
1465            @myParams = @{$params};
1466        }
1467        # Get the first object's structure so we have access to the searchable fields.
1468        my $object1Name = $objectNames->[$idx];
1469        my $object1Structure = $self->_GetStructure($object1Name);
1470        # Get the field list.
1471        if (! exists $object1Structure->{searchFields}) {
1472            Confess("No searchable index for $object1Name.");
1473        } else {
1474            # Get the field list.
1475            my @fields = @{$object1Structure->{searchFields}};
1476            # Clean the search expression.
1477            my $actualKeywords = $self->CleanKeywords($searchExpression);
1478            # Prefix a "+" to each uncontrolled word. This converts the default
1479            # search mode from OR to AND.
1480            $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;
1481            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1482            # We need two match expressions, one for the filter clause and one in the
1483            # query itself. Both will use a parameter mark, so we need to push the
1484            # search expression onto the front of the parameter list twice.
1485            unshift @myParams, $actualKeywords, $actualKeywords;
1486            # Build the match expression.
1487            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1488            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1489            # Process the SQL stuff.
1490            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1491                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1492            # Create the query. Note that the match clause is inserted at the front of
1493            # the select fields.
1494            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1495                ".* $suffix";
1496            my $sth = $self->_GetStatementHandle($command, \@myParams);
1497            # Now we create the relation map, which enables DBQuery to determine the order, name
1498            # and mapped name for each object in the query.
1499            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1500            # Return the statement object.
1501            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1502        }
1503        return $retVal;
1504    }
1505    
1506    =head3 GetFlat
1507    
1508    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1509    
1510    This is a variation of L</GetAll> that asks for only a single field per record and
1511    returns a single flattened list.
1512    
1513    =over 4
1514    
1515    =item objectNames
1516    
1517    List containing the names of the entity and relationship objects to be retrieved.
1518    
1519    =item filterClause
1520    
1521    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1522    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1523    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1524    parameter list as additional parameters. The fields in a filter clause can come from primary
1525    entity relations, relationship relations, or secondary entity relations; however, all of the
1526    entities and relationships involved must be included in the list of object names.
1527    
1528    =item parameterList
1529    
1530    List of the parameters to be substituted in for the parameters marks in the filter clause.
1531    
1532    =item field
1533    
1534    Name of the field to be used to get the elements of the list returned.
1535    
1536    =item RETURN
1537    
1538    Returns a list of values.
1539    
1540    =back
1541    
1542    =cut
1543    #: Return Type @;
1544    sub GetFlat {
1545        # Get the parameters.
1546        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1547        # Construct the query.
1548        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1549        # Create the result list.
1550        my @retVal = ();
1551        # Loop through the records, adding the field values found to the result list.
1552        while (my $row = $query->Fetch()) {
1553            push @retVal, $row->Value($field);
1554        }
1555        # Return the list created.
1556        return @retVal;
1557    }
1558    
1559    =head3 SpecialFields
1560    
1561    C<< my %specials = $erdb->SpecialFields($entityName); >>
1562    
1563    Return a hash mapping special fields in the specified entity to the value of their
1564    C<special> attribute. This enables the subclass to get access to the special field
1565    attributes without needed to plumb the internal ERDB data structures.
1566    
1567    =over 4
1568    
1569    =item entityName
1570    
1571    Name of the entity whose special fields are desired.
1572    
1573    =item RETURN
1574    
1575    Returns a hash. The keys of the hash are the special field names, and the values
1576    are the values from each special field's C<special> attribute.
1577    
1578    =back
1579    
1580    =cut
1581    
1582    sub SpecialFields {
1583        # Get the parameters.
1584        my ($self, $entityName) = @_;
1585        # Declare the return variable.
1586        my %retVal = ();
1587        # Find the entity's data structure.
1588        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1589        # Loop through its fields, adding each special field to the return hash.
1590        my $fieldHash = $entityData->{Fields};
1591        for my $fieldName (keys %{$fieldHash}) {
1592            my $fieldData = $fieldHash->{$fieldName};
1593            if (exists $fieldData->{special}) {
1594                $retVal{$fieldName} = $fieldData->{special};
1595            }
1596        }
1597        # Return the result.
1598        return %retVal;
1599    }
1600    
1601    =head3 Delete
1602    
1603    C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1604    
1605    Delete an entity instance from the database. The instance is deleted along with all entity and
1606    relationship instances dependent on it. The idea of dependence here is recursive. An object is
1607    always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1608    relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1609    dependent relationship.
1610    
1611    =over 4
1612    
1613    =item entityName
1614    
1615    Name of the entity type for the instance being deleted.
1616    
1617    =item objectID
1618    
1619    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1620    then it is presumed to by a LIKE pattern.
1621    
1622    =item testFlag
1623    
1624    If TRUE, the delete statements will be traced without being executed.
1625    
1626    =item RETURN
1627    
1628    Returns a statistics object indicating how many records of each particular table were
1629    deleted.
1630    
1631    =back
1632    
1633    =cut
1634    #: Return Type $%;
1635    sub Delete {
1636        # Get the parameters.
1637        my ($self, $entityName, $objectID, $testFlag) = @_;
1638        # Declare the return variable.
1639        my $retVal = Stats->new();
1640        # Get the DBKernel object.
1641        my $db = $self->{_dbh};
1642        # We're going to generate all the paths branching out from the starting entity. One of
1643        # the things we have to be careful about is preventing loops. We'll use a hash to
1644        # determine if we've hit a loop.
1645        my %alreadyFound = ();
1646        # These next lists will serve as our result stack. We start by pushing object lists onto
1647        # the stack, and then popping them off to do the deletes. This means the deletes will
1648        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1649        # sure we don't delete records that might be needed to forge relationships back to the
1650        # original item. We have two lists-- one for TO-relationships, and one for
1651        # FROM-relationships and entities.
1652        my @fromPathList = ();
1653        my @toPathList = ();
1654        # This final hash is used to remember what work still needs to be done. We push paths
1655        # onto the list, then pop them off to extend the paths. We prime it with the starting
1656        # point. Note that we will work hard to insure that the last item on a path in the
1657        # to-do list is always an entity.
1658        my @todoList = ([$entityName]);
1659        while (@todoList) {
1660            # Get the current path.
1661            my $current = pop @todoList;
1662            # Copy it into a list.
1663            my @stackedPath = @{$current};
1664            # Pull off the last item on the path. It will always be an entity.
1665            my $entityName = pop @stackedPath;
1666            # Add it to the alreadyFound list.
1667            $alreadyFound{$entityName} = 1;
1668            # Get the entity data.
1669            my $entityData = $self->_GetStructure($entityName);
1670            # The first task is to loop through the entity's relation. A DELETE command will
1671            # be needed for each of them.
1672            my $relations = $entityData->{Relations};
1673            for my $relation (keys %{$relations}) {
1674                my @augmentedList = (@stackedPath, $relation);
1675                push @fromPathList, \@augmentedList;
1676            }
1677            # Now we need to look for relationships connected to this entity.
1678            my $relationshipList = $self->{_metaData}->{Relationships};
1679            for my $relationshipName (keys %{$relationshipList}) {
1680                my $relationship = $relationshipList->{$relationshipName};
1681                # Check the FROM field. We're only interested if it's us.
1682                if ($relationship->{from} eq $entityName) {
1683                    # Add the path to this relationship.
1684                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1685                    push @fromPathList, \@augmentedList;
1686                    # Check the arity. If it's MM we're done. If it's 1M
1687                    # and the target hasn't been seen yet, we want to
1688                    # stack the entity for future processing.
1689                    if ($relationship->{arity} eq '1M') {
1690                        my $toEntity = $relationship->{to};
1691                        if (! exists $alreadyFound{$toEntity}) {
1692                            # Here we have a new entity that's dependent on
1693                            # the current entity, so we need to stack it.
1694                            my @stackList = (@augmentedList, $toEntity);
1695                            push @fromPathList, \@stackList;
1696                        } else {
1697                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1698                        }
1699                    }
1700                }
1701                # Now check the TO field. In this case only the relationship needs
1702                # deletion.
1703                if ($relationship->{to} eq $entityName) {
1704                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1705                    push @toPathList, \@augmentedList;
1706                }
1707            }
1708        }
1709        # Create the first qualifier for the WHERE clause. This selects the
1710        # keys of the primary entity records to be deleted. When we're deleting
1711        # from a dependent table, we construct a join page from the first qualifier
1712        # to the table containing the dependent records to delete.
1713        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1714        # We need to make two passes. The first is through the to-list, and
1715        # the second through the from-list. The from-list is second because
1716        # the to-list may need to pass through some of the entities the
1717        # from-list would delete.
1718        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1719        # Now it's time to do the deletes. We do it in two passes.
1720        for my $keyName ('to_link', 'from_link') {
1721            # Get the list for this key.
1722            my @pathList = @{$stackList{$keyName}};
1723            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1724            # Loop through this list.
1725            while (my $path = pop @pathList) {
1726                # Get the table whose rows are to be deleted.
1727                my @pathTables = @{$path};
1728                # Start the DELETE statement. We need to call DBKernel because the
1729                # syntax of a DELETE-USING varies among DBMSs.
1730                my $target = $pathTables[$#pathTables];
1731                my $stmt = $db->SetUsing(@pathTables);
1732                # Now start the WHERE. The first thing is the ID field from the starting table. That
1733                # starting table will either be the entity relation or one of the entity's
1734                # sub-relations.
1735                $stmt .= " WHERE $pathTables[0].id $qualifier";
1736                # Now we run through the remaining entities in the path, connecting them up.
1737                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1738                    # Connect the current relationship to the preceding entity.
1739                    my ($entity, $rel) = @pathTables[$i-1,$i];
1740                    # The style of connection depends on the direction of the relationship.
1741                    $stmt .= " AND $entity.id = $rel.$keyName";
1742                    if ($i + 1 <= $#pathTables) {
1743                        # Here there's a next entity, so connect that to the relationship's
1744                        # to-link.
1745                        my $entity2 = $pathTables[$i+1];
1746                        $stmt .= " AND $rel.to_link = $entity2.id";
1747                    }
1748                }
1749                # Now we have our desired DELETE statement.
1750                if ($testFlag) {
1751                    # Here the user wants to trace without executing.
1752                    Trace($stmt) if T(0);
1753                } else {
1754                    # Here we can delete. Note that the SQL method dies with a confessing
1755                    # if an error occurs, so we just go ahead and do it.
1756                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1757                    my $rv = $db->SQL($stmt, 0, $objectID);
1758                    # Accumulate the statistics for this delete. The only rows deleted
1759                    # are from the target table, so we use its name to record the
1760                    # statistic.
1761                    $retVal->Add($target, $rv);
1762                }
1763            }
1764        }
1765        # Return the result.
1766        return $retVal;
1767    }
1768    
1769    =head3 SortNeeded
1770    
1771    C<< my $parms = $erdb->SortNeeded($relationName); >>
1772    
1773    Return the pipe command for the sort that should be applied to the specified
1774    relation when creating the load file.
1775    
1776    For example, if the load file should be sorted ascending by the first
1777    field, this method would return
1778    
1779        sort -k1 -t"\t"
1780    
1781    If the first field is numeric, the method would return
1782    
1783        sort -k1n -t"\t"
1784    
1785    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1786    keys using a sort.
1787    
1788    =over 4
1789    
1790    =item relationName
1791    
1792    Name of the relation to be examined.
1793    
1794    =item
1795    
1796    Returns the sort command to use for sorting the relation, suitable for piping.
1797    
1798    =back
1799    
1800    =cut
1801    #: Return Type $;
1802    sub SortNeeded {
1803        # Get the parameters.
1804        my ($self, $relationName) = @_;
1805        # Declare a descriptor to hold the names of the key fields.
1806        my @keyNames = ();
1807        # Get the relation structure.
1808        my $relationData = $self->_FindRelation($relationName);
1809        # Find out if the relation is a primary entity relation,
1810        # a relationship relation, or a secondary entity relation.
1811        my $entityTable = $self->{_metaData}->{Entities};
1812        my $relationshipTable = $self->{_metaData}->{Relationships};
1813        if (exists $entityTable->{$relationName}) {
1814            # Here we have a primary entity relation.
1815            push @keyNames, "id";
1816        } elsif (exists $relationshipTable->{$relationName}) {
1817            # Here we have a relationship. We sort using the FROM index.
1818            my $relationshipData = $relationshipTable->{$relationName};
1819            my $index = $relationData->{Indexes}->{idxFrom};
1820            push @keyNames, @{$index->{IndexFields}};
1821        } else {
1822            # Here we have a secondary entity relation, so we have a sort on the ID field.
1823            push @keyNames, "id";
1824        }
1825        # Now we parse the key names into sort parameters. First, we prime the return
1826        # string.
1827        my $retVal = "sort -t\"\t\" ";
1828        # Get the relation's field list.
1829        my @fields = @{$relationData->{Fields}};
1830        # Loop through the keys.
1831        for my $keyData (@keyNames) {
1832            # Get the key and the ordering.
1833            my ($keyName, $ordering);
1834            if ($keyData =~ /^([^ ]+) DESC/) {
1835                ($keyName, $ordering) = ($1, "descending");
1836            } else {
1837                ($keyName, $ordering) = ($keyData, "ascending");
1838            }
1839            # Find the key's position and type.
1840            my $fieldSpec;
1841            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1842                my $thisField = $fields[$i];
1843                if ($thisField->{name} eq $keyName) {
1844                    # Get the sort modifier for this field type. The modifier
1845                    # decides whether we're using a character, numeric, or
1846                    # floating-point sort.
1847                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1848                    # If the index is descending for this field, denote we want
1849                    # to reverse the sort order on this field.
1850                    if ($ordering eq 'descending') {
1851                        $modifier .= "r";
1852                    }
1853                    # Store the position and modifier into the field spec, which
1854                    # will stop the inner loop. Note that the field number is
1855                    # 1-based in the sort command, so we have to increment the
1856                    # index.
1857                    $fieldSpec = ($i + 1) . $modifier;
1858                }
1859            }
1860            # Add this field to the sort command.
1861            $retVal .= " -k$fieldSpec";
1862        }
1863        # Return the result.
1864        return $retVal;
1865    }
1866    
1867    =head3 GetList
1868    
1869    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1870    
1871    Return a list of object descriptors for the specified objects as determined by the
1872    specified filter clause.
1873    
1874    This method is essentially the same as L</Get> except it returns a list of objects rather
1875    than a query object that can be used to get the results one record at a time.
1876    
1877    =over 4
1878    
1879    =item objectNames
1880    
1881    List containing the names of the entity and relationship objects to be retrieved.
1882    
1883    =item filterClause
1884    
1885    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1886    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1887    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1888    in the filter clause should be added to the parameter list as additional parameters. The
1889    fields in a filter clause can come from primary entity relations, relationship relations,
1890    or secondary entity relations; however, all of the entities and relationships involved must
1891    be included in the list of object names.
1892    
1893    The filter clause can also specify a sort order. To do this, simply follow the filter string
1894    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1895    particular genus and sorts them by species name.
1896    
1897    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1898    
1899    The rules for field references in a sort order are the same as those for field references in the
1900    filter clause in general; however, odd things may happen if a sort field is from a secondary
1901    relation.
1902    
1903    =item params
1904    
1905    Reference to a list of parameter values to be substituted into the filter clause.
1906    
1907    =item RETURN
1908    
1909    Returns a list of B<DBObject>s that satisfy the query conditions.
1910    
1911    =back
1912    
1913    =cut
1914    #: Return Type @%
1915    sub GetList {
1916        # Get the parameters.
1917        my ($self, $objectNames, $filterClause, $params) = @_;
1918        # Declare the return variable.
1919        my @retVal = ();
1920        # Perform the query.
1921        my $query = $self->Get($objectNames, $filterClause, $params);
1922        # Loop through the results.
1923        while (my $object = $query->Fetch) {
1924            push @retVal, $object;
1925        }
1926        # Return the result.
1927        return @retVal;
1928    }
1929    
1930    =head3 GetCount
1931    
1932    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1933    
1934    Return the number of rows found by a specified query. This method would
1935    normally be used to count the records in a single table. For example, in a
1936    genetics database
1937    
1938        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1939    
1940    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1941    to use it to return records based on a join. For example,
1942    
1943        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1944                                    ['homo %']);
1945    
1946    would return the number of features for genomes in the genus I<homo>. Note that
1947    only the rows from the first table are counted. If the above command were
1948    
1949        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1950                                    ['homo %']);
1951    
1952    it would return the number of genomes, not the number of genome/feature pairs.
1953    
1954    =over 4
1955    
1956    =item objectNames
1957    
1958    Reference to a list of the objects (entities and relationships) included in the
1959    query.
1960    
1961    =item filter
1962    
1963    A filter clause for restricting the query. The rules are the same as for the L</Get>
1964    method.
1965    
1966    =item params
1967    
1968    Reference to a list of the parameter values to be substituted for the parameter marks
1969    in the filter.
1970    
1971    =item RETURN
1972    
1973    Returns a count of the number of records in the first table that would satisfy
1974    the query.
1975    
1976    =back
1977    
1978    =cut
1979    
1980    sub GetCount {
1981        # Get the parameters.
1982        my ($self, $objectNames, $filter, $params) = @_;
1983        # Insure the params argument is an array reference if the caller left it off.
1984        if (! defined($params)) {
1985            $params = [];
1986        }
1987        # Declare the return variable.
1988        my $retVal;
1989        # Find out if we're counting an entity or a relationship.
1990        my $countedField;
1991        if ($self->IsEntity($objectNames->[0])) {
1992            $countedField = "id";
1993        } else {
1994            # For a relationship we count the to-link because it's usually more
1995            # numerous. Note we're automatically converting to the SQL form
1996            # of the field name (to_link vs. to-link).
1997            $countedField = "to_link";
1998        }
1999        # Create the SQL command suffix to get the desired records.
2000        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2001                                                                                $filter);
2002        # Prefix it with text telling it we want a record count.
2003        my $firstObject = $mappedNameListRef->[0];
2004        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2005        # Prepare and execute the command.
2006        my $sth = $self->_GetStatementHandle($command, $params);
2007        # Get the count value.
2008        ($retVal) = $sth->fetchrow_array();
2009        # Check for a problem.
2010        if (! defined($retVal)) {
2011            if ($sth->err) {
2012                # Here we had an SQL error.
2013                Confess("Error retrieving row count: " . $sth->errstr());
2014            } else {
2015                # Here we have no result.
2016                Confess("No result attempting to retrieve row count.");
2017            }
2018        }
2019        # Return the result.
2020        return $retVal;
2021    }
2022    
2023    =head3 ComputeObjectSentence
2024    
2025    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2026    
2027    Check an object name, and if it is a relationship convert it to a relationship sentence.
2028    
2029    =over 4
2030    
2031    =item objectName
2032    
2033    Name of the entity or relationship.
2034    
2035    =item RETURN
2036    
2037    Returns a string containing the entity name or a relationship sentence.
2038    
2039    =back
2040    
2041    =cut
2042    
2043    sub ComputeObjectSentence {
2044        # Get the parameters.
2045        my ($self, $objectName) = @_;
2046        # Set the default return value.
2047        my $retVal = $objectName;
2048        # Look for the object as a relationship.
2049        my $relTable = $self->{_metaData}->{Relationships};
2050        if (exists $relTable->{$objectName}) {
2051            # Get the relationship sentence.
2052            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2053        }
2054        # Return the result.
2055        return $retVal;
2056    }
2057    
2058    =head3 DumpRelations
2059    
2060    C<< $erdb->DumpRelations($outputDirectory); >>
2061    
2062    Write the contents of all the relations to tab-delimited files in the specified directory.
2063    Each file will have the same name as the relation dumped, with an extension of DTX.
2064    
2065    =over 4
2066    
2067    =item outputDirectory
2068    
2069    Name of the directory into which the relation files should be dumped.
2070    
2071    =back
2072    
2073    =cut
2074    
2075    sub DumpRelations {
2076        # Get the parameters.
2077        my ($self, $outputDirectory) = @_;
2078        # Now we need to run through all the relations. First, we loop through the entities.
2079        my $metaData = $self->{_metaData};
2080        my $entities = $metaData->{Entities};
2081        for my $entityName (keys %{$entities}) {
2082            my $entityStructure = $entities->{$entityName};
2083            # Get the entity's relations.
2084            my $relationList = $entityStructure->{Relations};
2085            # Loop through the relations, dumping them.
2086            for my $relationName (keys %{$relationList}) {
2087                my $relation = $relationList->{$relationName};
2088                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2089            }
2090        }
2091        # Next, we loop through the relationships.
2092        my $relationships = $metaData->{Relationships};
2093        for my $relationshipName (keys %{$relationships}) {
2094            my $relationshipStructure = $relationships->{$relationshipName};
2095            # Dump this relationship's relation.
2096            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2097        }
2098    }
2099    
2100    =head3 InsertValue
2101    
2102    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2103    
2104    This method will insert a new value into the database. The value must be one
2105    associated with a secondary relation, since primary values cannot be inserted:
2106    they occur exactly once. Secondary values, on the other hand, can be missing
2107    or multiply-occurring.
2108    
2109    =over 4
2110    
2111    =item entityID
2112    
2113    ID of the object that is to receive the new value.
2114    
2115    =item fieldName
2116    
2117    Field name for the new value-- this includes the entity name, since
2118    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2119    
2120    =item value
2121    
2122    New value to be put in the field.
2123    
2124    =back
2125    
2126    =cut
2127    
2128    sub InsertValue {
2129        # Get the parameters.
2130        my ($self, $entityID, $fieldName, $value) = @_;
2131        # Parse the entity name and the real field name.
2132        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2133            my $entityName = $1;
2134            my $fieldTitle = $2;
2135            # Get its descriptor.
2136            if (!$self->IsEntity($entityName)) {
2137                Confess("$entityName is not a valid entity.");
2138            } else {
2139                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2140                # Find the relation containing this field.
2141                my $fieldHash = $entityData->{Fields};
2142                if (! exists $fieldHash->{$fieldTitle}) {
2143                    Confess("$fieldTitle not found in $entityName.");
2144                } else {
2145                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2146                    if ($relation eq $entityName) {
2147                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2148                    } else {
2149                        # Now we can create an INSERT statement.
2150                        my $dbh = $self->{_dbh};
2151                        my $fixedName = _FixName($fieldTitle);
2152                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2153                        # Execute the command.
2154                        $dbh->SQL($statement, 0, $entityID, $value);
2155                    }
2156                }
2157            }
2158        } else {
2159            Confess("$fieldName is not a valid field name.");
2160        }
2161    }
2162    
2163    =head3 InsertObject
2164    
2165    C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2166    
2167    Insert an object into the database. The object is defined by a type name and then a hash
2168    of field names to values. Field values in the primary relation are represented by scalars.
2169    (Note that for relationships, the primary relation is the B<only> relation.)
2170    Field values for the other relations comprising the entity are always list references. For
2171    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2172    C<ZP_00210270.1> and C<gi|46206278>.
2173    
2174    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2175    
2176    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2177    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2178    
2179    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2180    
2181    =over 4
2182    
2183    =item newObjectType
2184    
2185    Type name of the object to insert.
2186    
2187    =item fieldHash
2188    
2189    Hash of field names to values.
2190    
2191    =item RETURN
2192    
2193    Returns 1 if successful, 0 if an error occurred.
2194    
2195    =back
2196    
2197    =cut
2198    
2199    sub InsertObject {
2200        # Get the parameters.
2201        my ($self, $newObjectType, $fieldHash) = @_;
2202        # Denote that so far we appear successful.
2203        my $retVal = 1;
2204        # Get the database handle.
2205        my $dbh = $self->{_dbh};
2206        # Get the relation list.
2207        my $relationTable = $self->_GetRelationTable($newObjectType);
2208        # Loop through the relations. We'll build insert statements for each one. If a relation is
2209        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2210        # stop the loop.
2211        my @relationList = keys %{$relationTable};
2212        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2213            my $relationName = $relationList[$i];
2214            my $relationDefinition = $relationTable->{$relationName};
2215            # Get the relation's fields. For each field we will collect a value in the corresponding
2216            # position of the @valueList array. If one of the fields is missing, we will add it to the
2217            # @missing list.
2218            my @fieldList = @{$relationDefinition->{Fields}};
2219            my @fieldNameList = ();
2220            my @valueList = ();
2221            my @missing = ();
2222            my $recordCount = 1;
2223            for my $fieldDescriptor (@fieldList) {
2224                # Get the field name and save it. Note we need to fix it up so the hyphens
2225                # are converted to underscores.
2226                my $fieldName = $fieldDescriptor->{name};
2227                push @fieldNameList, _FixName($fieldName);
2228                # Look for the named field in the incoming structure. Note that we are looking
2229                # for the real field name, not the fixed-up one!
2230                if (exists $fieldHash->{$fieldName}) {
2231                    # Here we found the field. Stash it in the value list.
2232                    my $value = $fieldHash->{$fieldName};
2233                    push @valueList, $value;
2234                    # If the value is a list, we may need to increment the record count.
2235                    if (ref $value eq "ARRAY") {
2236                        my $thisCount = @{$value};
2237                        if ($recordCount == 1) {
2238                            # Here we have our first list, so we save its count.
2239                            $recordCount = $thisCount;
2240                        } elsif ($recordCount != $thisCount) {
2241                            # Here we have a second list, so its length has to match the
2242                            # previous lists.
2243                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2244                            $retVal = 0;
2245                        }
2246                    }
2247                } else {
2248                    # Here the field is not present. Flag it as missing.
2249                    push @missing, $fieldName;
2250                }
2251            }
2252            # If we are the primary relation, add the new-record flag.
2253            if ($relationName eq $newObjectType) {
2254                push @valueList, 1;
2255                push @fieldNameList, "new_record";
2256            }
2257            # Only proceed if there are no missing fields.
2258            if (@missing > 0) {
2259                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2260                    join(' ', @missing)) if T(1);
2261                                  } else {                                  } else {
2262                                          # Get the field's relation.              # Build the INSERT statement.
2263                                          my $relationName = $fieldList->{$fieldName}->{relation};              my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2264                                          # Insure the relation is in the FROM clause.                  ") VALUES (";
2265                                          if (!exists $fromNames{$relationName}) {              # Create a marker list of the proper size and put it in the statement.
2266                                                  # Add the relation to the FROM clause.              my @markers = ();
2267                                                  $command .= ", $relationName";              while (@markers < @fieldNameList) { push @markers, '?'; }
2268                                                  # Create its join sub-clause.              $statement .= join(', ', @markers) . ")";
2269                                                  push @joinWhere, "$objectName.id = $relationName.id";              # We have the insert statement, so prepare it.
2270                                                  # Denote we have it available for future fields.              my $sth = $dbh->prepare_command($statement);
2271                                                  $fromNames{$relationName} = 1;              Trace("Insert statement prepared: $statement") if T(3);
2272                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2273                # a list, we use the current element. The values are stored in the @parameterList array.
2274                my $done = 0;
2275                for (my $i = 0; $i < $recordCount; $i++) {
2276                    # Clear the parameter list array.
2277                    my @parameterList = ();
2278                    # Loop through the values.
2279                    for my $value (@valueList) {
2280                        # Check to see if this is a scalar value.
2281                        if (ref $value eq "ARRAY") {
2282                            # Here we have a list value. Pull the current entry.
2283                            push @parameterList, $value->[$i];
2284                        } else {
2285                            # Here we have a scalar value. Use it unmodified.
2286                            push @parameterList, $value;
2287                                          }                                          }
                                         # Form an SQL field reference from the relation name and the field name.  
                                         my $sqlReference = "$relationName." . _FixName($fieldName);  
                                         # Put it into the filter string in place of the old value.  
                                         substr($filterString, $pos, $len) = $sqlReference;  
                                         # Reposition the search.  
                                         pos $filterString = $pos + length $sqlReference;  
2288                                  }                                  }
2289                    # Execute the INSERT statement with the specified parameter list.
2290                    $retVal = $sth->execute(@parameterList);
2291                    if (!$retVal) {
2292                        my $errorString = $sth->errstr();
2293                        Trace("Insert error: $errorString.") if T(0);
2294                          }                          }
2295                  }                  }
2296                  # The next step is to join the objects together. We only need to do this if there          }
2297                  # is more than one object in the object list. We start with the first object and      }
2298                  # run through the objects after it. Note also that we make a safety copy of the      # Return the success indicator.
2299                  # list before running through it.      return $retVal;
2300                  my @objectList = @{$objectNames};  }
2301                  my $lastObject = shift @objectList;  
2302                  # Get the join table.  =head3 LoadTable
2303                  my $joinTable = $self->{_metaData}->{Joins};  
2304                  # Loop through the object list.  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2305                  for my $thisObject (@objectList) {  
2306                          # Look for a join.  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2307                          my $joinKey = "$lastObject/$thisObject";  first.
2308                          if (!exists $joinTable->{$joinKey}) {  
2309                                  # Here there's no join, so we throw an error.  =over 4
2310                                  Confess("No join exists to connect from $lastObject to $thisObject.");  
2311    =item fileName
2312    
2313    Name of the file from which the table data should be loaded.
2314    
2315    =item relationName
2316    
2317    Name of the relation to be loaded. This is the same as the table name.
2318    
2319    =item truncateFlag
2320    
2321    TRUE if the table should be dropped and re-created, else FALSE
2322    
2323    =item RETURN
2324    
2325    Returns a statistical object containing a list of the error messages.
2326    
2327    =back
2328    
2329    =cut
2330    sub LoadTable {
2331        # Get the parameters.
2332        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2333        # Create the statistical return object.
2334        my $retVal = _GetLoadStats();
2335        # Trace the fact of the load.
2336        Trace("Loading table $relationName from $fileName") if T(2);
2337        # Get the database handle.
2338        my $dbh = $self->{_dbh};
2339        # Get the input file size.
2340        my $fileSize = -s $fileName;
2341        # Get the relation data.
2342        my $relation = $self->_FindRelation($relationName);
2343        # Check the truncation flag.
2344        if ($truncateFlag) {
2345            Trace("Creating table $relationName") if T(2);
2346            # Compute the row count estimate. We take the size of the load file,
2347            # divide it by the estimated row size, and then multiply by 1.5 to
2348            # leave extra room. We postulate a minimum row count of 1000 to
2349            # prevent problems with incoming empty load files.
2350            my $rowSize = $self->EstimateRowSize($relationName);
2351            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2352            # Re-create the table without its index.
2353            $self->CreateTable($relationName, 0, $estimate);
2354            # If this is a pre-index DBMS, create the index here.
2355            if ($dbh->{_preIndex}) {
2356                eval {
2357                    $self->CreateIndex($relationName);
2358                };
2359                if ($@) {
2360                    $retVal->AddMessage($@);
2361                }
2362            }
2363        }
2364        # Load the table.
2365        my $rv;
2366        eval {
2367            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2368        };
2369        if (!defined $rv) {
2370            $retVal->AddMessage($@) if ($@);
2371            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2372            Trace("Table load failed for $relationName.") if T(1);
2373                          } else {                          } else {
2374                                  # Get the join clause and add it to the WHERE list.          # Here we successfully loaded the table.
2375                                  push @joinWhere, $joinTable->{$joinKey};          $retVal->Add("tables");
2376                                  # Save this object as the last object for the next iteration.          my $size = -s $fileName;
2377                                  $lastObject = $thisObject;          Trace("$size bytes loaded into $relationName.") if T(2);
2378            # If we're rebuilding, we need to create the table indexes.
2379            if ($truncateFlag) {
2380                # Indexes are created here for PostGres. For PostGres, indexes are
2381                # best built at the end. For MySQL, the reverse is true.
2382                if (! $dbh->{_preIndex}) {
2383                    eval {
2384                        $self->CreateIndex($relationName);
2385                    };
2386                    if ($@) {
2387                        $retVal->AddMessage($@);
2388                          }                          }
2389                  }                  }
2390                  # Now we need to handle the whole ORDER BY thing. We'll put the order by clause              # The full-text index (if any) is always built last, even for MySQL.
2391                  # in the following variable.              # First we need to see if this table has a full-text index. Only
2392                  my $orderClause = "";              # primary relations are allowed that privilege.
2393                  # Locate the ORDER BY verb (if any).              if ($self->_IsPrimary($relationName)) {
2394                  if ($filterString =~ m/^(.*)ORDER BY/g) {                  # Get the relation's entity/relationship structure.
2395                          # Here we have an ORDER BY verb. Split it off of the filter string.                  my $structure = $self->_GetStructure($relationName);
2396                          my $pos = pos $filterString;                  # Check for a searchable fields list.
2397                          $orderClause = substr($filterString, $pos);                  if (exists $structure->{searchFields}) {
2398                          $filterString = $1;                      # Here we know that we need to create a full-text search index.
2399                        # Get an SQL-formatted field name list.
2400                        my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2401                        # Create the index.
2402                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2403                                           flds => $fields, kind => 'fulltext');
2404                  }                  }
                 # Add the filter and the join clauses (if any) to the SELECT command.  
                 if ($filterString) {  
                         push @joinWhere, "($filterString)";  
2405                  }                  }
                 if (@joinWhere) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
2406                  }                  }
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
2407                  }                  }
2408        # Analyze the table to improve performance.
2409        Trace("Analyzing and compacting $relationName.") if T(3);
2410        $dbh->vacuum_it($relationName);
2411        Trace("$relationName load completed.") if T(3);
2412        # Return the statistics.
2413        return $retVal;
2414    }
2415    
2416    =head3 DropRelation
2417    
2418    C<< $erdb->DropRelation($relationName); >>
2419    
2420    Physically drop a relation from the database.
2421    
2422    =over 4
2423    
2424    =item relationName
2425    
2426    Name of the relation to drop. If it does not exist, this method will have
2427    no effect.
2428    
2429    =back
2430    
2431    =cut
2432    
2433    sub DropRelation {
2434        # Get the parameters.
2435        my ($self, $relationName) = @_;
2436        # Get the database handle.
2437        my $dbh = $self->{_dbh};
2438        # Drop the relation. The method used here has no effect if the relation
2439        # does not exist.
2440        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2441        $dbh->drop_table(tbl => $relationName);
2442    }
2443    
2444    =head3 GetEntity
2445    
2446    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2447    
2448    Return an object describing the entity instance with a specified ID.
2449    
2450    =over 4
2451    
2452    =item entityType
2453    
2454    Entity type name.
2455    
2456    =item ID
2457    
2458    ID of the desired entity.
2459    
2460    =item RETURN
2461    
2462    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2463    instance is found with the specified key.
2464    
2465    =back
2466    
2467    =cut
2468    
2469    sub GetEntity {
2470        # Get the parameters.
2471        my ($self, $entityType, $ID) = @_;
2472        # Create a query.
2473        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2474        # Get the first (and only) object.
2475        my $retVal = $query->Fetch();
2476        # Return the result.
2477        return $retVal;
2478    }
2479    
2480    =head3 GetChoices
2481    
2482    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2483    
2484    Return a list of all the values for the specified field that are represented in the
2485    specified entity.
2486    
2487    Note that if the field is not indexed, then this will be a very slow operation.
2488    
2489    =over 4
2490    
2491    =item entityName
2492    
2493    Name of an entity in the database.
2494    
2495    =item fieldName
2496    
2497    Name of a field belonging to the entity. This is a raw field name without
2498    the standard parenthesized notation used in most calls.
2499    
2500    =item RETURN
2501    
2502    Returns a list of the distinct values for the specified field in the database.
2503    
2504    =back
2505    
2506    =cut
2507    
2508    sub GetChoices {
2509        # Get the parameters.
2510        my ($self, $entityName, $fieldName) = @_;
2511        # Declare the return variable.
2512        my @retVal;
2513        # Get the entity data structure.
2514        my $entityData = $self->_GetStructure($entityName);
2515        # Get the field.
2516        my $fieldHash = $entityData->{Fields};
2517        if (! exists $fieldHash->{$fieldName}) {
2518            Confess("$fieldName not found in $entityName.");
2519        } else {
2520            # Get the name of the relation containing the field.
2521            my $relation = $fieldHash->{$fieldName}->{relation};
2522            # Fix up the field name.
2523            my $realName = _FixName($fieldName);
2524            # Get the database handle.
2525            my $dbh = $self->{_dbh};
2526            # Query the database.
2527            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2528            # Clean the results. They are stored as a list of lists, and we just want the one list.
2529            @retVal = sort map { $_->[0] } @{$results};
2530        }
2531        # Return the result.
2532        return @retVal;
2533    }
2534    
2535    =head3 GetEntityValues
2536    
2537    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2538    
2539    Return a list of values from a specified entity instance. If the entity instance
2540    does not exist, an empty list is returned.
2541    
2542    =over 4
2543    
2544    =item entityType
2545    
2546    Entity type name.
2547    
2548    =item ID
2549    
2550    ID of the desired entity.
2551    
2552    =item fields
2553    
2554    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2555    
2556    =item RETURN
2557    
2558    Returns a flattened list of the values of the specified fields for the specified entity.
2559    
2560    =back
2561    
2562    =cut
2563    
2564    sub GetEntityValues {
2565        # Get the parameters.
2566        my ($self, $entityType, $ID, $fields) = @_;
2567        # Get the specified entity.
2568        my $entity = $self->GetEntity($entityType, $ID);
2569        # Declare the return list.
2570        my @retVal = ();
2571        # If we found the entity, push the values into the return list.
2572        if ($entity) {
2573            push @retVal, $entity->Values($fields);
2574        }
2575        # Return the result.
2576        return @retVal;
2577    }
2578    
2579    =head3 GetAll
2580    
2581    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2582    
2583    Return a list of values taken from the objects returned by a query. The first three
2584    parameters correspond to the parameters of the L</Get> method. The final parameter is
2585    a list of the fields desired from each record found by the query. The field name
2586    syntax is the standard syntax used for fields in the B<ERDB> system--
2587    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2588    or relationship and I<fieldName> is the name of the field.
2589    
2590    The list returned will be a list of lists. Each element of the list will contain
2591    the values returned for the fields specified in the fourth parameter. If one of the
2592    fields specified returns multiple values, they are flattened in with the rest. For
2593    example, the following call will return a list of the features in a particular
2594    spreadsheet cell, and each feature will be represented by a list containing the
2595    feature ID followed by all of its aliases.
2596    
2597    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2598    
2599    =over 4
2600    
2601    =item objectNames
2602    
2603    List containing the names of the entity and relationship objects to be retrieved.
2604    
2605    =item filterClause
2606    
2607    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2608    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2609    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2610    parameter list as additional parameters. The fields in a filter clause can come from primary
2611    entity relations, relationship relations, or secondary entity relations; however, all of the
2612    entities and relationships involved must be included in the list of object names.
2613    
2614    =item parameterList
2615    
2616    List of the parameters to be substituted in for the parameters marks in the filter clause.
2617    
2618    =item fields
2619    
2620    List of the fields to be returned in each element of the list returned.
2621    
2622    =item count
2623    
2624    Maximum number of records to return. If omitted or 0, all available records will be returned.
2625    
2626    =item RETURN
2627    
2628    Returns a list of list references. Each element of the return list contains the values for the
2629    fields specified in the B<fields> parameter.
2630    
2631    =back
2632    
2633    =cut
2634    #: Return Type @@;
2635    sub GetAll {
2636        # Get the parameters.
2637        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2638        # Translate the parameters from a list reference to a list. If the parameter
2639        # list is a scalar we convert it into a singleton list.
2640        my @parmList = ();
2641        if (ref $parameterList eq "ARRAY") {
2642            Trace("GetAll parm list is an array.") if T(4);
2643            @parmList = @{$parameterList};
2644        } else {
2645            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2646            push @parmList, $parameterList;
2647        }
2648        # Insure the counter has a value.
2649        if (!defined $count) {
2650            $count = 0;
2651        }
2652        # Add the row limit to the filter clause.
2653        if ($count > 0) {
2654            $filterClause .= " LIMIT $count";
2655        }
2656        # Create the query.
2657        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2658        # Set up a counter of the number of records read.
2659        my $fetched = 0;
2660        # Loop through the records returned, extracting the fields. Note that if the
2661        # counter is non-zero, we stop when the number of records read hits the count.
2662        my @retVal = ();
2663        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2664            my @rowData = $row->Values($fields);
2665            push @retVal, \@rowData;
2666            $fetched++;
2667        }
2668        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2669        # Return the resulting list.
2670        return @retVal;
2671          }          }
2672          Trace("SQL query: $command") if T(2);  
2673          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));  =head3 Exists
2674          my $sth = $dbh->prepare_command($command);  
2675          # Execute it with the parameters bound in.  C<< my $found = $sprout->Exists($entityName, $entityID); >>
2676          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
2677          # Return the statement object.  Return TRUE if an entity exists, else FALSE.
2678          my $retVal = DBQuery::_new($self, $sth, @{$objectNames});  
2679    =over 4
2680    
2681    =item entityName
2682    
2683    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2684    
2685    =item entityID
2686    
2687    ID of the entity instance whose existence is to be checked.
2688    
2689    =item RETURN
2690    
2691    Returns TRUE if the entity instance exists, else FALSE.
2692    
2693    =back
2694    
2695    =cut
2696    #: Return Type $;
2697    sub Exists {
2698        # Get the parameters.
2699        my ($self, $entityName, $entityID) = @_;
2700        # Check for the entity instance.
2701        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2702        my $testInstance = $self->GetEntity($entityName, $entityID);
2703        # Return an existence indicator.
2704        my $retVal = ($testInstance ? 1 : 0);
2705          return $retVal;          return $retVal;
2706  }  }
2707    
2708  =head3 ComputeObjectSentence  =head3 EstimateRowSize
2709    
2710  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2711    
2712  Check an object name, and if it is a relationship convert it to a relationship sentence.  Estimate the row size of the specified relation. The estimated row size is computed by adding
2713    up the average length for each data type.
2714    
2715  =over 4  =over 4
2716    
2717  =item objectName  =item relName
2718    
2719  Name of the entity or relationship.  Name of the relation whose estimated row size is desired.
2720    
2721  =item RETURN  =item RETURN
2722    
2723  Returns a string containing the entity name or a relationship sentence.  Returns an estimate of the row size for the specified relation.
2724    
2725  =back  =back
2726    
2727  =cut  =cut
2728    #: Return Type $;
2729  sub ComputeObjectSentence {  sub EstimateRowSize {
2730          # Get the parameters.          # Get the parameters.
2731          my ($self, $objectName) = @_;      my ($self, $relName) = @_;
2732          # Set the default return value.      # Declare the return variable.
2733          my $retVal = $objectName;      my $retVal = 0;
2734          # Look for the object as a relationship.      # Find the relation descriptor.
2735          my $relTable = $self->{_metaData}->{Relationships};      my $relation = $self->_FindRelation($relName);
2736          if (exists $relTable->{$objectName}) {      # Get the list of fields.
2737                  # Get the relationship sentence.      for my $fieldData (@{$relation->{Fields}}) {
2738                  $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          # Get the field type and add its length.
2739            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2740            $retVal += $fieldLen;
2741          }          }
2742          # Return the result.          # Return the result.
2743          return $retVal;          return $retVal;
2744  }  }
2745    
2746  =head3 DumpRelations  =head3 GetFieldTable
2747    
2748  C<< $database->DumpRelations($outputDirectory); >>  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2749    
2750  Write the contents of all the relations to tab-delimited files in the specified directory.  Get the field structure for a specified entity or relationship.
 Each file will have the same name as the relation dumped, with an extension of DTX.  
2751    
2752  =over 4  =over 4
2753    
2754  =item outputDirectory  =item objectName
2755    
2756  Name of the directory into which the relation files should be dumped.  Name of the desired entity or relationship.
2757    
2758    =item RETURN
2759    
2760    The table containing the field descriptors for the specified object.
2761    
2762  =back  =back
2763    
2764  =cut  =cut
2765    
2766  sub DumpRelations {  sub GetFieldTable {
2767          # Get the parameters.          # Get the parameters.
2768          my ($self, $outputDirectory) = @_;      my ($self, $objectName) = @_;
2769          # Now we need to run through all the relations. First, we loop through the entities.      # Get the descriptor from the metadata.
2770          my $metaData = $self->{_metaData};      my $objectData = $self->_GetStructure($objectName);
2771          my $entities = $metaData->{Entities};      # Return the object's field table.
2772          while (my ($entityName, $entityStructure) = each %{$entities}) {      return $objectData->{Fields};
                 # Get the entity's relations.  
                 my $relationList = $entityStructure->{Relations};  
                 # Loop through the relations, dumping them.  
                 while (my ($relationName, $relation) = each %{$relationList}) {  
                         $self->_DumpRelation($outputDirectory, $relationName, $relation);  
                 }  
         }  
         # Next, we loop through the relationships.  
         my $relationships = $metaData->{Relationships};  
         while (my ($relationshipName, $relationshipStructure) = each %{$relationships}) {  
                 # Dump this relationship's relation.  
                 $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});  
         }  
2773  }  }
2774    
2775  =head3 InsertObject  =head3 SplitKeywords
2776    
2777  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2778    
2779  Insert an object into the database. The object is defined by a type name and then a hash  This method returns a list of the positive keywords in the specified
2780  of field names to values. Field values in the primary relation are represented by scalars.  keyword string. All of the operators will have been stripped off,
2781  (Note that for relationships, the primary relation is the B<only> relation.)  and if the keyword is preceded by a minus operator (C<->), it will
2782  Field values for the other relations comprising the entity are always list references. For  not be in the list returned. The idea here is to get a list of the
2783  example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases  keywords the user wants to see. The list will be processed to remove
2784  C<ZP_00210270.1> and C<gi|46206278>.  duplicates.
2785    
2786  C<< $database->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>  It is possible to create a string that confuses this method. For example
2787    
2788  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and      frog toad -frog
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
2789    
2790  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  would return both C<frog> and C<toad>. If this is a problem we can deal
2791    with it later.
2792    
2793  =over 4  =over 4
2794    
2795  =item newObjectType  =item keywordString
2796    
2797  Type name of the object to insert.  The keyword string to be parsed.
2798    
2799  =item fieldHash  =item RETURN
2800    
2801  Hash of field names to values.  Returns a list of the words in the keyword string the user wants to
2802    see.
2803    
2804    =back
2805    
2806    =cut
2807    
2808    sub SplitKeywords {
2809        # Get the parameters.
2810        my ($keywordString) = @_;
2811        # Make a safety copy of the string. (This helps during debugging.)
2812        my $workString = $keywordString;
2813        # Convert operators we don't care about to spaces.
2814        $workString =~ tr/+"()<>/ /;
2815        # Split the rest of the string along space boundaries. Note that we
2816        # eliminate any words that are zero length or begin with a minus sign.
2817        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2818        # Use a hash to remove duplicates.
2819        my %words = map { $_ => 1 } @wordList;
2820        # Return the result.
2821        return sort keys %words;
2822    }
2823    
2824    =head3 ValidateFieldName
2825    
2826    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2827    
2828    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2829    be hyphenated words subject to certain restrictions.
2830    
2831    =over 4
2832    
2833    =item fieldName
2834    
2835    Field name to be validated.
2836    
2837  =item RETURN  =item RETURN
2838    
2839  Returns 1 if successful, 0 if an error occurred.  Returns TRUE if the field name is valid, else FALSE.
2840    
2841  =back  =back
2842    
2843  =cut  =cut
2844    
2845  sub InsertObject {  sub ValidateFieldName {
2846          # Get the parameters.          # Get the parameters.
2847          my ($self, $newObjectType, $fieldHash) = @_;      my ($fieldName) = @_;
2848          # Denote that so far we appear successful.      # Declare the return variable. The field name is valid until we hear
2849        # differently.
2850          my $retVal = 1;          my $retVal = 1;
2851          # Get the database handle.      # Look for bad stuff in the name.
2852          my $dbh = $self->{_dbh};      if ($fieldName =~ /--/) {
2853          # Get the relation list.          # Here we have a doubled minus sign.
2854          my $relationTable = $self->_GetRelationTable($newObjectType);          Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2855          # Loop through the relations. We'll build insert statements for each one. If a relation is          $retVal = 0;
2856          # secondary, we may end up generating multiple insert statements. If an error occurs, we      } elsif ($fieldName !~ /^[A-Za-z]/) {
2857          # stop the loop.          # Here the field name is missing the initial letter.
2858          while ($retVal && (my ($relationName, $relationDefinition) = each %{$relationTable})) {          Trace("Field name $fieldName does not begin with a letter.") if T(1);
                 # Get the relation's fields. For each field we will collect a value in the corresponding  
                 # position of the @valueList array. If one of the fields is missing, we will add it to the  
                 # @missing list.  
                 my @fieldList = @{$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);  
2859                                                  $retVal = 0;                                                  $retVal = 0;
                                         }  
                                 }  
2860                          } else {                          } else {
2861                                  # Here the field is not present. Flag it as missing.          # Strip out the minus signs. Everything remaining must be a letter,
2862                                  push @missing, $fieldName;          # underscore, or digit.
2863                          }          my $strippedName = $fieldName;
2864                  }          $strippedName =~ s/-//g;
2865                  # If we are the primary relation, add the new-record flag.          if ($strippedName !~ /^(\w|\d)+$/) {
2866                  if ($relationName eq $newObjectType) {              Trace("Field name $fieldName contains illegal characters.") if T(1);
2867                          push @valueList, 1;              $retVal = 0;
                         push @fieldNameList, "new_record";  
2868                  }                  }
                 # 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;  
2869                                          }                                          }
2870        # Return the result.
2871        return $retVal;
2872                                  }                                  }
2873                                  # Execute the INSERT statement with the specified parameter list.  
2874                                  $retVal = $sth->execute(@parameterList);  =head3 ReadMetaXML
2875                                  if (!$retVal) {  
2876                                          my $errorString = $sth->errstr();  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2877                                          Trace("Insert error: $errorString.") if T(0);  
2878    This method reads a raw database definition XML file and returns it.
2879    Normally, the metadata used by the ERDB system has been processed and
2880    modified to make it easier to load and retrieve the data; however,
2881    this method can be used to get the data in its raw form.
2882    
2883    =over 4
2884    
2885    =item fileName
2886    
2887    Name of the XML file to read.
2888    
2889    =item RETURN
2890    
2891    Returns a hash reference containing the raw XML data from the specified file.
2892    
2893    =back
2894    
2895    =cut
2896    
2897    sub ReadMetaXML {
2898        # Get the parameters.
2899        my ($fileName) = @_;
2900        # Read the XML.
2901        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2902        Trace("XML metadata loaded from file $fileName.") if T(1);
2903        # Return the result.
2904        return $retVal;
2905                                  }                                  }
2906    
2907    =head3 GetEntityFieldHash
2908    
2909    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2910    
2911    Get the field hash of the named entity in the specified raw XML structure.
2912    The field hash may not exist, in which case we need to create it.
2913    
2914    =over 4
2915    
2916    =item structure
2917    
2918    Raw XML structure defininng the database. This is not the run-time XML used by
2919    an ERDB object, since that has all sorts of optimizations built-in.
2920    
2921    =item entityName
2922    
2923    Name of the entity whose field structure is desired.
2924    
2925    =item RETURN
2926    
2927    Returns the field hash used to define the entity's fields.
2928    
2929    =back
2930    
2931    =cut
2932    
2933    sub GetEntityFieldHash {
2934        # Get the parameters.
2935        my ($structure, $entityName) = @_;
2936        # Get the entity structure.
2937        my $entityData = $structure->{Entities}->{$entityName};
2938        # Look for a field structure.
2939        my $retVal = $entityData->{Fields};
2940        # If it doesn't exist, create it.
2941        if (! defined($retVal)) {
2942            $entityData->{Fields} = {};
2943            $retVal = $entityData->{Fields};
2944                          }                          }
2945        # Return the result.
2946        return $retVal;
2947                  }                  }
2948    
2949    =head3 WriteMetaXML
2950    
2951    C<< ERDB::WriteMetaXML($structure, $fileName); >>
2952    
2953    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2954    used to update the database definition. It must be used with care, however, since it
2955    will only work on a raw structure, not on the processed structure created by an ERDB
2956    constructor.
2957    
2958    =over 4
2959    
2960    =item structure
2961    
2962    XML structure to be written to the file.
2963    
2964    =item fileName
2965    
2966    Name of the output file to which the updated XML should be stored.
2967    
2968    =back
2969    
2970    =cut
2971    
2972    sub WriteMetaXML {
2973        # Get the parameters.
2974        my ($structure, $fileName) = @_;
2975        # Compute the output.
2976        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2977        # Write it to the file.
2978        my $xmlOut = Open(undef, ">$fileName");
2979        print $xmlOut $fileString;
2980          }          }
2981          # Return the success indicator.  
2982    
2983    =head3 HTMLNote
2984    
2985    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2986    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
2987    Except for C<[p]>, all the codes are closed by slash-codes. So, for
2988    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
2989    
2990    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
2991    
2992    =over 4
2993    
2994    =item dataString
2995    
2996    String to convert to HTML.
2997    
2998    =item RETURN
2999    
3000    An HTML string derived from the input string.
3001    
3002    =back
3003    
3004    =cut
3005    
3006    sub HTMLNote {
3007        # Get the parameter.
3008        my ($dataString) = @_;
3009        # HTML-escape the text.
3010        my $retVal = CGI::escapeHTML($dataString);
3011        # Substitute the bulletin board codes.
3012        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3013        $retVal =~ s!\[p\]!</p><p>!g;
3014        # Return the result.
3015          return $retVal;          return $retVal;
3016  }  }
3017    
 =head3 LoadTable  
3018    
3019  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  =head2 Data Mining Methods
3020    
3021    =head3 GetUsefulCrossValues
3022    
3023  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3024    
3025    Return a list of the useful attributes that would be returned by a B<Cross> call
3026    from an entity of the source entity type through the specified relationship. This
3027    means it will return the fields of the target entity type and the intersection data
3028    fields in the relationship. Only primary table fields are returned. In other words,
3029    the field names returned will be for fields where there is always one and only one
3030    value.
3031    
3032  =over 4  =over 4
3033    
3034  =item fileName  =item sourceEntity
3035    
3036  Name of the file from which the table data should be loaded.  Name of the entity from which the relationship crossing will start.
3037    
3038  =item relationName  =item relationship
3039    
3040  Name of the relation to be loaded. This is the same as the table name.  Name of the relationship being crossed.
3041    
3042  =item truncateFlag  =item RETURN
3043    
3044  TRUE if the table should be dropped and re-created, else FALSE  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3045    
3046    =back
3047    
3048    =cut
3049    #: Return Type @;
3050    sub GetUsefulCrossValues {
3051        # Get the parameters.
3052        my ($self, $sourceEntity, $relationship) = @_;
3053        # Declare the return variable.
3054        my @retVal = ();
3055        # Determine the target entity for the relationship. This is whichever entity is not
3056        # the source entity. So, if the source entity is the FROM, we'll get the name of
3057        # the TO, and vice versa.
3058        my $relStructure = $self->_GetStructure($relationship);
3059        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3060        my $targetEntity = $relStructure->{$targetEntityType};
3061        # Get the field table for the entity.
3062        my $entityFields = $self->GetFieldTable($targetEntity);
3063        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3064        # For the entity fields, the key aspect of the target structure is that the {relation} value
3065        # must match the entity name.
3066        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3067                            keys %{$entityFields};
3068        # Push the fields found onto the return variable.
3069        push @retVal, sort @fieldList;
3070        # Get the field table for the relationship.
3071        my $relationshipFields = $self->GetFieldTable($relationship);
3072        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3073        # This may end up being an empty set.
3074        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3075                            keys %{$relationshipFields};
3076        # Push these onto the return list.
3077        push @retVal, sort @fieldList2;
3078        # Return the result.
3079        return @retVal;
3080    }
3081    
3082    =head3 FindColumn
3083    
3084    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3085    
3086    Return the location a desired column in a data mining header line. The data
3087    mining header line is a tab-separated list of column names. The column
3088    identifier is either the numerical index of a column or the actual column
3089    name.
3090    
3091    =over 4
3092    
3093    =item headerLine
3094    
3095    The header line from a data mining command, which consists of a tab-separated
3096    list of column names.
3097    
3098    =item columnIdentifier
3099    
3100    Either the ordinal number of the desired column (1-based), or the name of the
3101    desired column.
3102    
3103  =item RETURN  =item RETURN
3104    
3105  Returns a statistical object containing the number of records read and a list of the error messages.  Returns the array index (0-based) of the desired column.
3106    
3107  =back  =back
3108    
3109  =cut  =cut
3110  sub LoadTable {  
3111    sub FindColumn {
3112          # Get the parameters.          # Get the parameters.
3113          my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($headerLine, $columnIdentifier) = @_;
3114          # Create the statistical return object.      # Declare the return variable.
3115          my $retVal = _GetLoadStats();      my $retVal;
3116          # Trace the fact of the load.      # Split the header line into column names.
3117          Trace("Loading table $relationName from $fileName") if T(1);      my @headers = ParseColumns($headerLine);
3118          # Get the database handle.      # Determine whether we have a number or a name.
3119          my $dbh = $self->{_dbh};      if ($columnIdentifier =~ /^\d+$/) {
3120          # Get the relation data.          # Here we have a number. Subtract 1 and validate the result.
3121          my $relation = $self->_FindRelation($relationName);          $retVal = $columnIdentifier - 1;
3122          # Check the truncation flag.          if ($retVal < 0 || $retVal > $#headers) {
3123          if ($truncateFlag) {              Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
                 Trace("Creating table $relationName") if T(1);  
                 # Re-create the table without its index.  
                 $self->CreateTable($relationName, 0);  
3124          }          }
         # Determine whether or not this is a primary relation. Primary relations have an extra  
         # field indicating whether or not a given object is new or was loaded from the flat files.  
         my $primary = $self->_IsPrimary($relationName);  
         # Get the number of fields in this relation.  
         my @fieldList = @{$relation->{Fields}};  
         my $fieldCount = @fieldList;  
         # Record the number of expected fields.  
         my $expectedFields = $fieldCount + ($primary ? 1 : 0);  
         # Start a database transaction.  
         $dbh->begin_tran;  
         # Open the relation file. We need to create a cleaned-up copy before loading.  
         open TABLEIN, '<', $fileName;  
         my $tempName = "$fileName.tbl";  
         open TABLEOUT, '>', $tempName;  
         # Loop through the file.  
         while (<TABLEIN>) {  
                 # Chop off the new-line character.  
                 my $record = $_;  
                 chomp $record;  
         # Only proceed if the record is non-blank.  
         if ($record) {  
             # Escape all the backslashes found in the line.  
             $record =~ s/\\/\\\\/g;  
             # Eliminate any trailing tabs.  
             chop $record while substr($record, -1) eq "\t";  
             # If this is a primary relation, add a 0 for the new-record flag (indicating that  
             # this record is not new, but part of the original load).  
             if ($primary) {  
                 $record .= "\t0";  
             }  
             # Write the record.  
             print TABLEOUT "$record\n";  
             # Count the record read.  
             my $count = $retVal->Add('records');  
             my $len = length $record;  
             Trace("Record $count written with $len characters.") if T(4);  
         }  
         }  
         # Close the files.  
         close TABLEIN;  
         close TABLEOUT;  
     Trace("Temporary file $tempName created.") if T(4);  
     # Load the table.  
         my $rv;  
         eval {  
                 $rv = $dbh->load_table(file => $tempName, tbl => $relationName);  
         };  
         if (!defined $rv) {  
         $retVal->AddMessage($@) if ($@);  
         $retVal->AddMessage("Table load failed for $relationName using $tempName.");  
                 Trace("Table load failed for $relationName.") if T(1);  
3125          } else {          } else {
3126                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we have a name. We need to find it in the list.
3127                  Trace("$retVal->{records} records read for $relationName.") if T(1);          for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3128                  # If we're rebuilding, we need to create the table indexes.              if ($headers[$i] eq $columnIdentifier) {
3129                  if ($truncateFlag) {                  $retVal = $i;
                         eval {  
                                 $self->CreateIndex($relationName);  
                         };  
                         if ($@) {  
                                 $retVal->AddMessage($@);  
3130                          }                          }
3131                  }                  }
3132            if (! defined($retVal)) {
3133                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3134          }          }
3135          # Commit the database changes.      }
3136          $dbh->commit_tran;      # Return the result.
         # Delete the temporary file.  
         unlink $tempName;  
         # Return the statistics.  
3137          return $retVal;          return $retVal;
3138  }  }
3139    
3140  =head3 GenerateEntity  =head3 ParseColumns
3141    
3142  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3143    
3144  Generate the data for a new entity instance. This method creates a field hash suitable for  Convert the specified data line to a list of columns.
 passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest  
 of the fields are generated using information in the database schema.  
   
 Each data type has a default algorithm for generating random test data. This can be overridden  
 by including a B<DataGen> element in the field. If this happens, the content of the element is  
 executed as a PERL program in the context of this module. The element may make use of a C<$this>  
 variable which contains the field hash as it has been built up to the current point. If any  
 fields are dependent on other fields, the C<pass> attribute can be used to control the order  
 in which the fields are generated. A field with a high data pass number will be generated after  
 a field with a lower one. If any external values are needed, they should be passed in via the  
 optional third parameter, which will be available to the data generation script under the name  
 C<$value>. Several useful utility methods are provided for generating random values, including  
 L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated  
 in the form of a timestamp number rather than a string.  
3145    
3146  =over 4  =over 4
3147    
3148  =item id  =item line
   
 ID to assign to the new entity.  
   
 =item type  
3149    
3150  Type name for the new entity.  A data mining input, consisting of a tab-separated list of columns terminated by a
3151    new-line.
3152    
3153  =item values  =item RETURN
3154    
3155  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a list consisting of the column values.
3156    
3157  =back  =back
3158    
3159  =cut  =cut
3160    
3161  sub GenerateEntity {  sub ParseColumns {
3162          # Get the parameters.          # Get the parameters.
3163          my ($self, $id, $type, $values) = @_;      my ($line) = @_;
3164          # Create the return hash.      # Chop off the line-end.
3165          my $this = { id => $id };      chomp $line;
3166          # Get the metadata structure.      # Split it into a list.
3167          my $metadata = $self->{_metaData};      my @retVal = split(/\t/, $line);
3168          # Get this entity's list of fields.      # Return the result.
3169          if (!exists $metadata->{Entities}->{$type}) {      return @retVal;
                 Confess("Unrecognized entity type $type in GenerateEntity.");  
         } else {  
                 my $entity = $metadata->{Entities}->{$type};  
                 my $fields = $entity->{Fields};  
                 # Generate data from the fields.  
                 _GenerateFields($this, $fields, $type, $values);  
         }  
         # Return the hash created.  
         return $this;  
3170  }  }
3171    
3172    =head2 Virtual Methods
3173    
3174  =head2 Internal Utility Methods  =head3 CleanKeywords
3175    
3176  =head3 GetLoadStats  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3177    
3178  Return a blank statistics object for use by the load methods.  Clean up a search expression or keyword list. This is a virtual method that may
3179    be overridden by the subclass. The base-class method removes extra spaces
3180    and converts everything to lower case.
3181    
3182  This is a static method.  =over 4
3183    
3184    =item searchExpression
3185    
3186    Search expression or keyword list to clean. Note that a search expression may
3187    contain boolean operators which need to be preserved. This includes leading
3188    minus signs.
3189    
3190    =item RETURN
3191    
3192    Cleaned expression or keyword list.
3193    
3194    =back
3195    
3196  =cut  =cut
3197    
3198  sub _GetLoadStats {  sub CleanKeywords {
3199          return Stats->new('records');      # Get the parameters.
3200        my ($self, $searchExpression) = @_;
3201        # Lower-case the expression and copy it into the return variable. Note that we insure we
3202        # don't accidentally end up with an undefined value.
3203        my $retVal = lc($searchExpression || "");
3204        # Remove extra spaces.
3205        $retVal =~ s/\s+/ /g;
3206        $retVal =~ s/(^\s+)|(\s+$)//g;
3207        # Return the result.
3208        return $retVal;
3209  }  }
3210    
3211  =head3 GenerateFields  =head3 GetSourceObject
3212    
3213  Generate field values from a field structure and store in a specified table. The field names  C<< my $source = $erdb->GetSourceObject($entityName); >>
 are first sorted by pass count, certain pre-defined fields are removed from the list, and  
 then we rip through them evaluation the data generation string. Fields in the primary relation  
 are stored as scalars; fields in secondary relations are stored as value lists.  
3214    
3215  This is a static method.  Return the object to be used in loading special attributes of the specified entity. The
3216    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3217    XML
3218    
3219    =head2 Internal Utility Methods
3220    
3221    =head3 _RelationMap
3222    
3223    C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3224    
3225    Create the relation map for an SQL query. The relation map is used by B<DBObject>
3226    to determine how to interpret the results of the query.
3227    
3228  =over 4  =over 4
3229    
3230  =item this  =item mappedNameHashRef
3231    
3232  Hash table into which the field values should be placed.  Reference to a hash that maps modified object names to real object names.
3233    
3234  =item fields  =item mappedNameListRef
3235    
3236  Field structure from which the field descriptors should be taken.  Reference to a list of modified object names in the order they appear in the
3237    SELECT list.
3238    
3239  =item type  =item RETURN
3240    
3241    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3242    query followed by the actual name of that object. This enables the B<DBObject> to
3243    determine the order of the tables in the query and which object name belongs to each
3244    mapped object name. Most of the time these two values are the same; however, if a
3245    relation occurs twice in the query, the relation name in the field list and WHERE
3246    clause will use a mapped name (generally the actual relation name with a numeric
3247    suffix) that does not match the actual relation name.
3248    
3249    =back
3250    
3251    =cut
3252    
3253    sub _RelationMap {
3254        # Get the parameters.
3255        my ($mappedNameHashRef, $mappedNameListRef) = @_;
3256        # Declare the return variable.
3257        my @retVal = ();
3258        # Build the map.
3259        for my $mappedName (@{$mappedNameListRef}) {
3260            push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3261        }
3262        # Return it.
3263        return @retVal;
3264    }
3265    
3266    
3267    =head3 _SetupSQL
3268