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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 : parrello 1.74 all be from the same relation. The alternate indexes assist in ordering results
233 : parrello 1.8 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 : parrello 1.74 =head3 FindIndexForEntity
650 :    
651 :     C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
652 :    
653 :     This method locates the entry in an entity's index list that begins with the
654 :     specified attribute name. If the entity has no index list, one will be
655 :     created. This method works on raw XML, not a live ERDB object.
656 :    
657 :     =over 4
658 :    
659 :     =item xml
660 :    
661 :     The raw XML structure defining the database.
662 :    
663 :     =item entityName
664 :    
665 :     The name of the relevant entity.
666 :    
667 :     =item attributeName
668 :    
669 :     The name of the attribute relevant to the search.
670 :    
671 :     =item RETURN
672 :    
673 :     The numerical index in the index list of the index entry for the specified entity and
674 :     attribute, or C<undef> if no such index exists.
675 :    
676 :     =back
677 :    
678 :     =cut
679 :    
680 :     sub FindIndexForEntity {
681 :     # Get the parameters.
682 :     my ($xml, $entityName, $attributeName) = @_;
683 :     # Declare the return variable.
684 :     my $retVal;
685 :     # Get the named entity.
686 :     my $entityData = $xml->{Entities}->{$entityName};
687 :     if (! $entityData) {
688 :     Confess("Entity $entityName not found in DBD structure.");
689 :     } else {
690 :     # Insure it has an index list.
691 :     if (! exists $entityData->{Indexes}) {
692 :     $entityData->{Indexes} = [];
693 :     } else {
694 :     # Search for the desired index.
695 :     my $indexList = $entityData->{Indexes};
696 :     my $n = scalar @{$indexList};
697 :     Trace("Searching $n indexes in index list for $entityName.") if T(2);
698 :     # We use an indexed FOR here because we're returning an
699 :     # index number instead of an object. We do THAT so we can
700 :     # delete the index from the list if needed.
701 :     for (my $i = 0; $i < $n && !defined($retVal); $i++) {
702 :     my $index = $indexList->[$i];
703 :     my $fields = $index->{IndexFields};
704 :     # Technically this IF should be safe (that is, we are guaranteed
705 :     # the existence of a "$fields->[0]"), because when we load the XML
706 :     # we have SuppressEmpty specified.
707 :     if ($fields->[0]->{name} eq $attributeName) {
708 :     $retVal = $i;
709 :     }
710 :     }
711 :     }
712 :     }
713 :     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
714 :     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
715 :     # Return the result.
716 :     return $retVal;
717 :     }
718 :    
719 : parrello 1.1 =head3 CreateTables
720 :    
721 : parrello 1.18 C<< $erdb->CreateTables(); >>
722 : parrello 1.1
723 :     This method creates the tables for the database from the metadata structure loaded by the
724 :     constructor. It is expected this function will only be used on rare occasions, when the
725 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
726 : parrello 1.1 used by itself with the truncate flag turned on.
727 :    
728 :     =cut
729 :    
730 :     sub CreateTables {
731 : parrello 1.10 # Get the parameters.
732 :     my ($self) = @_;
733 : parrello 1.23 # Get the relation names.
734 :     my @relNames = $self->GetTableNames();
735 :     # Loop through the relations.
736 :     for my $relationName (@relNames) {
737 :     # Create a table for this relation.
738 :     $self->CreateTable($relationName);
739 :     Trace("Relation $relationName created.") if T(2);
740 : parrello 1.10 }
741 : parrello 1.1 }
742 :    
743 :     =head3 CreateTable
744 :    
745 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
746 : parrello 1.1
747 :     Create the table for a relation and optionally create its indexes.
748 :    
749 :     =over 4
750 :    
751 :     =item relationName
752 :    
753 :     Name of the relation (which will also be the table name).
754 :    
755 : parrello 1.18 =item indexFlag
756 : parrello 1.1
757 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
758 :     L</CreateIndexes> must be called later to bring the indexes into existence.
759 :    
760 : parrello 1.18 =item estimatedRows (optional)
761 :    
762 :     If specified, the estimated maximum number of rows for the relation. This
763 :     information allows the creation of tables using storage engines that are
764 :     faster but require size estimates, such as MyISAM.
765 :    
766 : parrello 1.1 =back
767 :    
768 :     =cut
769 :    
770 :     sub CreateTable {
771 : parrello 1.10 # Get the parameters.
772 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
773 : parrello 1.10 # Get the database handle.
774 :     my $dbh = $self->{_dbh};
775 :     # Get the relation data and determine whether or not the relation is primary.
776 :     my $relationData = $self->_FindRelation($relationName);
777 :     my $rootFlag = $self->_IsPrimary($relationName);
778 :     # Create a list of the field data.
779 :     my @fieldList;
780 :     for my $fieldData (@{$relationData->{Fields}}) {
781 :     # Assemble the field name and type.
782 :     my $fieldName = _FixName($fieldData->{name});
783 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
784 :     # Push the result into the field list.
785 :     push @fieldList, $fieldString;
786 :     }
787 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
788 :     if ($rootFlag) {
789 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
790 :     }
791 :     # Convert the field list into a comma-delimited string.
792 :     my $fieldThing = join(', ', @fieldList);
793 :     # Insure the table is not already there.
794 :     $dbh->drop_table(tbl => $relationName);
795 :     Trace("Table $relationName dropped.") if T(2);
796 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
797 :     # faster DB technologies.
798 :     my $estimation = undef;
799 :     if ($estimatedRows) {
800 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
801 :     }
802 : parrello 1.10 # Create the table.
803 :     Trace("Creating table $relationName: $fieldThing") if T(2);
804 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
805 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
806 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
807 :     # index will not be built until the table has been loaded.
808 : parrello 1.10 if ($indexFlag) {
809 :     $self->CreateIndex($relationName);
810 :     }
811 : parrello 1.1 }
812 :    
813 : parrello 1.31 =head3 VerifyFields
814 :    
815 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
816 :    
817 :     Run through the list of proposed field values, insuring that all the character fields are
818 :     below the maximum length. If any fields are too long, they will be truncated in place.
819 :    
820 :     =over 4
821 :    
822 :     =item relName
823 :    
824 :     Name of the relation for which the specified fields are destined.
825 :    
826 :     =item fieldList
827 :    
828 :     Reference to a list, in order, of the fields to be put into the relation.
829 :    
830 :     =item RETURN
831 :    
832 :     Returns the number of fields truncated.
833 :    
834 :     =back
835 :    
836 :     =cut
837 :    
838 :     sub VerifyFields {
839 :     # Get the parameters.
840 :     my ($self, $relName, $fieldList) = @_;
841 :     # Initialize the return value.
842 :     my $retVal = 0;
843 :     # Get the relation definition.
844 :     my $relData = $self->_FindRelation($relName);
845 :     # Get the list of field descriptors.
846 :     my $fieldTypes = $relData->{Fields};
847 :     my $fieldCount = scalar @{$fieldTypes};
848 :     # Loop through the two lists.
849 :     for (my $i = 0; $i < $fieldCount; $i++) {
850 :     # Get the type of the current field.
851 :     my $fieldType = $fieldTypes->[$i]->{type};
852 :     # If it's a character field, verify the length.
853 :     if ($fieldType =~ /string/) {
854 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
855 :     my $oldString = $fieldList->[$i];
856 :     if (length($oldString) > $maxLen) {
857 :     # Here it's too big, so we truncate it.
858 :     Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
859 :     $fieldList->[$i] = substr $oldString, 0, $maxLen;
860 :     $retVal++;
861 :     }
862 :     }
863 :     }
864 :     # Return the truncation count.
865 :     return $retVal;
866 :     }
867 :    
868 : parrello 1.42 =head3 DigestFields
869 :    
870 :     C<< $erdb->DigestFields($relName, $fieldList); >>
871 :    
872 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
873 :     specified relation.
874 :    
875 :     =over 4
876 :    
877 :     =item relName
878 :    
879 :     Name of the relation to which the fields belong.
880 :    
881 :     =item fieldList
882 :    
883 :     List of field contents to be loaded into the relation.
884 :    
885 :     =back
886 :    
887 :     =cut
888 :     #: Return Type ;
889 :     sub DigestFields {
890 :     # Get the parameters.
891 :     my ($self, $relName, $fieldList) = @_;
892 :     # Get the relation definition.
893 :     my $relData = $self->_FindRelation($relName);
894 :     # Get the list of field descriptors.
895 :     my $fieldTypes = $relData->{Fields};
896 :     my $fieldCount = scalar @{$fieldTypes};
897 :     # Loop through the two lists.
898 :     for (my $i = 0; $i < $fieldCount; $i++) {
899 :     # Get the type of the current field.
900 :     my $fieldType = $fieldTypes->[$i]->{type};
901 :     # If it's a hash string, digest it in place.
902 :     if ($fieldType eq 'hash-string') {
903 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
904 : parrello 1.42 }
905 :     }
906 :     }
907 :    
908 : parrello 1.46 =head3 DigestKey
909 :    
910 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
911 :    
912 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
913 :     key-based search into a table with key-type hash-string.
914 :    
915 :     Currently the digesting process is independent of the database structure, but that may not
916 :     always be the case, so this is an instance method instead of a static method.
917 :    
918 :     =over 4
919 :    
920 :     =item keyValue
921 :    
922 :     Key value to digest.
923 :    
924 :     =item RETURN
925 :    
926 : parrello 1.56 Digested value of the key.
927 : parrello 1.46
928 :     =back
929 :    
930 :     =cut
931 :    
932 :     sub DigestKey {
933 :     # Get the parameters.
934 :     my ($self, $keyValue) = @_;
935 :     # Compute the digest.
936 :     my $retVal = md5_base64($keyValue);
937 :     # Return the result.
938 :     return $retVal;
939 :     }
940 :    
941 : parrello 1.1 =head3 CreateIndex
942 :    
943 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
944 : parrello 1.1
945 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
946 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
947 :     If that is the case, then L</CreateTable> should be called with the index flag set to
948 :     FALSE, and this method used after the load to create the indexes for the table.
949 : parrello 1.1
950 :     =cut
951 :    
952 :     sub CreateIndex {
953 : parrello 1.10 # Get the parameters.
954 :     my ($self, $relationName) = @_;
955 :     # Get the relation's descriptor.
956 :     my $relationData = $self->_FindRelation($relationName);
957 :     # Get the database handle.
958 :     my $dbh = $self->{_dbh};
959 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
960 :     my $indexHash = $relationData->{Indexes};
961 :     for my $indexName (keys %{$indexHash}) {
962 :     my $indexData = $indexHash->{$indexName};
963 :     # Get the index's field list.
964 :     my @fieldList = _FixNames(@{$indexData->{IndexFields}});
965 :     my $flds = join(', ', @fieldList);
966 :     # Get the index's uniqueness flag.
967 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
968 : parrello 1.10 # Create the index.
969 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
970 : parrello 1.70 flds => $flds, kind => $unique);
971 : parrello 1.24 if ($rv) {
972 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
973 :     } else {
974 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
975 :     }
976 : parrello 1.10 }
977 : parrello 1.1 }
978 :    
979 :     =head3 LoadTables
980 :    
981 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
982 : parrello 1.1
983 :     This method will load the database tables from a directory. The tables must already have been created
984 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
985 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
986 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
987 :     line of the file will be loaded as a row of the target relation table. The field values should be in
988 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
989 :     erased before the new data is loaded in.
990 :    
991 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
992 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
993 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
994 :    
995 :     =over 4
996 :    
997 :     =item directoryName
998 :    
999 :     Name of the directory containing the relation files to be loaded.
1000 :    
1001 :     =item rebuild
1002 :    
1003 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1004 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
1005 :     by all of the DB engines we use.
1006 :    
1007 :     =item RETURN
1008 :    
1009 :     Returns a statistical object describing the number of records read and a list of the error messages.
1010 :    
1011 :     =back
1012 :    
1013 :     =cut
1014 :    
1015 :     sub LoadTables {
1016 : parrello 1.10 # Get the parameters.
1017 :     my ($self, $directoryName, $rebuild) = @_;
1018 :     # Start the timer.
1019 :     my $startTime = gettimeofday;
1020 :     # Clean any trailing slash from the directory name.
1021 :     $directoryName =~ s!/\\$!!;
1022 :     # Declare the return variable.
1023 :     my $retVal = Stats->new();
1024 : parrello 1.23 # Get the relation names.
1025 :     my @relNames = $self->GetTableNames();
1026 :     for my $relationName (@relNames) {
1027 :     # Try to load this relation.
1028 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1029 : parrello 1.10 # Accumulate the statistics.
1030 :     $retVal->Accumulate($result);
1031 :     }
1032 :     # Add the duration of the load to the statistical object.
1033 :     $retVal->Add('duration', gettimeofday - $startTime);
1034 :     # Return the accumulated statistics.
1035 :     return $retVal;
1036 : parrello 1.1 }
1037 :    
1038 : parrello 1.23
1039 : parrello 1.1 =head3 GetTableNames
1040 :    
1041 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
1042 : parrello 1.1
1043 :     Return a list of the relations required to implement this database.
1044 :    
1045 :     =cut
1046 :    
1047 :     sub GetTableNames {
1048 : parrello 1.10 # Get the parameters.
1049 :     my ($self) = @_;
1050 :     # Get the relation list from the metadata.
1051 :     my $relationTable = $self->{_metaData}->{RelationTable};
1052 :     # Return the relation names.
1053 :     return keys %{$relationTable};
1054 : parrello 1.1 }
1055 :    
1056 :     =head3 GetEntityTypes
1057 :    
1058 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
1059 : parrello 1.1
1060 :     Return a list of the entity type names.
1061 :    
1062 :     =cut
1063 :    
1064 :     sub GetEntityTypes {
1065 : parrello 1.10 # Get the database object.
1066 :     my ($self) = @_;
1067 :     # Get the entity list from the metadata object.
1068 :     my $entityList = $self->{_metaData}->{Entities};
1069 :     # Return the list of entity names in alphabetical order.
1070 :     return sort keys %{$entityList};
1071 : parrello 1.1 }
1072 :    
1073 : parrello 1.73 =head3 GetDataTypes
1074 :    
1075 :     C<< my %types = ERDB::GetDataTypes(); >>
1076 :    
1077 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1078 :     The keys of the big hash are the datatypes. Each smaller hash has several
1079 :     values used to manage the data. The most interesting is the SQL type (key
1080 :     C<sqlType>) and the descriptive node (key C<notes>).
1081 :    
1082 :     Note that changing the values in the smaller hashes will seriously break
1083 :     things, so this data should be treated as read-only.
1084 :    
1085 :     =cut
1086 :    
1087 :     sub GetDataTypes {
1088 :     return %TypeTable;
1089 :     }
1090 :    
1091 :    
1092 : parrello 1.20 =head3 IsEntity
1093 :    
1094 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1095 :    
1096 :     Return TRUE if the parameter is an entity name, else FALSE.
1097 :    
1098 :     =over 4
1099 :    
1100 :     =item entityName
1101 :    
1102 :     Object name to be tested.
1103 :    
1104 :     =item RETURN
1105 :    
1106 :     Returns TRUE if the specified string is an entity name, else FALSE.
1107 :    
1108 :     =back
1109 :    
1110 :     =cut
1111 :    
1112 :     sub IsEntity {
1113 :     # Get the parameters.
1114 :     my ($self, $entityName) = @_;
1115 :     # Test to see if it's an entity.
1116 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1117 :     }
1118 :    
1119 : parrello 1.1 =head3 Get
1120 :    
1121 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1122 : parrello 1.1
1123 :     This method returns a query object for entities of a specified type using a specified filter.
1124 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1125 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1126 :     following call requests all B<Genome> objects for the genus specified in the variable
1127 :     $genus.
1128 :    
1129 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1130 : parrello 1.1
1131 :     The WHERE clause contains a single question mark, so there is a single additional
1132 :     parameter representing the parameter value. It would also be possible to code
1133 :    
1134 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1135 : parrello 1.1
1136 :     however, this version of the call would generate a syntax error if there were any quote
1137 :     characters inside the variable C<$genus>.
1138 :    
1139 :     The use of the strange parenthesized notation for field names enables us to distinguish
1140 :     hyphens contained within field names from minus signs that participate in the computation
1141 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1142 :    
1143 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1144 :     one object's data at the same time, which allows highly complex joined queries. For example,
1145 :    
1146 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1147 : parrello 1.1
1148 :     If multiple names are specified, then the query processor will automatically determine a
1149 :     join path between the entities and relationships. The algorithm used is very simplistic.
1150 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1151 :     the entity and the relationship appear. For example, consider a recursive relationship
1152 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1153 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1154 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1155 :    
1156 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1157 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1158 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1159 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1160 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1161 :    
1162 : parrello 1.1 =over 4
1163 :    
1164 :     =item objectNames
1165 :    
1166 :     List containing the names of the entity and relationship objects to be retrieved.
1167 :    
1168 :     =item filterClause
1169 :    
1170 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1171 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1172 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1173 :     in the filter clause should be added to the parameter list as additional parameters. The
1174 :     fields in a filter clause can come from primary entity relations, relationship relations,
1175 :     or secondary entity relations; however, all of the entities and relationships involved must
1176 :     be included in the list of object names.
1177 :    
1178 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1179 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1180 :     particular genus and sorts them by species name.
1181 :    
1182 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1183 :    
1184 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1185 :     be processed. The idea is to make it less likely to find the verb by accident.
1186 :    
1187 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1188 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1189 :     relation.
1190 :    
1191 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1192 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1193 :     a positive number. So, for example
1194 :    
1195 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1196 :    
1197 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1198 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1199 :     use
1200 :    
1201 :     C<< "LIMIT 10" >>
1202 :    
1203 : parrello 1.45 =item params
1204 : parrello 1.1
1205 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1206 : parrello 1.1
1207 :     =item RETURN
1208 :    
1209 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1210 :    
1211 :     =back
1212 :    
1213 :     =cut
1214 :    
1215 :     sub Get {
1216 : parrello 1.10 # Get the parameters.
1217 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1218 :     # Process the SQL stuff.
1219 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1220 :     $self->_SetupSQL($objectNames, $filterClause);
1221 :     # Create the query.
1222 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1223 :     ".* $suffix";
1224 :     my $sth = $self->_GetStatementHandle($command, $params);
1225 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1226 :     # and mapped name for each object in the query.
1227 :     my @relationMap = ();
1228 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1229 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1230 : parrello 1.39 }
1231 : parrello 1.10 # Return the statement object.
1232 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1233 : parrello 1.10 return $retVal;
1234 : parrello 1.1 }
1235 :    
1236 : parrello 1.70 =head3 Search
1237 :    
1238 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1239 :    
1240 :     Perform a full text search with filtering. The search will be against a specified object
1241 :     in the object name list. That object will get an extra field containing the search
1242 :     relevance. Note that except for the search expression, the parameters of this method are
1243 :     the same as those for L</Get> and follow the same rules.
1244 :    
1245 :     =over 4
1246 :    
1247 :     =item searchExpression
1248 :    
1249 :     Boolean search expression for the text fields of the target object.
1250 :    
1251 :     =item idx
1252 :    
1253 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1254 :    
1255 :     =item objectNames
1256 :    
1257 :     List containing the names of the entity and relationship objects to be retrieved.
1258 :    
1259 :     =item filterClause
1260 :    
1261 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1262 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1263 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1264 :     in the filter clause should be added to the parameter list as additional parameters. The
1265 :     fields in a filter clause can come from primary entity relations, relationship relations,
1266 :     or secondary entity relations; however, all of the entities and relationships involved must
1267 :     be included in the list of object names.
1268 :    
1269 :     =item params
1270 :    
1271 :     Reference to a list of parameter values to be substituted into the filter clause.
1272 :    
1273 :     =item RETURN
1274 :    
1275 :     Returns a query object for the specified search.
1276 :    
1277 :     =back
1278 :    
1279 :     =cut
1280 :    
1281 :     sub Search {
1282 :     # Get the parameters.
1283 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1284 :     # Declare the return variable.
1285 :     my $retVal;
1286 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1287 :     # a parameter list exists before we copy it.
1288 :     my @myParams = ();
1289 :     if (defined $params) {
1290 :     @myParams = @{$params};
1291 :     }
1292 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1293 :     my $object1Name = $objectNames->[$idx];
1294 :     my $object1Structure = $self->_GetStructure($object1Name);
1295 :     # Get the field list.
1296 :     if (! exists $object1Structure->{searchFields}) {
1297 :     Confess("No searchable index for $object1Name.");
1298 :     } else {
1299 :     # Get the field list.
1300 :     my @fields = @{$object1Structure->{searchFields}};
1301 : parrello 1.71 # Clean the search expression.
1302 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1303 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1304 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1305 :     # query itself. Both will use a parameter mark, so we need to push the
1306 :     # search expression onto the front of the parameter list twice.
1307 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1308 : parrello 1.70 # Build the match expression.
1309 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1310 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1311 :     # Process the SQL stuff.
1312 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1313 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1314 :     # Create the query. Note that the match clause is inserted at the front of
1315 :     # the select fields.
1316 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1317 :     ".* $suffix";
1318 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1319 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1320 :     # and mapped name for each object in the query.
1321 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1322 :     # Return the statement object.
1323 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1324 :     }
1325 :     return $retVal;
1326 :     }
1327 :    
1328 : parrello 1.45 =head3 GetFlat
1329 :    
1330 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1331 :    
1332 :     This is a variation of L</GetAll> that asks for only a single field per record and
1333 :     returns a single flattened list.
1334 :    
1335 :     =over 4
1336 :    
1337 :     =item objectNames
1338 :    
1339 :     List containing the names of the entity and relationship objects to be retrieved.
1340 :    
1341 :     =item filterClause
1342 :    
1343 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1344 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1345 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1346 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1347 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1348 :     entities and relationships involved must be included in the list of object names.
1349 :    
1350 :     =item parameterList
1351 :    
1352 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1353 :    
1354 :     =item field
1355 :    
1356 :     Name of the field to be used to get the elements of the list returned.
1357 :    
1358 :     =item RETURN
1359 :    
1360 :     Returns a list of values.
1361 :    
1362 :     =back
1363 :    
1364 :     =cut
1365 :     #: Return Type @;
1366 :     sub GetFlat {
1367 :     # Get the parameters.
1368 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1369 :     # Construct the query.
1370 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1371 :     # Create the result list.
1372 :     my @retVal = ();
1373 :     # Loop through the records, adding the field values found to the result list.
1374 :     while (my $row = $query->Fetch()) {
1375 :     push @retVal, $row->Value($field);
1376 :     }
1377 :     # Return the list created.
1378 :     return @retVal;
1379 :     }
1380 :    
1381 : parrello 1.73 =head3 SpecialFields
1382 :    
1383 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1384 :    
1385 :     Return a hash mapping special fields in the specified entity to the value of their
1386 :     C<special> attribute. This enables the subclass to get access to the special field
1387 :     attributes without needed to plumb the internal ERDB data structures.
1388 :    
1389 :     =over 4
1390 :    
1391 :     =item entityName
1392 :    
1393 :     Name of the entity whose special fields are desired.
1394 :    
1395 :     =item RETURN
1396 :    
1397 :     Returns a hash. The keys of the hash are the special field names, and the values
1398 :     are the values from each special field's C<special> attribute.
1399 :    
1400 :     =back
1401 :    
1402 :     =cut
1403 :    
1404 :     sub SpecialFields {
1405 :     # Get the parameters.
1406 :     my ($self, $entityName) = @_;
1407 :     # Declare the return variable.
1408 :     my %retVal = ();
1409 :     # Find the entity's data structure.
1410 :     my $entityData = $self->{Entities}->{$entityName};
1411 :     # Loop through its fields, adding each special field to the return hash.
1412 :     my $fieldHash = $entityData->{Fields};
1413 :     for my $fieldName (keys %{$fieldHash}) {
1414 :     my $fieldData = $fieldHash->{$fieldName};
1415 :     if (exists $fieldData->{special}) {
1416 :     $retVal{$fieldName} = $fieldData->{special};
1417 :     }
1418 :     }
1419 :     # Return the result.
1420 :     return %retVal;
1421 :     }
1422 :    
1423 : parrello 1.32 =head3 Delete
1424 :    
1425 :     C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1426 :    
1427 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1428 :     relationship instances dependent on it. The idea of dependence here is recursive. An object is
1429 :     always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1430 :     relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1431 :     dependent relationship.
1432 :    
1433 :     =over 4
1434 :    
1435 :     =item entityName
1436 :    
1437 :     Name of the entity type for the instance being deleted.
1438 :    
1439 :     =item objectID
1440 :    
1441 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1442 :     then it is presumed to by a LIKE pattern.
1443 :    
1444 :     =item testFlag
1445 :    
1446 :     If TRUE, the delete statements will be traced without being executed.
1447 :    
1448 :     =item RETURN
1449 :    
1450 :     Returns a statistics object indicating how many records of each particular table were
1451 :     deleted.
1452 :    
1453 :     =back
1454 :    
1455 :     =cut
1456 :     #: Return Type $%;
1457 :     sub Delete {
1458 :     # Get the parameters.
1459 :     my ($self, $entityName, $objectID, $testFlag) = @_;
1460 :     # Declare the return variable.
1461 :     my $retVal = Stats->new();
1462 :     # Get the DBKernel object.
1463 :     my $db = $self->{_dbh};
1464 :     # We're going to generate all the paths branching out from the starting entity. One of
1465 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1466 :     # determine if we've hit a loop.
1467 :     my %alreadyFound = ();
1468 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1469 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1470 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1471 :     # sure we don't delete records that might be needed to forge relationships back to the
1472 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1473 :     # FROM-relationships and entities.
1474 :     my @fromPathList = ();
1475 :     my @toPathList = ();
1476 : parrello 1.32 # This final hash is used to remember what work still needs to be done. We push paths
1477 :     # onto the list, then pop them off to extend the paths. We prime it with the starting
1478 :     # point. Note that we will work hard to insure that the last item on a path in the
1479 :     # TODO list is always an entity.
1480 :     my @todoList = ([$entityName]);
1481 :     while (@todoList) {
1482 :     # Get the current path.
1483 :     my $current = pop @todoList;
1484 :     # Copy it into a list.
1485 :     my @stackedPath = @{$current};
1486 :     # Pull off the last item on the path. It will always be an entity.
1487 :     my $entityName = pop @stackedPath;
1488 :     # Add it to the alreadyFound list.
1489 :     $alreadyFound{$entityName} = 1;
1490 :     # Get the entity data.
1491 :     my $entityData = $self->_GetStructure($entityName);
1492 :     # The first task is to loop through the entity's relation. A DELETE command will
1493 :     # be needed for each of them.
1494 :     my $relations = $entityData->{Relations};
1495 :     for my $relation (keys %{$relations}) {
1496 :     my @augmentedList = (@stackedPath, $relation);
1497 : parrello 1.33 push @fromPathList, \@augmentedList;
1498 : parrello 1.32 }
1499 :     # Now we need to look for relationships connected to this entity.
1500 :     my $relationshipList = $self->{_metaData}->{Relationships};
1501 :     for my $relationshipName (keys %{$relationshipList}) {
1502 :     my $relationship = $relationshipList->{$relationshipName};
1503 :     # Check the FROM field. We're only interested if it's us.
1504 :     if ($relationship->{from} eq $entityName) {
1505 :     # Add the path to this relationship.
1506 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1507 : parrello 1.33 push @fromPathList, \@augmentedList;
1508 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1509 :     # and the target hasn't been seen yet, we want to
1510 :     # stack the entity for future processing.
1511 :     if ($relationship->{arity} eq '1M') {
1512 :     my $toEntity = $relationship->{to};
1513 :     if (! exists $alreadyFound{$toEntity}) {
1514 :     # Here we have a new entity that's dependent on
1515 :     # the current entity, so we need to stack it.
1516 :     my @stackList = (@augmentedList, $toEntity);
1517 : parrello 1.33 push @fromPathList, \@stackList;
1518 : parrello 1.34 } else {
1519 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1520 : parrello 1.32 }
1521 :     }
1522 :     }
1523 :     # Now check the TO field. In this case only the relationship needs
1524 : parrello 1.33 # deletion.
1525 : parrello 1.32 if ($relationship->{to} eq $entityName) {
1526 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1527 : parrello 1.33 push @toPathList, \@augmentedList;
1528 : parrello 1.32 }
1529 :     }
1530 :     }
1531 :     # Create the first qualifier for the WHERE clause. This selects the
1532 :     # keys of the primary entity records to be deleted. When we're deleting
1533 :     # from a dependent table, we construct a join page from the first qualifier
1534 :     # to the table containing the dependent records to delete.
1535 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1536 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1537 :     # the second through the from-list. The from-list is second because
1538 :     # the to-list may need to pass through some of the entities the
1539 :     # from-list would delete.
1540 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1541 :     # Now it's time to do the deletes. We do it in two passes.
1542 :     for my $keyName ('to_link', 'from_link') {
1543 :     # Get the list for this key.
1544 :     my @pathList = @{$stackList{$keyName}};
1545 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1546 : parrello 1.33 # Loop through this list.
1547 :     while (my $path = pop @pathList) {
1548 :     # Get the table whose rows are to be deleted.
1549 :     my @pathTables = @{$path};
1550 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1551 :     # syntax of a DELETE-USING varies among DBMSs.
1552 : parrello 1.33 my $target = $pathTables[$#pathTables];
1553 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1554 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1555 :     # starting table will either be the entity relation or one of the entity's
1556 :     # sub-relations.
1557 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1558 :     # Now we run through the remaining entities in the path, connecting them up.
1559 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1560 :     # Connect the current relationship to the preceding entity.
1561 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1562 :     # The style of connection depends on the direction of the relationship.
1563 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1564 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1565 :     # Here there's a next entity, so connect that to the relationship's
1566 :     # to-link.
1567 :     my $entity2 = $pathTables[$i+1];
1568 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1569 : parrello 1.32 }
1570 :     }
1571 : parrello 1.33 # Now we have our desired DELETE statement.
1572 :     if ($testFlag) {
1573 :     # Here the user wants to trace without executing.
1574 :     Trace($stmt) if T(0);
1575 :     } else {
1576 :     # Here we can delete. Note that the SQL method dies with a confessing
1577 :     # if an error occurs, so we just go ahead and do it.
1578 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1579 :     my $rv = $db->SQL($stmt, 0, $objectID);
1580 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1581 :     # are from the target table, so we use its name to record the
1582 :     # statistic.
1583 :     $retVal->Add($target, $rv);
1584 :     }
1585 : parrello 1.32 }
1586 :     }
1587 :     # Return the result.
1588 :     return $retVal;
1589 :     }
1590 :    
1591 : parrello 1.70 =head3 SortNeeded
1592 :    
1593 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
1594 :    
1595 :     Return the pipe command for the sort that should be applied to the specified
1596 :     relation when creating the load file.
1597 :    
1598 :     For example, if the load file should be sorted ascending by the first
1599 :     field, this method would return
1600 :    
1601 :     sort -k1 -t"\t"
1602 :    
1603 :     If the first field is numeric, the method would return
1604 :    
1605 :     sort -k1n -t"\t"
1606 :    
1607 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1608 :     keys using a sort.
1609 :    
1610 :     =over 4
1611 :    
1612 :     =item relationName
1613 :    
1614 :     Name of the relation to be examined.
1615 :    
1616 :     =item
1617 :    
1618 :     Returns the sort command to use for sorting the relation, suitable for piping.
1619 :    
1620 :     =back
1621 :    
1622 :     =cut
1623 :     #: Return Type $;
1624 :     sub SortNeeded {
1625 :     # Get the parameters.
1626 :     my ($self, $relationName) = @_;
1627 :     # Declare a descriptor to hold the names of the key fields.
1628 :     my @keyNames = ();
1629 :     # Get the relation structure.
1630 :     my $relationData = $self->_FindRelation($relationName);
1631 :     # Find out if the relation is a primary entity relation,
1632 :     # a relationship relation, or a secondary entity relation.
1633 :     my $entityTable = $self->{_metaData}->{Entities};
1634 :     my $relationshipTable = $self->{_metaData}->{Relationships};
1635 :     if (exists $entityTable->{$relationName}) {
1636 :     # Here we have a primary entity relation.
1637 :     push @keyNames, "id";
1638 :     } elsif (exists $relationshipTable->{$relationName}) {
1639 :     # Here we have a relationship. We sort using the FROM index.
1640 :     my $relationshipData = $relationshipTable->{$relationName};
1641 :     my $index = $relationData->{Indexes}->{"idx${relationName}From"};
1642 :     push @keyNames, @{$index->{IndexFields}};
1643 :     } else {
1644 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
1645 :     push @keyNames, "id";
1646 :     }
1647 :     # Now we parse the key names into sort parameters. First, we prime the return
1648 :     # string.
1649 :     my $retVal = "sort -t\"\t\" ";
1650 :     # Get the relation's field list.
1651 :     my @fields = @{$relationData->{Fields}};
1652 :     # Loop through the keys.
1653 :     for my $keyData (@keyNames) {
1654 :     # Get the key and the ordering.
1655 :     my ($keyName, $ordering);
1656 :     if ($keyData =~ /^([^ ]+) DESC/) {
1657 :     ($keyName, $ordering) = ($1, "descending");
1658 :     } else {
1659 :     ($keyName, $ordering) = ($keyData, "ascending");
1660 :     }
1661 :     # Find the key's position and type.
1662 :     my $fieldSpec;
1663 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1664 :     my $thisField = $fields[$i];
1665 :     if ($thisField->{name} eq $keyName) {
1666 :     # Get the sort modifier for this field type. The modifier
1667 :     # decides whether we're using a character, numeric, or
1668 :     # floating-point sort.
1669 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
1670 :     # If the index is descending for this field, denote we want
1671 :     # to reverse the sort order on this field.
1672 :     if ($ordering eq 'descending') {
1673 :     $modifier .= "r";
1674 :     }
1675 :     # Store the position and modifier into the field spec, which
1676 :     # will stop the inner loop. Note that the field number is
1677 :     # 1-based in the sort command, so we have to increment the
1678 :     # index.
1679 :     $fieldSpec = ($i + 1) . $modifier;
1680 :     }
1681 :     }
1682 :     # Add this field to the sort command.
1683 :     $retVal .= " -k$fieldSpec";
1684 :     }
1685 :     # Return the result.
1686 :     return $retVal;
1687 :     }
1688 :    
1689 : parrello 1.6 =head3 GetList
1690 :    
1691 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1692 : parrello 1.6
1693 :     Return a list of object descriptors for the specified objects as determined by the
1694 :     specified filter clause.
1695 :    
1696 :     This method is essentially the same as L</Get> except it returns a list of objects rather
1697 : parrello 1.7 than a query object that can be used to get the results one record at a time.
1698 : parrello 1.6
1699 :     =over 4
1700 :    
1701 :     =item objectNames
1702 :    
1703 :     List containing the names of the entity and relationship objects to be retrieved.
1704 :    
1705 :     =item filterClause
1706 :    
1707 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1708 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1709 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1710 :     in the filter clause should be added to the parameter list as additional parameters. The
1711 :     fields in a filter clause can come from primary entity relations, relationship relations,
1712 :     or secondary entity relations; however, all of the entities and relationships involved must
1713 :     be included in the list of object names.
1714 :    
1715 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1716 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1717 :     particular genus and sorts them by species name.
1718 :    
1719 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1720 :    
1721 :     The rules for field references in a sort order are the same as those for field references in the
1722 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1723 :     relation.
1724 :    
1725 : parrello 1.45 =item params
1726 : parrello 1.6
1727 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1728 : parrello 1.6
1729 :     =item RETURN
1730 :    
1731 :     Returns a list of B<DBObject>s that satisfy the query conditions.
1732 :    
1733 :     =back
1734 :    
1735 :     =cut
1736 :     #: Return Type @%
1737 :     sub GetList {
1738 :     # Get the parameters.
1739 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1740 : parrello 1.10 # Declare the return variable.
1741 :     my @retVal = ();
1742 :     # Perform the query.
1743 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
1744 : parrello 1.10 # Loop through the results.
1745 :     while (my $object = $query->Fetch) {
1746 :     push @retVal, $object;
1747 :     }
1748 : parrello 1.6 # Return the result.
1749 :     return @retVal;
1750 :     }
1751 :    
1752 : parrello 1.45 =head3 GetCount
1753 :    
1754 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1755 :    
1756 :     Return the number of rows found by a specified query. This method would
1757 :     normally be used to count the records in a single table. For example, in a
1758 :     genetics database
1759 :    
1760 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1761 :    
1762 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
1763 :     to use it to return records based on a join. For example,
1764 :    
1765 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1766 : parrello 1.45 ['homo %']);
1767 :    
1768 :     would return the number of features for genomes in the genus I<homo>. Note that
1769 :     only the rows from the first table are counted. If the above command were
1770 :    
1771 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1772 :     ['homo %']);
1773 :    
1774 :     it would return the number of genomes, not the number of genome/feature pairs.
1775 :    
1776 :     =over 4
1777 :    
1778 :     =item objectNames
1779 :    
1780 :     Reference to a list of the objects (entities and relationships) included in the
1781 :     query.
1782 :    
1783 :     =item filter
1784 :    
1785 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
1786 :     method.
1787 :    
1788 :     =item params
1789 :    
1790 :     Reference to a list of the parameter values to be substituted for the parameter marks
1791 :     in the filter.
1792 :    
1793 :     =item RETURN
1794 :    
1795 :     Returns a count of the number of records in the first table that would satisfy
1796 :     the query.
1797 :    
1798 :     =back
1799 :    
1800 :     =cut
1801 :    
1802 :     sub GetCount {
1803 :     # Get the parameters.
1804 :     my ($self, $objectNames, $filter, $params) = @_;
1805 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
1806 :     if (! defined($params)) {
1807 :     $params = [];
1808 :     }
1809 : parrello 1.45 # Declare the return variable.
1810 :     my $retVal;
1811 : parrello 1.47 # Find out if we're counting an entity or a relationship.
1812 :     my $countedField;
1813 :     if ($self->IsEntity($objectNames->[0])) {
1814 :     $countedField = "id";
1815 :     } else {
1816 :     # For a relationship we count the to-link because it's usually more
1817 :     # numerous. Note we're automatically converting to the SQL form
1818 :     # of the field name (to_link vs. to-link).
1819 :     $countedField = "to_link";
1820 :     }
1821 : parrello 1.45 # Create the SQL command suffix to get the desired records.
1822 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1823 :     $filter);
1824 :     # Prefix it with text telling it we want a record count.
1825 :     my $firstObject = $mappedNameListRef->[0];
1826 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
1827 : parrello 1.45 # Prepare and execute the command.
1828 :     my $sth = $self->_GetStatementHandle($command, $params);
1829 :     # Get the count value.
1830 :     ($retVal) = $sth->fetchrow_array();
1831 :     # Check for a problem.
1832 :     if (! defined($retVal)) {
1833 :     if ($sth->err) {
1834 :     # Here we had an SQL error.
1835 :     Confess("Error retrieving row count: " . $sth->errstr());
1836 :     } else {
1837 :     # Here we have no result.
1838 :     Confess("No result attempting to retrieve row count.");
1839 :     }
1840 :     }
1841 :     # Return the result.
1842 :     return $retVal;
1843 :     }
1844 :    
1845 : parrello 1.1 =head3 ComputeObjectSentence
1846 :    
1847 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1848 : parrello 1.1
1849 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
1850 :    
1851 :     =over 4
1852 :    
1853 :     =item objectName
1854 :    
1855 :     Name of the entity or relationship.
1856 :    
1857 :     =item RETURN
1858 :    
1859 :     Returns a string containing the entity name or a relationship sentence.
1860 :    
1861 :     =back
1862 :    
1863 :     =cut
1864 :    
1865 :     sub ComputeObjectSentence {
1866 : parrello 1.10 # Get the parameters.
1867 :     my ($self, $objectName) = @_;
1868 :     # Set the default return value.
1869 :     my $retVal = $objectName;
1870 :     # Look for the object as a relationship.
1871 :     my $relTable = $self->{_metaData}->{Relationships};
1872 :     if (exists $relTable->{$objectName}) {
1873 :     # Get the relationship sentence.
1874 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
1875 :     }
1876 :     # Return the result.
1877 :     return $retVal;
1878 : parrello 1.1 }
1879 :    
1880 :     =head3 DumpRelations
1881 :    
1882 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
1883 : parrello 1.1
1884 :     Write the contents of all the relations to tab-delimited files in the specified directory.
1885 :     Each file will have the same name as the relation dumped, with an extension of DTX.
1886 :    
1887 :     =over 4
1888 :    
1889 :     =item outputDirectory
1890 :    
1891 :     Name of the directory into which the relation files should be dumped.
1892 :    
1893 :     =back
1894 :    
1895 :     =cut
1896 :    
1897 :     sub DumpRelations {
1898 : parrello 1.10 # Get the parameters.
1899 :     my ($self, $outputDirectory) = @_;
1900 :     # Now we need to run through all the relations. First, we loop through the entities.
1901 :     my $metaData = $self->{_metaData};
1902 :     my $entities = $metaData->{Entities};
1903 :     for my $entityName (keys %{$entities}) {
1904 :     my $entityStructure = $entities->{$entityName};
1905 :     # Get the entity's relations.
1906 :     my $relationList = $entityStructure->{Relations};
1907 :     # Loop through the relations, dumping them.
1908 :     for my $relationName (keys %{$relationList}) {
1909 :     my $relation = $relationList->{$relationName};
1910 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
1911 :     }
1912 :     }
1913 :     # Next, we loop through the relationships.
1914 :     my $relationships = $metaData->{Relationships};
1915 :     for my $relationshipName (keys %{$relationships}) {
1916 :     my $relationshipStructure = $relationships->{$relationshipName};
1917 :     # Dump this relationship's relation.
1918 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
1919 :     }
1920 : parrello 1.1 }
1921 :    
1922 : parrello 1.51 =head3 InsertValue
1923 :    
1924 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
1925 :    
1926 :     This method will insert a new value into the database. The value must be one
1927 :     associated with a secondary relation, since primary values cannot be inserted:
1928 :     they occur exactly once. Secondary values, on the other hand, can be missing
1929 :     or multiply-occurring.
1930 :    
1931 :     =over 4
1932 :    
1933 :     =item entityID
1934 :    
1935 :     ID of the object that is to receive the new value.
1936 :    
1937 :     =item fieldName
1938 :    
1939 :     Field name for the new value-- this includes the entity name, since
1940 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
1941 :    
1942 :     =item value
1943 :    
1944 :     New value to be put in the field.
1945 :    
1946 :     =back
1947 :    
1948 :     =cut
1949 :    
1950 :     sub InsertValue {
1951 :     # Get the parameters.
1952 :     my ($self, $entityID, $fieldName, $value) = @_;
1953 :     # Parse the entity name and the real field name.
1954 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
1955 :     my $entityName = $1;
1956 :     my $fieldTitle = $2;
1957 :     # Get its descriptor.
1958 :     if (!$self->IsEntity($entityName)) {
1959 :     Confess("$entityName is not a valid entity.");
1960 :     } else {
1961 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1962 :     # Find the relation containing this field.
1963 :     my $fieldHash = $entityData->{Fields};
1964 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
1965 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
1966 :     } else {
1967 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
1968 :     if ($relation eq $entityName) {
1969 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
1970 :     } else {
1971 :     # Now we can create an INSERT statement.
1972 :     my $dbh = $self->{_dbh};
1973 :     my $fixedName = _FixName($fieldTitle);
1974 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
1975 : parrello 1.51 # Execute the command.
1976 :     $dbh->SQL($statement, 0, $entityID, $value);
1977 :     }
1978 :     }
1979 :     }
1980 :     } else {
1981 :     Confess("$fieldName is not a valid field name.");
1982 :     }
1983 :     }
1984 :    
1985 : parrello 1.1 =head3 InsertObject
1986 :    
1987 : parrello 1.18 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1988 : parrello 1.1
1989 :     Insert an object into the database. The object is defined by a type name and then a hash
1990 :     of field names to values. Field values in the primary relation are represented by scalars.
1991 :     (Note that for relationships, the primary relation is the B<only> relation.)
1992 :     Field values for the other relations comprising the entity are always list references. For
1993 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
1994 :     C<ZP_00210270.1> and C<gi|46206278>.
1995 :    
1996 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
1997 : parrello 1.1
1998 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
1999 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2000 :    
2001 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2002 : parrello 1.1
2003 :     =over 4
2004 :    
2005 :     =item newObjectType
2006 :    
2007 :     Type name of the object to insert.
2008 :    
2009 :     =item fieldHash
2010 :    
2011 :     Hash of field names to values.
2012 :    
2013 :     =item RETURN
2014 :    
2015 :     Returns 1 if successful, 0 if an error occurred.
2016 :    
2017 :     =back
2018 :    
2019 :     =cut
2020 :    
2021 :     sub InsertObject {
2022 : parrello 1.10 # Get the parameters.
2023 :     my ($self, $newObjectType, $fieldHash) = @_;
2024 :     # Denote that so far we appear successful.
2025 :     my $retVal = 1;
2026 :     # Get the database handle.
2027 :     my $dbh = $self->{_dbh};
2028 :     # Get the relation list.
2029 :     my $relationTable = $self->_GetRelationTable($newObjectType);
2030 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
2031 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
2032 :     # stop the loop.
2033 :     my @relationList = keys %{$relationTable};
2034 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2035 :     my $relationName = $relationList[$i];
2036 :     my $relationDefinition = $relationTable->{$relationName};
2037 :     # Get the relation's fields. For each field we will collect a value in the corresponding
2038 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
2039 :     # @missing list.
2040 :     my @fieldList = @{$relationDefinition->{Fields}};
2041 :     my @fieldNameList = ();
2042 :     my @valueList = ();
2043 :     my @missing = ();
2044 :     my $recordCount = 1;
2045 :     for my $fieldDescriptor (@fieldList) {
2046 :     # Get the field name and save it. Note we need to fix it up so the hyphens
2047 :     # are converted to underscores.
2048 :     my $fieldName = $fieldDescriptor->{name};
2049 :     push @fieldNameList, _FixName($fieldName);
2050 :     # Look for the named field in the incoming structure. Note that we are looking
2051 :     # for the real field name, not the fixed-up one!
2052 :     if (exists $fieldHash->{$fieldName}) {
2053 :     # Here we found the field. Stash it in the value list.
2054 :     my $value = $fieldHash->{$fieldName};
2055 :     push @valueList, $value;
2056 :     # If the value is a list, we may need to increment the record count.
2057 :     if (ref $value eq "ARRAY") {
2058 :     my $thisCount = @{$value};
2059 :     if ($recordCount == 1) {
2060 :     # Here we have our first list, so we save its count.
2061 :     $recordCount = $thisCount;
2062 :     } elsif ($recordCount != $thisCount) {
2063 :     # Here we have a second list, so its length has to match the
2064 :     # previous lists.
2065 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2066 :     $retVal = 0;
2067 :     }
2068 :     }
2069 :     } else {
2070 :     # Here the field is not present. Flag it as missing.
2071 :     push @missing, $fieldName;
2072 :     }
2073 :     }
2074 :     # If we are the primary relation, add the new-record flag.
2075 :     if ($relationName eq $newObjectType) {
2076 :     push @valueList, 1;
2077 :     push @fieldNameList, "new_record";
2078 :     }
2079 :     # Only proceed if there are no missing fields.
2080 :     if (@missing > 0) {
2081 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2082 :     join(' ', @missing)) if T(1);
2083 :     } else {
2084 :     # Build the INSERT statement.
2085 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2086 :     ") VALUES (";
2087 :     # Create a marker list of the proper size and put it in the statement.
2088 :     my @markers = ();
2089 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2090 :     $statement .= join(', ', @markers) . ")";
2091 :     # We have the insert statement, so prepare it.
2092 :     my $sth = $dbh->prepare_command($statement);
2093 :     Trace("Insert statement prepared: $statement") if T(3);
2094 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2095 :     # a list, we use the current element. The values are stored in the @parameterList array.
2096 :     my $done = 0;
2097 :     for (my $i = 0; $i < $recordCount; $i++) {
2098 :     # Clear the parameter list array.
2099 :     my @parameterList = ();
2100 :     # Loop through the values.
2101 :     for my $value (@valueList) {
2102 :     # Check to see if this is a scalar value.
2103 :     if (ref $value eq "ARRAY") {
2104 :     # Here we have a list value. Pull the current entry.
2105 :     push @parameterList, $value->[$i];
2106 :     } else {
2107 :     # Here we have a scalar value. Use it unmodified.
2108 :     push @parameterList, $value;
2109 :     }
2110 :     }
2111 :     # Execute the INSERT statement with the specified parameter list.
2112 :     $retVal = $sth->execute(@parameterList);
2113 :     if (!$retVal) {
2114 :     my $errorString = $sth->errstr();
2115 :     Trace("Insert error: $errorString.") if T(0);
2116 :     }
2117 :     }
2118 :     }
2119 :     }
2120 :     # Return the success indicator.
2121 :     return $retVal;
2122 : parrello 1.1 }
2123 :    
2124 :     =head3 LoadTable
2125 :    
2126 : parrello 1.18 C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2127 : parrello 1.1
2128 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2129 :     first.
2130 : parrello 1.1
2131 :     =over 4
2132 :    
2133 :     =item fileName
2134 :    
2135 :     Name of the file from which the table data should be loaded.
2136 :    
2137 :     =item relationName
2138 :    
2139 :     Name of the relation to be loaded. This is the same as the table name.
2140 :    
2141 :     =item truncateFlag
2142 :    
2143 :     TRUE if the table should be dropped and re-created, else FALSE
2144 :    
2145 :     =item RETURN
2146 :    
2147 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2148 : parrello 1.1
2149 :     =back
2150 :    
2151 :     =cut
2152 :     sub LoadTable {
2153 : parrello 1.10 # Get the parameters.
2154 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2155 :     # Create the statistical return object.
2156 :     my $retVal = _GetLoadStats();
2157 :     # Trace the fact of the load.
2158 :     Trace("Loading table $relationName from $fileName") if T(2);
2159 :     # Get the database handle.
2160 :     my $dbh = $self->{_dbh};
2161 : parrello 1.22 # Get the input file size.
2162 :     my $fileSize = -s $fileName;
2163 : parrello 1.10 # Get the relation data.
2164 :     my $relation = $self->_FindRelation($relationName);
2165 :     # Check the truncation flag.
2166 :     if ($truncateFlag) {
2167 :     Trace("Creating table $relationName") if T(2);
2168 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2169 :     # divide it by the estimated row size, and then multiply by 1.5 to
2170 :     # leave extra room. We postulate a minimum row count of 1000 to
2171 :     # prevent problems with incoming empty load files.
2172 :     my $rowSize = $self->EstimateRowSize($relationName);
2173 :     my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2174 : parrello 1.10 # Re-create the table without its index.
2175 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2176 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2177 :     if ($dbh->{_preIndex}) {
2178 :     eval {
2179 :     $self->CreateIndex($relationName);
2180 :     };
2181 :     if ($@) {
2182 :     $retVal->AddMessage($@);
2183 :     }
2184 :     }
2185 :     }
2186 : parrello 1.3 # Load the table.
2187 : parrello 1.10 my $rv;
2188 :     eval {
2189 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2190 : parrello 1.10 };
2191 :     if (!defined $rv) {
2192 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2193 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2194 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2195 :     } else {
2196 : parrello 1.22 # Here we successfully loaded the table.
2197 :     $retVal->Add("tables");
2198 :     my $size = -s $fileName;
2199 :     Trace("$size bytes loaded into $relationName.") if T(2);
2200 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2201 : parrello 1.70 if ($truncateFlag) {
2202 :     # Indexes are created here for PostGres. For PostGres, indexes are
2203 :     # best built at the end. For MySQL, the reverse is true.
2204 :     if (! $dbh->{_preIndex}) {
2205 :     eval {
2206 :     $self->CreateIndex($relationName);
2207 :     };
2208 :     if ($@) {
2209 :     $retVal->AddMessage($@);
2210 :     }
2211 :     }
2212 :     # The full-text index (if any) is always built last, even for MySQL.
2213 :     # First we need to see if this table has a full-text index. Only
2214 :     # primary relations are allowed that privilege.
2215 :     if ($self->_IsPrimary($relationName)) {
2216 :     # Get the relation's entity/relationship structure.
2217 :     my $structure = $self->_GetStructure($relationName);
2218 :     # Check for a searchable fields list.
2219 :     if (exists $structure->{searchFields}) {
2220 :     # Here we know that we need to create a full-text search index.
2221 :     # Get an SQL-formatted field name list.
2222 :     my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2223 :     # Create the index.
2224 :     $dbh->create_index(tbl => $relationName, idx => "search_idx_$relationName",
2225 :     flds => $fields, kind => 'fulltext');
2226 :     }
2227 : parrello 1.10 }
2228 :     }
2229 :     }
2230 : parrello 1.20 # Analyze the table to improve performance.
2231 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2232 : olson 1.16 $dbh->vacuum_it($relationName);
2233 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2234 : parrello 1.10 # Return the statistics.
2235 :     return $retVal;
2236 : parrello 1.1 }
2237 :    
2238 : parrello 1.73 =head3 DropRelation
2239 : parrello 1.1
2240 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2241 : parrello 1.1
2242 : parrello 1.73 Physically drop a relation from the database.
2243 : parrello 1.1
2244 :     =over 4
2245 :    
2246 : parrello 1.73 =item relationName
2247 : parrello 1.1
2248 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2249 :     no effect.
2250 : parrello 1.1
2251 :     =back
2252 :    
2253 :     =cut
2254 :    
2255 : parrello 1.73 sub DropRelation {
2256 : parrello 1.10 # Get the parameters.
2257 : parrello 1.73 my ($self, $relationName) = @_;
2258 :     # Get the database handle.
2259 :     my $dbh = $self->{_dbh};
2260 :     # Drop the relation. The method used here has no effect if the relation
2261 :     # does not exist.
2262 : parrello 1.74 Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2263 :     $dbh->drop_table(tbl => $relationName);
2264 : parrello 1.1 }
2265 :    
2266 : parrello 1.6 =head3 GetEntity
2267 :    
2268 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2269 : parrello 1.6
2270 :     Return an object describing the entity instance with a specified ID.
2271 :    
2272 :     =over 4
2273 :    
2274 :     =item entityType
2275 :    
2276 :     Entity type name.
2277 :    
2278 :     =item ID
2279 :    
2280 :     ID of the desired entity.
2281 :    
2282 :     =item RETURN
2283 :    
2284 :     Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2285 :     instance is found with the specified key.
2286 :    
2287 :     =back
2288 :    
2289 :     =cut
2290 :    
2291 :     sub GetEntity {
2292 : parrello 1.10 # Get the parameters.
2293 :     my ($self, $entityType, $ID) = @_;
2294 :     # Create a query.
2295 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2296 : parrello 1.10 # Get the first (and only) object.
2297 :     my $retVal = $query->Fetch();
2298 :     # Return the result.
2299 :     return $retVal;
2300 : parrello 1.6 }
2301 :    
2302 : parrello 1.69 =head3 GetChoices
2303 :    
2304 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2305 :    
2306 :     Return a list of all the values for the specified field that are represented in the
2307 :     specified entity.
2308 :    
2309 :     Note that if the field is not indexed, then this will be a very slow operation.
2310 :    
2311 :     =over 4
2312 :    
2313 :     =item entityName
2314 :    
2315 :     Name of an entity in the database.
2316 :    
2317 :     =item fieldName
2318 :    
2319 :     Name of a field belonging to the entity. This is a raw field name without
2320 :     the standard parenthesized notation used in most calls.
2321 :    
2322 :     =item RETURN
2323 :    
2324 :     Returns a list of the distinct values for the specified field in the database.
2325 :    
2326 :     =back
2327 :    
2328 :     =cut
2329 :    
2330 :     sub GetChoices {
2331 :     # Get the parameters.
2332 :     my ($self, $entityName, $fieldName) = @_;
2333 :     # Declare the return variable.
2334 :     my @retVal;
2335 :     # Get the entity data structure.
2336 :     my $entityData = $self->_GetStructure($entityName);
2337 :     # Get the field.
2338 :     my $fieldHash = $entityData->{Fields};
2339 :     if (! exists $fieldHash->{$fieldName}) {
2340 :     Confess("$fieldName not found in $entityName.");
2341 :     } else {
2342 :     # Get the name of the relation containing the field.
2343 :     my $relation = $fieldHash->{$fieldName}->{relation};
2344 :     # Fix up the field name.
2345 :     my $realName = _FixName($fieldName);
2346 :     # Get the database handle.
2347 :     my $dbh = $self->{_dbh};
2348 :     # Query the database.
2349 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2350 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
2351 :     @retVal = sort map { $_->[0] } @{$results};
2352 :     }
2353 :     # Return the result.
2354 :     return @retVal;
2355 :     }
2356 :    
2357 : parrello 1.6 =head3 GetEntityValues
2358 :    
2359 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2360 : parrello 1.6
2361 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
2362 :     does not exist, an empty list is returned.
2363 : parrello 1.6
2364 :     =over 4
2365 :    
2366 :     =item entityType
2367 :    
2368 :     Entity type name.
2369 :    
2370 :     =item ID
2371 :    
2372 :     ID of the desired entity.
2373 :    
2374 :     =item fields
2375 :    
2376 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2377 :    
2378 :     =item RETURN
2379 :    
2380 :     Returns a flattened list of the values of the specified fields for the specified entity.
2381 :    
2382 :     =back
2383 :    
2384 :     =cut
2385 :    
2386 :     sub GetEntityValues {
2387 : parrello 1.10 # Get the parameters.
2388 :     my ($self, $entityType, $ID, $fields) = @_;
2389 :     # Get the specified entity.
2390 :     my $entity = $self->GetEntity($entityType, $ID);
2391 :     # Declare the return list.
2392 :     my @retVal = ();
2393 :     # If we found the entity, push the values into the return list.
2394 :     if ($entity) {
2395 :     push @retVal, $entity->Values($fields);
2396 :     }
2397 :     # Return the result.
2398 :     return @retVal;
2399 : parrello 1.6 }
2400 : parrello 1.1
2401 : parrello 1.7 =head3 GetAll
2402 :    
2403 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2404 : parrello 1.7
2405 :     Return a list of values taken from the objects returned by a query. The first three
2406 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
2407 :     a list of the fields desired from each record found by the query. The field name
2408 :     syntax is the standard syntax used for fields in the B<ERDB> system--
2409 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2410 :     or relationship and I<fieldName> is the name of the field.
2411 :    
2412 :     The list returned will be a list of lists. Each element of the list will contain
2413 :     the values returned for the fields specified in the fourth parameter. If one of the
2414 :     fields specified returns multiple values, they are flattened in with the rest. For
2415 :     example, the following call will return a list of the features in a particular
2416 :     spreadsheet cell, and each feature will be represented by a list containing the
2417 :     feature ID followed by all of its aliases.
2418 :    
2419 : parrello 1.18 C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2420 : parrello 1.7
2421 :     =over 4
2422 :    
2423 :     =item objectNames
2424 :    
2425 :     List containing the names of the entity and relationship objects to be retrieved.
2426 :    
2427 :     =item filterClause
2428 :    
2429 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2430 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2431 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2432 :     parameter list as additional parameters. The fields in a filter clause can come from primary
2433 :     entity relations, relationship relations, or secondary entity relations; however, all of the
2434 :     entities and relationships involved must be included in the list of object names.
2435 :    
2436 :     =item parameterList
2437 :    
2438 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
2439 :    
2440 :     =item fields
2441 :    
2442 :     List of the fields to be returned in each element of the list returned.
2443 :    
2444 :     =item count
2445 :    
2446 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
2447 :    
2448 :     =item RETURN
2449 :    
2450 :     Returns a list of list references. Each element of the return list contains the values for the
2451 :     fields specified in the B<fields> parameter.
2452 :    
2453 :     =back
2454 :    
2455 :     =cut
2456 :     #: Return Type @@;
2457 :     sub GetAll {
2458 : parrello 1.10 # Get the parameters.
2459 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2460 :     # Translate the parameters from a list reference to a list. If the parameter
2461 :     # list is a scalar we convert it into a singleton list.
2462 :     my @parmList = ();
2463 :     if (ref $parameterList eq "ARRAY") {
2464 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
2465 : parrello 1.10 @parmList = @{$parameterList};
2466 :     } else {
2467 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2468 : parrello 1.10 push @parmList, $parameterList;
2469 :     }
2470 : parrello 1.30 # Insure the counter has a value.
2471 :     if (!defined $count) {
2472 :     $count = 0;
2473 :     }
2474 :     # Add the row limit to the filter clause.
2475 :     if ($count > 0) {
2476 :     $filterClause .= " LIMIT $count";
2477 :     }
2478 : parrello 1.10 # Create the query.
2479 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
2480 : parrello 1.10 # Set up a counter of the number of records read.
2481 :     my $fetched = 0;
2482 :     # Loop through the records returned, extracting the fields. Note that if the
2483 :     # counter is non-zero, we stop when the number of records read hits the count.
2484 :     my @retVal = ();
2485 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2486 :     my @rowData = $row->Values($fields);
2487 :     push @retVal, \@rowData;
2488 :     $fetched++;
2489 :     }
2490 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2491 : parrello 1.10 # Return the resulting list.
2492 :     return @retVal;
2493 : parrello 1.7 }
2494 :    
2495 : parrello 1.55 =head3 Exists
2496 :    
2497 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
2498 :    
2499 :     Return TRUE if an entity exists, else FALSE.
2500 :    
2501 :     =over 4
2502 :    
2503 :     =item entityName
2504 :    
2505 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2506 :    
2507 :     =item entityID
2508 :    
2509 :     ID of the entity instance whose existence is to be checked.
2510 :    
2511 :     =item RETURN
2512 :    
2513 :     Returns TRUE if the entity instance exists, else FALSE.
2514 :    
2515 :     =back
2516 :    
2517 :     =cut
2518 :     #: Return Type $;
2519 :     sub Exists {
2520 :     # Get the parameters.
2521 :     my ($self, $entityName, $entityID) = @_;
2522 :     # Check for the entity instance.
2523 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2524 :     my $testInstance = $self->GetEntity($entityName, $entityID);
2525 :     # Return an existence indicator.
2526 :     my $retVal = ($testInstance ? 1 : 0);
2527 :     return $retVal;
2528 :     }
2529 :    
2530 : parrello 1.18 =head3 EstimateRowSize
2531 :    
2532 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2533 :    
2534 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
2535 :     up the average length for each data type.
2536 :    
2537 :     =over 4
2538 :    
2539 :     =item relName
2540 :    
2541 :     Name of the relation whose estimated row size is desired.
2542 :    
2543 :     =item RETURN
2544 :    
2545 :     Returns an estimate of the row size for the specified relation.
2546 :    
2547 :     =back
2548 :    
2549 :     =cut
2550 :     #: Return Type $;
2551 :     sub EstimateRowSize {
2552 :     # Get the parameters.
2553 :     my ($self, $relName) = @_;
2554 :     # Declare the return variable.
2555 :     my $retVal = 0;
2556 :     # Find the relation descriptor.
2557 :     my $relation = $self->_FindRelation($relName);
2558 :     # Get the list of fields.
2559 :     for my $fieldData (@{$relation->{Fields}}) {
2560 :     # Get the field type and add its length.
2561 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2562 :     $retVal += $fieldLen;
2563 :     }
2564 :     # Return the result.
2565 :     return $retVal;
2566 :     }
2567 :    
2568 : parrello 1.38 =head3 GetFieldTable
2569 :    
2570 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2571 :    
2572 :     Get the field structure for a specified entity or relationship.
2573 :    
2574 :     =over 4
2575 :    
2576 :     =item objectName
2577 :    
2578 :     Name of the desired entity or relationship.
2579 :    
2580 :     =item RETURN
2581 :    
2582 :     The table containing the field descriptors for the specified object.
2583 :    
2584 :     =back
2585 :    
2586 :     =cut
2587 :    
2588 :     sub GetFieldTable {
2589 :     # Get the parameters.
2590 :     my ($self, $objectName) = @_;
2591 :     # Get the descriptor from the metadata.
2592 :     my $objectData = $self->_GetStructure($objectName);
2593 :     # Return the object's field table.
2594 :     return $objectData->{Fields};
2595 :     }
2596 :    
2597 : parrello 1.73 =head3 SplitKeywords
2598 :    
2599 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2600 :    
2601 :     This method returns a list of the positive keywords in the specified
2602 :     keyword string. All of the operators will have been stripped off,
2603 :     and if the keyword is preceded by a minus operator (C<->), it will
2604 :     not be in the list returned. The idea here is to get a list of the
2605 :     keywords the user wants to see. The list will be processed to remove
2606 :     duplicates.
2607 :    
2608 :     It is possible to create a string that confuses this method. For example
2609 :    
2610 :     frog toad -frog
2611 :    
2612 :     would return both C<frog> and C<toad>. If this is a problem we can deal
2613 :     with it later.
2614 :    
2615 :     =over 4
2616 :    
2617 :     =item keywordString
2618 :    
2619 :     The keyword string to be parsed.
2620 :    
2621 :     =item RETURN
2622 :    
2623 :     Returns a list of the words in the keyword string the user wants to
2624 :     see.
2625 :    
2626 :     =back
2627 :    
2628 :     =cut
2629 :    
2630 :     sub SplitKeywords {
2631 :     # Get the parameters.
2632 :     my ($keywordString) = @_;
2633 :     # Make a safety copy of the string. (This helps during debugging.)
2634 :     my $workString = $keywordString;
2635 :     # Convert operators we don't care about to spaces.
2636 :     $workString =~ tr/+"()<>/ /;
2637 :     # Split the rest of the string along space boundaries. Note that we
2638 :     # eliminate any words that are zero length or begin with a minus sign.
2639 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2640 :     # Use a hash to remove duplicates.
2641 :     my %words = map { $_ => 1 } @wordList;
2642 :     # Return the result.
2643 :     return sort keys %words;
2644 :     }
2645 :    
2646 :     =head3 ValidateFieldName
2647 :    
2648 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2649 :    
2650 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2651 :     be hyphenated words subject to certain restrictions.
2652 :    
2653 :     =over 4
2654 :    
2655 :     =item fieldName
2656 :    
2657 :     Field name to be validated.
2658 :    
2659 :     =item RETURN
2660 :    
2661 :     Returns TRUE if the field name is valid, else FALSE.
2662 :    
2663 :     =back
2664 :    
2665 :     =cut
2666 :    
2667 :     sub ValidateFieldName {
2668 :     # Get the parameters.
2669 :     my ($fieldName) = @_;
2670 :     # Declare the return variable. The field name is valid until we hear
2671 :     # differently.
2672 :     my $retVal = 1;
2673 :     # Look for bad stuff in the name.
2674 :     if ($fieldName =~ /--/) {
2675 :     # Here we have a doubled minus sign.
2676 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2677 :     $retVal = 0;
2678 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
2679 :     # Here the field name is missing the initial letter.
2680 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
2681 :     $retVal = 0;
2682 :     } else {
2683 :     # Strip out the minus signs. Everything remaining must be a letter
2684 :     # or digit.
2685 :     my $strippedName = $fieldName;
2686 :     $strippedName =~ s/-//g;
2687 :     if ($strippedName !~ /^[A-Za-z0-9]+$/) {
2688 :     Trace("Field name $fieldName contains illegal characters.") if T(1);
2689 :     $retVal = 0;
2690 :     }
2691 :     }
2692 :     # Return the result.
2693 :     return $retVal;
2694 :     }
2695 :    
2696 :     =head3 ReadMetaXML
2697 :    
2698 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2699 :    
2700 :     This method reads a raw database definition XML file and returns it.
2701 :     Normally, the metadata used by the ERDB system has been processed and
2702 :     modified to make it easier to load and retrieve the data; however,
2703 :     this method can be used to get the data in its raw form.
2704 :    
2705 :     =over 4
2706 :    
2707 :     =item fileName
2708 :    
2709 :     Name of the XML file to read.
2710 :    
2711 :     =item RETURN
2712 :    
2713 :     Returns a hash reference containing the raw XML data from the specified file.
2714 :    
2715 :     =back
2716 :    
2717 :     =cut
2718 :    
2719 :     sub ReadMetaXML {
2720 :     # Get the parameters.
2721 :     my ($fileName) = @_;
2722 :     # Read the XML.
2723 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2724 :     Trace("XML metadata loaded from file $fileName.") if T(1);
2725 :     # Return the result.
2726 :     return $retVal;
2727 :     }
2728 :    
2729 :     =head3 GetEntityFieldHash
2730 :    
2731 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2732 :    
2733 :     Get the field hash of the named entity in the specified raw XML structure.
2734 :     The field hash may not exist, in which case we need to create it.
2735 :    
2736 :     =over 4
2737 :    
2738 :     =item structure
2739 :    
2740 :     Raw XML structure defininng the database. This is not the run-time XML used by
2741 :     an ERDB object, since that has all sorts of optimizations built-in.
2742 :    
2743 :     =item entityName
2744 :    
2745 :     Name of the entity whose field structure is desired.
2746 :    
2747 :     =item RETURN
2748 :    
2749 :     Returns the field hash used to define the entity's fields.
2750 :    
2751 :     =back
2752 :    
2753 :     =cut
2754 :    
2755 :     sub GetEntityFieldHash {
2756 :     # Get the parameters.
2757 :     my ($structure, $entityName) = @_;
2758 :     # Get the entity structure.
2759 :     my $entityData = $structure->{Entities}->{$entityName};
2760 :     # Look for a field structure.
2761 :     my $retVal = $entityData->{Fields};
2762 :     # If it doesn't exist, create it.
2763 :     if (! defined($retVal)) {
2764 :     $entityData->{Fields} = {};
2765 :     $retVal = $entityData->{Fields};
2766 :     }
2767 :     # Return the result.
2768 :     return $retVal;
2769 :     }
2770 :    
2771 :     =head3 WriteMetaXML
2772 :    
2773 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
2774 :    
2775 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2776 :     used to update the database definition. It must be used with care, however, since it
2777 :     will only work on a raw structure, not on the processed structure created by an ERDB
2778 :     constructor.
2779 :    
2780 :     =over 4
2781 :    
2782 :     =item structure
2783 :    
2784 :     XML structure to be written to the file.
2785 :    
2786 :     =item fileName
2787 :    
2788 :     Name of the output file to which the updated XML should be stored.
2789 :    
2790 :     =back
2791 :    
2792 :     =cut
2793 :    
2794 :     sub WriteMetaXML {
2795 :     # Get the parameters.
2796 :     my ($structure, $fileName) = @_;
2797 :     # Compute the output.
2798 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2799 :     # Write it to the file.
2800 :     my $xmlOut = Open(undef, ">$fileName");
2801 :     print $xmlOut $fileString;
2802 :     }
2803 :    
2804 :    
2805 :     =head3 HTMLNote
2806 :    
2807 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2808 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
2809 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
2810 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
2811 :    
2812 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
2813 :    
2814 :     =over 4
2815 :    
2816 :     =item dataString
2817 :    
2818 :     String to convert to HTML.
2819 :    
2820 :     =item RETURN
2821 :    
2822 :     An HTML string derived from the input string.
2823 :    
2824 :     =back
2825 :    
2826 :     =cut
2827 :    
2828 :     sub HTMLNote {
2829 :     # Get the parameter.
2830 :     my ($dataString) = @_;
2831 :     # HTML-escape the text.
2832 :     my $retVal = CGI::escapeHTML($dataString);
2833 :     # Substitute the bulletin board codes.
2834 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
2835 :     $retVal =~ s!\[p\]!</p><p>!g;
2836 :     # Return the result.
2837 :     return $retVal;
2838 :     }
2839 :    
2840 :    
2841 : parrello 1.48 =head2 Data Mining Methods
2842 :    
2843 : parrello 1.38 =head3 GetUsefulCrossValues
2844 :    
2845 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
2846 :    
2847 :     Return a list of the useful attributes that would be returned by a B<Cross> call
2848 :     from an entity of the source entity type through the specified relationship. This
2849 :     means it will return the fields of the target entity type and the intersection data
2850 :     fields in the relationship. Only primary table fields are returned. In other words,
2851 :     the field names returned will be for fields where there is always one and only one
2852 :     value.
2853 :    
2854 :     =over 4
2855 :    
2856 :     =item sourceEntity
2857 :    
2858 :     Name of the entity from which the relationship crossing will start.
2859 :    
2860 :     =item relationship
2861 :    
2862 :     Name of the relationship being crossed.
2863 :    
2864 :     =item RETURN
2865 :    
2866 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
2867 :    
2868 :     =back
2869 :    
2870 :     =cut
2871 :     #: Return Type @;
2872 :     sub GetUsefulCrossValues {
2873 :     # Get the parameters.
2874 :     my ($self, $sourceEntity, $relationship) = @_;
2875 :     # Declare the return variable.
2876 :     my @retVal = ();
2877 :     # Determine the target entity for the relationship. This is whichever entity is not
2878 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
2879 :     # the TO, and vice versa.
2880 :     my $relStructure = $self->_GetStructure($relationship);
2881 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
2882 :     my $targetEntity = $relStructure->{$targetEntityType};
2883 :     # Get the field table for the entity.
2884 :     my $entityFields = $self->GetFieldTable($targetEntity);
2885 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
2886 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
2887 :     # must match the entity name.
2888 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
2889 :     keys %{$entityFields};
2890 :     # Push the fields found onto the return variable.
2891 :     push @retVal, sort @fieldList;
2892 :     # Get the field table for the relationship.
2893 :     my $relationshipFields = $self->GetFieldTable($relationship);
2894 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
2895 :     # This may end up being an empty set.
2896 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
2897 :     keys %{$relationshipFields};
2898 :     # Push these onto the return list.
2899 :     push @retVal, sort @fieldList2;
2900 :     # Return the result.
2901 :     return @retVal;
2902 :     }
2903 :    
2904 : parrello 1.48 =head3 FindColumn
2905 :    
2906 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2907 :    
2908 :     Return the location a desired column in a data mining header line. The data
2909 :     mining header line is a tab-separated list of column names. The column
2910 :     identifier is either the numerical index of a column or the actual column
2911 :     name.
2912 :    
2913 :     =over 4
2914 :    
2915 :     =item headerLine
2916 :    
2917 :     The header line from a data mining command, which consists of a tab-separated
2918 :     list of column names.
2919 :    
2920 :     =item columnIdentifier
2921 :    
2922 :     Either the ordinal number of the desired column (1-based), or the name of the
2923 :     desired column.
2924 :    
2925 :     =item RETURN
2926 :    
2927 :     Returns the array index (0-based) of the desired column.
2928 :    
2929 :     =back
2930 :    
2931 :     =cut
2932 :    
2933 :     sub FindColumn {
2934 :     # Get the parameters.
2935 :     my ($headerLine, $columnIdentifier) = @_;
2936 :     # Declare the return variable.
2937 :     my $retVal;
2938 :     # Split the header line into column names.
2939 :     my @headers = ParseColumns($headerLine);
2940 :     # Determine whether we have a number or a name.
2941 :     if ($columnIdentifier =~ /^\d+$/) {
2942 :     # Here we have a number. Subtract 1 and validate the result.
2943 :     $retVal = $columnIdentifier - 1;
2944 :     if ($retVal < 0 || $retVal > $#headers) {
2945 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2946 :     }
2947 :     } else {
2948 :     # Here we have a name. We need to find it in the list.
2949 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2950 :     if ($headers[$i] eq $columnIdentifier) {
2951 :     $retVal = $i;
2952 :     }
2953 :     }
2954 :     if (! defined($retVal)) {
2955 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2956 :     }
2957 :     }
2958 :     # Return the result.
2959 :     return $retVal;
2960 :     }
2961 :    
2962 :     =head3 ParseColumns
2963 :    
2964 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
2965 : parrello 1.48
2966 :     Convert the specified data line to a list of columns.
2967 :    
2968 :     =over 4
2969 :    
2970 :     =item line
2971 :    
2972 :     A data mining input, consisting of a tab-separated list of columns terminated by a
2973 :     new-line.
2974 :    
2975 :     =item RETURN
2976 :    
2977 :     Returns a list consisting of the column values.
2978 :    
2979 :     =back
2980 :    
2981 :     =cut
2982 :    
2983 :     sub ParseColumns {
2984 :     # Get the parameters.
2985 : parrello 1.50 my ($line) = @_;
2986 : parrello 1.48 # Chop off the line-end.
2987 :     chomp $line;
2988 :     # Split it into a list.
2989 :     my @retVal = split(/\t/, $line);
2990 :     # Return the result.
2991 :     return @retVal;
2992 :     }
2993 :    
2994 : parrello 1.71 =head2 Virtual Methods
2995 :    
2996 :     =head3 CleanKeywords
2997 :    
2998 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
2999 :    
3000 :     Clean up a search expression or keyword list. This is a virtual method that may
3001 :     be overridden by the subclass. The base-class method removes extra spaces
3002 :     and converts everything to lower case.
3003 :    
3004 :     =over 4
3005 :    
3006 :     =item searchExpression
3007 :    
3008 :     Search expression or keyword list to clean. Note that a search expression may
3009 :     contain boolean operators which need to be preserved. This includes leading
3010 :     minus signs.
3011 :    
3012 :     =item RETURN
3013 :    
3014 :     Cleaned expression or keyword list.
3015 :    
3016 :     =back
3017 :    
3018 :     =cut
3019 :    
3020 :     sub CleanKeywords {
3021 :     # Get the parameters.
3022 :     my ($self, $searchExpression) = @_;
3023 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
3024 :     # don't accidentally end up with an undefined value.
3025 :     my $retVal = lc($searchExpression || "");
3026 :     # Remove extra spaces.
3027 :     $retVal =~ s/\s+/ /g;
3028 :     $retVal =~ s/(^\s+)|(\s+$)//g;
3029 :     # Return the result.
3030 :     return $retVal;
3031 :     }
3032 :    
3033 : parrello 1.73 =head3 GetSourceObject
3034 :    
3035 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
3036 :    
3037 :     Return the object to be used in loading special attributes of the specified entity. The
3038 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
3039 :     XML
3040 :    
3041 : parrello 1.1 =head2 Internal Utility Methods
3042 :    
3043 : parrello 1.70 =head3 _RelationMap
3044 :    
3045 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3046 :    
3047 :     Create the relation map for an SQL query. The relation map is used by B<DBObject>
3048 :     to determine how to interpret the results of the query.
3049 :    
3050 :     =over 4
3051 :    
3052 :     =item mappedNameHashRef
3053 :    
3054 :     Reference to a hash that maps modified object names to real object names.
3055 :    
3056 :     =item mappedNameListRef
3057 :    
3058 :     Reference to a list of modified object names in the order they appear in the
3059 :     SELECT list.
3060 :    
3061 :     =item RETURN
3062 :    
3063 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3064 :     query followed by the actual name of that object. This enables the B<DBObject> to
3065 :     determine the order of the tables in the query and which object name belongs to each
3066 :     mapped object name. Most of the time these two values are the same; however, if a
3067 :     relation occurs twice in the query, the relation name in the field list and WHERE
3068 :     clause will use a mapped name (generally the actual relation name with a numeric
3069 :     suffix) that does not match the actual relation name.
3070 :    
3071 :     =back
3072 :    
3073 :     =cut
3074 :    
3075 :     sub _RelationMap {
3076 :     # Get the parameters.
3077 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3078 :     # Declare the return variable.
3079 :     my @retVal = ();
3080 :     # Build the map.
3081 :     for my $mappedName (@{$mappedNameListRef}) {
3082 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3083 :     }
3084 :     # Return it.
3085 :     return @retVal;
3086 :     }
3087 :    
3088 :    
3089 :     =head3 _SetupSQL
3090 : parrello 1.45
3091 :     Process a list of object names and a filter clause so that they can be used to
3092 :     build an SQL statement. This method takes in a reference to a list of object names
3093 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3094 :     names and the mapped name hash.
3095 :    
3096 :     This is an instance method.
3097 :    
3098 :     =over 4
3099 :    
3100 :     =item objectNames
3101 :    
3102 :     Reference to a list of the object names to be included in the query.
3103 :    
3104 :     =item filterClause
3105 :    
3106 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
3107 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
3108 :    
3109 : parrello 1.70 =item matchClause
3110 :    
3111 :     An optional full-text search clause. If specified, it will be inserted at the
3112 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
3113 :     field names should be in the form I<table>C<.>I<fieldName>.
3114 :    
3115 : parrello 1.45 =item RETURN
3116 :    
3117 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
3118 :     with the FROM clause. The second element is a reference to a list of the names to be
3119 :     used in retrieving the fields. The third element is a hash mapping the names to the
3120 :     objects they represent.
3121 :    
3122 :     =back
3123 :    
3124 :     =cut
3125 :    
3126 :     sub _SetupSQL {
3127 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
3128 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
3129 :     # same object. We start with a hash table keyed on object name that will
3130 :     # return the object suffix. The first time an object is encountered it will
3131 :     # not be found in the hash. The next time the hash will map the object name
3132 :     # to 2, then 3, and so forth.
3133 :     my %objectHash = ();
3134 :     # This list will contain the object names as they are to appear in the
3135 :     # FROM list.
3136 :     my @fromList = ();
3137 :     # This list contains the suffixed object name for each object. It is exactly
3138 :     # parallel to the list in the $objectNames parameter.
3139 :     my @mappedNameList = ();
3140 :     # Finally, this hash translates from a mapped name to its original object name.
3141 :     my %mappedNameHash = ();
3142 :     # Now we create the lists. Note that for every single name we push something into
3143 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
3144 :     # parallel to $objectNames.
3145 :     for my $objectName (@{$objectNames}) {
3146 :     # Get the next suffix for this object.
3147 :     my $suffix = $objectHash{$objectName};
3148 :     if (! $suffix) {
3149 :     # Here we are seeing the object for the first time. The object name
3150 :     # is used as is.
3151 :     push @mappedNameList, $objectName;
3152 :     push @fromList, $objectName;
3153 :     $mappedNameHash{$objectName} = $objectName;
3154 :     # Denote the next suffix will be 2.
3155 :     $objectHash{$objectName} = 2;
3156 :     } else {
3157 :     # Here we've seen the object before. We construct a new name using
3158 :     # the suffix from the hash and update the hash.
3159 :     my $mappedName = "$objectName$suffix";
3160 :     $objectHash{$objectName} = $suffix + 1;
3161 :     # The FROM list has the object name followed by the mapped name. This
3162 :     # tells SQL it's still the same table, but we're using a different name
3163 :     # for it to avoid confusion.
3164 :     push @fromList, "$objectName $mappedName";
3165 :     # The mapped-name list contains the real mapped name.
3166 :     push @mappedNameList, $mappedName;
3167 :     # Finally, enable us to get back from the mapped name to the object name.
3168 :     $mappedNameHash{$mappedName} = $objectName;
3169 :     }
3170 :     }
3171 :     # Begin the SELECT suffix. It starts with
3172 :     #
3173 :     # FROM name1, name2, ... nameN
3174 :     #
3175 :     my $suffix = "FROM " . join(', ', @fromList);
3176 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
3177 :     my $filterString = "";
3178 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
3179 :     # entities and relationships as well as primary relations to secondary ones.
3180 :     my @joinWhere = ();
3181 : parrello 1.45 # Check for a filter clause.
3182 :     if ($filterClause) {
3183 :     # Here we have one, so we convert its field names and add it to the query. First,
3184 :     # We create a copy of the filter string we can work with.
3185 : parrello 1.70 $filterString = $filterClause;
3186 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
3187 :     # object names inside other object names when we're doing our search and replace.
3188 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3189 :     # The final preparatory step is to create a hash table of relation names. The
3190 :     # table begins with the relation names already in the SELECT command. We may
3191 :     # need to add relations later if there is filtering on a field in a secondary
3192 :     # relation. The secondary relations are the ones that contain multiply-
3193 :     # occurring or optional fields.
3194 :     my %fromNames = map { $_ => 1 } @sortedNames;
3195 :     # We are ready to begin. We loop through the object names, replacing each
3196 :     # object name's field references by the corresponding SQL field reference.
3197 :     # Along the way, if we find a secondary relation, we will need to add it
3198 :     # to the FROM clause.
3199 :     for my $mappedName (@sortedNames) {
3200 :     # Get the length of the object name plus 2. This is the value we add to the
3201 :     # size of the field name to determine the size of the field reference as a
3202 :     # whole.
3203 :     my $nameLength = 2 + length $mappedName;
3204 :     # Get the real object name for this mapped name.
3205 :     my $objectName = $mappedNameHash{$mappedName};
3206 :     Trace("Processing $mappedName for object $objectName.") if T(4);
3207 :     # Get the object's field list.
3208 :     my $fieldList = $self->GetFieldTable($objectName);
3209 :     # Find the field references for this object.
3210 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3211 :     # At this point, $1 contains the field name, and the current position
3212 :     # is set immediately after the final parenthesis. We pull out the name of
3213 :     # the field and the position and length of the field reference as a whole.
3214 :     my $fieldName = $1;
3215 :     my $len = $nameLength + length $fieldName;
3216 :     my $pos = pos($filterString) - $len;
3217 :     # Insure the field exists.
3218 :     if (!exists $fieldList->{$fieldName}) {
3219 :     Confess("Field $fieldName not found for object $objectName.");
3220 :     } else {
3221 :     Trace("Processing $fieldName at position $pos.") if T(4);
3222 :     # Get the field's relation.
3223 :     my $relationName = $fieldList->{$fieldName}->{relation};
3224 :     # Now we have a secondary relation. We need to insure it matches the
3225 :     # mapped name of the primary relation. First we peel off the suffix
3226 :     # from the mapped name.
3227 :     my $mappingSuffix = substr $mappedName, length($objectName);
3228 :     # Put the mapping suffix onto the relation name to get the
3229 :     # mapped relation name.
3230 :     my $mappedRelationName = "$relationName$mappingSuffix";
3231 :     # Insure the relation is in the FROM clause.
3232 :     if (!exists $fromNames{$mappedRelationName}) {
3233 :     # Add the relation to the FROM clause.
3234 :     if ($mappedRelationName eq $relationName) {
3235 :     # The name is un-mapped, so we add it without
3236 :     # any frills.
3237 :     $suffix .= ", $relationName";
3238 :     push @joinWhere, "$objectName.id = $relationName.id";
3239 :     } else {
3240 :     # Here we have a mapping situation.
3241 :     $suffix .= ", $relationName $mappedRelationName";
3242 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3243 :     }
3244 :     # Denote we have this relation available for future fields.
3245 :     $fromNames{$mappedRelationName} = 1;
3246 :     }
3247 :     # Form an SQL field reference from the relation name and the field name.
3248 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3249 :     # Put it into the filter string in place of the old value.
3250 :     substr($filterString, $pos, $len) = $sqlReference;
3251 :     # Reposition the search.
3252 :     pos $filterString = $pos + length $sqlReference;
3253 :     }
3254 :     }
3255 :     }
3256 : parrello 1.70 }
3257 :     # The next step is to join the objects together. We only need to do this if there
3258 :     # is more than one object in the object list. We start with the first object and
3259 :     # run through the objects after it. Note also that we make a safety copy of the
3260 :     # list before running through it, because we shift off the first object before
3261 :     # processing the rest.
3262 :     my @mappedObjectList = @mappedNameList;
3263 :     my $lastMappedObject = shift @mappedObjectList;
3264 :     # Get the join table.
3265 :     my $joinTable = $self->{_metaData}->{Joins};
3266 :     # Loop through the object list.
3267 :     for my $thisMappedObject (@mappedObjectList) {
3268 :     # Look for a join using the real object names.
3269 :     my $lastObject = $mappedNameHash{$lastMappedObject};
3270 :     my $thisObject = $mappedNameHash{$thisMappedObject};
3271 :     my $joinKey = "$lastObject/$thisObject";
3272 :     if (!exists $joinTable->{$joinKey}) {
3273 :     # Here there's no join, so we throw an error.
3274 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3275 :     } else {
3276 :     # Get the join clause.
3277 :     my $unMappedJoin = $joinTable->{$joinKey};
3278 :     # Fix the names.
3279 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3280 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3281 :     push @joinWhere, $unMappedJoin;
3282 :     # Save this object as the last object for the next iteration.
3283 :     $lastMappedObject = $thisMappedObject;
3284 :     }
3285 :     }
3286 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3287 :     # here is we want the filter clause to be empty if there's no WHERE filter.
3288 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
3289 :     my $orderClause = "";
3290 :     # This is only necessary if we have a filter string in which the ORDER BY
3291 :     # and LIMIT clauses can live.
3292 :     if ($filterString) {
3293 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3294 :     # operator so that we find the first occurrence of either verb.
3295 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3296 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3297 :     my $pos = pos $filterString;
3298 :     $orderClause = $2 . substr($filterString, $pos);
3299 :     $filterString = $1;
3300 :     }
3301 : parrello 1.70 }
3302 :     # All the things that are supposed to be in the WHERE clause of the
3303 :     # SELECT command need to be put into @joinWhere so we can string them
3304 :     # together. We begin with the match clause. This is important,
3305 :     # because the match clause's parameter mark must precede any parameter
3306 :     # marks in the filter string.
3307 :     if ($matchClause) {
3308 :     push @joinWhere, $matchClause;
3309 :     }
3310 :     # Add the filter string. We put it in parentheses to avoid operator
3311 :     # precedence problems with the match clause or the joins.
3312 :     if ($filterString) {
3313 :     Trace("Filter string is \"$filterString\".") if T(4);
3314 :     push @joinWhere, "($filterString)";
3315 :     }
3316 :     # String it all together into a big filter clause.
3317 :     if (@joinWhere) {
3318 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
3319 :     }
3320 :     # Add the sort or limit clause (if any).
3321 :     if ($orderClause) {
3322 :     $suffix .= " $orderClause";
3323 : parrello 1.45 }
3324 :     # Return the suffix, the mapped name list, and the mapped name hash.
3325 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
3326 :     }
3327 :    
3328 : parrello 1.70 =head3 _GetStatementHandle
3329 : parrello 1.45
3330 :     This method will prepare and execute an SQL query, returning the statement handle.
3331 :     The main reason for doing this here is so that everybody who does SQL queries gets
3332 :     the benefit of tracing.
3333 :    
3334 :     This is an instance method.
3335 :    
3336 :     =over 4
3337 :    
3338 :     =item command
3339 :    
3340 :     Command to prepare and execute.
3341 :    
3342 :     =item params
3343 :    
3344 :     Reference to a list of the values to be substituted in for the parameter marks.
3345 :    
3346 :     =item RETURN
3347 :    
3348 :     Returns a prepared and executed statement handle from which the caller can extract
3349 :     results.
3350 :    
3351 :     =back
3352 :    
3353 :     =cut
3354 :    
3355 :     sub _GetStatementHandle {
3356 :     # Get the parameters.
3357 :     my ($self, $command, $params) = @_;
3358 :     # Trace the query.
3359 :     Trace("SQL query: $command") if T(SQL => 3);
3360 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3361 :     # Get the database handle.
3362 :     my $dbh = $self->{_dbh};
3363 :     # Prepare the command.
3364 :     my $sth = $dbh->prepare_command($command);
3365 :     # Execute it with the parameters bound in.
3366 :     $sth->execute(@{$params}) || Confess("SELECT error" . $sth->errstr());
3367 :     # Return the statement handle.
3368 :     return $sth;
3369 :     }
3370 :    
3371 : parrello 1.70 =head3 _GetLoadStats
3372 : parrello 1.1
3373 :     Return a blank statistics object for use by the load methods.
3374 :    
3375 :     This is a static method.
3376 :    
3377 :     =cut
3378 :    
3379 : parrello 1.29 sub _GetLoadStats{
3380 : parrello 1.28 return Stats->new();
3381 : parrello 1.1 }
3382 :    
3383 : parrello 1.70 =head3 _DumpRelation
3384 : parrello 1.1
3385 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
3386 : parrello 1.1
3387 :     This is an instance method.
3388 :    
3389 :     =over 4
3390 :    
3391 :     =item outputDirectory
3392 :    
3393 :     Directory to contain the output file.
3394 :    
3395 :     =item relationName
3396 :    
3397 :     Name of the relation to dump.
3398 :    
3399 :     =item relation
3400 :    
3401 :     Structure describing the relation to be dumped.
3402 :    
3403 :     =back
3404 :    
3405 :     =cut
3406 :    
3407 :     sub _DumpRelation {
3408 : parrello 1.10 # Get the parameters.
3409 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
3410 :     # Open the output file.
3411 :     my $fileName = "$outputDirectory/$relationName.dtx";
3412 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
3413 :     # Create a query for the specified relation.
3414 :     my $dbh = $self->{_dbh};
3415 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
3416 :     # Execute the query.
3417 :     $query->execute() || Confess("SELECT error dumping $relationName.");
3418 :     # Loop through the results.
3419 :     while (my @row = $query->fetchrow) {
3420 :     # Escape any tabs or new-lines in the row text.
3421 :     for my $field (@row) {
3422 :     $field =~ s/\n/\\n/g;
3423 :     $field =~ s/\t/\\t/g;
3424 :     }
3425 :     # Tab-join the row and write it to the output file.
3426 :     my $rowText = join("\t", @row);
3427 :     print DTXOUT "$rowText\n";
3428 :     }
3429 :     # Close the output file.
3430 :     close DTXOUT;
3431 : parrello 1.1 }
3432 :    
3433 : parrello 1.70 =head3 _GetStructure
3434 : parrello 1.1
3435 :     Get the data structure for a specified entity or relationship.
3436 :    
3437 :     This is an instance method.
3438 :    
3439 :     =over 4
3440 :    
3441 :     =item objectName
3442 :    
3443 :     Name of the desired entity or relationship.
3444 :    
3445 :     =item RETURN
3446 :    
3447 :     The descriptor for the specified object.
3448 :    
3449 :     =back
3450 :    
3451 :     =cut
3452 :    
3453 :     sub _GetStructure {
3454 : parrello 1.10 # Get the parameters.
3455 :     my ($self, $objectName) = @_;
3456 :     # Get the metadata structure.
3457 :     my $metadata = $self->{_metaData};
3458 :     # Declare the variable to receive the descriptor.
3459 :     my $retVal;
3460 :     # Get the descriptor from the metadata.
3461 :     if (exists $metadata->{Entities}->{$objectName}) {
3462 :     $retVal = $metadata->{Entities}->{$objectName};
3463 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
3464 :     $retVal = $metadata->{Relationships}->{$objectName};
3465 :     } else {
3466 :     Confess("Object $objectName not found in database.");
3467 :     }
3468 :     # Return the descriptor.
3469 :     return $retVal;
3470 : parrello 1.1 }
3471 :    
3472 : parrello 1.70
3473 :    
3474 :     =head3 _GetRelationTable
3475 : parrello 1.1
3476 :     Get the list of relations for a specified entity or relationship.
3477 :    
3478 :     This is an instance method.
3479 :    
3480 :     =over 4
3481 :    
3482 :     =item objectName
3483 :    
3484 :     Name of the desired entity or relationship.
3485 :    
3486 :     =item RETURN
3487 :    
3488 :     A table containing the relations for the specified object.
3489 :    
3490 :     =back
3491 :    
3492 :     =cut
3493 :    
3494 :     sub _GetRelationTable {
3495 : parrello 1.10 # Get the parameters.
3496 :     my ($self, $objectName) = @_;
3497 :     # Get the descriptor from the metadata.
3498 :     my $objectData = $self->_GetStructure($objectName);
3499 :     # Return the object's relation list.
3500 :     return $objectData->{Relations};
3501 : parrello 1.1 }
3502 :    
3503 : parrello 1.70 =head3 _ValidateFieldNames
3504 : parrello 1.1
3505 :     Determine whether or not the field names are valid. A description of the problems with the names
3506 :     will be written to the standard error output. If there is an error, this method will abort. This is
3507 :     a static method.
3508 :    
3509 :     =over 4
3510 :    
3511 :     =item metadata
3512 :    
3513 :     Metadata structure loaded from the XML data definition.
3514 :    
3515 :     =back
3516 :    
3517 :     =cut
3518 :    
3519 :     sub _ValidateFieldNames {
3520 : parrello 1.10 # Get the object.
3521 :     my ($metadata) = @_;
3522 :     # Declare the return value. We assume success.
3523 :     my $retVal = 1;
3524 :     # Loop through the sections of the database definition.
3525 :     for my $section ('Entities', 'Relationships') {
3526 :     # Loop through the objects in this section.
3527 :     for my $object (values %{$metadata->{$section}}) {
3528 :     # Loop through the object's fields.
3529 :     for my $fieldName (keys %{$object->{Fields}}) {
3530 : parrello 1.73 # If this field name is invalid, set the return value to zero
3531 :     # so we know we encountered an error.
3532 :     if (! ValidateFieldName($fieldName)) {
3533 : parrello 1.10 $retVal = 0;
3534 :     }
3535 :     }
3536 :     }
3537 :     }
3538 :     # If an error was found, fail.
3539 :     if ($retVal == 0) {
3540 :     Confess("Errors found in field names.");
3541 :     }
3542 : parrello 1.1 }
3543 :    
3544 : parrello 1.70 =head3 _LoadRelation
3545 : parrello 1.1
3546 :     Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
3547 :     file with the same name as the relation exists in the specified directory.
3548 :    
3549 :     This is an instance method.
3550 :    
3551 :     =over 4
3552 :    
3553 :     =item dbh
3554 :    
3555 :     DBKernel object for accessing the database.
3556 :    
3557 :     =item directoryName
3558 :    
3559 :     Name of the directory containing the tab-delimited data files.
3560 :    
3561 :     =item relationName
3562 :    
3563 :     Name of the relation to load.
3564 :    
3565 :     =item rebuild
3566 :    
3567 :     TRUE if the table should be dropped and re-created before loading.
3568 :    
3569 :     =item RETURN
3570 :    
3571 :     Returns a statistical object describing the number of records read and a list of error messages.
3572 :    
3573 :     =back
3574 :    
3575 :     =cut
3576 :    
3577 :     sub _LoadRelation {
3578 : parrello 1.10 # Get the parameters.
3579 :     my ($self, $directoryName, $relationName, $rebuild) = @_;
3580 :     # Create the file name.
3581 :     my $fileName = "$directoryName/$relationName";
3582 :     # If the file doesn't exist, try adding the .dtx suffix.
3583 :     if (! -e $fileName) {
3584 :     $fileName .= ".dtx";
3585 :     if (! -e $fileName) {
3586 :     $fileName = "";
3587 :     }
3588 :     }
3589 :     # Create the return object.
3590 :     my $retVal = _GetLoadStats();
3591 :     # If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
3592 :     # be a null string.
3593 :     if ($fileName ne "") {
3594 :     # Load the relation from the file.
3595 :     $retVal = $self->LoadTable($fileName, $relationName, $rebuild);
3596 :     } elsif ($rebuild) {
3597 :     # Here we are rebuilding, but no file exists, so we just re-create the table.
3598 :     $self->CreateTable($relationName, 1);
3599 :     }
3600 :     # Return the statistics from the load.
3601 :     return $retVal;
3602 : parrello 1.1 }
3603 :    
3604 : parrello 1.73
3605 : parrello 1.70 =head3 _LoadMetaData
3606 : parrello 1.1
3607 :     This method loads the data describing this database from an XML file into a metadata structure.
3608 :     The resulting structure is a set of nested hash tables containing all the information needed to
3609 :     load or use the database. The schema for the XML file is F<ERDatabase.xml>.
3610 :    
3611 :     This is a static method.
3612 :    
3613 :     =over 4
3614 :    
3615 :     =item filename
3616 :    
3617 :     Name of the file containing the database definition.
3618 :    
3619 :     =item RETURN
3620 :    
3621 :     Returns a structure describing the database.
3622 :    
3623 :     =back
3624 :    
3625 :     =cut
3626 :    
3627 :     sub _LoadMetaData {
3628 : parrello 1.10 # Get the parameters.
3629 :     my ($filename) = @_;
3630 : parrello 1.15 Trace("Reading Sprout DBD from $filename.") if T(2);
3631 : parrello 1.10 # Slurp the XML file into a variable. Extensive use of options is used to insure we
3632 :     # get the exact structure we want.
3633 : parrello 1.73 my $metadata = ReadMetaXML($filename);
3634 : parrello 1.10 # Before we go any farther, we need to validate the field and object names. If an error is found,
3635 :     # the method below will fail.
3636 :     _ValidateFieldNames($metadata);
3637 :     # Next we need to create a hash table for finding relations. The entities and relationships are
3638 :     # implemented as one or more database relations.
3639 :     my %masterRelationTable = ();
3640 :     # Loop through the entities.
3641 :     my $entityList = $metadata->{Entities};
3642 :     for my $entityName (keys %{$entityList}) {
3643 :     my $entityStructure = $entityList->{$entityName};
3644 :     #
3645 : parrello 1.12 # The first step is to create all the entity's default values. For C<Field> elements,
3646 : parrello 1.10 # the relation name must be added where it is not specified. For relationships,
3647 :     # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
3648 :     # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
3649 :     # added that can be used to pull the implicit fields to the top when displaying the field
3650 :     # documentation. The PrettySort values are 1-based and indicate in which pass through a
3651 :     # relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
3652 :     # and so on.
3653 :     #
3654 :     # Fix up this entity.
3655 :     _FixupFields($entityStructure, $entityName, 2, 3);
3656 :     # Add the ID field.
3657 :     _AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
3658 :     relation => $entityName,
3659 :     Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
3660 :     PrettySort => 1});
3661 :     #
3662 :     # The current field list enables us to quickly find the relation containing a particular field.
3663 :     # We also need a list that tells us the fields in each relation. We do this by creating a
3664 :     # Relations structure in the entity structure and collating the fields into it based on their
3665 :     # C<relation> property. There is one tricky bit, which is that every relation has to have the
3666 :     # C<id> field in it. Note also that the field list is put into a C<Fields> member of the
3667 :     # relation's structure so that it looks more like the entity and relationship structures.
3668 :     #
3669 :     # First we need to create the relations list.
3670 :     my $relationTable = { };
3671 :     # Loop through the fields. We use a list of field names to prevent a problem with
3672 :     # the hash table cursor losing its place during the loop.
3673 :     my $fieldList = $entityStructure->{Fields};
3674 :     my @fieldNames = keys %{$fieldList};
3675 :     for my $fieldName (@fieldNames) {
3676 :     my $fieldData = $fieldList->{$fieldName};
3677 :     # Get the current field's relation name.
3678 :     my $relationName = $fieldData->{relation};
3679 :     # Insure the relation exists.
3680 :     if (!exists $relationTable->{$relationName}) {
3681 :     $relationTable->{$relationName} = { Fields => { } };
3682 :     }
3683 :     # Add the field to the relation's field structure.
3684 :     $relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
3685 :     }
3686 :     # Now that we've organized all our fields by relation name we need to do some serious
3687 :     # housekeeping. We must add the C<id> field to every relation and convert each relation
3688 :     # to a list of fields. First, we need the ID field itself.
3689 :     my $idField = $fieldList->{id};
3690 :     # Loop through the relations.
3691 :     for my $relationName (keys %{$relationTable}) {
3692 :     my $relation = $relationTable->{$relationName};
3693 :     # Get the relation's field list.
3694 :     my $relationFieldList = $relation->{Fields};
3695 :     # Add the ID field to it. If the field's already there, it will not make any
3696 :     # difference.
3697 :     $relationFieldList->{id} = $idField;
3698 :     # Convert the field set from a hash into a list using the pretty-sort number.
3699 :     $relation->{Fields} = _ReOrderRelationTable($relationFieldList);
3700 :     # Add the relation to the master table.
3701 :     $masterRelationTable{$relationName} = $relation;
3702 :     }
3703 :     # The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
3704 :     # The other relations must have at least one index that begins with the ID field. In addition, the
3705 :     # metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
3706 :     # get the entity's field list and index list.
3707 :     my $indexList = $entityStructure->{Indexes};
3708 :     # Loop through the indexes.
3709 :     for my $indexData (@{$indexList}) {
3710 :     # We need to find this index's fields. All of them should belong to the same relation.
3711 :     # The ID field is an exception, since it's in all relations.
3712 :     my $relationName = '0';
3713 :     for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
3714 :     # Get this field's name.
3715 :     my $fieldName = $fieldDescriptor->{name};
3716 :     # Only proceed if it is NOT the ID field.
3717 :     if ($fieldName ne 'id') {
3718 :     # Find the relation containing the current index field.
3719 :     my $thisName = $fieldList->{$fieldName}->{relation};
3720 :     if ($relationName eq '0') {
3721 :     # Here we're looking at the first field, so we save its relation name.
3722 :     $relationName = $thisName;
3723 :     } elsif ($relationName ne $thisName) {
3724 :     # Here we have a field mismatch.
3725 :     Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
3726 :     }
3727 :     }
3728 :     }
3729 :     # Now $relationName is the name of the relation that contains this index. Add the index structure
3730 :     # to the relation.
3731 :     push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
3732 :     }
3733 :     # Now each index has been put in a relation. We need to add the primary index for the primary
3734 :     # relation.
3735 :     push @{$relationTable->{$entityName}->{Indexes}},
3736 :     { IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
3737 :     Notes => { content => "Primary index for $entityName." }
3738 :     };
3739 :     # The next step is to insure that each relation has at least one index that begins with the ID field.
3740 :     # After that, we convert each relation's index list to an index table. We first need to loop through
3741 :     # the relations.
3742 :     for my $relationName (keys %{$relationTable}) {
3743 :     my $relation = $relationTable->{$relationName};
3744 :     # Get the relation's index list.
3745 :     my $indexList = $relation->{Indexes};
3746 :     # Insure this relation has an ID index.
3747 :     my $found = 0;
3748 :     for my $index (@{$indexList}) {
3749 :     if ($index->{IndexFields}->[0]->{name} eq "id") {
3750 :     $found = 1;
3751 :     }
3752 :     }
3753 :     if ($found == 0) {
3754 :     push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
3755 :     }
3756 :     # Now we need to convert the relation's index list to an index table. We begin by creating
3757 :     # an empty table in the relation structure.
3758 :     $relation->{Indexes} = { };
3759 :     # Loop through the indexes.
3760 :     my $count = 0;
3761 :     for my $index (@{$indexList}) {
3762 :     # Add this index to the index table.
3763 :     _AddIndex("idx$relationName$count", $relation, $index);
3764 :     # Increment the counter so that the next index has a different name.
3765 :     $count++;
3766 :     }
3767 :     }
3768 :     # Finally, we add the relation structure to the entity.
3769 :     $entityStructure->{Relations} = $relationTable;
3770 :     }
3771 :     # Loop through the relationships. Relationships actually turn out to be much simpler than entities.
3772 :     # For one thing, there is only a single constituent relation.
3773 :     my $relationshipList = $metadata->{Relationships};
3774 :     for my $relationshipName (keys %{$relationshipList}) {
3775 :     my $relationshipStructure = $relationshipList->{$relationshipName};
3776 :     # Fix up this relationship.
3777 :     _FixupFields($relationshipStructure, $relationshipName, 2, 3);
3778 :     # Format a description for the FROM field.
3779 :     my $fromEntity = $relationshipStructure->{from};
3780 :     my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
3781 :     # Get the FROM entity's key type.
3782 :     my $fromType = $entityList->{$fromEntity}->{keyType};
3783 :     # Add the FROM field.
3784 :     _AddField($relationshipStructure, 'from-link', { type => $fromType,
3785 :     relation => $relationshipName,
3786 :     Notes => { content => $fromComment },
3787 :     PrettySort => 1});
3788 :     # Format a description for the TO field.
3789 :     my $toEntity = $relationshipStructure->{to};
3790 :     my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
3791 :     # Get the TO entity's key type.
3792 :     my $toType = $entityList->{$toEntity}->{keyType};
3793 :     # Add the TO field.
3794 :     _AddField($relationshipStructure, 'to-link', { type=> $toType,
3795 :     relation => $relationshipName,
3796 :     Notes => { content => $toComment },
3797 :     PrettySort => 1});
3798 :     # Create an index-free relation from the fields.
3799 :     my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
3800 :     Indexes => { } };
3801 :     $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
3802 :     # Create the FROM and TO indexes.
3803 :     _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
3804 :     _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
3805 :     # Add the relation to the master table.
3806 :     $masterRelationTable{$relationshipName} = $thisRelation;
3807 :     }
3808 :     # Now store the master relation table in the metadata structure.
3809 :     $metadata->{RelationTable} = \%masterRelationTable;
3810 :     # Our final task is to create the join table. The join table is a hash that describes all
3811 :     # the join clauses for traveling through the relationships. The join clause is an equality
3812 :     # condition that can be put into a WHERE clause in order to join two objects. Two relationships
3813 :     # can be joined if they share an entity in common; and an entity can be joined to a relationship
3814 :     # if the entity is at either end of the relationship.
3815 :     my %joinTable = ();
3816 :     # Loop through the entities.
3817 :     for my $entityName (keys %{$entityList}) {
3818 :     # Build three lists of the relationships connected to this entity. One will be
3819 :     # for relationships from the entity, one for relationships to the entity, and
3820 :     # one for recursive relationships.
3821 :     my @fromList = ();
3822 :     my @toList = ();
3823 :     my @bothList = ();
3824 : parrello 1.21 Trace("Join table build for $entityName.") if T(metadata => 4);
3825 : parrello 1.10 for my $relationshipName (keys %{$relationshipList}) {
3826 :     my $relationship = $relationshipList->{$relationshipName};
3827 :     # Determine if this relationship has our entity in one of its link fields.
3828 :     my $fromEntity = $relationship->{from};
3829 :     my $toEntity = $relationship->{to};
3830 : parrello 1.41 Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
3831 : parrello 1.10 if ($fromEntity eq $entityName) {
3832 :     if ($toEntity eq $entityName) {
3833 :     # Here the relationship is recursive.
3834 :     push @bothList, $relationshipName;
3835 : parrello 1.21 Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
3836 : parrello 1.10 } else {
3837 :     # Here the relationship comes from the entity.
3838 :     push @fromList, $relationshipName;
3839 : parrello 1.21 Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
3840 : parrello 1.10 }
3841 :     } elsif ($toEntity eq $entityName) {
3842 :     # Here the relationship goes to the entity.
3843 :     push @toList, $relationshipName;
3844 : parrello 1.21 Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
3845 : parrello 1.10 }
3846 :     }
3847 :     # Create the nonrecursive joins. Note that we build two hashes for running
3848 :     # through the nonrecursive relationships since we'll have an outer loop
3849 :     # and an inner loop, and we can't do two "each" iterations on the same
3850 :     # hash table at the same time.
3851 :     my %directRelationships = ( from => \@fromList, to => \@toList );
3852 :     my %otherRelationships = ( from => \@fromList, to => \@toList );
3853 :     for my $linkType (keys %directRelationships) {
3854 :     my $relationships = $directRelationships{$linkType};
3855 :     # Loop through all the relationships.
3856 :     for my $relationshipName (@{$relationships}) {
3857 :     # Create joins between the entity and this relationship.
3858 :     my $linkField = "$relationshipName.${linkType}_link";
3859 :     my $joinClause = "$entityName.id = $linkField";
3860 : parrello 1.21 Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
3861 : parrello 1.10 $joinTable{"$entityName/$relationshipName"} = $joinClause;
3862 :     $joinTable{"$relationshipName/$entityName"} = $joinClause;
3863 :     # Create joins between this relationship and the other relationships.
3864 :     for my $otherType (keys %otherRelationships) {
3865 :     my $otherships = $otherRelationships{$otherType};
3866 :     for my $otherName (@{$otherships}) {
3867 :     # Get the key for this join.
3868 :     my $joinKey = "$otherName/$relationshipName";
3869 :     # Check for a duplicate or a self-join.
3870 :     if (exists $joinTable{$joinKey}) {
3871 :     # Here we have a duplicate, which means that the join
3872 :     # path is ambiguous. We delete the join from the join
3873 :     # table to prevent it from being used.
3874 :     delete $joinTable{$joinKey};
3875 :     Trace("Deleting ambiguous join $joinKey.") if T(4);
3876 :     } elsif ($otherName ne $relationshipName) {
3877 :     # Here we have a valid join. Note that joins between a
3878 :     # relationship and itself are prohibited.
3879 :     my $relJoinClause = "$otherName.${otherType}_link = $linkField";
3880 :     $joinTable{$joinKey} = $relJoinClause;
3881 : parrello 1.21 Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
3882 : parrello 1.10 }
3883 :     }
3884 :     }
3885 :     # Create joins between this relationship and the recursive relationships.
3886 :     # We don't need to check for ambiguous joins here, because a recursive
3887 :     # relationship can only be ambiguous with another recursive relationship,
3888 :     # and the incoming relationship from the outer loop is never recursive.
3889 :     for my $otherName (@bothList) {
3890 : parrello 1.21 Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
3891 : parrello 1.10 # Join from the left.
3892 :     $joinTable{"$relationshipName/$otherName"} =
3893 :     "$linkField = $otherName.from_link";
3894 :     # Join from the right.
3895 :     $joinTable{"$otherName/$relationshipName"} =
3896 :     "$otherName.to_link = $linkField";
3897 :     }
3898 :     }
3899 :     }
3900 :     # Create entity joins for the recursive relationships. Unlike the non-recursive
3901 :     # joins, the direction makes a difference with the recursive joins. This can give
3902 :     # rise to situations where we can't create the path we want; however, it is always
3903 :     # possible to get the same effect using multiple queries.
3904 :     for my $relationshipName (@bothList) {
3905 : parrello 1.21 Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
3906 : parrello 1.10 # Join to the entity from each direction.
3907 :     $joinTable{"$entityName/$relationshipName"} =
3908 :     "$entityName.id = $relationshipName.from_link";
3909 :     $joinTable{"$relationshipName/$entityName"} =
3910 :     "$relationshipName.to_link = $entityName.id";
3911 :     }
3912 :     }
3913 :     # Add the join table to the structure.
3914 :     $metadata->{Joins} = \%joinTable;
3915 :     # Return the slurped and fixed-up structure.
3916 :     return $metadata;
3917 : parrello 1.1 }
3918 :    
3919 : parrello 1.70 =head3 _CreateRelationshipIndex
3920 : parrello 1.1
3921 :     Create an index for a relationship's relation.
3922 :    
3923 :     This is a static method.
3924 :    
3925 :     =over 4
3926 :    
3927 :     =item indexKey
3928 :    
3929 :     Type of index: either C<"From"> or C<"To">.
3930 :    
3931 :     =item relationshipName
3932 :    
3933 :     Name of the relationship.
3934 :    
3935 :     =item relationshipStructure
3936 :    
3937 :     Structure describing the relationship that the index will sort.
3938 :    
3939 :     =back
3940 :    
3941 :     =cut
3942 :    
3943 :     sub _CreateRelationshipIndex {
3944 : parrello 1.10 # Get the parameters.
3945 :     my ($indexKey, $relationshipName, $relationshipStructure) = @_;
3946 :     # Get the target relation.
3947 :     my $relationStructure = $relationshipStructure->{Relations}->{$relationshipName};
3948 :     # Create a descriptor for the link field that goes at the beginning of this index.
3949 :     my $firstField = { name => lcfirst $indexKey . '-link', order => 'ascending' };
3950 :     # Get the target index descriptor.
3951 :     my $newIndex = $relationshipStructure->{$indexKey . "Index"};
3952 :     # Add the first field to the index's field list. Due to the craziness of PERL, if the
3953 :     # index descriptor does not exist, it will be created automatically so we can add
3954 :     # the field to it.
3955 :     unshift @{$newIndex->{IndexFields}}, $firstField;
3956 : parrello 1.12 # If this is a one-to-many relationship, the "To" index is unique.
3957 :     if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
3958 :     $newIndex->{Unique} = 'true';
3959 :     }
3960 : parrello 1.10 # Add the index to the relation.
3961 :     _AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
3962 : parrello 1.1 }
3963 :    
3964 : parrello 1.70 =head3 _AddIndex
3965 : parrello 1.1
3966 :     Add an index to a relation structure.
3967 :    
3968 :     This is a static method.
3969 :    
3970 :     =over 4
3971 :    
3972 :     =item indexName
3973 :    
3974 :     Name to give to the new index.
3975 :    
3976 :     =item relationStructure
3977 :    
3978 :     Relation structure to which the new index should be added.
3979 :    
3980 :     =item newIndex
3981 :    
3982 :     New index to add.
3983 :    
3984 :     =back
3985 :    
3986 :     =cut
3987 :    
3988 :     sub _AddIndex {
3989 : parrello 1.10 # Get the parameters.
3990 :     my ($indexName, $relationStructure, $newIndex) = @_;
3991 :     # We want to re-do the index's field list. Instead of an object for each field,
3992 :     # we want a string consisting of the field name optionally followed by the token DESC.
3993 :     my @fieldList = ( );
3994 :     for my $field (@{$newIndex->{IndexFields}}) {
3995 :     # Create a string containing the field name.
3996 :     my $fieldString = $field->{name};
3997 :     # Add the ordering token if needed.
3998 :     if ($field->{order} eq "descending") {
3999 :     $fieldString .= " DESC";
4000 :     }
4001 :     # Push the result onto the field list.
4002 :     push @fieldList, $fieldString;
4003 :     }
4004 :     # Store the field list just created as the new index field list.
4005 :     $newIndex->{IndexFields} = \@fieldList;
4006 :     # Add the index to the relation's index list.
4007 :     $relationStructure->{Indexes}->{$indexName} = $newIndex;
4008 : parrello 1.1 }
4009 :    
4010 : parrello 1.70 =head3 _FixupFields
4011 : parrello 1.1
4012 :     This method fixes the field list for an entity or relationship. It will add the caller-specified
4013 :     relation name to fields that do not have a name and set the C<PrettySort> value as specified.
4014 :    
4015 :     This is a static method.
4016 :    
4017 :     =over 4
4018 :    
4019 :     =item structure
4020 :    
4021 :     Entity or relationship structure to be fixed up.
4022 :    
4023 :     =item defaultRelationName
4024 :    
4025 :     Default relation name to be added to the fields.
4026 :    
4027 :     =item prettySortValue
4028 :    
4029 :     C<PrettySort> value for the relation's normal fields.
4030 :    
4031 :     =item textPrettySortValue
4032 :    
4033 :     C<PrettySort> value for the relation's text fields. This value can be set to one greater than the
4034 :     normal pretty sort value so that text fields go at the end of each relation.
4035 :    
4036 :     =back
4037 :    
4038 :     =cut
4039 :    
4040 :     sub _FixupFields {
4041 : parrello 1.10 # Get the parameters.
4042 :     my ($structure, $defaultRelationName, $prettySortValue, $textPrettySortValue) = @_;
4043 :     # Insure the structure has a field list.
4044 :     if (!exists $structure->{Fields}) {
4045 :     # Here it doesn't, so we create a new one.
4046 :     $structure->{Fields} = { };
4047 :     } else {
4048 : parrello 1.70 # Here we have a field list. We need to track the searchable fields, so we
4049 :     # create a list for stashing them.
4050 :     my @textFields = ();
4051 :     # Loop through the fields.
4052 : parrello 1.10 my $fieldStructures = $structure->{Fields};
4053 :     for my $fieldName (keys %{$fieldStructures}) {
4054 : parrello 1.8 Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
4055 : parrello 1.10 my $fieldData = $fieldStructures->{$fieldName};
4056 :     # Get the field type.
4057 :     my $type = $fieldData->{type};
4058 :     # Plug in a relation name if it is needed.
4059 :     Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4060 : parrello 1.70 # Check for searchability.
4061 :     if ($fieldData->{searchable}) {
4062 :     # Only allow this for a primary relation.
4063 :     if ($fieldData->{relation} ne $defaultRelationName) {
4064 :     Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4065 :     } else {
4066 :     push @textFields, $fieldName;
4067 :     }
4068 :     }
4069 : parrello 1.10 # Add the PrettySortValue.
4070 :     $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4071 :     }
4072 : parrello 1.70 # If there are searchable fields, remember the fact.
4073 :     if (@textFields) {
4074 :     $structure->{searchFields} = \@textFields;
4075 :     }
4076 : parrello 1.10 }
4077 : parrello 1.1 }
4078 :    
4079 : parrello 1.70 =head3 _FixName
4080 : parrello 1.1
4081 :     Fix the incoming field name so that it is a legal SQL column name.
4082 :    
4083 :     This is a static method.
4084 :    
4085 :     =over 4
4086 :    
4087 :     =item fieldName
4088 :    
4089 :     Field name to fix.
4090 :    
4091 :     =item RETURN
4092 :    
4093 :     Returns the fixed-up field name.
4094 :    
4095 :     =back
4096 :    
4097 :     =cut
4098 :    
4099 :     sub _FixName {
4100 : parrello 1.10 # Get the parameter.
4101 :     my ($fieldName) = @_;
4102 :     # Replace its minus signs with underscores.
4103 :     $fieldName =~ s/-/_/g;
4104 :     # Return the result.
4105 :     return $fieldName;
4106 : parrello 1.1 }
4107 :    
4108 : parrello 1.70 =head3 _FixNames
4109 : parrello 1.1
4110 :     Fix all the field names in a list.
4111 :    
4112 :     This is a static method.
4113 :    
4114 :     =over 4
4115 :    
4116 :     =item field1, field2, field3, ... fieldn
4117 :    
4118 :     List of field names to fix.
4119 :    
4120 :     =item RETURN
4121 :    
4122 :     Returns a list of fixed-up versions of the incoming field names.
4123 :    
4124 :     =back
4125 :    
4126 :     =cut
4127 :    
4128 :     sub _FixNames {
4129 : parrello 1.10 # Create the result list.
4130 :     my @result = ( );
4131 :     # Loop through the incoming parameters.
4132 :     for my $field (@_) {
4133 :     push @result, _FixName($field);
4134 :     }
4135 :     # Return the result.
4136 :     return @result;
4137 : parrello 1.1 }
4138 :    
4139 : parrello 1.70 =head3 _AddField
4140 : parrello 1.1
4141 :     Add a field to a field list.
4142 :    
4143 :     This is a static method.
4144 :    
4145 :     =over 4
4146 :    
4147 :     =item structure
4148 :    
4149 :     Structure (usually an entity or relationship) that is to contain the field.
4150 :    
4151 :     =item fieldName
4152 :    
4153 :     Name of the new field.
4154 :    
4155 :     =item fieldData
4156 :    
4157 :     Structure containing the data to put in the field.
4158 :    
4159 :     =back
4160 :    
4161 :     =cut
4162 :    
4163 :     sub _AddField {
4164 : parrello 1.10 # Get the parameters.
4165 :     my ($structure, $fieldName, $fieldData) = @_;
4166 :     # Create the field structure by copying the incoming data.
4167 :     my $fieldStructure = {%{$fieldData}};
4168 :     # Get a reference to the field list itself.
4169 :     my $fieldList = $structure->{Fields};
4170 :     # Add the field to the field list.
4171 :     $fieldList->{$fieldName} = $fieldStructure;
4172 : parrello 1.1 }
4173 :    
4174 : parrello 1.70 =head3 _ReOrderRelationTable
4175 : parrello 1.1
4176 :     This method will take a relation table and re-sort it according to the implicit ordering of the
4177 :     C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
4178 :     This requires creating a new hash that contains the field name in the C<name> property but doesn't
4179 :     have the C<PrettySort> property, and then inserting that new hash into the field list.
4180 :    
4181 :     This is a static method.
4182 :    
4183 :     =over 4
4184 :    
4185 :     =item relationTable
4186 :    
4187 :     Relation hash to be reformatted into a list.
4188 :    
4189 :     =item RETURN
4190 :    
4191 :     A list of field hashes.
4192 :    
4193 :     =back
4194 :    
4195 :     =cut
4196 :    
4197 :     sub _ReOrderRelationTable {
4198 : parrello 1.10 # Get the parameters.
4199 :     my ($relationTable) = @_;
4200 :     # Create the return list.
4201 :     my @resultList;
4202 :     # Rather than copy all the fields in a single pass, we make multiple passes and only copy
4203 :     # fields whose PrettySort value matches the current pass number. This process continues
4204 :     # until we process all the fields in the relation.
4205 :     my $fieldsLeft = (values %{$relationTable});
4206 :     for (my $sortPass = 1; $fieldsLeft > 0; $sortPass++) {
4207 :     # Loop through the fields. Note that we lexically sort the fields. This makes field name
4208 :     # secondary to pretty-sort number in the final ordering.
4209 :     for my $fieldName (sort keys %{$relationTable}) {
4210 :     # Get this field's data.
4211 :     my $fieldData = $relationTable->{$fieldName};
4212 :     # Verify the sort pass.
4213 :     if ($fieldData->{PrettySort} == $sortPass) {
4214 :     # Here we're in the correct pass. Denote we've found a field.
4215 :     $fieldsLeft--;
4216 :     # The next step is to create the field structure. This done by copying all
4217 :     # of the field elements except PrettySort and adding the name.
4218 :     my %thisField;
4219 :     for my $property (keys %{$fieldData}) {
4220 :     if ($property ne 'PrettySort') {
4221 :     $thisField{$property} = $fieldData->{$property};
4222 :     }
4223 :     }
4224 :     $thisField{name} = $fieldName;
4225 :     # Now we add this field to the end of the result list.
4226 :     push @resultList, \%thisField;
4227 :     }
4228 :     }
4229 :     }
4230 :     # Return a reference to the result list.
4231 :     return \@resultList;
4232 : parrello 1.1
4233 :     }
4234 :    
4235 : parrello 1.70 =head3 _IsPrimary
4236 : parrello 1.1
4237 :     Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
4238 :     if it has the same name as an entity or relationship.
4239 :    
4240 :     This is an instance method.
4241 :    
4242 :     =over 4
4243 :    
4244 :     =item relationName
4245 :    
4246 :     Name of the relevant relation.
4247 :    
4248 :     =item RETURN
4249 :    
4250 :     Returns TRUE for a primary relation, else FALSE.
4251 :    
4252 :     =back
4253 :    
4254 :     =cut
4255 :    
4256 :     sub _IsPrimary {
4257 : parrello 1.10 # Get the parameters.
4258 :     my ($self, $relationName) = @_;
4259 :     # Check for the relation in the entity table.
4260 :     my $entityTable = $self->{_metaData}->{Entities};
4261 :     my $retVal = exists $entityTable->{$relationName};
4262 :     if (! $retVal) {
4263 :     # Check for it in the relationship table.
4264 :     my $relationshipTable = $self->{_metaData}->{Relationships};
4265 :     $retVal = exists $relationshipTable->{$relationName};
4266 :     }
4267 :     # Return the determination indicator.
4268 :     return $retVal;
4269 : parrello 1.1 }
4270 :    
4271 : parrello 1.70 =head3 _FindRelation
4272 : parrello 1.1
4273 :     Return the descriptor for the specified relation.
4274 :    
4275 :     This is an instance method.
4276 :    
4277 :     =over 4
4278 :    
4279 :     =item relationName
4280 :    
4281 :     Name of the relation whose descriptor is to be returned.
4282 :    
4283 :     =item RETURN
4284 :    
4285 :     Returns the object that describes the relation's indexes and fields.
4286 :    
4287 :     =back
4288 :    
4289 :     =cut
4290 :     sub _FindRelation {
4291 : parrello 1.10 # Get the parameters.
4292 :     my ($self, $relationName) = @_;
4293 :     # Get the relation's structure from the master relation table in the metadata structure.
4294 :     my $metaData = $self->{_metaData};
4295 :     my $retVal = $metaData->{RelationTable}->{$relationName};
4296 :     # Return it to the caller.
4297 :     return $retVal;
4298 : parrello 1.1 }
4299 :    
4300 :     =head2 HTML Documentation Utility Methods
4301 :    
4302 : parrello 1.70 =head3 _ComputeRelationshipSentence
4303 : parrello 1.1
4304 :     The relationship sentence consists of the relationship name between the names of the
4305 :     two related entities and an arity indicator.
4306 :    
4307 :     This is a static method.
4308 :    
4309 :     =over 4
4310 :    
4311 :     =item relationshipName
4312 :    
4313 :     Name of the relationship.
4314 :    
4315 :     =item relationshipStructure
4316 :    
4317 :     Relationship structure containing the relationship's description and properties.
4318 :    
4319 :     =item RETURN
4320 :    
4321 :     Returns a string containing the entity names on either side of the relationship name and an
4322 :     indicator of the arity.
4323 :    
4324 :     =back
4325 :    
4326 :     =cut
4327 :    
4328 :     sub _ComputeRelationshipSentence {
4329 : parrello 1.10 # Get the parameters.
4330 :     my ($relationshipName, $relationshipStructure) = @_;
4331 :     # Format the relationship sentence.
4332 :     my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";
4333 :     # Compute the arity.
4334 :     my $arityCode = $relationshipStructure->{arity};
4335 :     my $arity = $ArityTable{$arityCode};
4336 :     $result .= " ($arity)";
4337 :     return $result;
4338 : parrello 1.1 }
4339 :    
4340 : parrello 1.70 =head3 _ComputeRelationshipHeading
4341 : parrello 1.1
4342 :     The relationship heading is the L<relationship sentence|/ComputeRelationshipSentence> with the entity
4343 :     names hyperlinked to the appropriate entity sections of the document.
4344 :    
4345 :     This is a static method.
4346 :    
4347 :     =over 4
4348 :    
4349 :     =item relationshipName
4350 :    
4351