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revision 1.5, Tue Apr 5 05:17:01 2005 UTC revision 1.76, Wed Nov 15 12:08:26 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, $fieldValue); >>
1084    
1085    Delete secondary field values from the database. This method can be used to delete all
1086    values of a specified field for a particular entity instance, or only a single value.
1087    
1088    Secondary fields are stored in two-column relations separate from an entity's primary
1089    table, and as a result a secondary field can legitimately have no value or multiple
1090    values. Therefore, it makes sense to talk about deleting secondary fields where it
1091    would not make sense for primary fields.
1092    
1093    =over 4
1094    
1095    =item entityName
1096    
1097    Name of the entity from which the fields are to be deleted.
1098    
1099    =item id
1100    
1101    ID of the entity instance to be processed. If the instance is not found, this
1102    method will have no effect. If C<undef> is specified, all values for all of
1103    the entity instances will be deleted.
1104    
1105    =item fieldName
1106    
1107    Name of the field whose values are to be deleted.
1108    
1109    =item fieldValue (optional)
1110    
1111    Value to be deleted. If not specified, then all values of the specified field
1112    will be deleted for the entity instance. If specified, then only the values which
1113    match this parameter will be deleted.
1114    
1115    =item RETURN
1116    
1117    Returns the number of rows deleted.
1118    
1119    =back
1120    
1121    =cut
1122    
1123    sub DeleteValue {
1124        # Get the parameters.
1125        my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1126        # Declare the return value.
1127        my $retVal = 0;
1128        # We need to set up an SQL command to do the deletion. First, we
1129        # find the name of the field's relation.
1130        my $table = $self->GetFieldTable($entityName);
1131        my $field = $table->{$fieldName};
1132        my $relation = $field->{relation};
1133        # Make sure this is a secondary field.
1134        if ($relation eq $entityName) {
1135            Confess("Cannot delete values of $fieldName for $entityName.");
1136        } else {
1137            # Set up the SQL command to delete all values.
1138            my $sql = "DELETE FROM $relation";
1139            # Build the filter.
1140            my @filters = ();
1141            my @parms = ();
1142            # Check for a filter by ID.
1143            if (defined $id) {
1144                push @filters, "id = ?";
1145                push @parms, $id;
1146            }
1147            # Check for a filter by value.
1148            if (defined $fieldValue) {
1149                push @filters, "$fieldName = ?";
1150                push @parms, $fieldValue;
1151            }
1152            # Append the filters to the command.
1153            if (@filters) {
1154                $sql .= " WHERE " . join(" AND ", @filters);
1155            }
1156            # Execute the command.
1157            my $dbh = $self->{_dbh};
1158            $retVal = $dbh->SQL($sql, 0, @parms);
1159        }
1160        # Return the result.
1161        return $retVal;
1162    }
1163    
1164    =head3 LoadTables
1165    
1166    C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1167    
1168    This method will load the database tables from a directory. The tables must already have been created
1169    in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1170    all of the relations to be loaded must have a file in the directory with the same name as the relation
1171    (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1172    line of the file will be loaded as a row of the target relation table. The field values should be in
1173    the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1174    erased before the new data is loaded in.
1175    
1176    A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1177    tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1178    be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1179    
1180    =over 4
1181    
1182    =item directoryName
1183    
1184    Name of the directory containing the relation files to be loaded.
1185    
1186    =item rebuild
1187    
1188    TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1189    only way to erase existing data in the tables, since the TRUNCATE command is not supported
1190    by all of the DB engines we use.
1191    
1192    =item RETURN
1193    
1194    Returns a statistical object describing the number of records read and a list of the error messages.
1195    
1196    =back
1197    
1198    =cut
1199    
1200    sub LoadTables {
1201        # Get the parameters.
1202        my ($self, $directoryName, $rebuild) = @_;
1203        # Start the timer.
1204        my $startTime = gettimeofday;
1205        # Clean any trailing slash from the directory name.
1206        $directoryName =~ s!/\\$!!;
1207        # Declare the return variable.
1208        my $retVal = Stats->new();
1209        # Get the relation names.
1210        my @relNames = $self->GetTableNames();
1211        for my $relationName (@relNames) {
1212            # Try to load this relation.
1213            my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1214            # Accumulate the statistics.
1215            $retVal->Accumulate($result);
1216        }
1217        # Add the duration of the load to the statistical object.
1218        $retVal->Add('duration', gettimeofday - $startTime);
1219        # Return the accumulated statistics.
1220        return $retVal;
1221    }
1222    
1223    
1224    =head3 GetTableNames
1225    
1226    C<< my @names = $erdb->GetTableNames; >>
1227    
1228    Return a list of the relations required to implement this database.
1229    
1230    =cut
1231    
1232    sub GetTableNames {
1233          # Get the parameters.          # Get the parameters.
1234          my ($self) = @_;          my ($self) = @_;
1235          # Get the relation list from the metadata.          # Get the relation list from the metadata.
# Line 524  Line 1240 
1240    
1241  =head3 GetEntityTypes  =head3 GetEntityTypes
1242    
1243  C<< my @names = $database->GetEntityTypes; >>  C<< my @names = $erdb->GetEntityTypes; >>
1244    
1245  Return a list of the entity type names.  Return a list of the entity type names.
1246    
# Line 539  Line 1255 
1255          return sort keys %{$entityList};          return sort keys %{$entityList};
1256  }  }
1257    
1258    =head3 GetDataTypes
1259    
1260    C<< my %types = ERDB::GetDataTypes(); >>
1261    
1262    Return a table of ERDB data types. The table returned is a hash of hashes.
1263    The keys of the big hash are the datatypes. Each smaller hash has several
1264    values used to manage the data. The most interesting is the SQL type (key
1265    C<sqlType>) and the descriptive node (key C<notes>).
1266    
1267    Note that changing the values in the smaller hashes will seriously break
1268    things, so this data should be treated as read-only.
1269    
1270    =cut
1271    
1272    sub GetDataTypes {
1273        return %TypeTable;
1274    }
1275    
1276    
1277    =head3 IsEntity
1278    
1279    C<< my $flag = $erdb->IsEntity($entityName); >>
1280    
1281    Return TRUE if the parameter is an entity name, else FALSE.
1282    
1283    =over 4
1284    
1285    =item entityName
1286    
1287    Object name to be tested.
1288    
1289    =item RETURN
1290    
1291    Returns TRUE if the specified string is an entity name, else FALSE.
1292    
1293    =back
1294    
1295    =cut
1296    
1297    sub IsEntity {
1298        # Get the parameters.
1299        my ($self, $entityName) = @_;
1300        # Test to see if it's an entity.
1301        return exists $self->{_metaData}->{Entities}->{$entityName};
1302    }
1303    
1304  =head3 Get  =head3 Get
1305    
1306  C<< my $query = $database->Get(\@objectNames, $filterClause, $param1, $param2, ..., $paramN); >>  C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1307    
1308  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.
1309  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 1311 
1311  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
1312  $genus.  $genus.
1313    
1314  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1315    
1316  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
1317  parameter representing the parameter value. It would also be possible to code  parameter representing the parameter value. It would also be possible to code
1318    
1319  C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1320    
1321  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
1322  characters inside the variable C<$genus>.  characters inside the variable C<$genus>.
# Line 566  Line 1328 
1328  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
1329  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,
1330    
1331  C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", $genus); >>  C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1332    
1333  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
1334  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.
1335  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
1336  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
1337  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  
1338  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,
1339  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.
1340    
1341    If an entity or relationship is mentioned twice, the name for the second occurrence will
1342    be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1343    for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1344    B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1345    the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1346    
1347  =over 4  =over 4
1348    
1349  =item objectNames  =item objectNames
# Line 599  Line 1366 
1366    
1367  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>  C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1368    
1369    Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1370    be processed. The idea is to make it less likely to find the verb by accident.
1371    
1372  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
1373  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
1374  relation.  relation.
1375    
1376  =item param1, param2, ..., paramN  Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1377    be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1378    a positive number. So, for example
1379    
1380    C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1381    
1382  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
1383    required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1384    use
1385    
1386    C<< "LIMIT 10" >>
1387    
1388    =item params
1389    
1390    Reference to a list of parameter values to be substituted into the filter clause.
1391    
1392  =item RETURN  =item RETURN
1393    
# Line 617  Line 1399 
1399    
1400  sub Get {  sub Get {
1401          # Get the parameters.          # Get the parameters.
1402          my ($self, $objectNames, $filterClause, @params) = @_;      my ($self, $objectNames, $filterClause, $params) = @_;
1403          # Construct the SELECT statement. The general pattern is      # Process the SQL stuff.
1404          #      my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1405          # SELECT name1.*, name2.*, ... nameN.* FROM name1, name2, ... nameN          $self->_SetupSQL($objectNames, $filterClause);
1406          #      # Create the query.
1407          my $dbh = $self->{_dbh};      my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1408          my $command = "SELECT DISTINCT " . join('.*, ', @{$objectNames}) . ".* FROM " .          ".* $suffix";
1409                                  join(', ', @{$objectNames});      my $sth = $self->_GetStatementHandle($command, $params);
1410          # Check for a filter clause.      # Now we create the relation map, which enables DBQuery to determine the order, name
1411          if ($filterClause) {      # and mapped name for each object in the query.
1412                  # Here we have one, so we convert its field names and add it to the query. First,      my @relationMap = ();
1413                  # We create a copy of the filter string we can work with.      for my $mappedName (@{$mappedNameListRef}) {
1414                  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;  
1415                  }                  }
1416                  # We are ready to begin. We loop through the object names, replacing each      # Return the statement object.
1417                  # object name's field references by the corresponding SQL field reference.      my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1418                  # Along the way, if we find a secondary relation, we will need to add it      return $retVal;
1419                  # to the FROM clause.  }
1420                  for my $objectName (@sortedNames) {  
1421                          # Get the length of the object name plus 2. This is the value we add to the  =head3 Search
1422                          # size of the field name to determine the size of the field reference as a  
1423                          # whole.  C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1424                          my $nameLength = 2 + length $objectName;  
1425                          # Get the object's field list.  Perform a full text search with filtering. The search will be against a specified object
1426                          my $fieldList = $self->_GetFieldTable($objectName);  in the object name list. That object will get an extra field containing the search
1427                          # Find the field references for this object.  relevance. Note that except for the search expression, the parameters of this method are
1428                          while ($filterString =~ m/$objectName\(([^)]*)\)/g) {  the same as those for L</Get> and follow the same rules.
1429                                  # At this point, $1 contains the field name, and the current position  
1430                                  # is set immediately after the final parenthesis. We pull out the name of  =over 4
1431                                  # the field and the position and length of the field reference as a whole.  
1432                                  my $fieldName = $1;  =item searchExpression
1433                                  my $len = $nameLength + length $fieldName;  
1434                                  my $pos = pos($filterString) - $len;  Boolean search expression for the text fields of the target object. The default mode for
1435                                  # Insure the field exists.  a Boolean search expression is OR, but we want the default to be AND, so we will
1436                                  if (!exists $fieldList->{$fieldName}) {  add a C<+> operator to each word with no other operator before it.
1437                                          Confess("Field $fieldName not found for object $objectName.");  
1438    =item idx
1439    
1440    Index in the I<$objectNames> list of the table to be searched in full-text mode.
1441    
1442    =item objectNames
1443    
1444    List containing the names of the entity and relationship objects to be retrieved.
1445    
1446    =item filterClause
1447    
1448    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1449    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1450    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1451    in the filter clause should be added to the parameter list as additional parameters. The
1452    fields in a filter clause can come from primary entity relations, relationship relations,
1453    or secondary entity relations; however, all of the entities and relationships involved must
1454    be included in the list of object names.
1455    
1456    =item params
1457    
1458    Reference to a list of parameter values to be substituted into the filter clause.
1459    
1460    =item RETURN
1461    
1462    Returns a query object for the specified search.
1463    
1464    =back
1465    
1466    =cut
1467    
1468    sub Search {
1469        # Get the parameters.
1470        my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1471        # Declare the return variable.
1472        my $retVal;
1473        # Create a safety copy of the parameter list. Note we have to be careful to insure
1474        # a parameter list exists before we copy it.
1475        my @myParams = ();
1476        if (defined $params) {
1477            @myParams = @{$params};
1478        }
1479        # Get the first object's structure so we have access to the searchable fields.
1480        my $object1Name = $objectNames->[$idx];
1481        my $object1Structure = $self->_GetStructure($object1Name);
1482        # Get the field list.
1483        if (! exists $object1Structure->{searchFields}) {
1484            Confess("No searchable index for $object1Name.");
1485        } else {
1486            # Get the field list.
1487            my @fields = @{$object1Structure->{searchFields}};
1488            # Clean the search expression.
1489            my $actualKeywords = $self->CleanKeywords($searchExpression);
1490            # Prefix a "+" to each uncontrolled word. This converts the default
1491            # search mode from OR to AND.
1492            $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;
1493            Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1494            # We need two match expressions, one for the filter clause and one in the
1495            # query itself. Both will use a parameter mark, so we need to push the
1496            # search expression onto the front of the parameter list twice.
1497            unshift @myParams, $actualKeywords, $actualKeywords;
1498            # Build the match expression.
1499            my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1500            my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1501            # Process the SQL stuff.
1502            my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1503                $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1504            # Create the query. Note that the match clause is inserted at the front of
1505            # the select fields.
1506            my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1507                ".* $suffix";
1508            my $sth = $self->_GetStatementHandle($command, \@myParams);
1509            # Now we create the relation map, which enables DBQuery to determine the order, name
1510            # and mapped name for each object in the query.
1511            my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1512            # Return the statement object.
1513            $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1514        }
1515        return $retVal;
1516    }
1517    
1518    =head3 GetFlat
1519    
1520    C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1521    
1522    This is a variation of L</GetAll> that asks for only a single field per record and
1523    returns a single flattened list.
1524    
1525    =over 4
1526    
1527    =item objectNames
1528    
1529    List containing the names of the entity and relationship objects to be retrieved.
1530    
1531    =item filterClause
1532    
1533    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1534    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1535    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1536    parameter list as additional parameters. The fields in a filter clause can come from primary
1537    entity relations, relationship relations, or secondary entity relations; however, all of the
1538    entities and relationships involved must be included in the list of object names.
1539    
1540    =item parameterList
1541    
1542    List of the parameters to be substituted in for the parameters marks in the filter clause.
1543    
1544    =item field
1545    
1546    Name of the field to be used to get the elements of the list returned.
1547    
1548    =item RETURN
1549    
1550    Returns a list of values.
1551    
1552    =back
1553    
1554    =cut
1555    #: Return Type @;
1556    sub GetFlat {
1557        # Get the parameters.
1558        my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1559        # Construct the query.
1560        my $query = $self->Get($objectNames, $filterClause, $parameterList);
1561        # Create the result list.
1562        my @retVal = ();
1563        # Loop through the records, adding the field values found to the result list.
1564        while (my $row = $query->Fetch()) {
1565            push @retVal, $row->Value($field);
1566        }
1567        # Return the list created.
1568        return @retVal;
1569    }
1570    
1571    =head3 SpecialFields
1572    
1573    C<< my %specials = $erdb->SpecialFields($entityName); >>
1574    
1575    Return a hash mapping special fields in the specified entity to the value of their
1576    C<special> attribute. This enables the subclass to get access to the special field
1577    attributes without needed to plumb the internal ERDB data structures.
1578    
1579    =over 4
1580    
1581    =item entityName
1582    
1583    Name of the entity whose special fields are desired.
1584    
1585    =item RETURN
1586    
1587    Returns a hash. The keys of the hash are the special field names, and the values
1588    are the values from each special field's C<special> attribute.
1589    
1590    =back
1591    
1592    =cut
1593    
1594    sub SpecialFields {
1595        # Get the parameters.
1596        my ($self, $entityName) = @_;
1597        # Declare the return variable.
1598        my %retVal = ();
1599        # Find the entity's data structure.
1600        my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1601        # Loop through its fields, adding each special field to the return hash.
1602        my $fieldHash = $entityData->{Fields};
1603        for my $fieldName (keys %{$fieldHash}) {
1604            my $fieldData = $fieldHash->{$fieldName};
1605            if (exists $fieldData->{special}) {
1606                $retVal{$fieldName} = $fieldData->{special};
1607            }
1608        }
1609        # Return the result.
1610        return %retVal;
1611    }
1612    
1613    =head3 Delete
1614    
1615    C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1616    
1617    Delete an entity instance from the database. The instance is deleted along with all entity and
1618    relationship instances dependent on it. The idea of dependence here is recursive. An object is
1619    always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1620    relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1621    dependent relationship.
1622    
1623    =over 4
1624    
1625    =item entityName
1626    
1627    Name of the entity type for the instance being deleted.
1628    
1629    =item objectID
1630    
1631    ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1632    then it is presumed to by a LIKE pattern.
1633    
1634    =item testFlag
1635    
1636    If TRUE, the delete statements will be traced without being executed.
1637    
1638    =item RETURN
1639    
1640    Returns a statistics object indicating how many records of each particular table were
1641    deleted.
1642    
1643    =back
1644    
1645    =cut
1646    #: Return Type $%;
1647    sub Delete {
1648        # Get the parameters.
1649        my ($self, $entityName, $objectID, $testFlag) = @_;
1650        # Declare the return variable.
1651        my $retVal = Stats->new();
1652        # Get the DBKernel object.
1653        my $db = $self->{_dbh};
1654        # We're going to generate all the paths branching out from the starting entity. One of
1655        # the things we have to be careful about is preventing loops. We'll use a hash to
1656        # determine if we've hit a loop.
1657        my %alreadyFound = ();
1658        # These next lists will serve as our result stack. We start by pushing object lists onto
1659        # the stack, and then popping them off to do the deletes. This means the deletes will
1660        # start with the longer paths before getting to the shorter ones. That, in turn, makes
1661        # sure we don't delete records that might be needed to forge relationships back to the
1662        # original item. We have two lists-- one for TO-relationships, and one for
1663        # FROM-relationships and entities.
1664        my @fromPathList = ();
1665        my @toPathList = ();
1666        # This final hash is used to remember what work still needs to be done. We push paths
1667        # onto the list, then pop them off to extend the paths. We prime it with the starting
1668        # point. Note that we will work hard to insure that the last item on a path in the
1669        # to-do list is always an entity.
1670        my @todoList = ([$entityName]);
1671        while (@todoList) {
1672            # Get the current path.
1673            my $current = pop @todoList;
1674            # Copy it into a list.
1675            my @stackedPath = @{$current};
1676            # Pull off the last item on the path. It will always be an entity.
1677            my $entityName = pop @stackedPath;
1678            # Add it to the alreadyFound list.
1679            $alreadyFound{$entityName} = 1;
1680            # Get the entity data.
1681            my $entityData = $self->_GetStructure($entityName);
1682            # The first task is to loop through the entity's relation. A DELETE command will
1683            # be needed for each of them.
1684            my $relations = $entityData->{Relations};
1685            for my $relation (keys %{$relations}) {
1686                my @augmentedList = (@stackedPath, $relation);
1687                push @fromPathList, \@augmentedList;
1688            }
1689            # Now we need to look for relationships connected to this entity.
1690            my $relationshipList = $self->{_metaData}->{Relationships};
1691            for my $relationshipName (keys %{$relationshipList}) {
1692                my $relationship = $relationshipList->{$relationshipName};
1693                # Check the FROM field. We're only interested if it's us.
1694                if ($relationship->{from} eq $entityName) {
1695                    # Add the path to this relationship.
1696                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1697                    push @fromPathList, \@augmentedList;
1698                    # Check the arity. If it's MM we're done. If it's 1M
1699                    # and the target hasn't been seen yet, we want to
1700                    # stack the entity for future processing.
1701                    if ($relationship->{arity} eq '1M') {
1702                        my $toEntity = $relationship->{to};
1703                        if (! exists $alreadyFound{$toEntity}) {
1704                            # Here we have a new entity that's dependent on
1705                            # the current entity, so we need to stack it.
1706                            my @stackList = (@augmentedList, $toEntity);
1707                            push @fromPathList, \@stackList;
1708                        } else {
1709                            Trace("$toEntity ignored because it occurred previously.") if T(4);
1710                        }
1711                    }
1712                }
1713                # Now check the TO field. In this case only the relationship needs
1714                # deletion.
1715                if ($relationship->{to} eq $entityName) {
1716                    my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1717                    push @toPathList, \@augmentedList;
1718                }
1719            }
1720        }
1721        # Create the first qualifier for the WHERE clause. This selects the
1722        # keys of the primary entity records to be deleted. When we're deleting
1723        # from a dependent table, we construct a join page from the first qualifier
1724        # to the table containing the dependent records to delete.
1725        my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1726        # We need to make two passes. The first is through the to-list, and
1727        # the second through the from-list. The from-list is second because
1728        # the to-list may need to pass through some of the entities the
1729        # from-list would delete.
1730        my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1731        # Now it's time to do the deletes. We do it in two passes.
1732        for my $keyName ('to_link', 'from_link') {
1733            # Get the list for this key.
1734            my @pathList = @{$stackList{$keyName}};
1735            Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1736            # Loop through this list.
1737            while (my $path = pop @pathList) {
1738                # Get the table whose rows are to be deleted.
1739                my @pathTables = @{$path};
1740                # Start the DELETE statement. We need to call DBKernel because the
1741                # syntax of a DELETE-USING varies among DBMSs.
1742                my $target = $pathTables[$#pathTables];
1743                my $stmt = $db->SetUsing(@pathTables);
1744                # Now start the WHERE. The first thing is the ID field from the starting table. That
1745                # starting table will either be the entity relation or one of the entity's
1746                # sub-relations.
1747                $stmt .= " WHERE $pathTables[0].id $qualifier";
1748                # Now we run through the remaining entities in the path, connecting them up.
1749                for (my $i = 1; $i <= $#pathTables; $i += 2) {
1750                    # Connect the current relationship to the preceding entity.
1751                    my ($entity, $rel) = @pathTables[$i-1,$i];
1752                    # The style of connection depends on the direction of the relationship.
1753                    $stmt .= " AND $entity.id = $rel.$keyName";
1754                    if ($i + 1 <= $#pathTables) {
1755                        # Here there's a next entity, so connect that to the relationship's
1756                        # to-link.
1757                        my $entity2 = $pathTables[$i+1];
1758                        $stmt .= " AND $rel.to_link = $entity2.id";
1759                    }
1760                }
1761                # Now we have our desired DELETE statement.
1762                if ($testFlag) {
1763                    # Here the user wants to trace without executing.
1764                    Trace($stmt) if T(0);
1765                } else {
1766                    # Here we can delete. Note that the SQL method dies with a confessing
1767                    # if an error occurs, so we just go ahead and do it.
1768                    Trace("Executing delete from $target using '$objectID'.") if T(3);
1769                    my $rv = $db->SQL($stmt, 0, $objectID);
1770                    # Accumulate the statistics for this delete. The only rows deleted
1771                    # are from the target table, so we use its name to record the
1772                    # statistic.
1773                    $retVal->Add($target, $rv);
1774                }
1775            }
1776        }
1777        # Return the result.
1778        return $retVal;
1779    }
1780    
1781    =head3 SortNeeded
1782    
1783    C<< my $parms = $erdb->SortNeeded($relationName); >>
1784    
1785    Return the pipe command for the sort that should be applied to the specified
1786    relation when creating the load file.
1787    
1788    For example, if the load file should be sorted ascending by the first
1789    field, this method would return
1790    
1791        sort -k1 -t"\t"
1792    
1793    If the first field is numeric, the method would return
1794    
1795        sort -k1n -t"\t"
1796    
1797    Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1798    keys using a sort.
1799    
1800    =over 4
1801    
1802    =item relationName
1803    
1804    Name of the relation to be examined.
1805    
1806    =item
1807    
1808    Returns the sort command to use for sorting the relation, suitable for piping.
1809    
1810    =back
1811    
1812    =cut
1813    #: Return Type $;
1814    sub SortNeeded {
1815        # Get the parameters.
1816        my ($self, $relationName) = @_;
1817        # Declare a descriptor to hold the names of the key fields.
1818        my @keyNames = ();
1819        # Get the relation structure.
1820        my $relationData = $self->_FindRelation($relationName);
1821        # Find out if the relation is a primary entity relation,
1822        # a relationship relation, or a secondary entity relation.
1823        my $entityTable = $self->{_metaData}->{Entities};
1824        my $relationshipTable = $self->{_metaData}->{Relationships};
1825        if (exists $entityTable->{$relationName}) {
1826            # Here we have a primary entity relation.
1827            push @keyNames, "id";
1828        } elsif (exists $relationshipTable->{$relationName}) {
1829            # Here we have a relationship. We sort using the FROM index.
1830            my $relationshipData = $relationshipTable->{$relationName};
1831            my $index = $relationData->{Indexes}->{idxFrom};
1832            push @keyNames, @{$index->{IndexFields}};
1833        } else {
1834            # Here we have a secondary entity relation, so we have a sort on the ID field.
1835            push @keyNames, "id";
1836        }
1837        # Now we parse the key names into sort parameters. First, we prime the return
1838        # string.
1839        my $retVal = "sort -t\"\t\" ";
1840        # Get the relation's field list.
1841        my @fields = @{$relationData->{Fields}};
1842        # Loop through the keys.
1843        for my $keyData (@keyNames) {
1844            # Get the key and the ordering.
1845            my ($keyName, $ordering);
1846            if ($keyData =~ /^([^ ]+) DESC/) {
1847                ($keyName, $ordering) = ($1, "descending");
1848            } else {
1849                ($keyName, $ordering) = ($keyData, "ascending");
1850            }
1851            # Find the key's position and type.
1852            my $fieldSpec;
1853            for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1854                my $thisField = $fields[$i];
1855                if ($thisField->{name} eq $keyName) {
1856                    # Get the sort modifier for this field type. The modifier
1857                    # decides whether we're using a character, numeric, or
1858                    # floating-point sort.
1859                    my $modifier = $TypeTable{$thisField->{type}}->{sort};
1860                    # If the index is descending for this field, denote we want
1861                    # to reverse the sort order on this field.
1862                    if ($ordering eq 'descending') {
1863                        $modifier .= "r";
1864                    }
1865                    # Store the position and modifier into the field spec, which
1866                    # will stop the inner loop. Note that the field number is
1867                    # 1-based in the sort command, so we have to increment the
1868                    # index.
1869                    $fieldSpec = ($i + 1) . $modifier;
1870                }
1871            }
1872            # Add this field to the sort command.
1873            $retVal .= " -k$fieldSpec";
1874        }
1875        # Return the result.
1876        return $retVal;
1877    }
1878    
1879    =head3 GetList
1880    
1881    C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1882    
1883    Return a list of object descriptors for the specified objects as determined by the
1884    specified filter clause.
1885    
1886    This method is essentially the same as L</Get> except it returns a list of objects rather
1887    than a query object that can be used to get the results one record at a time.
1888    
1889    =over 4
1890    
1891    =item objectNames
1892    
1893    List containing the names of the entity and relationship objects to be retrieved.
1894    
1895    =item filterClause
1896    
1897    WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1898    be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1899    specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1900    in the filter clause should be added to the parameter list as additional parameters. The
1901    fields in a filter clause can come from primary entity relations, relationship relations,
1902    or secondary entity relations; however, all of the entities and relationships involved must
1903    be included in the list of object names.
1904    
1905    The filter clause can also specify a sort order. To do this, simply follow the filter string
1906    with an ORDER BY clause. For example, the following filter string gets all genomes for a
1907    particular genus and sorts them by species name.
1908    
1909    C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1910    
1911    The rules for field references in a sort order are the same as those for field references in the
1912    filter clause in general; however, odd things may happen if a sort field is from a secondary
1913    relation.
1914    
1915    =item params
1916    
1917    Reference to a list of parameter values to be substituted into the filter clause.
1918    
1919    =item RETURN
1920    
1921    Returns a list of B<DBObject>s that satisfy the query conditions.
1922    
1923    =back
1924    
1925    =cut
1926    #: Return Type @%
1927    sub GetList {
1928        # Get the parameters.
1929        my ($self, $objectNames, $filterClause, $params) = @_;
1930        # Declare the return variable.
1931        my @retVal = ();
1932        # Perform the query.
1933        my $query = $self->Get($objectNames, $filterClause, $params);
1934        # Loop through the results.
1935        while (my $object = $query->Fetch) {
1936            push @retVal, $object;
1937        }
1938        # Return the result.
1939        return @retVal;
1940    }
1941    
1942    =head3 GetCount
1943    
1944    C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1945    
1946    Return the number of rows found by a specified query. This method would
1947    normally be used to count the records in a single table. For example, in a
1948    genetics database
1949    
1950        my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1951    
1952    would return the number of genomes for the genus I<homo>. It is conceivable, however,
1953    to use it to return records based on a join. For example,
1954    
1955        my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1956                                    ['homo %']);
1957    
1958    would return the number of features for genomes in the genus I<homo>. Note that
1959    only the rows from the first table are counted. If the above command were
1960    
1961        my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1962                                    ['homo %']);
1963    
1964    it would return the number of genomes, not the number of genome/feature pairs.
1965    
1966    =over 4
1967    
1968    =item objectNames
1969    
1970    Reference to a list of the objects (entities and relationships) included in the
1971    query.
1972    
1973    =item filter
1974    
1975    A filter clause for restricting the query. The rules are the same as for the L</Get>
1976    method.
1977    
1978    =item params
1979    
1980    Reference to a list of the parameter values to be substituted for the parameter marks
1981    in the filter.
1982    
1983    =item RETURN
1984    
1985    Returns a count of the number of records in the first table that would satisfy
1986    the query.
1987    
1988    =back
1989    
1990    =cut
1991    
1992    sub GetCount {
1993        # Get the parameters.
1994        my ($self, $objectNames, $filter, $params) = @_;
1995        # Insure the params argument is an array reference if the caller left it off.
1996        if (! defined($params)) {
1997            $params = [];
1998        }
1999        # Declare the return variable.
2000        my $retVal;
2001        # Find out if we're counting an entity or a relationship.
2002        my $countedField;
2003        if ($self->IsEntity($objectNames->[0])) {
2004            $countedField = "id";
2005        } else {
2006            # For a relationship we count the to-link because it's usually more
2007            # numerous. Note we're automatically converting to the SQL form
2008            # of the field name (to_link vs. to-link).
2009            $countedField = "to_link";
2010        }
2011        # Create the SQL command suffix to get the desired records.
2012        my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2013                                                                                $filter);
2014        # Prefix it with text telling it we want a record count.
2015        my $firstObject = $mappedNameListRef->[0];
2016        my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2017        # Prepare and execute the command.
2018        my $sth = $self->_GetStatementHandle($command, $params);
2019        # Get the count value.
2020        ($retVal) = $sth->fetchrow_array();
2021        # Check for a problem.
2022        if (! defined($retVal)) {
2023            if ($sth->err) {
2024                # Here we had an SQL error.
2025                Confess("Error retrieving row count: " . $sth->errstr());
2026            } else {
2027                # Here we have no result.
2028                Confess("No result attempting to retrieve row count.");
2029            }
2030        }
2031        # Return the result.
2032        return $retVal;
2033    }
2034    
2035    =head3 ComputeObjectSentence
2036    
2037    C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2038    
2039    Check an object name, and if it is a relationship convert it to a relationship sentence.
2040    
2041    =over 4
2042    
2043    =item objectName
2044    
2045    Name of the entity or relationship.
2046    
2047    =item RETURN
2048    
2049    Returns a string containing the entity name or a relationship sentence.
2050    
2051    =back
2052    
2053    =cut
2054    
2055    sub ComputeObjectSentence {
2056        # Get the parameters.
2057        my ($self, $objectName) = @_;
2058        # Set the default return value.
2059        my $retVal = $objectName;
2060        # Look for the object as a relationship.
2061        my $relTable = $self->{_metaData}->{Relationships};
2062        if (exists $relTable->{$objectName}) {
2063            # Get the relationship sentence.
2064            $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2065        }
2066        # Return the result.
2067        return $retVal;
2068    }
2069    
2070    =head3 DumpRelations
2071    
2072    C<< $erdb->DumpRelations($outputDirectory); >>
2073    
2074    Write the contents of all the relations to tab-delimited files in the specified directory.
2075    Each file will have the same name as the relation dumped, with an extension of DTX.
2076    
2077    =over 4
2078    
2079    =item outputDirectory
2080    
2081    Name of the directory into which the relation files should be dumped.
2082    
2083    =back
2084    
2085    =cut
2086    
2087    sub DumpRelations {
2088        # Get the parameters.
2089        my ($self, $outputDirectory) = @_;
2090        # Now we need to run through all the relations. First, we loop through the entities.
2091        my $metaData = $self->{_metaData};
2092        my $entities = $metaData->{Entities};
2093        for my $entityName (keys %{$entities}) {
2094            my $entityStructure = $entities->{$entityName};
2095            # Get the entity's relations.
2096            my $relationList = $entityStructure->{Relations};
2097            # Loop through the relations, dumping them.
2098            for my $relationName (keys %{$relationList}) {
2099                my $relation = $relationList->{$relationName};
2100                $self->_DumpRelation($outputDirectory, $relationName, $relation);
2101            }
2102        }
2103        # Next, we loop through the relationships.
2104        my $relationships = $metaData->{Relationships};
2105        for my $relationshipName (keys %{$relationships}) {
2106            my $relationshipStructure = $relationships->{$relationshipName};
2107            # Dump this relationship's relation.
2108            $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2109        }
2110    }
2111    
2112    =head3 InsertValue
2113    
2114    C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2115    
2116    This method will insert a new value into the database. The value must be one
2117    associated with a secondary relation, since primary values cannot be inserted:
2118    they occur exactly once. Secondary values, on the other hand, can be missing
2119    or multiply-occurring.
2120    
2121    =over 4
2122    
2123    =item entityID
2124    
2125    ID of the object that is to receive the new value.
2126    
2127    =item fieldName
2128    
2129    Field name for the new value-- this includes the entity name, since
2130    field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2131    
2132    =item value
2133    
2134    New value to be put in the field.
2135    
2136    =back
2137    
2138    =cut
2139    
2140    sub InsertValue {
2141        # Get the parameters.
2142        my ($self, $entityID, $fieldName, $value) = @_;
2143        # Parse the entity name and the real field name.
2144        if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2145            my $entityName = $1;
2146            my $fieldTitle = $2;
2147            # Get its descriptor.
2148            if (!$self->IsEntity($entityName)) {
2149                Confess("$entityName is not a valid entity.");
2150            } else {
2151                my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2152                # Find the relation containing this field.
2153                my $fieldHash = $entityData->{Fields};
2154                if (! exists $fieldHash->{$fieldTitle}) {
2155                    Confess("$fieldTitle not found in $entityName.");
2156                } else {
2157                    my $relation = $fieldHash->{$fieldTitle}->{relation};
2158                    if ($relation eq $entityName) {
2159                        Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2160                    } else {
2161                        # Now we can create an INSERT statement.
2162                        my $dbh = $self->{_dbh};
2163                        my $fixedName = _FixName($fieldTitle);
2164                        my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2165                        # Execute the command.
2166                        $dbh->SQL($statement, 0, $entityID, $value);
2167                    }
2168                }
2169            }
2170        } else {
2171            Confess("$fieldName is not a valid field name.");
2172        }
2173    }
2174    
2175    =head3 InsertObject
2176    
2177    C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2178    
2179    Insert an object into the database. The object is defined by a type name and then a hash
2180    of field names to values. Field values in the primary relation are represented by scalars.
2181    (Note that for relationships, the primary relation is the B<only> relation.)
2182    Field values for the other relations comprising the entity are always list references. For
2183    example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2184    C<ZP_00210270.1> and C<gi|46206278>.
2185    
2186    C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2187    
2188    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2189    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2190    
2191    C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2192    
2193    =over 4
2194    
2195    =item newObjectType
2196    
2197    Type name of the object to insert.
2198    
2199    =item fieldHash
2200    
2201    Hash of field names to values.
2202    
2203    =item RETURN
2204    
2205    Returns 1 if successful, 0 if an error occurred.
2206    
2207    =back
2208    
2209    =cut
2210    
2211    sub InsertObject {
2212        # Get the parameters.
2213        my ($self, $newObjectType, $fieldHash) = @_;
2214        # Denote that so far we appear successful.
2215        my $retVal = 1;
2216        # Get the database handle.
2217        my $dbh = $self->{_dbh};
2218        # Get the relation list.
2219        my $relationTable = $self->_GetRelationTable($newObjectType);
2220        # Loop through the relations. We'll build insert statements for each one. If a relation is
2221        # secondary, we may end up generating multiple insert statements. If an error occurs, we
2222        # stop the loop.
2223        my @relationList = keys %{$relationTable};
2224        for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2225            my $relationName = $relationList[$i];
2226            my $relationDefinition = $relationTable->{$relationName};
2227            # Get the relation's fields. For each field we will collect a value in the corresponding
2228            # position of the @valueList array. If one of the fields is missing, we will add it to the
2229            # @missing list.
2230            my @fieldList = @{$relationDefinition->{Fields}};
2231            my @fieldNameList = ();
2232            my @valueList = ();
2233            my @missing = ();
2234            my $recordCount = 1;
2235            for my $fieldDescriptor (@fieldList) {
2236                # Get the field name and save it. Note we need to fix it up so the hyphens
2237                # are converted to underscores.
2238                my $fieldName = $fieldDescriptor->{name};
2239                push @fieldNameList, _FixName($fieldName);
2240                # Look for the named field in the incoming structure. Note that we are looking
2241                # for the real field name, not the fixed-up one!
2242                if (exists $fieldHash->{$fieldName}) {
2243                    # Here we found the field. Stash it in the value list.
2244                    my $value = $fieldHash->{$fieldName};
2245                    push @valueList, $value;
2246                    # If the value is a list, we may need to increment the record count.
2247                    if (ref $value eq "ARRAY") {
2248                        my $thisCount = @{$value};
2249                        if ($recordCount == 1) {
2250                            # Here we have our first list, so we save its count.
2251                            $recordCount = $thisCount;
2252                        } elsif ($recordCount != $thisCount) {
2253                            # Here we have a second list, so its length has to match the
2254                            # previous lists.
2255                            Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2256                            $retVal = 0;
2257                        }
2258                    }
2259                } else {
2260                    # Here the field is not present. Flag it as missing.
2261                    push @missing, $fieldName;
2262                }
2263            }
2264            # If we are the primary relation, add the new-record flag.
2265            if ($relationName eq $newObjectType) {
2266                push @valueList, 1;
2267                push @fieldNameList, "new_record";
2268            }
2269            # Only proceed if there are no missing fields.
2270            if (@missing > 0) {
2271                Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2272                    join(' ', @missing)) if T(1);
2273                                  } else {                                  } else {
2274                                          # Get the field's relation.              # Build the INSERT statement.
2275                                          my $relationName = $fieldList->{$fieldName}->{relation};              my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2276                                          # Insure the relation is in the FROM clause.                  ") VALUES (";
2277                                          if (!exists $fromNames{$relationName}) {              # Create a marker list of the proper size and put it in the statement.
2278                                                  # Add the relation to the FROM clause.              my @markers = ();
2279                                                  $command .= ", $relationName";              while (@markers < @fieldNameList) { push @markers, '?'; }
2280                                                  # Create its join sub-clause.              $statement .= join(', ', @markers) . ")";
2281                                                  push @joinWhere, "$objectName.id = $relationName.id";              # We have the insert statement, so prepare it.
2282                                                  # Denote we have it available for future fields.              my $sth = $dbh->prepare_command($statement);
2283                                                  $fromNames{$relationName} = 1;              Trace("Insert statement prepared: $statement") if T(3);
2284                # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2285                # a list, we use the current element. The values are stored in the @parameterList array.
2286                my $done = 0;
2287                for (my $i = 0; $i < $recordCount; $i++) {
2288                    # Clear the parameter list array.
2289                    my @parameterList = ();
2290                    # Loop through the values.
2291                    for my $value (@valueList) {
2292                        # Check to see if this is a scalar value.
2293                        if (ref $value eq "ARRAY") {
2294                            # Here we have a list value. Pull the current entry.
2295                            push @parameterList, $value->[$i];
2296                        } else {
2297                            # Here we have a scalar value. Use it unmodified.
2298                            push @parameterList, $value;
2299                                          }                                          }
                                         # 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;  
2300                                  }                                  }
2301                    # Execute the INSERT statement with the specified parameter list.
2302                    $retVal = $sth->execute(@parameterList);
2303                    if (!$retVal) {
2304                        my $errorString = $sth->errstr();
2305                        Trace("Insert error: $errorString.") if T(0);
2306                          }                          }
2307                  }                  }
2308                  # The next step is to join the objects together. We only need to do this if there          }
2309                  # is more than one object in the object list. We start with the first object and      }
2310                  # run through the objects after it. Note also that we make a safety copy of the      # Return the success indicator.
2311                  # list before running through it.      return $retVal;
2312                  my @objectList = @{$objectNames};  }
2313                  my $lastObject = shift @objectList;  
2314                  # Get the join table.  =head3 LoadTable
2315                  my $joinTable = $self->{_metaData}->{Joins};  
2316                  # Loop through the object list.  C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2317                  for my $thisObject (@objectList) {  
2318                          # Look for a join.  Load data from a tab-delimited file into a specified table, optionally re-creating the table
2319                          my $joinKey = "$lastObject/$thisObject";  first.
2320                          if (!exists $joinTable->{$joinKey}) {  
2321                                  # Here there's no join, so we throw an error.  =over 4
2322                                  Confess("No join exists to connect from $lastObject to $thisObject.");  
2323    =item fileName
2324    
2325    Name of the file from which the table data should be loaded.
2326    
2327    =item relationName
2328    
2329    Name of the relation to be loaded. This is the same as the table name.
2330    
2331    =item truncateFlag
2332    
2333    TRUE if the table should be dropped and re-created, else FALSE
2334    
2335    =item RETURN
2336    
2337    Returns a statistical object containing a list of the error messages.
2338    
2339    =back
2340    
2341    =cut
2342    sub LoadTable {
2343        # Get the parameters.
2344        my ($self, $fileName, $relationName, $truncateFlag) = @_;
2345        # Create the statistical return object.
2346        my $retVal = _GetLoadStats();
2347        # Trace the fact of the load.
2348        Trace("Loading table $relationName from $fileName") if T(2);
2349        # Get the database handle.
2350        my $dbh = $self->{_dbh};
2351        # Get the input file size.
2352        my $fileSize = -s $fileName;
2353        # Get the relation data.
2354        my $relation = $self->_FindRelation($relationName);
2355        # Check the truncation flag.
2356        if ($truncateFlag) {
2357            Trace("Creating table $relationName") if T(2);
2358            # Compute the row count estimate. We take the size of the load file,
2359            # divide it by the estimated row size, and then multiply by 1.5 to
2360            # leave extra room. We postulate a minimum row count of 1000 to
2361            # prevent problems with incoming empty load files.
2362            my $rowSize = $self->EstimateRowSize($relationName);
2363            my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2364            # Re-create the table without its index.
2365            $self->CreateTable($relationName, 0, $estimate);
2366            # If this is a pre-index DBMS, create the index here.
2367            if ($dbh->{_preIndex}) {
2368                eval {
2369                    $self->CreateIndex($relationName);
2370                };
2371                if ($@) {
2372                    $retVal->AddMessage($@);
2373                }
2374            }
2375        }
2376        # Load the table.
2377        my $rv;
2378        eval {
2379            $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2380        };
2381        if (!defined $rv) {
2382            $retVal->AddMessage($@) if ($@);
2383            $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2384            Trace("Table load failed for $relationName.") if T(1);
2385                          } else {                          } else {
2386                                  # Get the join clause and add it to the WHERE list.          # Here we successfully loaded the table.
2387                                  push @joinWhere, $joinTable->{$joinKey};          $retVal->Add("tables");
2388                                  # Save this object as the last object for the next iteration.          my $size = -s $fileName;
2389                                  $lastObject = $thisObject;          Trace("$size bytes loaded into $relationName.") if T(2);
2390            # If we're rebuilding, we need to create the table indexes.
2391            if ($truncateFlag) {
2392                # Indexes are created here for PostGres. For PostGres, indexes are
2393                # best built at the end. For MySQL, the reverse is true.
2394                if (! $dbh->{_preIndex}) {
2395                    eval {
2396                        $self->CreateIndex($relationName);
2397                    };
2398                    if ($@) {
2399                        $retVal->AddMessage($@);
2400                          }                          }
2401                  }                  }
2402                  # 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.
2403                  # in the following variable.              # First we need to see if this table has a full-text index. Only
2404                  my $orderClause = "";              # primary relations are allowed that privilege.
2405                  # Locate the ORDER BY verb (if any).              if ($self->_IsPrimary($relationName)) {
2406                  if ($filterString =~ m/^(.*)ORDER BY/g) {                  # Get the relation's entity/relationship structure.
2407                          # Here we have an ORDER BY verb. Split it off of the filter string.                  my $structure = $self->_GetStructure($relationName);
2408                          my $pos = pos $filterString;                  # Check for a searchable fields list.
2409                          $orderClause = substr($filterString, $pos);                  if (exists $structure->{searchFields}) {
2410                          $filterString = $1;                      # Here we know that we need to create a full-text search index.
2411                        # Get an SQL-formatted field name list.
2412                        my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2413                        # Create the index.
2414                        $dbh->create_index(tbl => $relationName, idx => "search_idx",
2415                                           flds => $fields, kind => 'fulltext');
2416                  }                  }
                 # Add the filter and the join clauses (if any) to the SELECT command.  
                 if ($filterString) {  
                         push @joinWhere, "($filterString)";  
2417                  }                  }
                 if (@joinWhere) {  
                         $command .= " WHERE " . join(' AND ', @joinWhere);  
2418                  }                  }
                 # Add the sort clause (if any) to the SELECT command.  
                 if ($orderClause) {  
                         $command .= " ORDER BY $orderClause";  
2419                  }                  }
2420        # Analyze the table to improve performance.
2421        Trace("Analyzing and compacting $relationName.") if T(3);
2422        $dbh->vacuum_it($relationName);
2423        Trace("$relationName load completed.") if T(3);
2424        # Return the statistics.
2425        return $retVal;
2426    }
2427    
2428    =head3 DropRelation
2429    
2430    C<< $erdb->DropRelation($relationName); >>
2431    
2432    Physically drop a relation from the database.
2433    
2434    =over 4
2435    
2436    =item relationName
2437    
2438    Name of the relation to drop. If it does not exist, this method will have
2439    no effect.
2440    
2441    =back
2442    
2443    =cut
2444    
2445    sub DropRelation {
2446        # Get the parameters.
2447        my ($self, $relationName) = @_;
2448        # Get the database handle.
2449        my $dbh = $self->{_dbh};
2450        # Drop the relation. The method used here has no effect if the relation
2451        # does not exist.
2452        Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2453        $dbh->drop_table(tbl => $relationName);
2454    }
2455    
2456    =head3 GetEntity
2457    
2458    C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2459    
2460    Return an object describing the entity instance with a specified ID.
2461    
2462    =over 4
2463    
2464    =item entityType
2465    
2466    Entity type name.
2467    
2468    =item ID
2469    
2470    ID of the desired entity.
2471    
2472    =item RETURN
2473    
2474    Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2475    instance is found with the specified key.
2476    
2477    =back
2478    
2479    =cut
2480    
2481    sub GetEntity {
2482        # Get the parameters.
2483        my ($self, $entityType, $ID) = @_;
2484        # Create a query.
2485        my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2486        # Get the first (and only) object.
2487        my $retVal = $query->Fetch();
2488        # Return the result.
2489        return $retVal;
2490    }
2491    
2492    =head3 GetChoices
2493    
2494    C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2495    
2496    Return a list of all the values for the specified field that are represented in the
2497    specified entity.
2498    
2499    Note that if the field is not indexed, then this will be a very slow operation.
2500    
2501    =over 4
2502    
2503    =item entityName
2504    
2505    Name of an entity in the database.
2506    
2507    =item fieldName
2508    
2509    Name of a field belonging to the entity. This is a raw field name without
2510    the standard parenthesized notation used in most calls.
2511    
2512    =item RETURN
2513    
2514    Returns a list of the distinct values for the specified field in the database.
2515    
2516    =back
2517    
2518    =cut
2519    
2520    sub GetChoices {
2521        # Get the parameters.
2522        my ($self, $entityName, $fieldName) = @_;
2523        # Declare the return variable.
2524        my @retVal;
2525        # Get the entity data structure.
2526        my $entityData = $self->_GetStructure($entityName);
2527        # Get the field.
2528        my $fieldHash = $entityData->{Fields};
2529        if (! exists $fieldHash->{$fieldName}) {
2530            Confess("$fieldName not found in $entityName.");
2531        } else {
2532            # Get the name of the relation containing the field.
2533            my $relation = $fieldHash->{$fieldName}->{relation};
2534            # Fix up the field name.
2535            my $realName = _FixName($fieldName);
2536            # Get the database handle.
2537            my $dbh = $self->{_dbh};
2538            # Query the database.
2539            my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2540            # Clean the results. They are stored as a list of lists, and we just want the one list.
2541            @retVal = sort map { $_->[0] } @{$results};
2542        }
2543        # Return the result.
2544        return @retVal;
2545    }
2546    
2547    =head3 GetEntityValues
2548    
2549    C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2550    
2551    Return a list of values from a specified entity instance. If the entity instance
2552    does not exist, an empty list is returned.
2553    
2554    =over 4
2555    
2556    =item entityType
2557    
2558    Entity type name.
2559    
2560    =item ID
2561    
2562    ID of the desired entity.
2563    
2564    =item fields
2565    
2566    List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2567    
2568    =item RETURN
2569    
2570    Returns a flattened list of the values of the specified fields for the specified entity.
2571    
2572    =back
2573    
2574    =cut
2575    
2576    sub GetEntityValues {
2577        # Get the parameters.
2578        my ($self, $entityType, $ID, $fields) = @_;
2579        # Get the specified entity.
2580        my $entity = $self->GetEntity($entityType, $ID);
2581        # Declare the return list.
2582        my @retVal = ();
2583        # If we found the entity, push the values into the return list.
2584        if ($entity) {
2585            push @retVal, $entity->Values($fields);
2586        }
2587        # Return the result.
2588        return @retVal;
2589    }
2590    
2591    =head3 GetAll
2592    
2593    C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2594    
2595    Return a list of values taken from the objects returned by a query. The first three
2596    parameters correspond to the parameters of the L</Get> method. The final parameter is
2597    a list of the fields desired from each record found by the query. The field name
2598    syntax is the standard syntax used for fields in the B<ERDB> system--
2599    B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2600    or relationship and I<fieldName> is the name of the field.
2601    
2602    The list returned will be a list of lists. Each element of the list will contain
2603    the values returned for the fields specified in the fourth parameter. If one of the
2604    fields specified returns multiple values, they are flattened in with the rest. For
2605    example, the following call will return a list of the features in a particular
2606    spreadsheet cell, and each feature will be represented by a list containing the
2607    feature ID followed by all of its aliases.
2608    
2609    C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2610    
2611    =over 4
2612    
2613    =item objectNames
2614    
2615    List containing the names of the entity and relationship objects to be retrieved.
2616    
2617    =item filterClause
2618    
2619    WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2620    be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2621    B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2622    parameter list as additional parameters. The fields in a filter clause can come from primary
2623    entity relations, relationship relations, or secondary entity relations; however, all of the
2624    entities and relationships involved must be included in the list of object names.
2625    
2626    =item parameterList
2627    
2628    List of the parameters to be substituted in for the parameters marks in the filter clause.
2629    
2630    =item fields
2631    
2632    List of the fields to be returned in each element of the list returned.
2633    
2634    =item count
2635    
2636    Maximum number of records to return. If omitted or 0, all available records will be returned.
2637    
2638    =item RETURN
2639    
2640    Returns a list of list references. Each element of the return list contains the values for the
2641    fields specified in the B<fields> parameter.
2642    
2643    =back
2644    
2645    =cut
2646    #: Return Type @@;
2647    sub GetAll {
2648        # Get the parameters.
2649        my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2650        # Translate the parameters from a list reference to a list. If the parameter
2651        # list is a scalar we convert it into a singleton list.
2652        my @parmList = ();
2653        if (ref $parameterList eq "ARRAY") {
2654            Trace("GetAll parm list is an array.") if T(4);
2655            @parmList = @{$parameterList};
2656        } else {
2657            Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2658            push @parmList, $parameterList;
2659        }
2660        # Insure the counter has a value.
2661        if (!defined $count) {
2662            $count = 0;
2663        }
2664        # Add the row limit to the filter clause.
2665        if ($count > 0) {
2666            $filterClause .= " LIMIT $count";
2667        }
2668        # Create the query.
2669        my $query = $self->Get($objectNames, $filterClause, \@parmList);
2670        # Set up a counter of the number of records read.
2671        my $fetched = 0;
2672        # Loop through the records returned, extracting the fields. Note that if the
2673        # counter is non-zero, we stop when the number of records read hits the count.
2674        my @retVal = ();
2675        while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2676            my @rowData = $row->Values($fields);
2677            push @retVal, \@rowData;
2678            $fetched++;
2679        }
2680        Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2681        # Return the resulting list.
2682        return @retVal;
2683          }          }
2684          Trace("SQL query: $command") if T(2);  
2685          Trace("PARMS: '" . (join "', '", @params) . "'") if (T(3) && (@params > 0));  =head3 Exists
2686          my $sth = $dbh->prepare_command($command);  
2687          # Execute it with the parameters bound in.  C<< my $found = $sprout->Exists($entityName, $entityID); >>
2688          $sth->execute(@params) || Confess("SELECT error" . $sth->errstr());  
2689          # Return the statement object.  Return TRUE if an entity exists, else FALSE.
2690          my $retVal = DBQuery::_new($self, $sth, @{$objectNames});  
2691    =over 4
2692    
2693    =item entityName
2694    
2695    Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2696    
2697    =item entityID
2698    
2699    ID of the entity instance whose existence is to be checked.
2700    
2701    =item RETURN
2702    
2703    Returns TRUE if the entity instance exists, else FALSE.
2704    
2705    =back
2706    
2707    =cut
2708    #: Return Type $;
2709    sub Exists {
2710        # Get the parameters.
2711        my ($self, $entityName, $entityID) = @_;
2712        # Check for the entity instance.
2713        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2714        my $testInstance = $self->GetEntity($entityName, $entityID);
2715        # Return an existence indicator.
2716        my $retVal = ($testInstance ? 1 : 0);
2717          return $retVal;          return $retVal;
2718  }  }
2719    
2720  =head3 ComputeObjectSentence  =head3 EstimateRowSize
2721    
2722  C<< my $sentence = $database->ComputeObjectSentence($objectName); >>  C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2723    
2724  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
2725    up the average length for each data type.
2726    
2727  =over 4  =over 4
2728    
2729  =item objectName  =item relName
2730    
2731  Name of the entity or relationship.  Name of the relation whose estimated row size is desired.
2732    
2733  =item RETURN  =item RETURN
2734    
2735  Returns a string containing the entity name or a relationship sentence.  Returns an estimate of the row size for the specified relation.
2736    
2737  =back  =back
2738    
2739  =cut  =cut
2740    #: Return Type $;
2741  sub ComputeObjectSentence {  sub EstimateRowSize {
2742          # Get the parameters.          # Get the parameters.
2743          my ($self, $objectName) = @_;      my ($self, $relName) = @_;
2744          # Set the default return value.      # Declare the return variable.
2745          my $retVal = $objectName;      my $retVal = 0;
2746          # Look for the object as a relationship.      # Find the relation descriptor.
2747          my $relTable = $self->{_metaData}->{Relationships};      my $relation = $self->_FindRelation($relName);
2748          if (exists $relTable->{$objectName}) {      # Get the list of fields.
2749                  # Get the relationship sentence.      for my $fieldData (@{$relation->{Fields}}) {
2750                  $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});          # Get the field type and add its length.
2751            my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2752            $retVal += $fieldLen;
2753          }          }
2754          # Return the result.          # Return the result.
2755          return $retVal;          return $retVal;
2756  }  }
2757    
2758  =head3 DumpRelations  =head3 GetFieldTable
2759    
2760  C<< $database->DumpRelations($outputDirectory); >>  C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2761    
2762  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.  
2763    
2764  =over 4  =over 4
2765    
2766  =item outputDirectory  =item objectName
2767    
2768  Name of the directory into which the relation files should be dumped.  Name of the desired entity or relationship.
2769    
2770    =item RETURN
2771    
2772    The table containing the field descriptors for the specified object.
2773    
2774  =back  =back
2775    
2776  =cut  =cut
2777    
2778  sub DumpRelations {  sub GetFieldTable {
2779          # Get the parameters.          # Get the parameters.
2780          my ($self, $outputDirectory) = @_;      my ($self, $objectName) = @_;
2781          # Now we need to run through all the relations. First, we loop through the entities.      # Get the descriptor from the metadata.
2782          my $metaData = $self->{_metaData};      my $objectData = $self->_GetStructure($objectName);
2783          my $entities = $metaData->{Entities};      # Return the object's field table.
2784          while (my ($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});  
         }  
2785  }  }
2786    
2787  =head3 InsertObject  =head3 SplitKeywords
2788    
2789  C<< my $ok = $database->InsertObject($objectType, \%fieldHash); >>  C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2790    
2791  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
2792  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,
2793  (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
2794  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
2795  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
2796  C<ZP_00210270.1> and C<gi|46206278>.  duplicates.
2797    
2798  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
2799    
2800  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>.  
2801    
2802  C<< $database->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  would return both C<frog> and C<toad>. If this is a problem we can deal
2803    with it later.
2804    
2805  =over 4  =over 4
2806    
2807  =item newObjectType  =item keywordString
2808    
2809  Type name of the object to insert.  The keyword string to be parsed.
2810    
2811  =item fieldHash  =item RETURN
2812    
2813  Hash of field names to values.  Returns a list of the words in the keyword string the user wants to
2814    see.
2815    
2816    =back
2817    
2818    =cut
2819    
2820    sub SplitKeywords {
2821        # Get the parameters.
2822        my ($keywordString) = @_;
2823        # Make a safety copy of the string. (This helps during debugging.)
2824        my $workString = $keywordString;
2825        # Convert operators we don't care about to spaces.
2826        $workString =~ tr/+"()<>/ /;
2827        # Split the rest of the string along space boundaries. Note that we
2828        # eliminate any words that are zero length or begin with a minus sign.
2829        my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2830        # Use a hash to remove duplicates.
2831        my %words = map { $_ => 1 } @wordList;
2832        # Return the result.
2833        return sort keys %words;
2834    }
2835    
2836    =head3 ValidateFieldName
2837    
2838    C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2839    
2840    Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2841    be hyphenated words subject to certain restrictions.
2842    
2843    =over 4
2844    
2845    =item fieldName
2846    
2847    Field name to be validated.
2848    
2849  =item RETURN  =item RETURN
2850    
2851  Returns 1 if successful, 0 if an error occurred.  Returns TRUE if the field name is valid, else FALSE.
2852    
2853  =back  =back
2854    
2855  =cut  =cut
2856    
2857  sub InsertObject {  sub ValidateFieldName {
2858          # Get the parameters.          # Get the parameters.
2859          my ($self, $newObjectType, $fieldHash) = @_;      my ($fieldName) = @_;
2860          # Denote that so far we appear successful.      # Declare the return variable. The field name is valid until we hear
2861        # differently.
2862          my $retVal = 1;          my $retVal = 1;
2863          # Get the database handle.      # Look for bad stuff in the name.
2864          my $dbh = $self->{_dbh};      if ($fieldName =~ /--/) {
2865          # Get the relation list.          # Here we have a doubled minus sign.
2866          my $relationTable = $self->_GetRelationTable($newObjectType);          Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2867          # Loop through the relations. We'll build insert statements for each one. If a relation is          $retVal = 0;
2868          # secondary, we may end up generating multiple insert statements. If an error occurs, we      } elsif ($fieldName !~ /^[A-Za-z]/) {
2869          # stop the loop.          # Here the field name is missing the initial letter.
2870          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);  
2871                                                  $retVal = 0;                                                  $retVal = 0;
                                         }  
                                 }  
2872                          } else {                          } else {
2873                                  # Here the field is not present. Flag it as missing.          # Strip out the minus signs. Everything remaining must be a letter,
2874                                  push @missing, $fieldName;          # underscore, or digit.
2875                          }          my $strippedName = $fieldName;
2876                  }          $strippedName =~ s/-//g;
2877                  # If we are the primary relation, add the new-record flag.          if ($strippedName !~ /^(\w|\d)+$/) {
2878                  if ($relationName eq $newObjectType) {              Trace("Field name $fieldName contains illegal characters.") if T(1);
2879                          push @valueList, 1;              $retVal = 0;
                         push @fieldNameList, "new_record";  
2880                  }                  }
                 # 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;  
2881                                          }                                          }
2882        # Return the result.
2883        return $retVal;
2884                                  }                                  }
2885                                  # Execute the INSERT statement with the specified parameter list.  
2886                                  $retVal = $sth->execute(@parameterList);  =head3 ReadMetaXML
2887                                  if (!$retVal) {  
2888                                          my $errorString = $sth->errstr();  C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2889                                          Trace("Insert error: $errorString.") if T(0);  
2890    This method reads a raw database definition XML file and returns it.
2891    Normally, the metadata used by the ERDB system has been processed and
2892    modified to make it easier to load and retrieve the data; however,
2893    this method can be used to get the data in its raw form.
2894    
2895    =over 4
2896    
2897    =item fileName
2898    
2899    Name of the XML file to read.
2900    
2901    =item RETURN
2902    
2903    Returns a hash reference containing the raw XML data from the specified file.
2904    
2905    =back
2906    
2907    =cut
2908    
2909    sub ReadMetaXML {
2910        # Get the parameters.
2911        my ($fileName) = @_;
2912        # Read the XML.
2913        my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2914        Trace("XML metadata loaded from file $fileName.") if T(1);
2915        # Return the result.
2916        return $retVal;
2917                                  }                                  }
2918    
2919    =head3 GetEntityFieldHash
2920    
2921    C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2922    
2923    Get the field hash of the named entity in the specified raw XML structure.
2924    The field hash may not exist, in which case we need to create it.
2925    
2926    =over 4
2927    
2928    =item structure
2929    
2930    Raw XML structure defininng the database. This is not the run-time XML used by
2931    an ERDB object, since that has all sorts of optimizations built-in.
2932    
2933    =item entityName
2934    
2935    Name of the entity whose field structure is desired.
2936    
2937    =item RETURN
2938    
2939    Returns the field hash used to define the entity's fields.
2940    
2941    =back
2942    
2943    =cut
2944    
2945    sub GetEntityFieldHash {
2946        # Get the parameters.
2947        my ($structure, $entityName) = @_;
2948        # Get the entity structure.
2949        my $entityData = $structure->{Entities}->{$entityName};
2950        # Look for a field structure.
2951        my $retVal = $entityData->{Fields};
2952        # If it doesn't exist, create it.
2953        if (! defined($retVal)) {
2954            $entityData->{Fields} = {};
2955            $retVal = $entityData->{Fields};
2956                          }                          }
2957        # Return the result.
2958        return $retVal;
2959                  }                  }
2960    
2961    =head3 WriteMetaXML
2962    
2963    C<< ERDB::WriteMetaXML($structure, $fileName); >>
2964    
2965    Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2966    used to update the database definition. It must be used with care, however, since it
2967    will only work on a raw structure, not on the processed structure created by an ERDB
2968    constructor.
2969    
2970    =over 4
2971    
2972    =item structure
2973    
2974    XML structure to be written to the file.
2975    
2976    =item fileName
2977    
2978    Name of the output file to which the updated XML should be stored.
2979    
2980    =back
2981    
2982    =cut
2983    
2984    sub WriteMetaXML {
2985        # Get the parameters.
2986        my ($structure, $fileName) = @_;
2987        # Compute the output.
2988        my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2989        # Write it to the file.
2990        my $xmlOut = Open(undef, ">$fileName");
2991        print $xmlOut $fileString;
2992          }          }
2993          # Return the success indicator.  
2994    
2995    =head3 HTMLNote
2996    
2997    Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2998    supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
2999    Except for C<[p]>, all the codes are closed by slash-codes. So, for
3000    example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3001    
3002    C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3003    
3004    =over 4
3005    
3006    =item dataString
3007    
3008    String to convert to HTML.
3009    
3010    =item RETURN
3011    
3012    An HTML string derived from the input string.
3013    
3014    =back
3015    
3016    =cut
3017    
3018    sub HTMLNote {
3019        # Get the parameter.
3020        my ($dataString) = @_;
3021        # HTML-escape the text.
3022        my $retVal = CGI::escapeHTML($dataString);
3023        # Substitute the bulletin board codes.
3024        $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3025        $retVal =~ s!\[p\]!</p><p>!g;
3026        # Return the result.
3027          return $retVal;          return $retVal;
3028  }  }
3029    
 =head3 LoadTable  
3030    
3031  C<< my %results = $database->LoadTable($fileName, $relationName, $truncateFlag); >>  =head2 Data Mining Methods
3032    
3033    =head3 GetUsefulCrossValues
3034    
3035  Load data from a tab-delimited file into a specified table, optionally re-creating the table first.  C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3036    
3037    Return a list of the useful attributes that would be returned by a B<Cross> call
3038    from an entity of the source entity type through the specified relationship. This
3039    means it will return the fields of the target entity type and the intersection data
3040    fields in the relationship. Only primary table fields are returned. In other words,
3041    the field names returned will be for fields where there is always one and only one
3042    value.
3043    
3044  =over 4  =over 4
3045    
3046  =item fileName  =item sourceEntity
3047    
3048  Name of the file from which the table data should be loaded.  Name of the entity from which the relationship crossing will start.
3049    
3050  =item relationName  =item relationship
3051    
3052  Name of the relation to be loaded. This is the same as the table name.  Name of the relationship being crossed.
3053    
3054  =item truncateFlag  =item RETURN
3055    
3056  TRUE if the table should be dropped and re-created, else FALSE  Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3057    
3058    =back
3059    
3060    =cut
3061    #: Return Type @;
3062    sub GetUsefulCrossValues {
3063        # Get the parameters.
3064        my ($self, $sourceEntity, $relationship) = @_;
3065        # Declare the return variable.
3066        my @retVal = ();
3067        # Determine the target entity for the relationship. This is whichever entity is not
3068        # the source entity. So, if the source entity is the FROM, we'll get the name of
3069        # the TO, and vice versa.
3070        my $relStructure = $self->_GetStructure($relationship);
3071        my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3072        my $targetEntity = $relStructure->{$targetEntityType};
3073        # Get the field table for the entity.
3074        my $entityFields = $self->GetFieldTable($targetEntity);
3075        # The field table is a hash. The hash key is the field name. The hash value is a structure.
3076        # For the entity fields, the key aspect of the target structure is that the {relation} value
3077        # must match the entity name.
3078        my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3079                            keys %{$entityFields};
3080        # Push the fields found onto the return variable.
3081        push @retVal, sort @fieldList;
3082        # Get the field table for the relationship.
3083        my $relationshipFields = $self->GetFieldTable($relationship);
3084        # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3085        # This may end up being an empty set.
3086        my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3087                            keys %{$relationshipFields};
3088        # Push these onto the return list.
3089        push @retVal, sort @fieldList2;
3090        # Return the result.
3091        return @retVal;
3092    }
3093    
3094    =head3 FindColumn
3095    
3096    C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3097    
3098    Return the location a desired column in a data mining header line. The data
3099    mining header line is a tab-separated list of column names. The column
3100    identifier is either the numerical index of a column or the actual column
3101    name.
3102    
3103    =over 4
3104    
3105    =item headerLine
3106    
3107    The header line from a data mining command, which consists of a tab-separated
3108    list of column names.
3109    
3110    =item columnIdentifier
3111    
3112    Either the ordinal number of the desired column (1-based), or the name of the
3113    desired column.
3114    
3115  =item RETURN  =item RETURN
3116    
3117  Returns a statistical object containing the number of records read and a list of the error messages.  Returns the array index (0-based) of the desired column.
3118    
3119  =back  =back
3120    
3121  =cut  =cut
3122  sub LoadTable {  
3123    sub FindColumn {
3124          # Get the parameters.          # Get the parameters.
3125          my ($self, $fileName, $relationName, $truncateFlag) = @_;      my ($headerLine, $columnIdentifier) = @_;
3126          # Create the statistical return object.      # Declare the return variable.
3127          my $retVal = _GetLoadStats();      my $retVal;
3128          # Trace the fact of the load.      # Split the header line into column names.
3129          Trace("Loading table $relationName from $fileName") if T(1);      my @headers = ParseColumns($headerLine);
3130          # Get the database handle.      # Determine whether we have a number or a name.
3131          my $dbh = $self->{_dbh};      if ($columnIdentifier =~ /^\d+$/) {
3132          # Get the relation data.          # Here we have a number. Subtract 1 and validate the result.
3133          my $relation = $self->_FindRelation($relationName);          $retVal = $columnIdentifier - 1;
3134          # Check the truncation flag.          if ($retVal < 0 || $retVal > $#headers) {
3135          if ($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);  
3136          }          }
         # 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 $relationName.") if T(1);  
3137          } else {          } else {
3138                  # Here we successfully loaded the table. Trace the number of records loaded.          # Here we have a name. We need to find it in the list.
3139                  Trace("$retVal->{records} records read for $relationName.") if T(1);          for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3140                  # If we're rebuilding, we need to create the table indexes.              if ($headers[$i] eq $columnIdentifier) {
3141                  if ($truncateFlag) {                  $retVal = $i;
                         eval {  
                                 $self->CreateIndex($relationName);  
                         };  
                         if ($@) {  
                                 $retVal->AddMessage($@);  
3142                          }                          }
3143                  }                  }
3144            if (! defined($retVal)) {
3145                Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3146          }          }
3147          # Commit the database changes.      }
3148          $dbh->commit_tran;      # Return the result.
         # Delete the temporary file.  
         unlink $tempName;  
         # Return the statistics.  
3149          return $retVal;          return $retVal;
3150  }  }
3151    
3152  =head3 GenerateEntity  =head3 ParseColumns
3153    
3154  C<< my $fieldHash = $database->GenerateEntity($id, $type, \%values); >>  C<< my @columns = ERDB::ParseColumns($line); >>
3155    
3156  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.  
3157    
3158  =over 4  =over 4
3159    
3160  =item id  =item line
   
 ID to assign to the new entity.  
   
 =item type  
3161    
3162  Type name for the new entity.  A data mining input, consisting of a tab-separated list of columns terminated by a
3163    new-line.
3164    
3165  =item values  =item RETURN
3166    
3167  Hash containing additional values that might be needed by the data generation methods (optional).  Returns a list consisting of the column values.
3168    
3169  =back  =back
3170    
3171  =cut  =cut
3172    
3173  sub GenerateEntity {  sub ParseColumns {
3174          # Get the parameters.          # Get the parameters.
3175          my ($self, $id, $type, $values) = @_;      my ($line) = @_;
3176          # Create the return hash.      # Chop off the line-end.
3177          my $this = { id => $id };      chomp $line;
3178          # Get the metadata structure.      # Split it into a list.
3179          my $metadata = $self->{_metaData};      my @retVal = split(/\t/, $line);
3180          # Get this entity's list of fields.      # Return the result.
3181          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;  
3182  }  }
3183    
3184    =head2 Virtual Methods
3185    
3186  =head2 Internal Utility Methods  =head3 CleanKeywords
3187    
3188  =head3 GetLoadStats  C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3189    
3190  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
3191    be overridden by the subclass. The base-class method removes extra spaces
3192    and converts everything to lower case.
3193    
3194  This is a static method.  =over 4
3195    
3196    =item searchExpression
3197    
3198    Search expression or keyword list to clean. Note that a search expression may
3199    contain boolean operators which need to be preserved. This includes leading
3200    minus signs.
3201    
3202    =item RETURN
3203    
3204    Cleaned expression or keyword list.
3205    
3206    =back
3207    
3208  =cut  =cut
3209    
3210  sub _GetLoadStats {  sub CleanKeywords {
3211          return Stats->new('records');      # Get the parameters.
3212        my ($self, $searchExpression) = @_;
3213        # Lower-case the expression and copy it into the return variable. Note that we insure we
3214        # don't accidentally end up with an undefined value.
3215        my $retVal = lc($searchExpression || "");
3216        # Remove extra spaces.
3217        $retVal =~ s/\s+/ /g;
3218        $retVal =~ s/(^\s+)|(\s+$)//g;
3219        # Return the result.
3220        return $retVal;
3221  }  }
3222    
3223  =head3 GenerateFields  =head3 GetSourceObject
3224    
3225  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.  
3226    
3227  This is a static method.  Return the object to be used in loading special attributes of the specified entity. The
3228    algorithm for loading special attributes is stored in the C<DataGen> elements of the
3229    XML
3230    
3231    =head2 Internal Utility Methods
3232    
3233    =head3 _RelationMap
3234    
3235    C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3236    
3237    Create the relation map for an SQL query. The relation map is used by B<DBObject>
3238    to determine how to interpret the results of the query.
3239    
3240  =over 4  =over 4
3241    
3242  =item this  =item mappedNameHashRef
3243    
3244  Hash table into which the field values should be placed.  Reference to a hash that maps modified object names to real object names.
3245    
3246  =item fields  =item mappedNameListRef
3247    
3248  Field structure from which the field descriptors should be taken.  Reference to a list of modified object names in the order they appear in the
3249    SELECT list.
3250    
3251  =item type  =item RETURN
3252    
3253    Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3254    query followed by the actual name of that object. This enables the B<DBObject> to
3255    determine the order of the tables in the query and which object name belongs to each
3256    mapped object name. Most of the time these two values are the same; however, if a
3257    relation occurs twice in the query, the relation name in the field list and WHERE
3258    clause will use a mapped name (generally the actual relation name with a numeric
3259    suffix) that does not match the actual relation name.
3260    
3261    =back
3262    
3263    =cut
3264    
3265    sub _RelationMap {
3266        # Get the parameters.
3267        my ($mappedNameHashRef, $mappedNameListRef) = @_;