[Bio] / Sprout / ERDB.pm Repository:
ViewVC logotype

Annotation of /Sprout/ERDB.pm

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.73 - (view) (download) (as text)

1 : parrello 1.1 package ERDB;
2 :    
3 : parrello 1.10 use strict;
4 :     use Tracer;
5 : olson 1.14 use DBrtns;
6 : parrello 1.10 use Data::Dumper;
7 :     use XML::Simple;
8 :     use DBQuery;
9 :     use DBObject;
10 :     use Stats;
11 :     use Time::HiRes qw(gettimeofday);
12 : parrello 1.42 use Digest::MD5 qw(md5_base64);
13 : parrello 1.19 use FIG;
14 : parrello 1.73 use CGI;
15 : parrello 1.1
16 :     =head1 Entity-Relationship Database Package
17 :    
18 :     =head2 Introduction
19 :    
20 :     The Entity-Relationship Database Package allows the client to create an easily-configurable
21 :     database of Entities connected by Relationships. Each entity is represented by one or more
22 :     relations in an underlying SQL database. Each relationship is represented by a single
23 :     relation that connects two entities.
24 :    
25 :     Although this package is designed for general use, all examples are derived from the
26 :     Sprout database, which is the first database implemented using this package.
27 :    
28 :     Each entity has at least one relation, the I<primary relation>, that has the same name as
29 :     the entity. The primary relation contains a field named C<id> that contains the unique
30 :     identifier of each entity instance. An entity may have additional relations that contain
31 :     fields which are optional or can occur more than once. For example, the B<FEATURE> entity
32 :     has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
33 :     is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
34 :     however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
35 :     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
37 :     as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38 : parrello 1.8 (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39 :     the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40 :     number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41 :     C<FeatureVirulence>.
42 : parrello 1.1
43 :     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>),
45 :     or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
46 :     ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
47 :     of the relationship is generally a verb phrase with the source entity as the subject and the
48 :     target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
49 :     and B<SOURCE> entities, and indicates that a particular source organization participated in the
50 :     mapping of the genome. A source organization frequently participates in the mapping
51 :     of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
52 :     this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
53 :     relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
54 :     and C<to-link>, which contains a source ID.
55 :    
56 :     A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
57 :     are implemented as additional fields in the relationship's relation. So, for example, the
58 :     B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
59 :     to determine which sequences make up a contig. The relationship has as an attribute the
60 :     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.
62 :    
63 : parrello 1.73 The database itself is described by an XML file. In addition to all the data required to define
64 :     the entities, relationships, and attributes, the schema provides space for notes describing
65 :     the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66 :     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 : parrello 1.1
72 :     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
74 :     was inserted by the L</InsertObject> method.
75 :    
76 : parrello 1.8 =head2 XML Database Description
77 :    
78 :     =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 : parrello 1.60 =item counter
96 :    
97 :     32-bit unsigned integer
98 :    
99 : parrello 1.8 =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 : parrello 1.44 =item id-string
119 :    
120 :     variable-length string, maximum 25 characters
121 :    
122 : parrello 1.8 =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 : parrello 1.42 =item hash-string
139 :    
140 :     variable-length string, maximum 22 characters
141 :    
142 : parrello 1.8 =back
143 :    
144 : parrello 1.42 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 : parrello 1.8 =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 : parrello 1.10 <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 : parrello 1.8
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 : parrello 1.10 <Entity ... >
181 :     <Fields>
182 :     ... Field tags ...
183 :     </Fields>
184 :     </Entity>
185 : parrello 1.8
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 : parrello 1.70 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 : parrello 1.8
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 : parrello 1.70 =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 : parrello 1.73 =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 : parrello 1.8 =back
228 :    
229 :     =head3 Indexes
230 :    
231 :     An entity can have multiple alternate indexes associated with it. The fields must
232 :     be from the primary 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 : parrello 1.1 =cut
333 :    
334 :     # GLOBALS
335 :    
336 :     # 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
338 : parrello 1.73 # of the specified type. "avgLen" is the average byte length for estimating
339 :     # 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, avgLen => 1, sort => "",
341 :     notes => "single ASCII character"},
342 :     int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n",
343 :     notes => "signed 32-bit integer"},
344 :     counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n",
345 :     notes => "unsigned 32-bit integer"},
346 :     string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "",
347 :     notes => "character string, 0 to 255 characters"},
348 :     text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "",
349 :     notes => "character string, nearly unlimited length, cannot be indexed"},
350 :     date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n",
351 :     notes => "signed, 64-bit integer"},
352 :     float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g",
353 :     notes => "64-bit double precision floating-point number"},
354 :     boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n",
355 :     notes => "boolean value: 0 if false, 1 if true"},
356 : parrello 1.42 'hash-string' =>
357 : parrello 1.73 { sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "",
358 :     notes => "string stored in digested form, used for certain types of key fields"},
359 : parrello 1.44 'id-string' =>
360 : parrello 1.73 { sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "",
361 :     notes => "character string, 0 to 25 characters"},
362 : parrello 1.10 'key-string' =>
363 : parrello 1.73 { sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "",
364 :     notes => "character string, 0 to 40 characters"},
365 : parrello 1.10 'name-string' =>
366 : parrello 1.73 { sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "",
367 :     notes => "character string, 0 to 80 characters"},
368 : parrello 1.10 'medium-string' =>
369 : parrello 1.73 { sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "",
370 :     notes => "character string, 0 to 160 characters"},
371 : parrello 1.10 );
372 : parrello 1.1
373 :     # Table translating arities into natural language.
374 :     my %ArityTable = ( '11' => 'one-to-one',
375 : parrello 1.10 '1M' => 'one-to-many',
376 :     'MM' => 'many-to-many'
377 :     );
378 : parrello 1.1
379 : parrello 1.73 # Options for XML input and output.
380 :    
381 :     my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
382 :     Entities => 'Entity',
383 :     Fields => 'Field',
384 :     Indexes => 'Index',
385 :     IndexFields => 'IndexField'
386 :     },
387 :     KeyAttr => { Relationship => 'name',
388 :     Entity => 'name',
389 :     Field => 'name'
390 :     },
391 :     SuppressEmpty => 1,
392 :     );
393 :    
394 :     my %XmlInOpts = (
395 :     ForceArray => ['Field', 'Index', 'IndexField'],
396 :     ForceContent => 1,
397 :     NormalizeSpace => 2,
398 :     );
399 :     my %XmlOutOpts = (
400 :     RootName => 'Database',
401 :     XMLDecl => 1,
402 :     );
403 : parrello 1.1
404 :    
405 :     =head2 Public Methods
406 :    
407 :     =head3 new
408 :    
409 : parrello 1.5 C<< my $database = ERDB->new($dbh, $metaFileName); >>
410 : parrello 1.1
411 :     Create a new ERDB object.
412 :    
413 :     =over 4
414 :    
415 :     =item dbh
416 :    
417 :     DBKernel database object for the target database.
418 :    
419 :     =item metaFileName
420 :    
421 :     Name of the XML file containing the metadata.
422 :    
423 :     =back
424 :    
425 :     =cut
426 :    
427 :     sub new {
428 : parrello 1.10 # Get the parameters.
429 :     my ($class, $dbh, $metaFileName, $options) = @_;
430 :     # Load the meta-data.
431 :     my $metaData = _LoadMetaData($metaFileName);
432 :     # Create the object.
433 :     my $self = { _dbh => $dbh,
434 :     _metaData => $metaData
435 :     };
436 :     # Bless and return it.
437 :     bless $self, $class;
438 :     return $self;
439 : parrello 1.1 }
440 :    
441 :     =head3 ShowMetaData
442 :    
443 : parrello 1.18 C<< $erdb->ShowMetaData($fileName); >>
444 : parrello 1.1
445 :     This method outputs a description of the database. This description can be used to help users create
446 :     the data to be loaded into the relations.
447 :    
448 :     =over 4
449 :    
450 :     =item filename
451 :    
452 :     The name of the output file.
453 :    
454 :     =back
455 :    
456 :     =cut
457 :    
458 :     sub ShowMetaData {
459 : parrello 1.10 # Get the parameters.
460 :     my ($self, $filename) = @_;
461 :     # Get the metadata and the title string.
462 :     my $metadata = $self->{_metaData};
463 :     # Get the title string.
464 :     my $title = $metadata->{Title};
465 :     # Get the entity and relationship lists.
466 :     my $entityList = $metadata->{Entities};
467 :     my $relationshipList = $metadata->{Relationships};
468 :     # Open the output file.
469 :     open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
470 :     Trace("Building MetaData table of contents.") if T(4);
471 :     # Write the HTML heading stuff.
472 :     print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
473 :     print HTMLOUT "</head>\n<body>\n";
474 : parrello 1.45 # Write the documentation.
475 :     print HTMLOUT $self->DisplayMetaData();
476 :     # Close the document.
477 :     print HTMLOUT "</body>\n</html>\n";
478 :     # Close the file.
479 :     close HTMLOUT;
480 :     }
481 :    
482 :     =head3 DisplayMetaData
483 :    
484 :     C<< my $html = $erdb->DisplayMetaData(); >>
485 :    
486 :     Return an HTML description of the database. This description can be used to help users create
487 :     the data to be loaded into the relations and form queries. The output is raw includable HTML
488 :     without any HEAD or BODY tags.
489 :    
490 :     =over 4
491 :    
492 :     =item filename
493 :    
494 :     The name of the output file.
495 :    
496 :     =back
497 :    
498 :     =cut
499 :    
500 :     sub DisplayMetaData {
501 :     # Get the parameters.
502 :     my ($self) = @_;
503 :     # Get the metadata and the title string.
504 :     my $metadata = $self->{_metaData};
505 :     # Get the title string.
506 :     my $title = $metadata->{Title};
507 :     # Get the entity and relationship lists.
508 :     my $entityList = $metadata->{Entities};
509 :     my $relationshipList = $metadata->{Relationships};
510 :     # Declare the return variable.
511 :     my $retVal = "";
512 :     # Open the output file.
513 :     Trace("Building MetaData table of contents.") if T(4);
514 : parrello 1.10 # Here we do the table of contents. It starts as an unordered list of section names. Each
515 :     # section contains an ordered list of entity or relationship subsections.
516 : parrello 1.45 $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
517 : parrello 1.10 # Loop through the Entities, displaying a list item for each.
518 :     foreach my $key (sort keys %{$entityList}) {
519 :     # Display this item.
520 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
521 : parrello 1.10 }
522 :     # Close off the entity section and start the relationship section.
523 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
524 : parrello 1.10 # Loop through the Relationships.
525 :     foreach my $key (sort keys %{$relationshipList}) {
526 :     # Display this item.
527 :     my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
528 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
529 : parrello 1.10 }
530 :     # Close off the relationship section and list the join table section.
531 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
532 : parrello 1.10 # Close off the table of contents itself.
533 : parrello 1.45 $retVal .= "</ul>\n";
534 : parrello 1.10 # Now we start with the actual data. Denote we're starting the entity section.
535 : parrello 1.45 $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
536 : parrello 1.10 # Loop through the entities.
537 :     for my $key (sort keys %{$entityList}) {
538 :     Trace("Building MetaData entry for $key entity.") if T(4);
539 :     # Create the entity header. It contains a bookmark and the entity name.
540 : parrello 1.45 $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
541 : parrello 1.10 # Get the entity data.
542 :     my $entityData = $entityList->{$key};
543 :     # If there's descriptive text, display it.
544 :     if (my $notes = $entityData->{Notes}) {
545 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
546 : parrello 1.10 }
547 :     # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
548 : parrello 1.45 $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
549 : parrello 1.10 # Loop through the relationships.
550 :     for my $relationship (sort keys %{$relationshipList}) {
551 :     # Get the relationship data.
552 :     my $relationshipStructure = $relationshipList->{$relationship};
553 :     # Only use the relationship if if has this entity in its FROM or TO fields.
554 :     if ($relationshipStructure->{from} eq $key || $relationshipStructure->{to} eq $key) {
555 :     # Get the relationship sentence and append the arity.
556 :     my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
557 :     # Display the relationship data.
558 : parrello 1.45 $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
559 : parrello 1.10 }
560 :     }
561 :     # Close off the relationship list.
562 : parrello 1.45 $retVal .= "</ul>\n";
563 : parrello 1.10 # Get the entity's relations.
564 :     my $relationList = $entityData->{Relations};
565 :     # Create a header for the relation subsection.
566 : parrello 1.45 $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
567 : parrello 1.10 # Loop through the relations, displaying them.
568 :     for my $relation (sort keys %{$relationList}) {
569 :     my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
570 : parrello 1.45 $retVal .= $htmlString;
571 : parrello 1.10 }
572 :     }
573 :     # Denote we're starting the relationship section.
574 : parrello 1.45 $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
575 : parrello 1.10 # Loop through the relationships.
576 :     for my $key (sort keys %{$relationshipList}) {
577 :     Trace("Building MetaData entry for $key relationship.") if T(4);
578 :     # Get the relationship's structure.
579 :     my $relationshipStructure = $relationshipList->{$key};
580 :     # Create the relationship header.
581 :     my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
582 : parrello 1.45 $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
583 : parrello 1.10 # Get the entity names.
584 :     my $fromEntity = $relationshipStructure->{from};
585 :     my $toEntity = $relationshipStructure->{to};
586 :     # Describe the relationship arity. Note there's a bit of trickiness involving recursive
587 :     # many-to-many relationships. In a normal many-to-many we use two sentences to describe
588 :     # the arity (one for each direction). This is a bad idea for a recursive relationship,
589 :     # since both sentences will say the same thing.
590 :     my $arity = $relationshipStructure->{arity};
591 :     if ($arity eq "11") {
592 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
593 : parrello 1.10 } else {
594 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
595 : parrello 1.10 if ($arity eq "MM" && $fromEntity ne $toEntity) {
596 : parrello 1.45 $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
597 : parrello 1.10 }
598 :     }
599 : parrello 1.45 $retVal .= "</p>\n";
600 : parrello 1.10 # If there are notes on this relationship, display them.
601 :     if (my $notes = $relationshipStructure->{Notes}) {
602 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
603 : parrello 1.10 }
604 :     # Generate the relationship's relation table.
605 :     my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
606 : parrello 1.45 $retVal .= $htmlString;
607 : parrello 1.10 }
608 :     Trace("Building MetaData join table.") if T(4);
609 :     # Denote we're starting the join table.
610 : parrello 1.45 $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
611 : parrello 1.10 # Create a table header.
612 : parrello 1.45 $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
613 : parrello 1.10 # Loop through the joins.
614 :     my $joinTable = $metadata->{Joins};
615 :     my @joinKeys = keys %{$joinTable};
616 :     for my $joinKey (sort @joinKeys) {
617 :     # Separate out the source, the target, and the join clause.
618 :     $joinKey =~ m!^([^/]+)/(.+)$!;
619 :     my ($sourceRelation, $targetRelation) = ($1, $2);
620 : parrello 1.30 Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
621 : parrello 1.10 my $source = $self->ComputeObjectSentence($sourceRelation);
622 :     my $target = $self->ComputeObjectSentence($targetRelation);
623 :     my $clause = $joinTable->{$joinKey};
624 :     # Display them in a table row.
625 : parrello 1.45 $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
626 : parrello 1.10 }
627 :     # Close the table.
628 : parrello 1.45 $retVal .= _CloseTable();
629 :     Trace("Built MetaData HTML.") if T(3);
630 :     # Return the HTML.
631 :     return $retVal;
632 : parrello 1.1 }
633 :    
634 :     =head3 DumpMetaData
635 :    
636 : parrello 1.18 C<< $erdb->DumpMetaData(); >>
637 : parrello 1.1
638 :     Return a dump of the metadata structure.
639 :    
640 :     =cut
641 :    
642 :     sub DumpMetaData {
643 : parrello 1.10 # Get the parameters.
644 :     my ($self) = @_;
645 :     # Dump the meta-data.
646 :     return Data::Dumper::Dumper($self->{_metaData});
647 : parrello 1.1 }
648 :    
649 :     =head3 CreateTables
650 :    
651 : parrello 1.18 C<< $erdb->CreateTables(); >>
652 : parrello 1.1
653 :     This method creates the tables for the database from the metadata structure loaded by the
654 :     constructor. It is expected this function will only be used on rare occasions, when the
655 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
656 : parrello 1.1 used by itself with the truncate flag turned on.
657 :    
658 :     =cut
659 :    
660 :     sub CreateTables {
661 : parrello 1.10 # Get the parameters.
662 :     my ($self) = @_;
663 : parrello 1.23 # Get the relation names.
664 :     my @relNames = $self->GetTableNames();
665 :     # Loop through the relations.
666 :     for my $relationName (@relNames) {
667 :     # Create a table for this relation.
668 :     $self->CreateTable($relationName);
669 :     Trace("Relation $relationName created.") if T(2);
670 : parrello 1.10 }
671 : parrello 1.1 }
672 :    
673 :     =head3 CreateTable
674 :    
675 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
676 : parrello 1.1
677 :     Create the table for a relation and optionally create its indexes.
678 :    
679 :     =over 4
680 :    
681 :     =item relationName
682 :    
683 :     Name of the relation (which will also be the table name).
684 :    
685 : parrello 1.18 =item indexFlag
686 : parrello 1.1
687 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
688 :     L</CreateIndexes> must be called later to bring the indexes into existence.
689 :    
690 : parrello 1.18 =item estimatedRows (optional)
691 :    
692 :     If specified, the estimated maximum number of rows for the relation. This
693 :     information allows the creation of tables using storage engines that are
694 :     faster but require size estimates, such as MyISAM.
695 :    
696 : parrello 1.1 =back
697 :    
698 :     =cut
699 :    
700 :     sub CreateTable {
701 : parrello 1.10 # Get the parameters.
702 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
703 : parrello 1.10 # Get the database handle.
704 :     my $dbh = $self->{_dbh};
705 :     # Get the relation data and determine whether or not the relation is primary.
706 :     my $relationData = $self->_FindRelation($relationName);
707 :     my $rootFlag = $self->_IsPrimary($relationName);
708 :     # Create a list of the field data.
709 :     my @fieldList;
710 :     for my $fieldData (@{$relationData->{Fields}}) {
711 :     # Assemble the field name and type.
712 :     my $fieldName = _FixName($fieldData->{name});
713 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
714 :     # Push the result into the field list.
715 :     push @fieldList, $fieldString;
716 :     }
717 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
718 :     if ($rootFlag) {
719 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
720 :     }
721 :     # Convert the field list into a comma-delimited string.
722 :     my $fieldThing = join(', ', @fieldList);
723 :     # Insure the table is not already there.
724 :     $dbh->drop_table(tbl => $relationName);
725 :     Trace("Table $relationName dropped.") if T(2);
726 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
727 :     # faster DB technologies.
728 :     my $estimation = undef;
729 :     if ($estimatedRows) {
730 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
731 :     }
732 : parrello 1.10 # Create the table.
733 :     Trace("Creating table $relationName: $fieldThing") if T(2);
734 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
735 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
736 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
737 :     # index will not be built until the table has been loaded.
738 : parrello 1.10 if ($indexFlag) {
739 :     $self->CreateIndex($relationName);
740 :     }
741 : parrello 1.1 }
742 :    
743 : parrello 1.31 =head3 VerifyFields
744 :    
745 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
746 :    
747 :     Run through the list of proposed field values, insuring that all the character fields are
748 :     below the maximum length. If any fields are too long, they will be truncated in place.
749 :    
750 :     =over 4
751 :    
752 :     =item relName
753 :    
754 :     Name of the relation for which the specified fields are destined.
755 :    
756 :     =item fieldList
757 :    
758 :     Reference to a list, in order, of the fields to be put into the relation.
759 :    
760 :     =item RETURN
761 :    
762 :     Returns the number of fields truncated.
763 :    
764 :     =back
765 :    
766 :     =cut
767 :    
768 :     sub VerifyFields {
769 :     # Get the parameters.
770 :     my ($self, $relName, $fieldList) = @_;
771 :     # Initialize the return value.
772 :     my $retVal = 0;
773 :     # Get the relation definition.
774 :     my $relData = $self->_FindRelation($relName);
775 :     # Get the list of field descriptors.
776 :     my $fieldTypes = $relData->{Fields};
777 :     my $fieldCount = scalar @{$fieldTypes};
778 :     # Loop through the two lists.
779 :     for (my $i = 0; $i < $fieldCount; $i++) {
780 :     # Get the type of the current field.
781 :     my $fieldType = $fieldTypes->[$i]->{type};
782 :     # If it's a character field, verify the length.
783 :     if ($fieldType =~ /string/) {
784 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
785 :     my $oldString = $fieldList->[$i];
786 :     if (length($oldString) > $maxLen) {
787 :     # Here it's too big, so we truncate it.
788 :     Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
789 :     $fieldList->[$i] = substr $oldString, 0, $maxLen;
790 :     $retVal++;
791 :     }
792 :     }
793 :     }
794 :     # Return the truncation count.
795 :     return $retVal;
796 :     }
797 :    
798 : parrello 1.42 =head3 DigestFields
799 :    
800 :     C<< $erdb->DigestFields($relName, $fieldList); >>
801 :    
802 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
803 :     specified relation.
804 :    
805 :     =over 4
806 :    
807 :     =item relName
808 :    
809 :     Name of the relation to which the fields belong.
810 :    
811 :     =item fieldList
812 :    
813 :     List of field contents to be loaded into the relation.
814 :    
815 :     =back
816 :    
817 :     =cut
818 :     #: Return Type ;
819 :     sub DigestFields {
820 :     # Get the parameters.
821 :     my ($self, $relName, $fieldList) = @_;
822 :     # Get the relation definition.
823 :     my $relData = $self->_FindRelation($relName);
824 :     # Get the list of field descriptors.
825 :     my $fieldTypes = $relData->{Fields};
826 :     my $fieldCount = scalar @{$fieldTypes};
827 :     # Loop through the two lists.
828 :     for (my $i = 0; $i < $fieldCount; $i++) {
829 :     # Get the type of the current field.
830 :     my $fieldType = $fieldTypes->[$i]->{type};
831 :     # If it's a hash string, digest it in place.
832 :     if ($fieldType eq 'hash-string') {
833 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
834 : parrello 1.42 }
835 :     }
836 :     }
837 :    
838 : parrello 1.46 =head3 DigestKey
839 :    
840 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
841 :    
842 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
843 :     key-based search into a table with key-type hash-string.
844 :    
845 :     Currently the digesting process is independent of the database structure, but that may not
846 :     always be the case, so this is an instance method instead of a static method.
847 :    
848 :     =over 4
849 :    
850 :     =item keyValue
851 :    
852 :     Key value to digest.
853 :    
854 :     =item RETURN
855 :    
856 : parrello 1.56 Digested value of the key.
857 : parrello 1.46
858 :     =back
859 :    
860 :     =cut
861 :    
862 :     sub DigestKey {
863 :     # Get the parameters.
864 :     my ($self, $keyValue) = @_;
865 :     # Compute the digest.
866 :     my $retVal = md5_base64($keyValue);
867 :     # Return the result.
868 :     return $retVal;
869 :     }
870 :    
871 : parrello 1.1 =head3 CreateIndex
872 :    
873 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
874 : parrello 1.1
875 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
876 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
877 :     If that is the case, then L</CreateTable> should be called with the index flag set to
878 :     FALSE, and this method used after the load to create the indexes for the table.
879 : parrello 1.1
880 :     =cut
881 :    
882 :     sub CreateIndex {
883 : parrello 1.10 # Get the parameters.
884 :     my ($self, $relationName) = @_;
885 :     # Get the relation's descriptor.
886 :     my $relationData = $self->_FindRelation($relationName);
887 :     # Get the database handle.
888 :     my $dbh = $self->{_dbh};
889 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
890 :     my $indexHash = $relationData->{Indexes};
891 :     for my $indexName (keys %{$indexHash}) {
892 :     my $indexData = $indexHash->{$indexName};
893 :     # Get the index's field list.
894 :     my @fieldList = _FixNames(@{$indexData->{IndexFields}});
895 :     my $flds = join(', ', @fieldList);
896 :     # Get the index's uniqueness flag.
897 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
898 : parrello 1.10 # Create the index.
899 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
900 : parrello 1.70 flds => $flds, kind => $unique);
901 : parrello 1.24 if ($rv) {
902 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
903 :     } else {
904 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
905 :     }
906 : parrello 1.10 }
907 : parrello 1.1 }
908 :    
909 :     =head3 LoadTables
910 :    
911 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
912 : parrello 1.1
913 :     This method will load the database tables from a directory. The tables must already have been created
914 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
915 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
916 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
917 :     line of the file will be loaded as a row of the target relation table. The field values should be in
918 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
919 :     erased before the new data is loaded in.
920 :    
921 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
922 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
923 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
924 :    
925 :     =over 4
926 :    
927 :     =item directoryName
928 :    
929 :     Name of the directory containing the relation files to be loaded.
930 :    
931 :     =item rebuild
932 :    
933 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
934 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
935 :     by all of the DB engines we use.
936 :    
937 :     =item RETURN
938 :    
939 :     Returns a statistical object describing the number of records read and a list of the error messages.
940 :    
941 :     =back
942 :    
943 :     =cut
944 :    
945 :     sub LoadTables {
946 : parrello 1.10 # Get the parameters.
947 :     my ($self, $directoryName, $rebuild) = @_;
948 :     # Start the timer.
949 :     my $startTime = gettimeofday;
950 :     # Clean any trailing slash from the directory name.
951 :     $directoryName =~ s!/\\$!!;
952 :     # Declare the return variable.
953 :     my $retVal = Stats->new();
954 : parrello 1.23 # Get the relation names.
955 :     my @relNames = $self->GetTableNames();
956 :     for my $relationName (@relNames) {
957 :     # Try to load this relation.
958 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
959 : parrello 1.10 # Accumulate the statistics.
960 :     $retVal->Accumulate($result);
961 :     }
962 :     # Add the duration of the load to the statistical object.
963 :     $retVal->Add('duration', gettimeofday - $startTime);
964 :     # Return the accumulated statistics.
965 :     return $retVal;
966 : parrello 1.1 }
967 :    
968 : parrello 1.23
969 : parrello 1.1 =head3 GetTableNames
970 :    
971 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
972 : parrello 1.1
973 :     Return a list of the relations required to implement this database.
974 :    
975 :     =cut
976 :    
977 :     sub GetTableNames {
978 : parrello 1.10 # Get the parameters.
979 :     my ($self) = @_;
980 :     # Get the relation list from the metadata.
981 :     my $relationTable = $self->{_metaData}->{RelationTable};
982 :     # Return the relation names.
983 :     return keys %{$relationTable};
984 : parrello 1.1 }
985 :    
986 :     =head3 GetEntityTypes
987 :    
988 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
989 : parrello 1.1
990 :     Return a list of the entity type names.
991 :    
992 :     =cut
993 :    
994 :     sub GetEntityTypes {
995 : parrello 1.10 # Get the database object.
996 :     my ($self) = @_;
997 :     # Get the entity list from the metadata object.
998 :     my $entityList = $self->{_metaData}->{Entities};
999 :     # Return the list of entity names in alphabetical order.
1000 :     return sort keys %{$entityList};
1001 : parrello 1.1 }
1002 :    
1003 : parrello 1.73 =head3 GetDataTypes
1004 :    
1005 :     C<< my %types = ERDB::GetDataTypes(); >>
1006 :    
1007 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1008 :     The keys of the big hash are the datatypes. Each smaller hash has several
1009 :     values used to manage the data. The most interesting is the SQL type (key
1010 :     C<sqlType>) and the descriptive node (key C<notes>).
1011 :    
1012 :     Note that changing the values in the smaller hashes will seriously break
1013 :     things, so this data should be treated as read-only.
1014 :    
1015 :     =cut
1016 :    
1017 :     sub GetDataTypes {
1018 :     return %TypeTable;
1019 :     }
1020 :    
1021 :    
1022 : parrello 1.20 =head3 IsEntity
1023 :    
1024 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1025 :    
1026 :     Return TRUE if the parameter is an entity name, else FALSE.
1027 :    
1028 :     =over 4
1029 :    
1030 :     =item entityName
1031 :    
1032 :     Object name to be tested.
1033 :    
1034 :     =item RETURN
1035 :    
1036 :     Returns TRUE if the specified string is an entity name, else FALSE.
1037 :    
1038 :     =back
1039 :    
1040 :     =cut
1041 :    
1042 :     sub IsEntity {
1043 :     # Get the parameters.
1044 :     my ($self, $entityName) = @_;
1045 :     # Test to see if it's an entity.
1046 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1047 :     }
1048 :    
1049 : parrello 1.1 =head3 Get
1050 :    
1051 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1052 : parrello 1.1
1053 :     This method returns a query object for entities of a specified type using a specified filter.
1054 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1055 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1056 :     following call requests all B<Genome> objects for the genus specified in the variable
1057 :     $genus.
1058 :    
1059 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1060 : parrello 1.1
1061 :     The WHERE clause contains a single question mark, so there is a single additional
1062 :     parameter representing the parameter value. It would also be possible to code
1063 :    
1064 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1065 : parrello 1.1
1066 :     however, this version of the call would generate a syntax error if there were any quote
1067 :     characters inside the variable C<$genus>.
1068 :    
1069 :     The use of the strange parenthesized notation for field names enables us to distinguish
1070 :     hyphens contained within field names from minus signs that participate in the computation
1071 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1072 :    
1073 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1074 :     one object's data at the same time, which allows highly complex joined queries. For example,
1075 :    
1076 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1077 : parrello 1.1
1078 :     If multiple names are specified, then the query processor will automatically determine a
1079 :     join path between the entities and relationships. The algorithm used is very simplistic.
1080 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1081 :     the entity and the relationship appear. For example, consider a recursive relationship
1082 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1083 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1084 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1085 :    
1086 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1087 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1088 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1089 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1090 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1091 :    
1092 : parrello 1.1 =over 4
1093 :    
1094 :     =item objectNames
1095 :    
1096 :     List containing the names of the entity and relationship objects to be retrieved.
1097 :    
1098 :     =item filterClause
1099 :    
1100 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1101 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1102 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1103 :     in the filter clause should be added to the parameter list as additional parameters. The
1104 :     fields in a filter clause can come from primary entity relations, relationship relations,
1105 :     or secondary entity relations; however, all of the entities and relationships involved must
1106 :     be included in the list of object names.
1107 :    
1108 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1109 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1110 :     particular genus and sorts them by species name.
1111 :    
1112 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1113 :    
1114 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1115 :     be processed. The idea is to make it less likely to find the verb by accident.
1116 :    
1117 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1118 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1119 :     relation.
1120 :    
1121 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1122 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1123 :     a positive number. So, for example
1124 :    
1125 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1126 :    
1127 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1128 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1129 :     use
1130 :    
1131 :     C<< "LIMIT 10" >>
1132 :    
1133 : parrello 1.45 =item params
1134 : parrello 1.1
1135 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1136 : parrello 1.1
1137 :     =item RETURN
1138 :    
1139 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1140 :    
1141 :     =back
1142 :    
1143 :     =cut
1144 :    
1145 :     sub Get {
1146 : parrello 1.10 # Get the parameters.
1147 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1148 :     # Process the SQL stuff.
1149 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1150 :     $self->_SetupSQL($objectNames, $filterClause);
1151 :     # Create the query.
1152 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1153 :     ".* $suffix";
1154 :     my $sth = $self->_GetStatementHandle($command, $params);
1155 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1156 :     # and mapped name for each object in the query.
1157 :     my @relationMap = ();
1158 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1159 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1160 : parrello 1.39 }
1161 : parrello 1.10 # Return the statement object.
1162 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1163 : parrello 1.10 return $retVal;
1164 : parrello 1.1 }
1165 :    
1166 : parrello 1.70 =head3 Search
1167 :    
1168 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1169 :    
1170 :     Perform a full text search with filtering. The search will be against a specified object
1171 :     in the object name list. That object will get an extra field containing the search
1172 :     relevance. Note that except for the search expression, the parameters of this method are
1173 :     the same as those for L</Get> and follow the same rules.
1174 :    
1175 :     =over 4
1176 :    
1177 :     =item searchExpression
1178 :    
1179 :     Boolean search expression for the text fields of the target object.
1180 :    
1181 :     =item idx
1182 :    
1183 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1184 :    
1185 :     =item objectNames
1186 :    
1187 :     List containing the names of the entity and relationship objects to be retrieved.
1188 :    
1189 :     =item filterClause
1190 :    
1191 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1192 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1193 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1194 :     in the filter clause should be added to the parameter list as additional parameters. The
1195 :     fields in a filter clause can come from primary entity relations, relationship relations,
1196 :     or secondary entity relations; however, all of the entities and relationships involved must
1197 :     be included in the list of object names.
1198 :    
1199 :     =item params
1200 :    
1201 :     Reference to a list of parameter values to be substituted into the filter clause.
1202 :    
1203 :     =item RETURN
1204 :    
1205 :     Returns a query object for the specified search.
1206 :    
1207 :     =back
1208 :    
1209 :     =cut
1210 :    
1211 :     sub Search {
1212 :     # Get the parameters.
1213 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1214 :     # Declare the return variable.
1215 :     my $retVal;
1216 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1217 :     # a parameter list exists before we copy it.
1218 :     my @myParams = ();
1219 :     if (defined $params) {
1220 :     @myParams = @{$params};
1221 :     }
1222 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1223 :     my $object1Name = $objectNames->[$idx];
1224 :     my $object1Structure = $self->_GetStructure($object1Name);
1225 :     # Get the field list.
1226 :     if (! exists $object1Structure->{searchFields}) {
1227 :     Confess("No searchable index for $object1Name.");
1228 :     } else {
1229 :     # Get the field list.
1230 :     my @fields = @{$object1Structure->{searchFields}};
1231 : parrello 1.71 # Clean the search expression.
1232 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1233 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1234 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1235 :     # query itself. Both will use a parameter mark, so we need to push the
1236 :     # search expression onto the front of the parameter list twice.
1237 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1238 : parrello 1.70 # Build the match expression.
1239 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1240 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1241 :     # Process the SQL stuff.
1242 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1243 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1244 :     # Create the query. Note that the match clause is inserted at the front of
1245 :     # the select fields.
1246 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1247 :     ".* $suffix";
1248 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1249 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1250 :     # and mapped name for each object in the query.
1251 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1252 :     # Return the statement object.
1253 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1254 :     }
1255 :     return $retVal;
1256 :     }
1257 :    
1258 : parrello 1.45 =head3 GetFlat
1259 :    
1260 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1261 :    
1262 :     This is a variation of L</GetAll> that asks for only a single field per record and
1263 :     returns a single flattened list.
1264 :    
1265 :     =over 4
1266 :    
1267 :     =item objectNames
1268 :    
1269 :     List containing the names of the entity and relationship objects to be retrieved.
1270 :    
1271 :     =item filterClause
1272 :    
1273 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1274 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1275 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1276 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1277 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1278 :     entities and relationships involved must be included in the list of object names.
1279 :    
1280 :     =item parameterList
1281 :    
1282 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1283 :    
1284 :     =item field
1285 :    
1286 :     Name of the field to be used to get the elements of the list returned.
1287 :    
1288 :     =item RETURN
1289 :    
1290 :     Returns a list of values.
1291 :    
1292 :     =back
1293 :    
1294 :     =cut
1295 :     #: Return Type @;
1296 :     sub GetFlat {
1297 :     # Get the parameters.
1298 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1299 :     # Construct the query.
1300 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1301 :     # Create the result list.
1302 :     my @retVal = ();
1303 :     # Loop through the records, adding the field values found to the result list.
1304 :     while (my $row = $query->Fetch()) {
1305 :     push @retVal, $row->Value($field);
1306 :     }
1307 :     # Return the list created.
1308 :     return @retVal;
1309 :     }
1310 :    
1311 : parrello 1.73 =head3 SpecialFields
1312 :    
1313 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1314 :    
1315 :     Return a hash mapping special fields in the specified entity to the value of their
1316 :     C<special> attribute. This enables the subclass to get access to the special field
1317 :     attributes without needed to plumb the internal ERDB data structures.
1318 :    
1319 :     =over 4
1320 :    
1321 :     =item entityName
1322 :    
1323 :     Name of the entity whose special fields are desired.
1324 :    
1325 :     =item RETURN
1326 :    
1327 :     Returns a hash. The keys of the hash are the special field names, and the values
1328 :     are the values from each special field's C<special> attribute.
1329 :    
1330 :     =back
1331 :    
1332 :     =cut
1333 :    
1334 :     sub SpecialFields {
1335 :     # Get the parameters.
1336 :     my ($self, $entityName) = @_;
1337 :     # Declare the return variable.
1338 :     my %retVal = ();
1339 :     # Find the entity's data structure.
1340 :     my $entityData = $self->{Entities}->{$entityName};
1341 :     # Loop through its fields, adding each special field to the return hash.
1342 :     my $fieldHash = $entityData->{Fields};
1343 :     for my $fieldName (keys %{$fieldHash}) {
1344 :     my $fieldData = $fieldHash->{$fieldName};
1345 :     if (exists $fieldData->{special}) {
1346 :     $retVal{$fieldName} = $fieldData->{special};
1347 :     }
1348 :     }
1349 :     # Return the result.
1350 :     return %retVal;
1351 :     }
1352 :    
1353 : parrello 1.32 =head3 Delete
1354 :    
1355 :     C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1356 :    
1357 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1358 :     relationship instances dependent on it. The idea of dependence here is recursive. An object is
1359 :     always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1360 :     relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1361 :     dependent relationship.
1362 :    
1363 :     =over 4
1364 :    
1365 :     =item entityName
1366 :    
1367 :     Name of the entity type for the instance being deleted.
1368 :    
1369 :     =item objectID
1370 :    
1371 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1372 :     then it is presumed to by a LIKE pattern.
1373 :    
1374 :     =item testFlag
1375 :    
1376 :     If TRUE, the delete statements will be traced without being executed.
1377 :    
1378 :     =item RETURN
1379 :    
1380 :     Returns a statistics object indicating how many records of each particular table were
1381 :     deleted.
1382 :    
1383 :     =back
1384 :    
1385 :     =cut
1386 :     #: Return Type $%;
1387 :     sub Delete {
1388 :     # Get the parameters.
1389 :     my ($self, $entityName, $objectID, $testFlag) = @_;
1390 :     # Declare the return variable.
1391 :     my $retVal = Stats->new();
1392 :     # Get the DBKernel object.
1393 :     my $db = $self->{_dbh};
1394 :     # We're going to generate all the paths branching out from the starting entity. One of
1395 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1396 :     # determine if we've hit a loop.
1397 :     my %alreadyFound = ();
1398 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1399 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1400 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1401 :     # sure we don't delete records that might be needed to forge relationships back to the
1402 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1403 :     # FROM-relationships and entities.
1404 :     my @fromPathList = ();
1405 :     my @toPathList = ();
1406 : parrello 1.32 # This final hash is used to remember what work still needs to be done. We push paths
1407 :     # onto the list, then pop them off to extend the paths. We prime it with the starting
1408 :     # point. Note that we will work hard to insure that the last item on a path in the
1409 :     # TODO list is always an entity.
1410 :     my @todoList = ([$entityName]);
1411 :     while (@todoList) {
1412 :     # Get the current path.
1413 :     my $current = pop @todoList;
1414 :     # Copy it into a list.
1415 :     my @stackedPath = @{$current};
1416 :     # Pull off the last item on the path. It will always be an entity.
1417 :     my $entityName = pop @stackedPath;
1418 :     # Add it to the alreadyFound list.
1419 :     $alreadyFound{$entityName} = 1;
1420 :     # Get the entity data.
1421 :     my $entityData = $self->_GetStructure($entityName);
1422 :     # The first task is to loop through the entity's relation. A DELETE command will
1423 :     # be needed for each of them.
1424 :     my $relations = $entityData->{Relations};
1425 :     for my $relation (keys %{$relations}) {
1426 :     my @augmentedList = (@stackedPath, $relation);
1427 : parrello 1.33 push @fromPathList, \@augmentedList;
1428 : parrello 1.32 }
1429 :     # Now we need to look for relationships connected to this entity.
1430 :     my $relationshipList = $self->{_metaData}->{Relationships};
1431 :     for my $relationshipName (keys %{$relationshipList}) {
1432 :     my $relationship = $relationshipList->{$relationshipName};
1433 :     # Check the FROM field. We're only interested if it's us.
1434 :     if ($relationship->{from} eq $entityName) {
1435 :     # Add the path to this relationship.
1436 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1437 : parrello 1.33 push @fromPathList, \@augmentedList;
1438 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1439 :     # and the target hasn't been seen yet, we want to
1440 :     # stack the entity for future processing.
1441 :     if ($relationship->{arity} eq '1M') {
1442 :     my $toEntity = $relationship->{to};
1443 :     if (! exists $alreadyFound{$toEntity}) {
1444 :     # Here we have a new entity that's dependent on
1445 :     # the current entity, so we need to stack it.
1446 :     my @stackList = (@augmentedList, $toEntity);
1447 : parrello 1.33 push @fromPathList, \@stackList;
1448 : parrello 1.34 } else {
1449 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1450 : parrello 1.32 }
1451 :     }
1452 :     }
1453 :     # Now check the TO field. In this case only the relationship needs
1454 : parrello 1.33 # deletion.
1455 : parrello 1.32 if ($relationship->{to} eq $entityName) {
1456 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1457 : parrello 1.33 push @toPathList, \@augmentedList;
1458 : parrello 1.32 }
1459 :     }
1460 :     }
1461 :     # Create the first qualifier for the WHERE clause. This selects the
1462 :     # keys of the primary entity records to be deleted. When we're deleting
1463 :     # from a dependent table, we construct a join page from the first qualifier
1464 :     # to the table containing the dependent records to delete.
1465 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1466 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1467 :     # the second through the from-list. The from-list is second because
1468 :     # the to-list may need to pass through some of the entities the
1469 :     # from-list would delete.
1470 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1471 :     # Now it's time to do the deletes. We do it in two passes.
1472 :     for my $keyName ('to_link', 'from_link') {
1473 :     # Get the list for this key.
1474 :     my @pathList = @{$stackList{$keyName}};
1475 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1476 : parrello 1.33 # Loop through this list.
1477 :     while (my $path = pop @pathList) {
1478 :     # Get the table whose rows are to be deleted.
1479 :     my @pathTables = @{$path};
1480 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1481 :     # syntax of a DELETE-USING varies among DBMSs.
1482 : parrello 1.33 my $target = $pathTables[$#pathTables];
1483 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1484 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1485 :     # starting table will either be the entity relation or one of the entity's
1486 :     # sub-relations.
1487 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1488 :     # Now we run through the remaining entities in the path, connecting them up.
1489 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1490 :     # Connect the current relationship to the preceding entity.
1491 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1492 :     # The style of connection depends on the direction of the relationship.
1493 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1494 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1495 :     # Here there's a next entity, so connect that to the relationship's
1496 :     # to-link.
1497 :     my $entity2 = $pathTables[$i+1];
1498 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1499 : parrello 1.32 }
1500 :     }
1501 : parrello 1.33 # Now we have our desired DELETE statement.
1502 :     if ($testFlag) {
1503 :     # Here the user wants to trace without executing.
1504 :     Trace($stmt) if T(0);
1505 :     } else {
1506 :     # Here we can delete. Note that the SQL method dies with a confessing
1507 :     # if an error occurs, so we just go ahead and do it.
1508 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1509 :     my $rv = $db->SQL($stmt, 0, $objectID);
1510 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1511 :     # are from the target table, so we use its name to record the
1512 :     # statistic.
1513 :     $retVal->Add($target, $rv);
1514 :     }
1515 : parrello 1.32 }
1516 :     }
1517 :     # Return the result.
1518 :     return $retVal;
1519 :     }
1520 :    
1521 : parrello 1.70 =head3 SortNeeded
1522 :    
1523 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
1524 :    
1525 :     Return the pipe command for the sort that should be applied to the specified
1526 :     relation when creating the load file.
1527 :    
1528 :     For example, if the load file should be sorted ascending by the first
1529 :     field, this method would return
1530 :    
1531 :     sort -k1 -t"\t"
1532 :    
1533 :     If the first field is numeric, the method would return
1534 :    
1535 :     sort -k1n -t"\t"
1536 :    
1537 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1538 :     keys using a sort.
1539 :    
1540 :     =over 4
1541 :    
1542 :     =item relationName
1543 :    
1544 :     Name of the relation to be examined.
1545 :    
1546 :     =item
1547 :    
1548 :     Returns the sort command to use for sorting the relation, suitable for piping.
1549 :    
1550 :     =back
1551 :    
1552 :     =cut
1553 :     #: Return Type $;
1554 :     sub SortNeeded {
1555 :     # Get the parameters.
1556 :     my ($self, $relationName) = @_;
1557 :     # Declare a descriptor to hold the names of the key fields.
1558 :     my @keyNames = ();
1559 :     # Get the relation structure.
1560 :     my $relationData = $self->_FindRelation($relationName);
1561 :     # Find out if the relation is a primary entity relation,
1562 :     # a relationship relation, or a secondary entity relation.
1563 :     my $entityTable = $self->{_metaData}->{Entities};
1564 :     my $relationshipTable = $self->{_metaData}->{Relationships};
1565 :     if (exists $entityTable->{$relationName}) {
1566 :     # Here we have a primary entity relation.
1567 :     push @keyNames, "id";
1568 :     } elsif (exists $relationshipTable->{$relationName}) {
1569 :     # Here we have a relationship. We sort using the FROM index.
1570 :     my $relationshipData = $relationshipTable->{$relationName};
1571 :     my $index = $relationData->{Indexes}->{"idx${relationName}From"};
1572 :     push @keyNames, @{$index->{IndexFields}};
1573 :     } else {
1574 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
1575 :     push @keyNames, "id";
1576 :     }
1577 :     # Now we parse the key names into sort parameters. First, we prime the return
1578 :     # string.
1579 :     my $retVal = "sort -t\"\t\" ";
1580 :     # Get the relation's field list.
1581 :     my @fields = @{$relationData->{Fields}};
1582 :     # Loop through the keys.
1583 :     for my $keyData (@keyNames) {
1584 :     # Get the key and the ordering.
1585 :     my ($keyName, $ordering);
1586 :     if ($keyData =~ /^([^ ]+) DESC/) {
1587 :     ($keyName, $ordering) = ($1, "descending");
1588 :     } else {
1589 :     ($keyName, $ordering) = ($keyData, "ascending");
1590 :     }
1591 :     # Find the key's position and type.
1592 :     my $fieldSpec;
1593 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1594 :     my $thisField = $fields[$i];
1595 :     if ($thisField->{name} eq $keyName) {
1596 :     # Get the sort modifier for this field type. The modifier
1597 :     # decides whether we're using a character, numeric, or
1598 :     # floating-point sort.
1599 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
1600 :     # If the index is descending for this field, denote we want
1601 :     # to reverse the sort order on this field.
1602 :     if ($ordering eq 'descending') {
1603 :     $modifier .= "r";
1604 :     }
1605 :     # Store the position and modifier into the field spec, which
1606 :     # will stop the inner loop. Note that the field number is
1607 :     # 1-based in the sort command, so we have to increment the
1608 :     # index.
1609 :     $fieldSpec = ($i + 1) . $modifier;
1610 :     }
1611 :     }
1612 :     # Add this field to the sort command.
1613 :     $retVal .= " -k$fieldSpec";
1614 :     }
1615 :     # Return the result.
1616 :     return $retVal;
1617 :     }
1618 :    
1619 : parrello 1.6 =head3 GetList
1620 :    
1621 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1622 : parrello 1.6
1623 :     Return a list of object descriptors for the specified objects as determined by the
1624 :     specified filter clause.
1625 :    
1626 :     This method is essentially the same as L</Get> except it returns a list of objects rather
1627 : parrello 1.7 than a query object that can be used to get the results one record at a time.
1628 : parrello 1.6
1629 :     =over 4
1630 :    
1631 :     =item objectNames
1632 :    
1633 :     List containing the names of the entity and relationship objects to be retrieved.
1634 :    
1635 :     =item filterClause
1636 :    
1637 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1638 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1639 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1640 :     in the filter clause should be added to the parameter list as additional parameters. The
1641 :     fields in a filter clause can come from primary entity relations, relationship relations,
1642 :     or secondary entity relations; however, all of the entities and relationships involved must
1643 :     be included in the list of object names.
1644 :    
1645 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1646 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1647 :     particular genus and sorts them by species name.
1648 :    
1649 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1650 :    
1651 :     The rules for field references in a sort order are the same as those for field references in the
1652 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1653 :     relation.
1654 :    
1655 : parrello 1.45 =item params
1656 : parrello 1.6
1657 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1658 : parrello 1.6
1659 :     =item RETURN
1660 :    
1661 :     Returns a list of B<DBObject>s that satisfy the query conditions.
1662 :    
1663 :     =back
1664 :    
1665 :     =cut
1666 :     #: Return Type @%
1667 :     sub GetList {
1668 :     # Get the parameters.
1669 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1670 : parrello 1.10 # Declare the return variable.
1671 :     my @retVal = ();
1672 :     # Perform the query.
1673 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
1674 : parrello 1.10 # Loop through the results.
1675 :     while (my $object = $query->Fetch) {
1676 :     push @retVal, $object;
1677 :     }
1678 : parrello 1.6 # Return the result.
1679 :     return @retVal;
1680 :     }
1681 :    
1682 : parrello 1.45 =head3 GetCount
1683 :    
1684 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1685 :    
1686 :     Return the number of rows found by a specified query. This method would
1687 :     normally be used to count the records in a single table. For example, in a
1688 :     genetics database
1689 :    
1690 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1691 :    
1692 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
1693 :     to use it to return records based on a join. For example,
1694 :    
1695 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1696 : parrello 1.45 ['homo %']);
1697 :    
1698 :     would return the number of features for genomes in the genus I<homo>. Note that
1699 :     only the rows from the first table are counted. If the above command were
1700 :    
1701 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1702 :     ['homo %']);
1703 :    
1704 :     it would return the number of genomes, not the number of genome/feature pairs.
1705 :    
1706 :     =over 4
1707 :    
1708 :     =item objectNames
1709 :    
1710 :     Reference to a list of the objects (entities and relationships) included in the
1711 :     query.
1712 :    
1713 :     =item filter
1714 :    
1715 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
1716 :     method.
1717 :    
1718 :     =item params
1719 :    
1720 :     Reference to a list of the parameter values to be substituted for the parameter marks
1721 :     in the filter.
1722 :    
1723 :     =item RETURN
1724 :    
1725 :     Returns a count of the number of records in the first table that would satisfy
1726 :     the query.
1727 :    
1728 :     =back
1729 :    
1730 :     =cut
1731 :    
1732 :     sub GetCount {
1733 :     # Get the parameters.
1734 :     my ($self, $objectNames, $filter, $params) = @_;
1735 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
1736 :     if (! defined($params)) {
1737 :     $params = [];
1738 :     }
1739 : parrello 1.45 # Declare the return variable.
1740 :     my $retVal;
1741 : parrello 1.47 # Find out if we're counting an entity or a relationship.
1742 :     my $countedField;
1743 :     if ($self->IsEntity($objectNames->[0])) {
1744 :     $countedField = "id";
1745 :     } else {
1746 :     # For a relationship we count the to-link because it's usually more
1747 :     # numerous. Note we're automatically converting to the SQL form
1748 :     # of the field name (to_link vs. to-link).
1749 :     $countedField = "to_link";
1750 :     }
1751 : parrello 1.45 # Create the SQL command suffix to get the desired records.
1752 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1753 :     $filter);
1754 :     # Prefix it with text telling it we want a record count.
1755 :     my $firstObject = $mappedNameListRef->[0];
1756 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
1757 : parrello 1.45 # Prepare and execute the command.
1758 :     my $sth = $self->_GetStatementHandle($command, $params);
1759 :     # Get the count value.
1760 :     ($retVal) = $sth->fetchrow_array();
1761 :     # Check for a problem.
1762 :     if (! defined($retVal)) {
1763 :     if ($sth->err) {
1764 :     # Here we had an SQL error.
1765 :     Confess("Error retrieving row count: " . $sth->errstr());
1766 :     } else {
1767 :     # Here we have no result.
1768 :     Confess("No result attempting to retrieve row count.");
1769 :     }
1770 :     }
1771 :     # Return the result.
1772 :     return $retVal;
1773 :     }
1774 :    
1775 : parrello 1.1 =head3 ComputeObjectSentence
1776 :    
1777 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1778 : parrello 1.1
1779 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
1780 :    
1781 :     =over 4
1782 :    
1783 :     =item objectName
1784 :    
1785 :     Name of the entity or relationship.
1786 :    
1787 :     =item RETURN
1788 :    
1789 :     Returns a string containing the entity name or a relationship sentence.
1790 :    
1791 :     =back
1792 :    
1793 :     =cut
1794 :    
1795 :     sub ComputeObjectSentence {
1796 : parrello 1.10 # Get the parameters.
1797 :     my ($self, $objectName) = @_;
1798 :     # Set the default return value.
1799 :     my $retVal = $objectName;
1800 :     # Look for the object as a relationship.
1801 :     my $relTable = $self->{_metaData}->{Relationships};
1802 :     if (exists $relTable->{$objectName}) {
1803 :     # Get the relationship sentence.
1804 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
1805 :     }
1806 :     # Return the result.
1807 :     return $retVal;
1808 : parrello 1.1 }
1809 :    
1810 :     =head3 DumpRelations
1811 :    
1812 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
1813 : parrello 1.1
1814 :     Write the contents of all the relations to tab-delimited files in the specified directory.
1815 :     Each file will have the same name as the relation dumped, with an extension of DTX.
1816 :    
1817 :     =over 4
1818 :    
1819 :     =item outputDirectory
1820 :    
1821 :     Name of the directory into which the relation files should be dumped.
1822 :    
1823 :     =back
1824 :    
1825 :     =cut
1826 :    
1827 :     sub DumpRelations {
1828 : parrello 1.10 # Get the parameters.
1829 :     my ($self, $outputDirectory) = @_;
1830 :     # Now we need to run through all the relations. First, we loop through the entities.
1831 :     my $metaData = $self->{_metaData};
1832 :     my $entities = $metaData->{Entities};
1833 :     for my $entityName (keys %{$entities}) {
1834 :     my $entityStructure = $entities->{$entityName};
1835 :     # Get the entity's relations.
1836 :     my $relationList = $entityStructure->{Relations};
1837 :     # Loop through the relations, dumping them.
1838 :     for my $relationName (keys %{$relationList}) {
1839 :     my $relation = $relationList->{$relationName};
1840 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
1841 :     }
1842 :     }
1843 :     # Next, we loop through the relationships.
1844 :     my $relationships = $metaData->{Relationships};
1845 :     for my $relationshipName (keys %{$relationships}) {
1846 :     my $relationshipStructure = $relationships->{$relationshipName};
1847 :     # Dump this relationship's relation.
1848 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
1849 :     }
1850 : parrello 1.1 }
1851 :    
1852 : parrello 1.51 =head3 InsertValue
1853 :    
1854 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
1855 :    
1856 :     This method will insert a new value into the database. The value must be one
1857 :     associated with a secondary relation, since primary values cannot be inserted:
1858 :     they occur exactly once. Secondary values, on the other hand, can be missing
1859 :     or multiply-occurring.
1860 :    
1861 :     =over 4
1862 :    
1863 :     =item entityID
1864 :    
1865 :     ID of the object that is to receive the new value.
1866 :    
1867 :     =item fieldName
1868 :    
1869 :     Field name for the new value-- this includes the entity name, since
1870 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
1871 :    
1872 :     =item value
1873 :    
1874 :     New value to be put in the field.
1875 :    
1876 :     =back
1877 :    
1878 :     =cut
1879 :    
1880 :     sub InsertValue {
1881 :     # Get the parameters.
1882 :     my ($self, $entityID, $fieldName, $value) = @_;
1883 :     # Parse the entity name and the real field name.
1884 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
1885 :     my $entityName = $1;
1886 :     my $fieldTitle = $2;
1887 :     # Get its descriptor.
1888 :     if (!$self->IsEntity($entityName)) {
1889 :     Confess("$entityName is not a valid entity.");
1890 :     } else {
1891 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1892 :     # Find the relation containing this field.
1893 :     my $fieldHash = $entityData->{Fields};
1894 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
1895 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
1896 :     } else {
1897 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
1898 :     if ($relation eq $entityName) {
1899 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
1900 :     } else {
1901 :     # Now we can create an INSERT statement.
1902 :     my $dbh = $self->{_dbh};
1903 :     my $fixedName = _FixName($fieldTitle);
1904 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
1905 : parrello 1.51 # Execute the command.
1906 :     $dbh->SQL($statement, 0, $entityID, $value);
1907 :     }
1908 :     }
1909 :     }
1910 :     } else {
1911 :     Confess("$fieldName is not a valid field name.");
1912 :     }
1913 :     }
1914 :    
1915 : parrello 1.1 =head3 InsertObject
1916 :    
1917 : parrello 1.18 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1918 : parrello 1.1
1919 :     Insert an object into the database. The object is defined by a type name and then a hash
1920 :     of field names to values. Field values in the primary relation are represented by scalars.
1921 :     (Note that for relationships, the primary relation is the B<only> relation.)
1922 :     Field values for the other relations comprising the entity are always list references. For
1923 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
1924 :     C<ZP_00210270.1> and C<gi|46206278>.
1925 :    
1926 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
1927 : parrello 1.1
1928 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
1929 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
1930 :    
1931 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1932 : parrello 1.1
1933 :     =over 4
1934 :    
1935 :     =item newObjectType
1936 :    
1937 :     Type name of the object to insert.
1938 :    
1939 :     =item fieldHash
1940 :    
1941 :     Hash of field names to values.
1942 :    
1943 :     =item RETURN
1944 :    
1945 :     Returns 1 if successful, 0 if an error occurred.
1946 :    
1947 :     =back
1948 :    
1949 :     =cut
1950 :    
1951 :     sub InsertObject {
1952 : parrello 1.10 # Get the parameters.
1953 :     my ($self, $newObjectType, $fieldHash) = @_;
1954 :     # Denote that so far we appear successful.
1955 :     my $retVal = 1;
1956 :     # Get the database handle.
1957 :     my $dbh = $self->{_dbh};
1958 :     # Get the relation list.
1959 :     my $relationTable = $self->_GetRelationTable($newObjectType);
1960 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
1961 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
1962 :     # stop the loop.
1963 :     my @relationList = keys %{$relationTable};
1964 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
1965 :     my $relationName = $relationList[$i];
1966 :     my $relationDefinition = $relationTable->{$relationName};
1967 :     # Get the relation's fields. For each field we will collect a value in the corresponding
1968 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
1969 :     # @missing list.
1970 :     my @fieldList = @{$relationDefinition->{Fields}};
1971 :     my @fieldNameList = ();
1972 :     my @valueList = ();
1973 :     my @missing = ();
1974 :     my $recordCount = 1;
1975 :     for my $fieldDescriptor (@fieldList) {
1976 :     # Get the field name and save it. Note we need to fix it up so the hyphens
1977 :     # are converted to underscores.
1978 :     my $fieldName = $fieldDescriptor->{name};
1979 :     push @fieldNameList, _FixName($fieldName);
1980 :     # Look for the named field in the incoming structure. Note that we are looking
1981 :     # for the real field name, not the fixed-up one!
1982 :     if (exists $fieldHash->{$fieldName}) {
1983 :     # Here we found the field. Stash it in the value list.
1984 :     my $value = $fieldHash->{$fieldName};
1985 :     push @valueList, $value;
1986 :     # If the value is a list, we may need to increment the record count.
1987 :     if (ref $value eq "ARRAY") {
1988 :     my $thisCount = @{$value};
1989 :     if ($recordCount == 1) {
1990 :     # Here we have our first list, so we save its count.
1991 :     $recordCount = $thisCount;
1992 :     } elsif ($recordCount != $thisCount) {
1993 :     # Here we have a second list, so its length has to match the
1994 :     # previous lists.
1995 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
1996 :     $retVal = 0;
1997 :     }
1998 :     }
1999 :     } else {
2000 :     # Here the field is not present. Flag it as missing.
2001 :     push @missing, $fieldName;
2002 :     }
2003 :     }
2004 :     # If we are the primary relation, add the new-record flag.
2005 :     if ($relationName eq $newObjectType) {
2006 :     push @valueList, 1;
2007 :     push @fieldNameList, "new_record";
2008 :     }
2009 :     # Only proceed if there are no missing fields.
2010 :     if (@missing > 0) {
2011 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2012 :     join(' ', @missing)) if T(1);
2013 :     } else {
2014 :     # Build the INSERT statement.
2015 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2016 :     ") VALUES (";
2017 :     # Create a marker list of the proper size and put it in the statement.
2018 :     my @markers = ();
2019 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2020 :     $statement .= join(', ', @markers) . ")";
2021 :     # We have the insert statement, so prepare it.
2022 :     my $sth = $dbh->prepare_command($statement);
2023 :     Trace("Insert statement prepared: $statement") if T(3);
2024 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2025 :     # a list, we use the current element. The values are stored in the @parameterList array.
2026 :     my $done = 0;
2027 :     for (my $i = 0; $i < $recordCount; $i++) {
2028 :     # Clear the parameter list array.
2029 :     my @parameterList = ();
2030 :     # Loop through the values.
2031 :     for my $value (@valueList) {
2032 :     # Check to see if this is a scalar value.
2033 :     if (ref $value eq "ARRAY") {
2034 :     # Here we have a list value. Pull the current entry.
2035 :     push @parameterList, $value->[$i];
2036 :     } else {
2037 :     # Here we have a scalar value. Use it unmodified.
2038 :     push @parameterList, $value;
2039 :     }
2040 :     }
2041 :     # Execute the INSERT statement with the specified parameter list.
2042 :     $retVal = $sth->execute(@parameterList);
2043 :     if (!$retVal) {
2044 :     my $errorString = $sth->errstr();
2045 :     Trace("Insert error: $errorString.") if T(0);
2046 :     }
2047 :     }
2048 :     }
2049 :     }
2050 :     # Return the success indicator.
2051 :     return $retVal;
2052 : parrello 1.1 }
2053 :    
2054 :     =head3 LoadTable
2055 :    
2056 : parrello 1.18 C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2057 : parrello 1.1
2058 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2059 :     first.
2060 : parrello 1.1
2061 :     =over 4
2062 :    
2063 :     =item fileName
2064 :    
2065 :     Name of the file from which the table data should be loaded.
2066 :    
2067 :     =item relationName
2068 :    
2069 :     Name of the relation to be loaded. This is the same as the table name.
2070 :    
2071 :     =item truncateFlag
2072 :    
2073 :     TRUE if the table should be dropped and re-created, else FALSE
2074 :    
2075 :     =item RETURN
2076 :    
2077 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2078 : parrello 1.1
2079 :     =back
2080 :    
2081 :     =cut
2082 :     sub LoadTable {
2083 : parrello 1.10 # Get the parameters.
2084 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2085 :     # Create the statistical return object.
2086 :     my $retVal = _GetLoadStats();
2087 :     # Trace the fact of the load.
2088 :     Trace("Loading table $relationName from $fileName") if T(2);
2089 :     # Get the database handle.
2090 :     my $dbh = $self->{_dbh};
2091 : parrello 1.22 # Get the input file size.
2092 :     my $fileSize = -s $fileName;
2093 : parrello 1.10 # Get the relation data.
2094 :     my $relation = $self->_FindRelation($relationName);
2095 :     # Check the truncation flag.
2096 :     if ($truncateFlag) {
2097 :     Trace("Creating table $relationName") if T(2);
2098 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2099 :     # divide it by the estimated row size, and then multiply by 1.5 to
2100 :     # leave extra room. We postulate a minimum row count of 1000 to
2101 :     # prevent problems with incoming empty load files.
2102 :     my $rowSize = $self->EstimateRowSize($relationName);
2103 :     my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2104 : parrello 1.10 # Re-create the table without its index.
2105 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2106 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2107 :     if ($dbh->{_preIndex}) {
2108 :     eval {
2109 :     $self->CreateIndex($relationName);
2110 :     };
2111 :     if ($@) {
2112 :     $retVal->AddMessage($@);
2113 :     }
2114 :     }
2115 :     }
2116 : parrello 1.3 # Load the table.
2117 : parrello 1.10 my $rv;
2118 :     eval {
2119 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2120 : parrello 1.10 };
2121 :     if (!defined $rv) {
2122 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2123 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2124 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2125 :     } else {
2126 : parrello 1.22 # Here we successfully loaded the table.
2127 :     $retVal->Add("tables");
2128 :     my $size = -s $fileName;
2129 :     Trace("$size bytes loaded into $relationName.") if T(2);
2130 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2131 : parrello 1.70 if ($truncateFlag) {
2132 :     # Indexes are created here for PostGres. For PostGres, indexes are
2133 :     # best built at the end. For MySQL, the reverse is true.
2134 :     if (! $dbh->{_preIndex}) {
2135 :     eval {
2136 :     $self->CreateIndex($relationName);
2137 :     };
2138 :     if ($@) {
2139 :     $retVal->AddMessage($@);
2140 :     }
2141 :     }
2142 :     # The full-text index (if any) is always built last, even for MySQL.
2143 :     # First we need to see if this table has a full-text index. Only
2144 :     # primary relations are allowed that privilege.
2145 :     if ($self->_IsPrimary($relationName)) {
2146 :     # Get the relation's entity/relationship structure.
2147 :     my $structure = $self->_GetStructure($relationName);
2148 :     # Check for a searchable fields list.
2149 :     if (exists $structure->{searchFields}) {
2150 :     # Here we know that we need to create a full-text search index.
2151 :     # Get an SQL-formatted field name list.
2152 :     my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2153 :     # Create the index.
2154 :     $dbh->create_index(tbl => $relationName, idx => "search_idx_$relationName",
2155 :     flds => $fields, kind => 'fulltext');
2156 :     }
2157 : parrello 1.10 }
2158 :     }
2159 :     }
2160 : parrello 1.20 # Analyze the table to improve performance.
2161 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2162 : olson 1.16 $dbh->vacuum_it($relationName);
2163 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2164 : parrello 1.10 # Return the statistics.
2165 :     return $retVal;
2166 : parrello 1.1 }
2167 :    
2168 : parrello 1.73 =head3 DropRelation
2169 : parrello 1.1
2170 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2171 : parrello 1.1
2172 : parrello 1.73 Physically drop a relation from the database.
2173 : parrello 1.1
2174 :     =over 4
2175 :    
2176 : parrello 1.73 =item relationName
2177 : parrello 1.1
2178 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2179 :     no effect.
2180 : parrello 1.1
2181 :     =back
2182 :    
2183 :     =cut
2184 :    
2185 : parrello 1.73 sub DropRelation {
2186 : parrello 1.10 # Get the parameters.
2187 : parrello 1.73 my ($self, $relationName) = @_;
2188 :     # Get the database handle.
2189 :     my $dbh = $self->{_dbh};
2190 :     # Drop the relation. The method used here has no effect if the relation
2191 :     # does not exist.
2192 :     $dbh->drop_table($relationName);
2193 : parrello 1.1 }
2194 :    
2195 : parrello 1.6 =head3 GetEntity
2196 :    
2197 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2198 : parrello 1.6
2199 :     Return an object describing the entity instance with a specified ID.
2200 :    
2201 :     =over 4
2202 :    
2203 :     =item entityType
2204 :    
2205 :     Entity type name.
2206 :    
2207 :     =item ID
2208 :    
2209 :     ID of the desired entity.
2210 :    
2211 :     =item RETURN
2212 :    
2213 :     Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2214 :     instance is found with the specified key.
2215 :    
2216 :     =back
2217 :    
2218 :     =cut
2219 :    
2220 :     sub GetEntity {
2221 : parrello 1.10 # Get the parameters.
2222 :     my ($self, $entityType, $ID) = @_;
2223 :     # Create a query.
2224 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2225 : parrello 1.10 # Get the first (and only) object.
2226 :     my $retVal = $query->Fetch();
2227 :     # Return the result.
2228 :     return $retVal;
2229 : parrello 1.6 }
2230 :    
2231 : parrello 1.69 =head3 GetChoices
2232 :    
2233 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2234 :    
2235 :     Return a list of all the values for the specified field that are represented in the
2236 :     specified entity.
2237 :    
2238 :     Note that if the field is not indexed, then this will be a very slow operation.
2239 :    
2240 :     =over 4
2241 :    
2242 :     =item entityName
2243 :    
2244 :     Name of an entity in the database.
2245 :    
2246 :     =item fieldName
2247 :    
2248 :     Name of a field belonging to the entity. This is a raw field name without
2249 :     the standard parenthesized notation used in most calls.
2250 :    
2251 :     =item RETURN
2252 :    
2253 :     Returns a list of the distinct values for the specified field in the database.
2254 :    
2255 :     =back
2256 :    
2257 :     =cut
2258 :    
2259 :     sub GetChoices {
2260 :     # Get the parameters.
2261 :     my ($self, $entityName, $fieldName) = @_;
2262 :     # Declare the return variable.
2263 :     my @retVal;
2264 :     # Get the entity data structure.
2265 :     my $entityData = $self->_GetStructure($entityName);
2266 :     # Get the field.
2267 :     my $fieldHash = $entityData->{Fields};
2268 :     if (! exists $fieldHash->{$fieldName}) {
2269 :     Confess("$fieldName not found in $entityName.");
2270 :     } else {
2271 :     # Get the name of the relation containing the field.
2272 :     my $relation = $fieldHash->{$fieldName}->{relation};
2273 :     # Fix up the field name.
2274 :     my $realName = _FixName($fieldName);
2275 :     # Get the database handle.
2276 :     my $dbh = $self->{_dbh};
2277 :     # Query the database.
2278 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2279 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
2280 :     @retVal = sort map { $_->[0] } @{$results};
2281 :     }
2282 :     # Return the result.
2283 :     return @retVal;
2284 :     }
2285 :    
2286 : parrello 1.6 =head3 GetEntityValues
2287 :    
2288 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2289 : parrello 1.6
2290 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
2291 :     does not exist, an empty list is returned.
2292 : parrello 1.6
2293 :     =over 4
2294 :    
2295 :     =item entityType
2296 :    
2297 :     Entity type name.
2298 :    
2299 :     =item ID
2300 :    
2301 :     ID of the desired entity.
2302 :    
2303 :     =item fields
2304 :    
2305 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2306 :    
2307 :     =item RETURN
2308 :    
2309 :     Returns a flattened list of the values of the specified fields for the specified entity.
2310 :    
2311 :     =back
2312 :    
2313 :     =cut
2314 :    
2315 :     sub GetEntityValues {
2316 : parrello 1.10 # Get the parameters.
2317 :     my ($self, $entityType, $ID, $fields) = @_;
2318 :     # Get the specified entity.
2319 :     my $entity = $self->GetEntity($entityType, $ID);
2320 :     # Declare the return list.
2321 :     my @retVal = ();
2322 :     # If we found the entity, push the values into the return list.
2323 :     if ($entity) {
2324 :     push @retVal, $entity->Values($fields);
2325 :     }
2326 :     # Return the result.
2327 :     return @retVal;
2328 : parrello 1.6 }
2329 : parrello 1.1
2330 : parrello 1.7 =head3 GetAll
2331 :    
2332 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2333 : parrello 1.7
2334 :     Return a list of values taken from the objects returned by a query. The first three
2335 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
2336 :     a list of the fields desired from each record found by the query. The field name
2337 :     syntax is the standard syntax used for fields in the B<ERDB> system--
2338 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2339 :     or relationship and I<fieldName> is the name of the field.
2340 :    
2341 :     The list returned will be a list of lists. Each element of the list will contain
2342 :     the values returned for the fields specified in the fourth parameter. If one of the
2343 :     fields specified returns multiple values, they are flattened in with the rest. For
2344 :     example, the following call will return a list of the features in a particular
2345 :     spreadsheet cell, and each feature will be represented by a list containing the
2346 :     feature ID followed by all of its aliases.
2347 :    
2348 : parrello 1.18 C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2349 : parrello 1.7
2350 :     =over 4
2351 :    
2352 :     =item objectNames
2353 :    
2354 :     List containing the names of the entity and relationship objects to be retrieved.
2355 :    
2356 :     =item filterClause
2357 :    
2358 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2359 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2360 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2361 :     parameter list as additional parameters. The fields in a filter clause can come from primary
2362 :     entity relations, relationship relations, or secondary entity relations; however, all of the
2363 :     entities and relationships involved must be included in the list of object names.
2364 :    
2365 :     =item parameterList
2366 :    
2367 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
2368 :    
2369 :     =item fields
2370 :    
2371 :     List of the fields to be returned in each element of the list returned.
2372 :    
2373 :     =item count
2374 :    
2375 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
2376 :    
2377 :     =item RETURN
2378 :    
2379 :     Returns a list of list references. Each element of the return list contains the values for the
2380 :     fields specified in the B<fields> parameter.
2381 :    
2382 :     =back
2383 :    
2384 :     =cut
2385 :     #: Return Type @@;
2386 :     sub GetAll {
2387 : parrello 1.10 # Get the parameters.
2388 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2389 :     # Translate the parameters from a list reference to a list. If the parameter
2390 :     # list is a scalar we convert it into a singleton list.
2391 :     my @parmList = ();
2392 :     if (ref $parameterList eq "ARRAY") {
2393 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
2394 : parrello 1.10 @parmList = @{$parameterList};
2395 :     } else {
2396 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2397 : parrello 1.10 push @parmList, $parameterList;
2398 :     }
2399 : parrello 1.30 # Insure the counter has a value.
2400 :     if (!defined $count) {
2401 :     $count = 0;
2402 :     }
2403 :     # Add the row limit to the filter clause.
2404 :     if ($count > 0) {
2405 :     $filterClause .= " LIMIT $count";
2406 :     }
2407 : parrello 1.10 # Create the query.
2408 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
2409 : parrello 1.10 # Set up a counter of the number of records read.
2410 :     my $fetched = 0;
2411 :     # Loop through the records returned, extracting the fields. Note that if the
2412 :     # counter is non-zero, we stop when the number of records read hits the count.
2413 :     my @retVal = ();
2414 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2415 :     my @rowData = $row->Values($fields);
2416 :     push @retVal, \@rowData;
2417 :     $fetched++;
2418 :     }
2419 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2420 : parrello 1.10 # Return the resulting list.
2421 :     return @retVal;
2422 : parrello 1.7 }
2423 :    
2424 : parrello 1.55 =head3 Exists
2425 :    
2426 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
2427 :    
2428 :     Return TRUE if an entity exists, else FALSE.
2429 :    
2430 :     =over 4
2431 :    
2432 :     =item entityName
2433 :    
2434 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2435 :    
2436 :     =item entityID
2437 :    
2438 :     ID of the entity instance whose existence is to be checked.
2439 :    
2440 :     =item RETURN
2441 :    
2442 :     Returns TRUE if the entity instance exists, else FALSE.
2443 :    
2444 :     =back
2445 :    
2446 :     =cut
2447 :     #: Return Type $;
2448 :     sub Exists {
2449 :     # Get the parameters.
2450 :     my ($self, $entityName, $entityID) = @_;
2451 :     # Check for the entity instance.
2452 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2453 :     my $testInstance = $self->GetEntity($entityName, $entityID);
2454 :     # Return an existence indicator.
2455 :     my $retVal = ($testInstance ? 1 : 0);
2456 :     return $retVal;
2457 :     }
2458 :    
2459 : parrello 1.18 =head3 EstimateRowSize
2460 :    
2461 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2462 :    
2463 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
2464 :     up the average length for each data type.
2465 :    
2466 :     =over 4
2467 :    
2468 :     =item relName
2469 :    
2470 :     Name of the relation whose estimated row size is desired.
2471 :    
2472 :     =item RETURN
2473 :    
2474 :     Returns an estimate of the row size for the specified relation.
2475 :    
2476 :     =back
2477 :    
2478 :     =cut
2479 :     #: Return Type $;
2480 :     sub EstimateRowSize {
2481 :     # Get the parameters.
2482 :     my ($self, $relName) = @_;
2483 :     # Declare the return variable.
2484 :     my $retVal = 0;
2485 :     # Find the relation descriptor.
2486 :     my $relation = $self->_FindRelation($relName);
2487 :     # Get the list of fields.
2488 :     for my $fieldData (@{$relation->{Fields}}) {
2489 :     # Get the field type and add its length.
2490 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2491 :     $retVal += $fieldLen;
2492 :     }
2493 :     # Return the result.
2494 :     return $retVal;
2495 :     }
2496 :    
2497 : parrello 1.38 =head3 GetFieldTable
2498 :    
2499 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2500 :    
2501 :     Get the field structure for a specified entity or relationship.
2502 :    
2503 :     =over 4
2504 :    
2505 :     =item objectName
2506 :    
2507 :     Name of the desired entity or relationship.
2508 :    
2509 :     =item RETURN
2510 :    
2511 :     The table containing the field descriptors for the specified object.
2512 :    
2513 :     =back
2514 :    
2515 :     =cut
2516 :    
2517 :     sub GetFieldTable {
2518 :     # Get the parameters.
2519 :     my ($self, $objectName) = @_;
2520 :     # Get the descriptor from the metadata.
2521 :     my $objectData = $self->_GetStructure($objectName);
2522 :     # Return the object's field table.
2523 :     return $objectData->{Fields};
2524 :     }
2525 :    
2526 : parrello 1.73 =head3 SplitKeywords
2527 :    
2528 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2529 :    
2530 :     This method returns a list of the positive keywords in the specified
2531 :     keyword string. All of the operators will have been stripped off,
2532 :     and if the keyword is preceded by a minus operator (C<->), it will
2533 :     not be in the list returned. The idea here is to get a list of the
2534 :     keywords the user wants to see. The list will be processed to remove
2535 :     duplicates.
2536 :    
2537 :     It is possible to create a string that confuses this method. For example
2538 :    
2539 :     frog toad -frog
2540 :    
2541 :     would return both C<frog> and C<toad>. If this is a problem we can deal
2542 :     with it later.
2543 :    
2544 :     =over 4
2545 :    
2546 :     =item keywordString
2547 :    
2548 :     The keyword string to be parsed.
2549 :    
2550 :     =item RETURN
2551 :    
2552 :     Returns a list of the words in the keyword string the user wants to
2553 :     see.
2554 :    
2555 :     =back
2556 :    
2557 :     =cut
2558 :    
2559 :     sub SplitKeywords {
2560 :     # Get the parameters.
2561 :     my ($keywordString) = @_;
2562 :     # Make a safety copy of the string. (This helps during debugging.)
2563 :     my $workString = $keywordString;
2564 :     # Convert operators we don't care about to spaces.
2565 :     $workString =~ tr/+"()<>/ /;
2566 :     # Split the rest of the string along space boundaries. Note that we
2567 :     # eliminate any words that are zero length or begin with a minus sign.
2568 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2569 :     # Use a hash to remove duplicates.
2570 :     my %words = map { $_ => 1 } @wordList;
2571 :     # Return the result.
2572 :     return sort keys %words;
2573 :     }
2574 :    
2575 :     =head3 ValidateFieldName
2576 :    
2577 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2578 :    
2579 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2580 :     be hyphenated words subject to certain restrictions.
2581 :    
2582 :     =over 4
2583 :    
2584 :     =item fieldName
2585 :    
2586 :     Field name to be validated.
2587 :    
2588 :     =item RETURN
2589 :    
2590 :     Returns TRUE if the field name is valid, else FALSE.
2591 :    
2592 :     =back
2593 :    
2594 :     =cut
2595 :    
2596 :     sub ValidateFieldName {
2597 :     # Get the parameters.
2598 :     my ($fieldName) = @_;
2599 :     # Declare the return variable. The field name is valid until we hear
2600 :     # differently.
2601 :     my $retVal = 1;
2602 :     # Look for bad stuff in the name.
2603 :     if ($fieldName =~ /--/) {
2604 :     # Here we have a doubled minus sign.
2605 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2606 :     $retVal = 0;
2607 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
2608 :     # Here the field name is missing the initial letter.
2609 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
2610 :     $retVal = 0;
2611 :     } else {
2612 :     # Strip out the minus signs. Everything remaining must be a letter
2613 :     # or digit.
2614 :     my $strippedName = $fieldName;
2615 :     $strippedName =~ s/-//g;
2616 :     if ($strippedName !~ /^[A-Za-z0-9]+$/) {
2617 :     Trace("Field name $fieldName contains illegal characters.") if T(1);
2618 :     $retVal = 0;
2619 :     }
2620 :     }
2621 :     # Return the result.
2622 :     return $retVal;
2623 :     }
2624 :    
2625 :     =head3 ReadMetaXML
2626 :    
2627 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2628 :    
2629 :     This method reads a raw database definition XML file and returns it.
2630 :     Normally, the metadata used by the ERDB system has been processed and
2631 :     modified to make it easier to load and retrieve the data; however,
2632 :     this method can be used to get the data in its raw form.
2633 :    
2634 :     =over 4
2635 :    
2636 :     =item fileName
2637 :    
2638 :     Name of the XML file to read.
2639 :    
2640 :     =item RETURN
2641 :    
2642 :     Returns a hash reference containing the raw XML data from the specified file.
2643 :    
2644 :     =back
2645 :    
2646 :     =cut
2647 :    
2648 :     sub ReadMetaXML {
2649 :     # Get the parameters.
2650 :     my ($fileName) = @_;
2651 :     # Read the XML.
2652 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2653 :     Trace("XML metadata loaded from file $fileName.") if T(1);
2654 :     # Return the result.
2655 :     return $retVal;
2656 :     }
2657 :    
2658 :     =head3 GetEntityFieldHash
2659 :    
2660 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2661 :    
2662 :     Get the field hash of the named entity in the specified raw XML structure.
2663 :     The field hash may not exist, in which case we need to create it.
2664 :    
2665 :     =over 4
2666 :    
2667 :     =item structure
2668 :    
2669 :     Raw XML structure defininng the database. This is not the run-time XML used by
2670 :     an ERDB object, since that has all sorts of optimizations built-in.
2671 :    
2672 :     =item entityName
2673 :    
2674 :     Name of the entity whose field structure is desired.
2675 :    
2676 :     =item RETURN
2677 :    
2678 :     Returns the field hash used to define the entity's fields.
2679 :    
2680 :     =back
2681 :    
2682 :     =cut
2683 :    
2684 :     sub GetEntityFieldHash {
2685 :     # Get the parameters.
2686 :     my ($structure, $entityName) = @_;
2687 :     # Get the entity structure.
2688 :     my $entityData = $structure->{Entities}->{$entityName};
2689 :     # Look for a field structure.
2690 :     my $retVal = $entityData->{Fields};
2691 :     # If it doesn't exist, create it.
2692 :     if (! defined($retVal)) {
2693 :     $entityData->{Fields} = {};
2694 :     $retVal = $entityData->{Fields};
2695 :     }
2696 :     # Return the result.
2697 :     return $retVal;
2698 :     }
2699 :    
2700 :     =head3 WriteMetaXML
2701 :    
2702 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
2703 :    
2704 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2705 :     used to update the database definition. It must be used with care, however, since it
2706 :     will only work on a raw structure, not on the processed structure created by an ERDB
2707 :     constructor.
2708 :    
2709 :     =over 4
2710 :    
2711 :     =item structure
2712 :    
2713 :     XML structure to be written to the file.
2714 :    
2715 :     =item fileName
2716 :    
2717 :     Name of the output file to which the updated XML should be stored.
2718 :    
2719 :     =back
2720 :    
2721 :     =cut
2722 :    
2723 :     sub WriteMetaXML {
2724 :     # Get the parameters.
2725 :     my ($structure, $fileName) = @_;
2726 :     # Compute the output.
2727 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2728 :     # Write it to the file.
2729 :     my $xmlOut = Open(undef, ">$fileName");
2730 :     print $xmlOut $fileString;
2731 :     }
2732 :    
2733 :    
2734 :     =head3 HTMLNote
2735 :    
2736 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2737 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
2738 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
2739 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
2740 :    
2741 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
2742 :    
2743 :     =over 4
2744 :    
2745 :     =item dataString
2746 :    
2747 :     String to convert to HTML.
2748 :    
2749 :     =item RETURN
2750 :    
2751 :     An HTML string derived from the input string.
2752 :    
2753 :     =back
2754 :    
2755 :     =cut
2756 :    
2757 :     sub HTMLNote {
2758 :     # Get the parameter.
2759 :     my ($dataString) = @_;
2760 :     # HTML-escape the text.
2761 :     my $retVal = CGI::escapeHTML($dataString);
2762 :     # Substitute the bulletin board codes.
2763 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
2764 :     $retVal =~ s!\[p\]!</p><p>!g;
2765 :     # Return the result.
2766 :     return $retVal;
2767 :     }
2768 :    
2769 :    
2770 : parrello 1.48 =head2 Data Mining Methods
2771 :    
2772 : parrello 1.38 =head3 GetUsefulCrossValues
2773 :    
2774 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
2775 :    
2776 :     Return a list of the useful attributes that would be returned by a B<Cross> call
2777 :     from an entity of the source entity type through the specified relationship. This
2778 :     means it will return the fields of the target entity type and the intersection data
2779 :     fields in the relationship. Only primary table fields are returned. In other words,
2780 :     the field names returned will be for fields where there is always one and only one
2781 :     value.
2782 :    
2783 :     =over 4
2784 :    
2785 :     =item sourceEntity
2786 :    
2787 :     Name of the entity from which the relationship crossing will start.
2788 :    
2789 :     =item relationship
2790 :    
2791 :     Name of the relationship being crossed.
2792 :    
2793 :     =item RETURN
2794 :    
2795 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
2796 :    
2797 :     =back
2798 :    
2799 :     =cut
2800 :     #: Return Type @;
2801 :     sub GetUsefulCrossValues {
2802 :     # Get the parameters.
2803 :     my ($self, $sourceEntity, $relationship) = @_;
2804 :     # Declare the return variable.
2805 :     my @retVal = ();
2806 :     # Determine the target entity for the relationship. This is whichever entity is not
2807 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
2808 :     # the TO, and vice versa.
2809 :     my $relStructure = $self->_GetStructure($relationship);
2810 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
2811 :     my $targetEntity = $relStructure->{$targetEntityType};
2812 :     # Get the field table for the entity.
2813 :     my $entityFields = $self->GetFieldTable($targetEntity);
2814 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
2815 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
2816 :     # must match the entity name.
2817 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
2818 :     keys %{$entityFields};
2819 :     # Push the fields found onto the return variable.
2820 :     push @retVal, sort @fieldList;
2821 :     # Get the field table for the relationship.
2822 :     my $relationshipFields = $self->GetFieldTable($relationship);
2823 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
2824 :     # This may end up being an empty set.
2825 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
2826 :     keys %{$relationshipFields};
2827 :     # Push these onto the return list.
2828 :     push @retVal, sort @fieldList2;
2829 :     # Return the result.
2830 :     return @retVal;
2831 :     }
2832 :    
2833 : parrello 1.48 =head3 FindColumn
2834 :    
2835 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2836 :    
2837 :     Return the location a desired column in a data mining header line. The data
2838 :     mining header line is a tab-separated list of column names. The column
2839 :     identifier is either the numerical index of a column or the actual column
2840 :     name.
2841 :    
2842 :     =over 4
2843 :    
2844 :     =item headerLine
2845 :    
2846 :     The header line from a data mining command, which consists of a tab-separated
2847 :     list of column names.
2848 :    
2849 :     =item columnIdentifier
2850 :    
2851 :     Either the ordinal number of the desired column (1-based), or the name of the
2852 :     desired column.
2853 :    
2854 :     =item RETURN
2855 :    
2856 :     Returns the array index (0-based) of the desired column.
2857 :    
2858 :     =back
2859 :    
2860 :     =cut
2861 :    
2862 :     sub FindColumn {
2863 :     # Get the parameters.
2864 :     my ($headerLine, $columnIdentifier) = @_;
2865 :     # Declare the return variable.
2866 :     my $retVal;
2867 :     # Split the header line into column names.
2868 :     my @headers = ParseColumns($headerLine);
2869 :     # Determine whether we have a number or a name.
2870 :     if ($columnIdentifier =~ /^\d+$/) {
2871 :     # Here we have a number. Subtract 1 and validate the result.
2872 :     $retVal = $columnIdentifier - 1;
2873 :     if ($retVal < 0 || $retVal > $#headers) {
2874 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2875 :     }
2876 :     } else {
2877 :     # Here we have a name. We need to find it in the list.
2878 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2879 :     if ($headers[$i] eq $columnIdentifier) {
2880 :     $retVal = $i;
2881 :     }
2882 :     }
2883 :     if (! defined($retVal)) {
2884 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2885 :     }
2886 :     }
2887 :     # Return the result.
2888 :     return $retVal;
2889 :     }
2890 :    
2891 :     =head3 ParseColumns
2892 :    
2893 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
2894 : parrello 1.48
2895 :     Convert the specified data line to a list of columns.
2896 :    
2897 :     =over 4
2898 :    
2899 :     =item line
2900 :    
2901 :     A data mining input, consisting of a tab-separated list of columns terminated by a
2902 :     new-line.
2903 :    
2904 :     =item RETURN
2905 :    
2906 :     Returns a list consisting of the column values.
2907 :    
2908 :     =back
2909 :    
2910 :     =cut
2911 :    
2912 :     sub ParseColumns {
2913 :     # Get the parameters.
2914 : parrello 1.50 my ($line) = @_;
2915 : parrello 1.48 # Chop off the line-end.
2916 :     chomp $line;
2917 :     # Split it into a list.
2918 :     my @retVal = split(/\t/, $line);
2919 :     # Return the result.
2920 :     return @retVal;
2921 :     }
2922 :    
2923 : parrello 1.71 =head2 Virtual Methods
2924 :    
2925 :     =head3 CleanKeywords
2926 :    
2927 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
2928 :    
2929 :     Clean up a search expression or keyword list. This is a virtual method that may
2930 :     be overridden by the subclass. The base-class method removes extra spaces
2931 :     and converts everything to lower case.
2932 :    
2933 :     =over 4
2934 :    
2935 :     =item searchExpression
2936 :    
2937 :     Search expression or keyword list to clean. Note that a search expression may
2938 :     contain boolean operators which need to be preserved. This includes leading
2939 :     minus signs.
2940 :    
2941 :     =item RETURN
2942 :    
2943 :     Cleaned expression or keyword list.
2944 :    
2945 :     =back
2946 :    
2947 :     =cut
2948 :    
2949 :     sub CleanKeywords {
2950 :     # Get the parameters.
2951 :     my ($self, $searchExpression) = @_;
2952 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
2953 :     # don't accidentally end up with an undefined value.
2954 :     my $retVal = lc($searchExpression || "");
2955 :     # Remove extra spaces.
2956 :     $retVal =~ s/\s+/ /g;
2957 :     $retVal =~ s/(^\s+)|(\s+$)//g;
2958 :     # Return the result.
2959 :     return $retVal;
2960 :     }
2961 :    
2962 : parrello 1.73 =head3 GetSourceObject
2963 :    
2964 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
2965 :    
2966 :     Return the object to be used in loading special attributes of the specified entity. The
2967 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
2968 :     XML
2969 :    
2970 : parrello 1.1 =head2 Internal Utility Methods
2971 :    
2972 : parrello 1.70 =head3 _RelationMap
2973 :    
2974 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
2975 :    
2976 :     Create the relation map for an SQL query. The relation map is used by B<DBObject>
2977 :     to determine how to interpret the results of the query.
2978 :    
2979 :     =over 4
2980 :    
2981 :     =item mappedNameHashRef
2982 :    
2983 :     Reference to a hash that maps modified object names to real object names.
2984 :    
2985 :     =item mappedNameListRef
2986 :    
2987 :     Reference to a list of modified object names in the order they appear in the
2988 :     SELECT list.
2989 :    
2990 :     =item RETURN
2991 :    
2992 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
2993 :     query followed by the actual name of that object. This enables the B<DBObject> to
2994 :     determine the order of the tables in the query and which object name belongs to each
2995 :     mapped object name. Most of the time these two values are the same; however, if a
2996 :     relation occurs twice in the query, the relation name in the field list and WHERE
2997 :     clause will use a mapped name (generally the actual relation name with a numeric
2998 :     suffix) that does not match the actual relation name.
2999 :    
3000 :     =back
3001 :    
3002 :     =cut
3003 :    
3004 :     sub _RelationMap {
3005 :     # Get the parameters.
3006 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3007 :     # Declare the return variable.
3008 :     my @retVal = ();
3009 :     # Build the map.
3010 :     for my $mappedName (@{$mappedNameListRef}) {
3011 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3012 :     }
3013 :     # Return it.
3014 :     return @retVal;
3015 :     }
3016 :    
3017 :    
3018 :     =head3 _SetupSQL
3019 : parrello 1.45
3020 :     Process a list of object names and a filter clause so that they can be used to
3021 :     build an SQL statement. This method takes in a reference to a list of object names
3022 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3023 :     names and the mapped name hash.
3024 :    
3025 :     This is an instance method.
3026 :    
3027 :     =over 4
3028 :    
3029 :     =item objectNames
3030 :    
3031 :     Reference to a list of the object names to be included in the query.
3032 :    
3033 :     =item filterClause
3034 :    
3035 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
3036 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
3037 :    
3038 : parrello 1.70 =item matchClause
3039 :    
3040 :     An optional full-text search clause. If specified, it will be inserted at the
3041 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
3042 :     field names should be in the form I<table>C<.>I<fieldName>.
3043 :    
3044 : parrello 1.45 =item RETURN
3045 :    
3046 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
3047 :     with the FROM clause. The second element is a reference to a list of the names to be
3048 :     used in retrieving the fields. The third element is a hash mapping the names to the
3049 :     objects they represent.
3050 :    
3051 :     =back
3052 :    
3053 :     =cut
3054 :    
3055 :     sub _SetupSQL {
3056 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
3057 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
3058 :     # same object. We start with a hash table keyed on object name that will
3059 :     # return the object suffix. The first time an object is encountered it will
3060 :     # not be found in the hash. The next time the hash will map the object name
3061 :     # to 2, then 3, and so forth.
3062 :     my %objectHash = ();
3063 :     # This list will contain the object names as they are to appear in the
3064 :     # FROM list.
3065 :     my @fromList = ();
3066 :     # This list contains the suffixed object name for each object. It is exactly
3067 :     # parallel to the list in the $objectNames parameter.
3068 :     my @mappedNameList = ();
3069 :     # Finally, this hash translates from a mapped name to its original object name.
3070 :     my %mappedNameHash = ();
3071 :     # Now we create the lists. Note that for every single name we push something into
3072 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
3073 :     # parallel to $objectNames.
3074 :     for my $objectName (@{$objectNames}) {
3075 :     # Get the next suffix for this object.
3076 :     my $suffix = $objectHash{$objectName};
3077 :     if (! $suffix) {
3078 :     # Here we are seeing the object for the first time. The object name
3079 :     # is used as is.
3080 :     push @mappedNameList, $objectName;
3081 :     push @fromList, $objectName;
3082 :     $mappedNameHash{$objectName} = $objectName;
3083 :     # Denote the next suffix will be 2.
3084 :     $objectHash{$objectName} = 2;
3085 :     } else {
3086 :     # Here we've seen the object before. We construct a new name using
3087 :     # the suffix from the hash and update the hash.
3088 :     my $mappedName = "$objectName$suffix";
3089 :     $objectHash{$objectName} = $suffix + 1;
3090 :     # The FROM list has the object name followed by the mapped name. This
3091 :     # tells SQL it's still the same table, but we're using a different name
3092 :     # for it to avoid confusion.
3093 :     push @fromList, "$objectName $mappedName";
3094 :     # The mapped-name list contains the real mapped name.
3095 :     push @mappedNameList, $mappedName;
3096 :     # Finally, enable us to get back from the mapped name to the object name.
3097 :     $mappedNameHash{$mappedName} = $objectName;
3098 :     }
3099 :     }
3100 :     # Begin the SELECT suffix. It starts with
3101 :     #
3102 :     # FROM name1, name2, ... nameN
3103 :     #
3104 :     my $suffix = "FROM " . join(', ', @fromList);
3105 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
3106 :     my $filterString = "";
3107 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
3108 :     # entities and relationships as well as primary relations to secondary ones.
3109 :     my @joinWhere = ();
3110 : parrello 1.45 # Check for a filter clause.
3111 :     if ($filterClause) {
3112 :     # Here we have one, so we convert its field names and add it to the query. First,
3113 :     # We create a copy of the filter string we can work with.
3114 : parrello 1.70 $filterString = $filterClause;
3115 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
3116 :     # object names inside other object names when we're doing our search and replace.
3117 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3118 :     # The final preparatory step is to create a hash table of relation names. The
3119 :     # table begins with the relation names already in the SELECT command. We may
3120 :     # need to add relations later if there is filtering on a field in a secondary
3121 :     # relation. The secondary relations are the ones that contain multiply-
3122 :     # occurring or optional fields.
3123 :     my %fromNames = map { $_ => 1 } @sortedNames;
3124 :     # We are ready to begin. We loop through the object names, replacing each
3125 :     # object name's field references by the corresponding SQL field reference.
3126 :     # Along the way, if we find a secondary relation, we will need to add it
3127 :     # to the FROM clause.
3128 :     for my $mappedName (@sortedNames) {
3129 :     # Get the length of the object name plus 2. This is the value we add to the
3130 :     # size of the field name to determine the size of the field reference as a
3131 :     # whole.
3132 :     my $nameLength = 2 + length $mappedName;
3133 :     # Get the real object name for this mapped name.
3134 :     my $objectName = $mappedNameHash{$mappedName};
3135 :     Trace("Processing $mappedName for object $objectName.") if T(4);
3136 :     # Get the object's field list.
3137 :     my $fieldList = $self->GetFieldTable($objectName);
3138 :     # Find the field references for this object.
3139 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3140 :     # At this point, $1 contains the field name, and the current position
3141 :     # is set immediately after the final parenthesis. We pull out the name of
3142 :     # the field and the position and length of the field reference as a whole.
3143 :     my $fieldName = $1;
3144 :     my $len = $nameLength + length $fieldName;
3145 :     my $pos = pos($filterString) - $len;
3146 :     # Insure the field exists.
3147 :     if (!exists $fieldList->{$fieldName}) {
3148 :     Confess("Field $fieldName not found for object $objectName.");
3149 :     } else {
3150 :     Trace("Processing $fieldName at position $pos.") if T(4);
3151 :     # Get the field's relation.
3152 :     my $relationName = $fieldList->{$fieldName}->{relation};
3153 :     # Now we have a secondary relation. We need to insure it matches the
3154 :     # mapped name of the primary relation. First we peel off the suffix
3155 :     # from the mapped name.
3156 :     my $mappingSuffix = substr $mappedName, length($objectName);
3157 :     # Put the mapping suffix onto the relation name to get the
3158 :     # mapped relation name.
3159 :     my $mappedRelationName = "$relationName$mappingSuffix";
3160 :     # Insure the relation is in the FROM clause.
3161 :     if (!exists $fromNames{$mappedRelationName}) {
3162 :     # Add the relation to the FROM clause.
3163 :     if ($mappedRelationName eq $relationName) {
3164 :     # The name is un-mapped, so we add it without
3165 :     # any frills.
3166 :     $suffix .= ", $relationName";
3167 :     push @joinWhere, "$objectName.id = $relationName.id";
3168 :     } else {
3169 :     # Here we have a mapping situation.
3170 :     $suffix .= ", $relationName $mappedRelationName";
3171 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3172 :     }
3173 :     # Denote we have this relation available for future fields.
3174 :     $fromNames{$mappedRelationName} = 1;
3175 :     }
3176 :     # Form an SQL field reference from the relation name and the field name.
3177 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3178 :     # Put it into the filter string in place of the old value.
3179 :     substr($filterString, $pos, $len) = $sqlReference;
3180 :     # Reposition the search.
3181 :     pos $filterString = $pos + length $sqlReference;
3182 :     }
3183 :     }
3184 :     }
3185 : parrello 1.70 }
3186 :     # The next step is to join the objects together. We only need to do this if there
3187 :     # is more than one object in the object list. We start with the first object and
3188 :     # run through the objects after it. Note also that we make a safety copy of the
3189 :     # list before running through it, because we shift off the first object before
3190 :     # processing the rest.
3191 :     my @mappedObjectList = @mappedNameList;
3192 :     my $lastMappedObject = shift @mappedObjectList;
3193 :     # Get the join table.
3194 :     my $joinTable = $self->{_metaData}->{Joins};
3195 :     # Loop through the object list.
3196 :     for my $thisMappedObject (@mappedObjectList) {
3197 :     # Look for a join using the real object names.
3198 :     my $lastObject = $mappedNameHash{$lastMappedObject};
3199 :     my $thisObject = $mappedNameHash{$thisMappedObject};
3200 :     my $joinKey = "$lastObject/$thisObject";
3201 :     if (!exists $joinTable->{$joinKey}) {
3202 :     # Here there's no join, so we throw an error.
3203 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3204 :     } else {
3205 :     # Get the join clause.
3206 :     my $unMappedJoin = $joinTable->{$joinKey};
3207 :     # Fix the names.
3208 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3209 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3210 :     push @joinWhere, $unMappedJoin;
3211 :     # Save this object as the last object for the next iteration.
3212 :     $lastMappedObject = $thisMappedObject;
3213 :     }
3214 :     }
3215 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3216 :     # here is we want the filter clause to be empty if there's no WHERE filter.
3217 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
3218 :     my $orderClause = "";
3219 :     # This is only necessary if we have a filter string in which the ORDER BY
3220 :     # and LIMIT clauses can live.
3221 :     if ($filterString) {
3222 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3223 :     # operator so that we find the first occurrence of either verb.
3224 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3225 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3226 :     my $pos = pos $filterString;
3227 :     $orderClause = $2 . substr($filterString, $pos);
3228 :     $filterString = $1;
3229 :     }
3230 : parrello 1.70 }
3231 :     # All the things that are supposed to be in the WHERE clause of the
3232 :     # SELECT command need to be put into @joinWhere so we can string them
3233 :     # together. We begin with the match clause. This is important,
3234 :     # because the match clause's parameter mark must precede any parameter
3235 :     # marks in the filter string.
3236 :     if ($matchClause) {
3237 :     push @joinWhere, $matchClause;
3238 :     }
3239 :     # Add the filter string. We put it in parentheses to avoid operator
3240 :     # precedence problems with the match clause or the joins.
3241 :     if ($filterString) {
3242 :     Trace("Filter string is \"$filterString\".") if T(4);
3243 :     push @joinWhere, "($filterString)";
3244 :     }
3245 :     # String it all together into a big filter clause.
3246 :     if (@joinWhere) {
3247 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
3248 :     }
3249 :     # Add the sort or limit clause (if any).
3250 :     if ($orderClause) {
3251 :     $suffix .= " $orderClause";
3252 : parrello 1.45 }
3253 :     # Return the suffix, the mapped name list, and the mapped name hash.
3254 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
3255 :     }
3256 :    
3257 : parrello 1.70 =head3 _GetStatementHandle
3258 : parrello 1.45
3259 :     This method will prepare and execute an SQL query, returning the statement handle.
3260 :     The main reason for doing this here is so that everybody who does SQL queries gets
3261 :     the benefit of tracing.
3262 :    
3263 :     This is an instance method.
3264 :    
3265 :     =over 4
3266 :    
3267 :     =item command
3268 :    
3269 :     Command to prepare and execute.
3270 :    
3271 :     =item params
3272 :    
3273 :     Reference to a list of the values to be substituted in for the parameter marks.
3274 :    
3275 :     =item RETURN
3276 :    
3277 :     Returns a prepared and executed statement handle from which the caller can extract
3278 :     results.
3279 :    
3280 :     =back
3281 :    
3282 :     =cut
3283 :    
3284 :     sub _GetStatementHandle {
3285 :     # Get the parameters.
3286 :     my ($self, $command, $params) = @_;
3287 :     # Trace the query.
3288 :     Trace("SQL query: $command") if T(SQL => 3);
3289 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3290 :     # Get the database handle.
3291 :     my $dbh = $self->{_dbh};
3292 :     # Prepare the command.
3293 :     my $sth = $dbh->prepare_command($command);
3294 :     # Execute it with the parameters bound in.
3295 :     $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
3296 :     # Return the statement handle.
3297 :     return $sth;
3298 :     }
3299 :    
3300 : parrello 1.70 =head3 _GetLoadStats
3301 : parrello 1.1
3302 :     Return a blank statistics object for use by the load methods.
3303 :    
3304 :     This is a static method.
3305 :    
3306 :     =cut
3307 :    
3308 : parrello 1.29 sub _GetLoadStats{
3309 : parrello 1.28 return Stats->new();
3310 : parrello 1.1 }
3311 :    
3312 : parrello 1.70 =head3 _DumpRelation
3313 : parrello 1.1
3314 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
3315 : parrello 1.1
3316 :     This is an instance method.
3317 :    
3318 :     =over 4
3319 :    
3320 :     =item outputDirectory
3321 :    
3322 :     Directory to contain the output file.
3323 :    
3324 :     =item relationName
3325 :    
3326 :     Name of the relation to dump.
3327 :    
3328 :     =item relation
3329 :    
3330 :     Structure describing the relation to be dumped.
3331 :    
3332 :     =back
3333 :    
3334 :     =cut
3335 :    
3336 :     sub _DumpRelation {
3337 : parrello 1.10 # Get the parameters.
3338 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
3339 :     # Open the output file.
3340 :     my $fileName = "$outputDirectory/$relationName.dtx";
3341 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
3342 :     # Create a query for the specified relation.
3343 :     my $dbh = $self->{_dbh};
3344 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
3345 :     # Execute the query.
3346 :     $query->execute() || Confess("SELECT error dumping $relationName.");
3347 :     # Loop through the results.
3348 :     while (my @row = $query->fetchrow) {
3349 :     # Escape any tabs or new-lines in the row text.
3350 :     for my $field (@row) {
3351 :     $field =~ s/\n/\\n/g;
3352 :     $field =~ s/\t/\\t/g;
3353 :     }
3354 :     # Tab-join the row and write it to the output file.
3355 :     my $rowText = join("\t", @row);
3356 :     print DTXOUT "$rowText\n";
3357 :     }
3358 :     # Close the output file.
3359 :     close DTXOUT;
3360 : parrello 1.1 }
3361 :    
3362 : parrello 1.70 =head3 _GetStructure
3363 : parrello 1.1
3364 :     Get the data structure for a specified entity or relationship.
3365 :    
3366 :     This is an instance method.
3367 :    
3368 :     =over 4
3369 :    
3370 :     =item objectName
3371 :    
3372 :     Name of the desired entity or relationship.
3373 :    
3374 :     =item RETURN
3375 :    
3376 :     The descriptor for the specified object.
3377 :    
3378 :     =back
3379 :    
3380 :     =cut
3381 :    
3382 :     sub _GetStructure {
3383 : parrello 1.10 # Get the parameters.
3384 :     my ($self, $objectName) = @_;
3385 :     # Get the metadata structure.
3386 :     my $metadata = $self->{_metaData};
3387 :     # Declare the variable to receive the descriptor.
3388 :     my $retVal;
3389 :     # Get the descriptor from the metadata.
3390 :     if (exists $metadata->{Entities}->{$objectName}) {
3391 :     $retVal = $metadata->{Entities}->{$objectName};
3392 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
3393 :     $retVal = $metadata->{Relationships}->{$objectName};
3394 :     } else {
3395 :     Confess("Object $objectName not found in database.");
3396 :     }
3397 :     # Return the descriptor.
3398 :     return $retVal;
3399 : parrello 1.1 }
3400 :    
3401 : parrello 1.70
3402 :    
3403 :     =head3 _GetRelationTable
3404 : parrello 1.1
3405 :     Get the list of relations for a specified entity or relationship.
3406 :    
3407 :     This is an instance method.
3408 :    
3409 :     =over 4
3410 :    
3411 :     =item objectName
3412 :    
3413 :     Name of the desired entity or relationship.
3414 :    
3415 :     =item RETURN
3416 :    
3417 :     A table containing the relations for the specified object.
3418 :    
3419 :     =back
3420 :    
3421 :     =cut
3422 :    
3423 :     sub _GetRelationTable {
3424 : parrello 1.10 # Get the parameters.
3425 :     my ($self, $objectName) = @_;
3426 :     # Get the descriptor from the metadata.
3427 :     my $objectData = $self->_GetStructure($objectName);
3428 :     # Return the object's relation list.
3429 :     return $objectData->{Relations};
3430 : parrello 1.1 }
3431 :    
3432 : parrello 1.70 =head3 _ValidateFieldNames
3433 : parrello 1.1
3434 :     Determine whether or not the field names are valid. A description of the problems with the names
3435 :     will be written to the standard error output. If there is an error, this method will abort. This is
3436 :     a static method.
3437 :    
3438 :     =over 4
3439 :    
3440 :     =item metadata
3441 :    
3442 :     Metadata structure loaded from the XML data definition.
3443 :    
3444 :     =back
3445 :    
3446 :     =cut
3447 :    
3448 :     sub _ValidateFieldNames {
3449 : parrello 1.10 # Get the object.
3450 :     my ($metadata) = @_;
3451 :     # Declare the return value. We assume success.
3452 :     my $retVal = 1;
3453 :     # Loop through the sections of the database definition.
3454 :     for my $section ('Entities', 'Relationships') {
3455 :     # Loop through the objects in this section.
3456 :     for my $object (values %{$metadata->{$section}}) {
3457 :     # Loop through the object's fields.
3458 :     for my $fieldName (keys %{$object->{Fields}}) {
3459 : parrello 1.73 # If this field name is invalid, set the return value to zero
3460 :     # so we know we encountered an error.
3461 :     if (! ValidateFieldName($fieldName)) {
3462 : parrello 1.10 $retVal = 0;
3463 :     }
3464 :     }
3465 :     }
3466 :     }
3467 :     # If an error was found, fail.
3468 :     if ($retVal == 0) {
3469 :     Confess("Errors found in field names.");
3470 :     }
3471 : parrello 1.1 }
3472 :    
3473 : parrello 1.70 =head3 _LoadRelation
3474 : parrello 1.1
3475 :     Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
3476 :     file with the same name as the relation exists in the specified directory.
3477 :    
3478 :     This is an instance method.
3479 :    
3480 :     =over 4
3481 :    
3482 :     =item dbh
3483 :    
3484 :     DBKernel object for accessing the database.
3485 :    
3486 :     =item directoryName
3487 :    
3488 :     Name of the directory containing the tab-delimited data files.
3489 :    
3490 :     =item relationName
3491 :    
3492 :     Name of the relation to load.
3493 :    
3494 :     =item rebuild
3495 :    
3496 :     TRUE if the table should be dropped and re-created before loading.
3497 :    
3498 :     =item RETURN
3499 :    
3500 :     Returns a statistical object describing the number of records read and a list of error messages.
3501 :    
3502 :     =back
3503 :    
3504 :     =cut
3505 :    
3506 :     sub _LoadRelation {
3507 : parrello 1.10 # Get the parameters.
3508 :     my ($self, $directoryName, $relationName, $rebuild) = @_;
3509 :     # Create the file name.
3510 :     my $fileName = "$directoryName/$relationName";
3511 :     # If the file doesn't exist, try adding the .dtx suffix.
3512 :     if (! -e $fileName) {
3513 :     $fileName .= ".dtx";
3514 :     if (! -e $fileName) {
3515 :     $fileName = "";
3516 :     }
3517 :     }
3518 :     # Create the return object.
3519 :     my $retVal = _GetLoadStats();
3520 :     # If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
3521 :     # be a null string.
3522 :     if ($fileName ne "") {
3523 :     # Load the relation from the file.
3524 :     $retVal = $self->LoadTable($fileName, $relationName, $rebuild);
3525 :     } elsif ($rebuild) {
3526 :     # Here we are rebuilding, but no file exists, so we just re-create the table.
3527 :     $self->CreateTable($relationName, 1);
3528 :     }
3529 :     # Return the statistics from the load.
3530 :     return $retVal;
3531 : parrello 1.1 }
3532 :    
3533 : parrello 1.73
3534 : parrello 1.70 =head3 _LoadMetaData
3535 : parrello 1.1
3536 :     This method loads the data describing this database from an XML file into a metadata structure.
3537 :     The resulting structure is a set of nested hash tables containing all the information needed to
3538 :     load or use the database. The schema for the XML file is F<ERDatabase.xml>.
3539 :    
3540 :     This is a static method.
3541 :    
3542 :     =over 4
3543 :    
3544 :     =item filename
3545 :    
3546 :     Name of the file containing the database definition.
3547 :    
3548 :     =item RETURN
3549 :    
3550 :     Returns a structure describing the database.
3551 :    
3552 :     =back
3553 :    
3554 :     =cut
3555 :    
3556 :     sub _LoadMetaData {
3557 : parrello 1.10 # Get the parameters.
3558 :     my ($filename) = @_;
3559 : parrello 1.15 Trace("Reading Sprout DBD from $filename.") if T(2);
3560 : parrello 1.10 # Slurp the XML file into a variable. Extensive use of options is used to insure we
3561 :     # get the exact structure we want.
3562 : parrello 1.73 my $metadata = ReadMetaXML($filename);
3563 : parrello 1.10 # Before we go any farther, we need to validate the field and object names. If an error is found,
3564 :     # the method below will fail.
3565 :     _ValidateFieldNames($metadata);
3566 :     # Next we need to create a hash table for finding relations. The entities and relationships are
3567 :     # implemented as one or more database relations.
3568 :     my %masterRelationTable = ();
3569 :     # Loop through the entities.
3570 :     my $entityList = $metadata->{Entities};
3571 :     for my $entityName (keys %{$entityList}) {
3572 :     my $entityStructure = $entityList->{$entityName};
3573 :     #
3574 : parrello 1.12 # The first step is to create all the entity's default values. For C<Field> elements,
3575 : parrello 1.10 # the relation name must be added where it is not specified. For relationships,
3576 :     # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
3577 :     # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
3578 :     # added that can be used to pull the implicit fields to the top when displaying the field
3579 :     # documentation. The PrettySort values are 1-based and indicate in which pass through a
3580 :     # relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
3581 :     # and so on.
3582 :     #
3583 :     # Fix up this entity.
3584 :     _FixupFields($entityStructure, $entityName, 2, 3);
3585 :     # Add the ID field.
3586 :     _AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
3587 :     relation => $entityName,
3588 :     Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
3589 :     PrettySort => 1});
3590 :     #
3591 :     # The current field list enables us to quickly find the relation containing a particular field.
3592 :     # We also need a list that tells us the fields in each relation. We do this by creating a
3593 :     # Relations structure in the entity structure and collating the fields into it based on their
3594 :     # C<relation> property. There is one tricky bit, which is that every relation has to have the
3595 :     # C<id> field in it. Note also that the field list is put into a C<Fields> member of the
3596 :     # relation's structure so that it looks more like the entity and relationship structures.
3597 :     #
3598 :     # First we need to create the relations list.
3599 :     my $relationTable = { };
3600 :     # Loop through the fields. We use a list of field names to prevent a problem with
3601 :     # the hash table cursor losing its place during the loop.
3602 :     my $fieldList = $entityStructure->{Fields};
3603 :     my @fieldNames = keys %{$fieldList};
3604 :     for my $fieldName (@fieldNames) {
3605 :     my $fieldData = $fieldList->{$fieldName};
3606 :     # Get the current field's relation name.
3607 :     my $relationName = $fieldData->{relation};
3608 :     # Insure the relation exists.
3609 :     if (!exists $relationTable->{$relationName}) {
3610 :     $relationTable->{$relationName} = { Fields => { } };
3611 :     }
3612 :     # Add the field to the relation's field structure.
3613 :     $relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
3614 :     }
3615 :     # Now that we've organized all our fields by relation name we need to do some serious
3616 :     # housekeeping. We must add the C<id> field to every relation and convert each relation
3617 :     # to a list of fields. First, we need the ID field itself.
3618 :     my $idField = $fieldList->{id};
3619 :     # Loop through the relations.
3620 :     for my $relationName (keys %{$relationTable}) {
3621 :     my $relation = $relationTable->{$relationName};
3622 :     # Get the relation's field list.
3623 :     my $relationFieldList = $relation->{Fields};
3624 :     # Add the ID field to it. If the field's already there, it will not make any
3625 :     # difference.
3626 :     $relationFieldList->{id} = $idField;
3627 :     # Convert the field set from a hash into a list using the pretty-sort number.
3628 :     $relation->{Fields} = _ReOrderRelationTable($relationFieldList);
3629 :     # Add the relation to the master table.
3630 :     $masterRelationTable{$relationName} = $relation;
3631 :     }
3632 :     # The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
3633 :     # The other relations must have at least one index that begins with the ID field. In addition, the
3634 :     # metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
3635 :     # get the entity's field list and index list.
3636 :     my $indexList = $entityStructure->{Indexes};
3637 :     # Loop through the indexes.
3638 :     for my $indexData (@{$indexList}) {
3639 :     # We need to find this index's fields. All of them should belong to the same relation.
3640 :     # The ID field is an exception, since it's in all relations.
3641 :     my $relationName = '0';
3642 :     for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
3643 :     # Get this field's name.
3644 :     my $fieldName = $fieldDescriptor->{name};
3645 :     # Only proceed if it is NOT the ID field.
3646 :     if ($fieldName ne 'id') {
3647 :     # Find the relation containing the current index field.
3648 :     my $thisName = $fieldList->{$fieldName}->{relation};
3649 :     if ($relationName eq '0') {
3650 :     # Here we're looking at the first field, so we save its relation name.
3651 :     $relationName = $thisName;
3652 :     } elsif ($relationName ne $thisName) {
3653 :     # Here we have a field mismatch.
3654 :     Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
3655 :     }
3656 :     }
3657 :     }
3658 :     # Now $relationName is the name of the relation that contains this index. Add the index structure
3659 :     # to the relation.
3660 :     push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
3661 :     }
3662 :     # Now each index has been put in a relation. We need to add the primary index for the primary
3663 :     # relation.
3664 :     push @{$relationTable->{$entityName}->{Indexes}},
3665 :     { IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
3666 :     Notes => { content => "Primary index for $entityName." }
3667 :     };
3668 :     # The next step is to insure that each relation has at least one index that begins with the ID field.
3669 :     # After that, we convert each relation's index list to an index table. We first need to loop through
3670 :     # the relations.
3671 :     for my $relationName (keys %{$relationTable}) {
3672 :     my $relation = $relationTable->{$relationName};
3673 :     # Get the relation's index list.
3674 :     my $indexList = $relation->{Indexes};
3675 :     # Insure this relation has an ID index.
3676 :     my $found = 0;
3677 :     for my $index (@{$indexList}) {
3678 :     if ($index->{IndexFields}->[0]->{name} eq "id") {
3679 :     $found = 1;
3680 :     }
3681 :     }
3682 :     if ($found == 0) {
3683 :     push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
3684 :     }
3685 :     # Now we need to convert the relation's index list to an index table. We begin by creating
3686 :     # an empty table in the relation structure.
3687 :     $relation->{Indexes} = { };
3688 :     # Loop through the indexes.
3689 :     my $count = 0;
3690 :     for my $index (@{$indexList}) {
3691 :     # Add this index to the index table.
3692 :     _AddIndex("idx$relationName$count", $relation, $index);
3693 :     # Increment the counter so that the next index has a different name.
3694 :     $count++;
3695 :     }
3696 :     }
3697 :     # Finally, we add the relation structure to the entity.
3698 :     $entityStructure->{Relations} = $relationTable;
3699 :     }
3700 :     # Loop through the relationships. Relationships actually turn out to be much simpler than entities.
3701 :     # For one thing, there is only a single constituent relation.
3702 :     my $relationshipList = $metadata->{Relationships};
3703 :     for my $relationshipName (keys %{$relationshipList}) {
3704 :     my $relationshipStructure = $relationshipList->{$relationshipName};
3705 :     # Fix up this relationship.
3706 :     _FixupFields($relationshipStructure, $relationshipName, 2, 3);
3707 :     # Format a description for the FROM field.
3708 :     my $fromEntity = $relationshipStructure->{from};
3709 :     my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
3710 :     # Get the FROM entity's key type.
3711 :     my $fromType = $entityList->{$fromEntity}->{keyType};
3712 :     # Add the FROM field.
3713 :     _AddField($relationshipStructure, 'from-link', { type => $fromType,
3714 :     relation => $relationshipName,
3715 :     Notes => { content => $fromComment },
3716 :     PrettySort => 1});
3717 :     # Format a description for the TO field.
3718 :     my $toEntity = $relationshipStructure->{to};
3719 :     my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
3720 :     # Get the TO entity's key type.
3721 :     my $toType = $entityList->{$toEntity}->{keyType};
3722 :     # Add the TO field.
3723 :     _AddField($relationshipStructure, 'to-link', { type=> $toType,
3724 :     relation => $relationshipName,
3725 :     Notes => { content => $toComment },
3726 :     PrettySort => 1});
3727 :     # Create an index-free relation from the fields.
3728 :     my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
3729 :     Indexes => { } };
3730 :     $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
3731 :     # Create the FROM and TO indexes.
3732 :     _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
3733 :     _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
3734 :     # Add the relation to the master table.
3735 :     $masterRelationTable{$relationshipName} = $thisRelation;
3736 :     }
3737 :     # Now store the master relation table in the metadata structure.
3738 :     $metadata->{RelationTable} = \%masterRelationTable;
3739 :     # Our final task is to create the join table. The join table is a hash that describes all
3740 :     # the join clauses for traveling through the relationships. The join clause is an equality
3741 :     # condition that can be put into a WHERE clause in order to join two objects. Two relationships
3742 :     # can be joined if they share an entity in common; and an entity can be joined to a relationship
3743 :     # if the entity is at either end of the relationship.
3744 :     my %joinTable = ();
3745 :     # Loop through the entities.
3746 :     for my $entityName (keys %{$entityList}) {
3747 :     # Build three lists of the relationships connected to this entity. One will be
3748 :     # for relationships from the entity, one for relationships to the entity, and
3749 :     # one for recursive relationships.
3750 :     my @fromList = ();
3751 :     my @toList = ();
3752 :     my @bothList = ();
3753 : parrello 1.21 Trace("Join table build for $entityName.") if T(metadata => 4);
3754 : parrello 1.10 for my $relationshipName (keys %{$relationshipList}) {
3755 :     my $relationship = $relationshipList->{$relationshipName};
3756 :     # Determine if this relationship has our entity in one of its link fields.
3757 :     my $fromEntity = $relationship->{from};
3758 :     my $toEntity = $relationship->{to};
3759 : parrello 1.41 Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
3760 : parrello 1.10 if ($fromEntity eq $entityName) {
3761 :     if ($toEntity eq $entityName) {
3762 :     # Here the relationship is recursive.
3763 :     push @bothList, $relationshipName;
3764 : parrello 1.21 Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
3765 : parrello 1.10 } else {
3766 :     # Here the relationship comes from the entity.
3767 :     push @fromList, $relationshipName;
3768 : parrello 1.21 Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
3769 : parrello 1.10 }
3770 :     } elsif ($toEntity eq $entityName) {
3771 :     # Here the relationship goes to the entity.
3772 :     push @toList, $relationshipName;
3773 : parrello 1.21 Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
3774 : parrello 1.10 }
3775 :     }
3776 :     # Create the nonrecursive joins. Note that we build two hashes for running
3777 :     # through the nonrecursive relationships since we'll have an outer loop
3778 :     # and an inner loop, and we can't do two "each" iterations on the same
3779 :     # hash table at the same time.
3780 :     my %directRelationships = ( from => \@fromList, to => \@toList );
3781 :     my %otherRelationships = ( from => \@fromList, to => \@toList );
3782 :     for my $linkType (keys %directRelationships) {
3783 :     my $relationships = $directRelationships{$linkType};
3784 :     # Loop through all the relationships.
3785 :     for my $relationshipName (@{$relationships}) {
3786 :     # Create joins between the entity and this relationship.
3787 :     my $linkField = "$relationshipName.${linkType}_link";
3788 :     my $joinClause = "$entityName.id = $linkField";
3789 : parrello 1.21 Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
3790 : parrello 1.10 $joinTable{"$entityName/$relationshipName"} = $joinClause;
3791 :     $joinTable{"$relationshipName/$entityName"} = $joinClause;
3792 :     # Create joins between this relationship and the other relationships.
3793 :     for my $otherType (keys %otherRelationships) {
3794 :     my $otherships = $otherRelationships{$otherType};
3795 :     for my $otherName (@{$otherships}) {
3796 :     # Get the key for this join.
3797 :     my $joinKey = "$otherName/$relationshipName";
3798 :     # Check for a duplicate or a self-join.
3799 :     if (exists $joinTable{$joinKey}) {
3800 :     # Here we have a duplicate, which means that the join
3801 :     # path is ambiguous. We delete the join from the join
3802 :     # table to prevent it from being used.
3803 :     delete $joinTable{$joinKey};
3804 :     Trace("Deleting ambiguous join $joinKey.") if T(4);
3805 :     } elsif ($otherName ne $relationshipName) {
3806 :     # Here we have a valid join. Note that joins between a
3807 :     # relationship and itself are prohibited.
3808 :     my $relJoinClause = "$otherName.${otherType}_link = $linkField";
3809 :     $joinTable{$joinKey} = $relJoinClause;
3810 : parrello 1.21 Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
3811 : parrello 1.10 }
3812 :     }
3813 :     }
3814 :     # Create joins between this relationship and the recursive relationships.
3815 :     # We don't need to check for ambiguous joins here, because a recursive
3816 :     # relationship can only be ambiguous with another recursive relationship,
3817 :     # and the incoming relationship from the outer loop is never recursive.
3818 :     for my $otherName (@bothList) {
3819 : parrello 1.21 Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
3820 : parrello 1.10 # Join from the left.
3821 :     $joinTable{"$relationshipName/$otherName"} =
3822 :     "$linkField = $otherName.from_link";
3823 :     # Join from the right.
3824 :     $joinTable{"$otherName/$relationshipName"} =
3825 :     "$otherName.to_link = $linkField";
3826 :     }
3827 :     }
3828 :     }
3829 :     # Create entity joins for the recursive relationships. Unlike the non-recursive
3830 :     # joins, the direction makes a difference with the recursive joins. This can give
3831 :     # rise to situations where we can't create the path we want; however, it is always
3832 :     # possible to get the same effect using multiple queries.
3833 :     for my $relationshipName (@bothList) {
3834 : parrello 1.21 Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
3835 : parrello 1.10 # Join to the entity from each direction.
3836 :     $joinTable{"$entityName/$relationshipName"} =
3837 :     "$entityName.id = $relationshipName.from_link";
3838 :     $joinTable{"$relationshipName/$entityName"} =
3839 :     "$relationshipName.to_link = $entityName.id";
3840 :     }
3841 :     }
3842 :     # Add the join table to the structure.
3843 :     $metadata->{Joins} = \%joinTable;
3844 :     # Return the slurped and fixed-up structure.
3845 :     return $metadata;
3846 : parrello 1.1 }
3847 :    
3848 : parrello 1.70 =head3 _CreateRelationshipIndex
3849 : parrello 1.1
3850 :     Create an index for a relationship's relation.
3851 :    
3852 :     This is a static method.
3853 :    
3854 :     =over 4
3855 :    
3856 :     =item indexKey
3857 :    
3858 :     Type of index: either C<"From"> or C<"To">.
3859 :    
3860 :     =item relationshipName
3861 :    
3862 :     Name of the relationship.
3863 :    
3864 :     =item relationshipStructure
3865 :    
3866 :     Structure describing the relationship that the index will sort.
3867 :    
3868 :     =back
3869 :    
3870 :     =cut
3871 :    
3872 :     sub _CreateRelationshipIndex {
3873 : parrello 1.10 # Get the parameters.
3874 :     my ($indexKey, $relationshipName, $relationshipStructure) = @_;
3875 :     # Get the target relation.
3876 :     my $relationStructure = $relationshipStructure->{Relations}->{$relationshipName};
3877 :     # Create a descriptor for the link field that goes at the beginning of this index.
3878 :     my $firstField = { name => lcfirst $indexKey . '-link', order => 'ascending' };
3879 :     # Get the target index descriptor.
3880 :     my $newIndex = $relationshipStructure->{$indexKey . "Index"};
3881 :     # Add the first field to the index's field list. Due to the craziness of PERL, if the
3882 :     # index descriptor does not exist, it will be created automatically so we can add
3883 :     # the field to it.
3884 :     unshift @{$newIndex->{IndexFields}}, $firstField;
3885 : parrello 1.12 # If this is a one-to-many relationship, the "To" index is unique.
3886 :     if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
3887 :     $newIndex->{Unique} = 'true';
3888 :     }
3889 : parrello 1.10 # Add the index to the relation.
3890 :     _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
3891 : parrello 1.1 }
3892 :    
3893 : parrello 1.70 =head3 _AddIndex
3894 : parrello 1.1
3895 :     Add an index to a relation structure.
3896 :    
3897 :     This is a static method.
3898 :    
3899 :     =over 4
3900 :    
3901 :     =item indexName
3902 :    
3903 :     Name to give to the new index.
3904 :    
3905 :     =item relationStructure
3906 :    
3907 :     Relation structure to which the new index should be added.
3908 :    
3909 :     =item newIndex
3910 :    
3911 :     New index to add.
3912 :    
3913 :     =back
3914 :    
3915 :     =cut
3916 :    
3917 :     sub _AddIndex {
3918 : parrello 1.10 # Get the parameters.
3919 :     my ($indexName, $relationStructure, $newIndex) = @_;
3920 :     # We want to re-do the index's field list. Instead of an object for each field,
3921 :     # we want a string consisting of the field name optionally followed by the token DESC.
3922 :     my @fieldList = ( );
3923 :     for my $field (@{$newIndex->{IndexFields}}) {
3924 :     # Create a string containing the field name.
3925 :     my $fieldString = $field->{name};
3926 :     # Add the ordering token if needed.
3927 :     if ($field->{order} eq "descending") {
3928 :     $fieldString .= " DESC";
3929 :     }
3930 :     # Push the result onto the field list.
3931 :     push @fieldList, $fieldString;
3932 :     }
3933 :     # Store the field list just created as the new index field list.
3934 :     $newIndex->{IndexFields} = \@fieldList;
3935 :     # Add the index to the relation's index list.
3936 :     $relationStructure->{Indexes}->{$indexName} = $newIndex;
3937 : parrello 1.1 }
3938 :    
3939 : parrello 1.70 =head3 _FixupFields
3940 : parrello 1.1
3941 :     This method fixes the field list for an entity or relationship. It will add the caller-specified
3942 :     relation name to fields that do not have a name and set the C<PrettySort> value as specified.
3943 :    
3944 :     This is a static method.
3945 :    
3946 :     =over 4
3947 :    
3948 :     =item structure
3949 :    
3950 :     Entity or relationship structure to be fixed up.
3951 :    
3952 :     =item defaultRelationName
3953 :    
3954 :     Default relation name to be added to the fields.
3955 :    
3956 :     =item prettySortValue
3957 :    
3958 :     C<PrettySort> value for the relation's normal fields.
3959 :    
3960 :     =item textPrettySortValue
3961 :    
3962 :     C<PrettySort> value for the relation's text fields. This value can be set to one greater than the
3963 :     normal pretty sort value so that text fields go at the end of each relation.
3964 :    
3965 :     =back
3966 :    
3967 :     =cut
3968 :    
3969 :     sub _FixupFields {
3970 : parrello 1.10 # Get the parameters.
3971 :     my ($structure, $defaultRelationName, $prettySortValue, $textPrettySortValue) = @_;
3972 :     # Insure the structure has a field list.
3973 :     if (!exists $structure->{Fields}) {
3974 :     # Here it doesn't, so we create a new one.
3975 :     $structure->{Fields} = { };
3976 :     } else {
3977 : parrello 1.70 # Here we have a field list. We need to track the searchable fields, so we
3978 :     # create a list for stashing them.
3979 :     my @textFields = ();
3980 :     # Loop through the fields.
3981 : parrello 1.10 my $fieldStructures = $structure->{Fields};
3982 :     for my $fieldName (keys %{$fieldStructures}) {
3983 : parrello 1.8 Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
3984 : parrello 1.10 my $fieldData = $fieldStructures->{$fieldName};
3985 :     # Get the field type.
3986 :     my $type = $fieldData->{type};
3987 :     # Plug in a relation name if it is needed.
3988 :     Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
3989 : parrello 1.70 # Check for searchability.
3990 :     if ($fieldData->{searchable}) {
3991 :     # Only allow this for a primary relation.
3992 :     if ($fieldData->{relation} ne $defaultRelationName) {
3993 :     Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
3994 :     } else {
3995 :     push @textFields, $fieldName;
3996 :     }
3997 :     }
3998 : parrello 1.10 # Add the PrettySortValue.
3999 :     $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4000 :     }
4001 : parrello 1.70 # If there are searchable fields, remember the fact.
4002 :     if (@textFields) {
4003 :     $structure->{searchFields} = \@textFields;
4004 :     }
4005 : parrello 1.10 }
4006 : parrello 1.1 }
4007 :    
4008 : parrello 1.70 =head3 _FixName
4009 : parrello 1.1
4010 :     Fix the incoming field name so that it is a legal SQL column name.
4011 :    
4012 :     This is a static method.
4013 :    
4014 :     =over 4
4015 :    
4016 :     =item fieldName
4017 :    
4018 :     Field name to fix.
4019 :    
4020 :     =item RETURN
4021 :    
4022 :     Returns the fixed-up field name.
4023 :    
4024 :     =back
4025 :    
4026 :     =cut
4027 :    
4028 :     sub _FixName {
4029 : parrello 1.10 # Get the parameter.
4030 :     my ($fieldName) = @_;
4031 :     # Replace its minus signs with underscores.
4032 :     $fieldName =~ s/-/_/g;
4033 :     # Return the result.
4034 :     return $fieldName;
4035 : parrello 1.1 }
4036 :    
4037 : parrello 1.70 =head3 _FixNames
4038 : parrello 1.1
4039 :     Fix all the field names in a list.
4040 :    
4041 :     This is a static method.
4042 :    
4043 :     =over 4
4044 :    
4045 :     =item field1, field2, field3, ... fieldn
4046 :    
4047 :     List of field names to fix.
4048 :    
4049 :     =item RETURN
4050 :    
4051 :     Returns a list of fixed-up versions of the incoming field names.
4052 :    
4053 :     =back
4054 :    
4055 :     =cut
4056 :    
4057 :     sub _FixNames {
4058 : parrello 1.10 # Create the result list.
4059 :     my @result = ( );
4060 :     # Loop through the incoming parameters.
4061 :     for my $field (@_) {
4062 :     push @result, _FixName($field);
4063 :     }
4064 :     # Return the result.
4065 :     return @result;
4066 : parrello 1.1 }
4067 :    
4068 : parrello 1.70 =head3 _AddField
4069 : parrello 1.1
4070 :     Add a field to a field list.
4071 :    
4072 :     This is a static method.
4073 :    
4074 :     =over 4
4075 :    
4076 :     =item structure
4077 :    
4078 :     Structure (usually an entity or relationship) that is to contain the field.
4079 :    
4080 :     =item fieldName
4081 :    
4082 :     Name of the new field.
4083 :    
4084 :     =item fieldData
4085 :    
4086 :     Structure containing the data to put in the field.
4087 :    
4088 :     =back
4089 :    
4090 :     =cut
4091 :    
4092 :     sub _AddField {
4093 : parrello 1.10 # Get the parameters.
4094 :     my ($structure, $fieldName, $fieldData) = @_;
4095 :     # Create the field structure by copying the incoming data.
4096 :     my $fieldStructure = {%{$fieldData}};
4097 :     # Get a reference to the field list itself.
4098 :     my $fieldList = $structure->{Fields};
4099 :     # Add the field to the field list.
4100 :     $fieldList->{$fieldName} = $fieldStructure;
4101 : parrello 1.1 }
4102 :    
4103 : parrello 1.70 =head3 _ReOrderRelationTable
4104 : parrello 1.1
4105 :     This method will take a relation table and re-sort it according to the implicit ordering of the
4106 :     C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
4107 :     This requires creating a new hash that contains the field name in the C<name> property but doesn't
4108 :     have the C<PrettySort> property, and then inserting that new hash into the field list.
4109 :    
4110 :     This is a static method.
4111 :    
4112 :     =over 4
4113 :    
4114 :     =item relationTable
4115 :    
4116 :     Relation hash to be reformatted into a list.
4117 :    
4118 :     =item RETURN
4119 :    
4120 :     A list of field hashes.
4121 :    
4122 :     =back
4123 :    
4124 :     =cut
4125 :    
4126 :     sub _ReOrderRelationTable {
4127 : parrello 1.10 # Get the parameters.
4128 :     my ($relationTable) = @_;
4129 :     # Create the return list.
4130 :     my @resultList;
4131 :     # Rather than copy all the fields in a single pass, we make multiple passes and only copy
4132 :     # fields whose PrettySort value matches the current pass number. This process continues
4133 :     # until we process all the fields in the relation.
4134 :     my $fieldsLeft = (values %{$relationTable});
4135 :     for (my $sortPass = 1; $fieldsLeft > 0; $sortPass++) {
4136 :     # Loop through the fields. Note that we lexically sort the fields. This makes field name
4137 :     # secondary to pretty-sort number in the final ordering.
4138 :     for my $fieldName (sort keys %{$relationTable}) {
4139 :     # Get this field's data.
4140 :     my $fieldData = $relationTable->{$fieldName};
4141 :     # Verify the sort pass.
4142 :     if ($fieldData->{PrettySort} == $sortPass) {
4143 :     # Here we're in the correct pass. Denote we've found a field.
4144 :     $fieldsLeft--;
4145 :     # The next step is to create the field structure. This done by copying all
4146 :     # of the field elements except PrettySort and adding the name.
4147 :     my %thisField;
4148 :     for my $property (keys %{$fieldData}) {
4149 :     if ($property ne 'PrettySort') {
4150 :     $thisField{$property} = $fieldData->{$property};
4151 :     }
4152 :     }
4153 :     $thisField{name} = $fieldName;
4154 :     # Now we add this field to the end of the result list.
4155 :     push @resultList, \%thisField;
4156 :     }
4157 :     }
4158 :     }
4159 :     # Return a reference to the result list.
4160 :     return \@resultList;
4161 : parrello 1.1
4162 :     }
4163 :    
4164 : parrello 1.70 =head3 _IsPrimary
4165 : parrello 1.1
4166 :     Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
4167 :     if it has the same name as an entity or relationship.
4168 :    
4169 :     This is an instance method.
4170 :    
4171 :     =over 4
4172 :    
4173 :     =item relationName
4174 :    
4175 :     Name of the relevant relation.
4176 :    
4177 :     =item RETURN
4178 :    
4179 :     Returns TRUE for a primary relation, else FALSE.
4180 :    
4181 :     =back
4182 :    
4183 :     =cut
4184 :    
4185 :     sub _IsPrimary {
4186 : parrello 1.10 # Get the parameters.
4187 :     my ($self, $relationName) = @_;
4188 :     # Check for the relation in the entity table.
4189 :     my $entityTable = $self->{_metaData}->{Entities};
4190 :     my $retVal = exists $entityTable->{$relationName};
4191 :     if (! $retVal) {
4192 :     # Check for it in the relationship table.
4193 :     my $relationshipTable = $self->{_metaData}->{Relationships};
4194 :     $retVal = exists $relationshipTable->{$relationName};
4195 :     }
4196 :     # Return the determination indicator.
4197 :     return $retVal;
4198 : parrello 1.1 }
4199 :    
4200 : parrello 1.70 =head3 _FindRelation
4201 : parrello 1.1
4202 :     Return the descriptor for the specified relation.
4203 :    
4204 :     This is an instance method.
4205 :    
4206 :     =over 4
4207 :    
4208 :     =item relationName
4209 :    
4210 :     Name of the relation whose descriptor is to be returned.
4211 :    
4212 :     =item RETURN
4213 :    
4214 :     Returns the object that describes the relation's indexes and fields.
4215 :    
4216 :     =back
4217 :    
4218 :     =cut
4219 :     sub _FindRelation {
4220 : parrello 1.10 # Get the parameters.
4221 :     my ($self, $relationName) = @_;
4222 :     # Get the relation's structure from the master relation table in the metadata structure.
4223 :     my $metaData = $self->{_metaData};
4224 :     my $retVal = $metaData->{RelationTable}->{$relationName};
4225 :     # Return it to the caller.
4226 :     return $retVal;
4227 : parrello 1.1 }
4228 :    
4229 :     =head2 HTML Documentation Utility Methods
4230 :    
4231 : parrello 1.70 =head3 _ComputeRelationshipSentence
4232 : parrello 1.1
4233 :     The relationship sentence consists of the relationship name between the names of the
4234 :     two related entities and an arity indicator.
4235 :    
4236 :     This is a static method.
4237 :    
4238 :     =over 4
4239 :    
4240 :     =item relationshipName
4241 :    
4242 :     Name of the relationship.
4243 :    
4244 :     =item relationshipStructure
4245 :    
4246 :     Relationship structure containing the relationship's description and properties.
4247 :    
4248 :     =item RETURN
4249 :    
4250 :     Returns a string containing the entity names on either side of the relationship name and an
4251 :     indicator of the arity.
4252 :    
4253 :     =back
4254 :    
4255 :     =cut
4256 :    
4257 :     sub _ComputeRelationshipSentence {
4258 : parrello 1.10 # Get the parameters.
4259 :     my ($relationshipName, $relationshipStructure) = @_;
4260 :     # Format the relationship sentence.
4261 :     my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";
4262 :     # Compute the arity.
4263 :     my $arityCode = $relationshipStructure->{arity};
4264 :     my $arity = $ArityTable{$arityCode};
4265 :     $result .= " ($arity)";
4266 :     return $result;
4267 : parrello 1.1 }
4268 :    
4269 : parrello 1.70 =head3 _ComputeRelationshipHeading
4270 : parrello 1.1
4271 :     The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
4272 :     names hyperlinked to the appropriate entity sections of the document.
4273 :    
4274 :     This is a static method.
4275 :    
4276 :     =over 4
4277 :    
4278 :     =item relationshipName
4279 :    
4280 :     Name of the relationship.
4281 :    
4282 :     =item relationshipStructure
4283 :    
4284 :     Relationship structure containing the relationship's description and properties.
4285 :    
4286 :     =item RETURN
4287 :    
4288 :     Returns a string containing the entity names on either side of the relationship name with the entity
4289 :     names hyperlinked.
4290 :    
4291 :     =back
4292 :    
4293 :     =cut
4294 :    
4295 :     sub _ComputeRelationshipHeading {
4296 : parrello 1.10 # Get the parameters.
4297 :     my ($relationshipName, $relationshipStructure) = @_;
4298 :     # Get the FROM and TO entity names.
4299 :     my $fromEntity = $relationshipStructure->{from};
4300 :     my $toEntity = $relationshipStructure->{to};
4301 :     # Format a relationship sentence with hyperlinks in it.
4302 :     my $result = "<a href=\"#$fromEntity\">$fromEntity</a> $relationshipName <a href=\"#$toEntity\">$toEntity</a>";
4303 :     return $result;
4304 : parrello 1.1 }
4305 :    
4306 : parrello 1.70 =head3 _ShowRelationTable
4307 : parrello 1.1
4308 :     Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
4309 :     table with three columns-- the field name, the field type, and the field description.
4310 :    
4311 :     This is a static method.
4312 :    
4313 :     =over 4
4314 :    
4315 :     =item relationName
4316 :    
4317 :     Name of the relation being formatted.
4318 :    
4319 :     =item relationData
4320 :    
4321 :     Hash containing the relation's fields and indexes.
4322 :    
4323 :     =item RETURN
4324 :    
4325 :     Returns an HTML string that can be used to display the relation name and all of its fields.
4326 :    
4327 :     =back
4328 :    
4329 :     =cut
4330 :    
4331 :     sub _ShowRelationTable {
4332 : parrello 1.10 # Get the parameters.
4333 :     my ($relationName, $relationData) = @_;
4334 :     # Start the relation's field table.
4335 :     my $htmlString = _OpenFieldTable($relationName);
4336 :     # Loop through the fields.
4337 :     for my $field (@{$relationData->{Fields}}) {
4338 :     $htmlString .= _ShowField($field);
4339 :     }
4340 :     # Close this relation's field table.
4341 :     $htmlString .= &_CloseTable;
4342 :     # Now we show the relation's indexes.
4343 :     $htmlString .= "<ul>\n";
4344 :     my $indexTable = $relationData->{Indexes};
4345 :     for my $indexName (sort keys %{$indexTable}) {
4346 :     my $indexData = $indexTable->{$indexName};
4347 :     # Determine whether or not the index is unique.
4348 :     my $fullName = $indexName;
4349 :     if (exists $indexData->{Unique} && $indexData->{Unique} eq "true") {
4350 :     $fullName .= " (unique)";
4351 :     }
4352 :     # Start an HTML list item for this index.
4353 :     $htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
4354 :     # Add any note text.
4355 :     if (my $note = $indexData->{Notes}) {