Annotation of /Sprout/ERDB.pm

Revision 1.65 - (view) (download) (as text)

1 :	parrello	1.1	package ERDB;
2 :
3 :	parrello	1.10	use strict;
4 :			use Tracer;
5 :	olson	1.14	use DBrtns;
6 :	parrello	1.10	use Data::Dumper;
7 :			use XML::Simple;
8 :			use DBQuery;
9 :			use DBObject;
10 :			use Stats;
11 :			use Time::HiRes qw(gettimeofday);
12 :	parrello	1.42	use Digest::MD5 qw(md5_base64);
13 :	parrello	1.19	use FIG;
14 :	parrello	1.1
15 :			=head1 Entity-Relationship Database Package
16 :
17 :			=head2 Introduction
18 :
19 :			The Entity-Relationship Database Package allows the client to create an easily-configurable
20 :			database of Entities connected by Relationships. Each entity is represented by one or more
21 :			relations in an underlying SQL database. Each relationship is represented by a single
22 :			relation that connects two entities.
23 :
24 :			Although this package is designed for general use, all examples are derived from the
25 :			Sprout database, which is the first database implemented using this package.
26 :
27 :			Each entity has at least one relation, the I<primary relation>, that has the same name as
28 :			the entity. The primary relation contains a field named C<id> that contains the unique
29 :			identifier of each entity instance. An entity may have additional relations that contain
30 :			fields which are optional or can occur more than once. For example, the B<FEATURE> entity
31 :			has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
32 :			is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
33 :			however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
34 :			relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
35 :			The B<FEATURE> entity also contains an optional virulence number. This is implemented
36 :			as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
37 :	parrello	1.8	(C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
38 :			the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
39 :			number. If the virulence of I<ABC> is not known, there will not be any rows for it in
40 :			C<FeatureVirulence>.
41 :	parrello	1.1
42 :			Entities are connected by binary relationships implemented using single relations possessing the
43 :			same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
44 :			or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
45 :			ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
46 :			of the relationship is generally a verb phrase with the source entity as the subject and the
47 :			target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
48 :			and B<SOURCE> entities, and indicates that a particular source organization participated in the
49 :			mapping of the genome. A source organization frequently participates in the mapping
50 :			of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
51 :			this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
52 :			relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
53 :			and C<to-link>, which contains a source ID.
54 :
55 :			A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
56 :			are implemented as additional fields in the relationship's relation. So, for example, the
57 :			B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
58 :			to determine which sequences make up a contig. The relationship has as an attribute the
59 :			B<start-position>, which indicates where in the contig that the sequence begins. This attribute
60 :			is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
61 :
62 :			The database itself is described by an XML file using the F<ERDatabase.xsd> schema. In addition to
63 :			all the data required to define the entities, relationships, and attributes, the schema provides
64 :			space for notes describing the data and what it means. These notes are used by L</ShowMetaData>
65 :			to generate documentation for the database.
66 :
67 :			Finally, every entity and relationship object has a flag indicating if it is new or old. The object
68 :			is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
69 :			was inserted by the L</InsertObject> method.
70 :
71 :			To facilitate testing, the ERDB module supports automatic generation of test data. This process
72 :	parrello	1.5	is described in the L</GenerateEntity> and L</GenerateConnection> methods, though it is not yet
73 :			fully implemented.
74 :	parrello	1.1
75 :	parrello	1.8	=head2 XML Database Description
76 :
77 :			=head3 Data Types
78 :
79 :			The ERDB system supports the following data types. Note that there are numerous string
80 :			types depending on the maximum length. Some database packages limit the total number of
81 :			characters you have in an index key; to insure the database works in all environments,
82 :			the type of string should be the shortest one possible that supports all the known values.
83 :
84 :			=over 4
85 :
86 :			=item char
87 :
88 :			single ASCII character
89 :
90 :			=item int
91 :
92 :			32-bit signed integer
93 :
94 :	parrello	1.60	=item counter
95 :
96 :			32-bit unsigned integer
97 :
98 :	parrello	1.8	=item date
99 :
100 :			64-bit unsigned integer, representing a PERL date/time value
101 :
102 :			=item text
103 :
104 :			long string; Text fields cannot be used in indexes or sorting and do not support the
105 :			normal syntax of filter clauses, but can be up to a billion character in length
106 :
107 :			=item float
108 :
109 :			double-precision floating-point number
110 :
111 :			=item boolean
112 :
113 :			single-bit numeric value; The value is stored as a 16-bit signed integer (for
114 :			compatability with certain database packages), but the only values supported are
115 :			0 and 1.
116 :
117 :	parrello	1.44	=item id-string
118 :
119 :			variable-length string, maximum 25 characters
120 :
121 :	parrello	1.8	=item key-string
122 :
123 :			variable-length string, maximum 40 characters
124 :
125 :			=item name-string
126 :
127 :			variable-length string, maximum 80 characters
128 :
129 :			=item medium-string
130 :
131 :			variable-length string, maximum 160 characters
132 :
133 :			=item string
134 :
135 :			variable-length string, maximum 255 characters
136 :
137 :	parrello	1.42	=item hash-string
138 :
139 :			variable-length string, maximum 22 characters
140 :
141 :	parrello	1.8	=back
142 :
143 :	parrello	1.42	The hash-string data type has a special meaning. The actual key passed into the loader will
144 :			be a string, but it will be digested into a 22-character MD5 code to save space. Although the
145 :			MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
146 :			digest. Therefore, it is presumed the keys will be unique. When the database is actually
147 :			in use, the hashed keys will be presented rather than the original values. For this reason,
148 :			they should not be used for entities where the key is meaningful.
149 :
150 :	parrello	1.8	=head3 Global Tags
151 :
152 :			The entire database definition must be inside a B<Database> tag. The display name of
153 :			the database is given by the text associated with the B<Title> tag. The display name
154 :			is only used in the automated documentation. It has no other effect. The entities and
155 :			relationships are listed inside the B<Entities> and B<Relationships> tags,
156 :			respectively. None of these tags have attributes.
157 :
158 :	parrello	1.10	<Database>
159 :			<Title>... display title here...</Title>
160 :			<Entities>
161 :			... entity definitions here ...
162 :			</Entities>
163 :			<Relationships>
164 :			... relationship definitions here...
165 :			</Relationships>
166 :			</Database>
167 :	parrello	1.8
168 :			Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
169 :			The text inside the B<Notes> tag contains comments that will appear when the database
170 :			documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
171 :			italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
172 :
173 :			=head3 Fields
174 :
175 :			Both entities and relationships have fields described by B<Field> tags. A B<Field>
176 :			tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
177 :			object mus be inside B<Fields> tags.
178 :
179 :	parrello	1.10	<Entity ... >
180 :			<Fields>
181 :			... Field tags ...
182 :			</Fields>
183 :			</Entity>
184 :	parrello	1.8
185 :			The attributes for the B<Field> tag are as follows.
186 :
187 :			=over 4
188 :
189 :			=item name
190 :
191 :			Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
192 :			and the first character should be a letter. Most underlying databases are case-insensitive
193 :			with the respect to field names, so a best practice is to use lower-case letters only.
194 :
195 :			=item type
196 :
197 :			Data type of the field. The legal data types are given above.
198 :
199 :			=item relation
200 :
201 :			Name of the relation containing the field. This should only be specified for entity
202 :			fields. The ERDB system does not support optional fields or multi-occurring fields
203 :			in the primary relation of an entity. Instead, they are put into secondary relations.
204 :			So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
205 :			grouping used to select a subset of the genomes. A given genome may not be in any
206 :			groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
207 :			value. The relation name specified must be a valid table name. By convention, it is
208 :			usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
209 :			entity, the fields without a relation attribute are said to belong to the
210 :			I<primary relation>. This relation has the same name as the entity itself.
211 :
212 :			=back
213 :
214 :			=head3 Indexes
215 :
216 :			An entity can have multiple alternate indexes associated with it. The fields must
217 :			be from the primary relation. The alternate indexes assist in ordering results
218 :			from a query. A relationship can have up to two indexes-- a I<to-index> and a
219 :			I<from-index>. These order the results when crossing the relationship. For
220 :			example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
221 :			from-index would order the contigs of a ganome, and the to-index would order
222 :			the genomes of a contig. A relationship's index must specify only fields in
223 :			the relationship.
224 :
225 :			The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
226 :			of a relationship is specified using the B<FromIndex> tag; the to-index is specified
227 :			using the B<ToIndex> tag.
228 :
229 :			Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
230 :			tag containing the B<IndexField> tags. These specify, in order, the fields used in
231 :			the index. The attributes of an B<IndexField> tag are as follows.
232 :
233 :			=over 4
234 :
235 :			=item name
236 :
237 :			Name of the field.
238 :
239 :			=item order
240 :
241 :			Sort order of the field-- C<ascending> or C<descending>.
242 :
243 :			=back
244 :
245 :			The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
246 :
247 :			=head3 Object and Field Names
248 :
249 :			By convention entity and relationship names use capital casing (e.g. C<Genome> or
250 :			C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
251 :			with respect to relation names, converting them internally to all-upper case or
252 :			all-lower case.
253 :
254 :			If syntax or parsing errors occur when you try to load or use an ERDB database, the
255 :			most likely reason is that one of your objects has an SQL reserved word as its name.
256 :			The list of SQL reserved words keeps increasing; however, most are unlikely to show
257 :			up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
258 :			C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
259 :			C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
260 :
261 :			Every entity has a field called C<id> that acts as its primary key. Every relationship
262 :			has fields called C<from-link> and C<to-link> that contain copies of the relevant
263 :			entity IDs. These are essentially ERDB's reserved words, and should not be used
264 :			for user-defined field names.
265 :
266 :			=head3 Entities
267 :
268 :			An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
269 :			B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
270 :			containing one or more fields. The attributes of the B<Entity> tag are as follows.
271 :
272 :			=over 4
273 :
274 :			=item name
275 :
276 :			Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
277 :			or C<GroupBlock>) and should be a noun or noun phrase.
278 :
279 :			=item keyType
280 :
281 :			Data type of the primary key. The primary key is always named C<id>.
282 :
283 :			=back
284 :
285 :			=head3 Relationships
286 :
287 :			A relationship is described by the C<Relationship> tag. Within a relationship,
288 :			there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
289 :			fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
290 :			the to-index.
291 :
292 :			The C<Relationship> tag has the following attributes.
293 :
294 :			=over 4
295 :
296 :			=item name
297 :
298 :			Name of the relationship. The relationship name, by convention, uses capital casing
299 :			(e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
300 :			phrase, designed to fit between the from-entity and the to-entity (e.g.
301 :			Block C<ContainsRegionIn> Genome).
302 :
303 :			=item from
304 :
305 :			Name of the entity from which the relationship starts.
306 :
307 :			=item to
308 :
309 :			Name of the entity to which the relationship proceeds.
310 :
311 :			=item arity
312 :
313 :			Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
314 :
315 :			=back
316 :
317 :	parrello	1.1	=cut
318 :
319 :			# GLOBALS
320 :
321 :			# Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
322 :			# "maxLen" is the maximum permissible length of the incoming string data used to populate a field
323 :			# of the specified type. "dataGen" is PERL string that will be evaluated if no test data generation
324 :	parrello	1.18	# string is specified in the field definition. "avgLen" is the average byte length for estimating
325 :	parrello	1.60	# record sizes. "sort" is the key modifier for the sort command.
326 :			my %TypeTable = ( char => { sqlType => 'CHAR(1)', maxLen => 1, avgLen => 1, sort => "", dataGen => "StringGen('A')" },
327 :			int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n", dataGen => "IntGen(0, 99999999)" },
328 :			counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n", dataGen => "IntGen(0, 99999999)" },
329 :			string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "", dataGen => "StringGen(IntGen(10,250))" },
330 :			text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "", dataGen => "StringGen(IntGen(80,1000))" },
331 :			date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n", dataGen => "DateGen(-7, 7, IntGen(0,1400))" },
332 :			float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g", dataGen => "FloatGen(0.0, 100.0)" },
333 :			boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n", dataGen => "IntGen(0, 1)" },
334 :	parrello	1.42	'hash-string' =>
335 :	parrello	1.60	{ sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "", dataGen => "SringGen(22)" },
336 :	parrello	1.44	'id-string' =>
337 :	parrello	1.60	{ sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "", dataGen => "SringGen(22)" },
338 :	parrello	1.10	'key-string' =>
339 :	parrello	1.60	{ sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "", dataGen => "StringGen(IntGen(10,40))" },
340 :	parrello	1.10	'name-string' =>
341 :	parrello	1.60	{ sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "", dataGen => "StringGen(IntGen(10,80))" },
342 :	parrello	1.10	'medium-string' =>
343 :	parrello	1.60	{ sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "", dataGen => "StringGen(IntGen(10,160))" },
344 :	parrello	1.10	);
345 :	parrello	1.1
346 :			# Table translating arities into natural language.
347 :			my %ArityTable = ( '11' => 'one-to-one',
348 :	parrello	1.10	'1M' => 'one-to-many',
349 :			'MM' => 'many-to-many'
350 :			);
351 :	parrello	1.1
352 :			# Table for interpreting string patterns.
353 :
354 :			my %PictureTable = ( 'A' => "abcdefghijklmnopqrstuvwxyz",
355 :	parrello	1.10	'9' => "0123456789",
356 :			'X' => "abcdefghijklmnopqrstuvwxyz0123456789",
357 :			'V' => "aeiou",
358 :			'K' => "bcdfghjklmnoprstvwxyz"
359 :			);
360 :	parrello	1.1
361 :			=head2 Public Methods
362 :
363 :			=head3 new
364 :
365 :	parrello	1.5	C<< my $database = ERDB->new($dbh, $metaFileName); >>
366 :	parrello	1.1
367 :			Create a new ERDB object.
368 :
369 :			=over 4
370 :
371 :			=item dbh
372 :
373 :			DBKernel database object for the target database.
374 :
375 :			=item metaFileName
376 :
377 :			Name of the XML file containing the metadata.
378 :
379 :			=back
380 :
381 :			=cut
382 :
383 :			sub new {
384 :	parrello	1.10	# Get the parameters.
385 :			my ($class, $dbh, $metaFileName, $options) = @_;
386 :			# Load the meta-data.
387 :			my $metaData = _LoadMetaData($metaFileName);
388 :			# Create the object.
389 :			my $self = { _dbh => $dbh,
390 :			_metaData => $metaData
391 :			};
392 :			# Bless and return it.
393 :			bless $self, $class;
394 :			return $self;
395 :	parrello	1.1	}
396 :
397 :			=head3 ShowMetaData
398 :
399 :	parrello	1.18	C<< $erdb->ShowMetaData($fileName); >>
400 :	parrello	1.1
401 :			This method outputs a description of the database. This description can be used to help users create
402 :			the data to be loaded into the relations.
403 :
404 :			=over 4
405 :
406 :			=item filename
407 :
408 :			The name of the output file.
409 :
410 :			=back
411 :
412 :			=cut
413 :
414 :			sub ShowMetaData {
415 :	parrello	1.10	# Get the parameters.
416 :			my ($self, $filename) = @_;
417 :			# Get the metadata and the title string.
418 :			my $metadata = $self->{_metaData};
419 :			# Get the title string.
420 :			my $title = $metadata->{Title};
421 :			# Get the entity and relationship lists.
422 :			my $entityList = $metadata->{Entities};
423 :			my $relationshipList = $metadata->{Relationships};
424 :			# Open the output file.
425 :			open(HTMLOUT, ">$filename") \|\| Confess("Could not open MetaData display file $filename: $!");
426 :			Trace("Building MetaData table of contents.") if T(4);
427 :			# Write the HTML heading stuff.
428 :			print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
429 :			print HTMLOUT "</head>\n<body>\n";
430 :	parrello	1.45	# Write the documentation.
431 :			print HTMLOUT $self->DisplayMetaData();
432 :			# Close the document.
433 :			print HTMLOUT "</body>\n</html>\n";
434 :			# Close the file.
435 :			close HTMLOUT;
436 :			}
437 :
438 :			=head3 DisplayMetaData
439 :
440 :			C<< my $html = $erdb->DisplayMetaData(); >>
441 :
442 :			Return an HTML description of the database. This description can be used to help users create
443 :			the data to be loaded into the relations and form queries. The output is raw includable HTML
444 :			without any HEAD or BODY tags.
445 :
446 :			=over 4
447 :
448 :			=item filename
449 :
450 :			The name of the output file.
451 :
452 :			=back
453 :
454 :			=cut
455 :
456 :			sub DisplayMetaData {
457 :			# Get the parameters.
458 :			my ($self) = @_;
459 :			# Get the metadata and the title string.
460 :			my $metadata = $self->{_metaData};
461 :			# Get the title string.
462 :			my $title = $metadata->{Title};
463 :			# Get the entity and relationship lists.
464 :			my $entityList = $metadata->{Entities};
465 :			my $relationshipList = $metadata->{Relationships};
466 :			# Declare the return variable.
467 :			my $retVal = "";
468 :			# Open the output file.
469 :			Trace("Building MetaData table of contents.") if T(4);
470 :	parrello	1.10	# Here we do the table of contents. It starts as an unordered list of section names. Each
471 :			# section contains an ordered list of entity or relationship subsections.
472 :	parrello	1.45	$retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
473 :	parrello	1.10	# Loop through the Entities, displaying a list item for each.
474 :			foreach my $key (sort keys %{$entityList}) {
475 :			# Display this item.
476 :	parrello	1.45	$retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
477 :	parrello	1.10	}
478 :			# Close off the entity section and start the relationship section.
479 :	parrello	1.45	$retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
480 :	parrello	1.10	# Loop through the Relationships.
481 :			foreach my $key (sort keys %{$relationshipList}) {
482 :			# Display this item.
483 :			my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
484 :	parrello	1.45	$retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
485 :	parrello	1.10	}
486 :			# Close off the relationship section and list the join table section.
487 :	parrello	1.45	$retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
488 :	parrello	1.10	# Close off the table of contents itself.
489 :	parrello	1.45	$retVal .= "</ul>\n";
490 :	parrello	1.10	# Now we start with the actual data. Denote we're starting the entity section.
491 :	parrello	1.45	$retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
492 :	parrello	1.10	# Loop through the entities.
493 :			for my $key (sort keys %{$entityList}) {
494 :			Trace("Building MetaData entry for $key entity.") if T(4);
495 :			# Create the entity header. It contains a bookmark and the entity name.
496 :	parrello	1.45	$retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
497 :	parrello	1.10	# Get the entity data.
498 :			my $entityData = $entityList->{$key};
499 :			# If there's descriptive text, display it.
500 :			if (my $notes = $entityData->{Notes}) {
501 :	parrello	1.45	$retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
502 :	parrello	1.10	}
503 :			# Now we want a list of the entity's relationships. First, we set up the relationship subsection.
504 :	parrello	1.45	$retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
505 :	parrello	1.10	# Loop through the relationships.
506 :			for my $relationship (sort keys %{$relationshipList}) {
507 :			# Get the relationship data.
508 :			my $relationshipStructure = $relationshipList->{$relationship};
509 :			# Only use the relationship if if has this entity in its FROM or TO fields.
510 :			if ($relationshipStructure->{from} eq $key \|\| $relationshipStructure->{to} eq $key) {
511 :			# Get the relationship sentence and append the arity.
512 :			my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
513 :			# Display the relationship data.
514 :	parrello	1.45	$retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
515 :	parrello	1.10	}
516 :			}
517 :			# Close off the relationship list.
518 :	parrello	1.45	$retVal .= "</ul>\n";
519 :	parrello	1.10	# Get the entity's relations.
520 :			my $relationList = $entityData->{Relations};
521 :			# Create a header for the relation subsection.
522 :	parrello	1.45	$retVal .= "<h4>Relations for <b>$key</b></h4>\n";
523 :	parrello	1.10	# Loop through the relations, displaying them.
524 :			for my $relation (sort keys %{$relationList}) {
525 :			my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
526 :	parrello	1.45	$retVal .= $htmlString;
527 :	parrello	1.10	}
528 :			}
529 :			# Denote we're starting the relationship section.
530 :	parrello	1.45	$retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
531 :	parrello	1.10	# Loop through the relationships.
532 :			for my $key (sort keys %{$relationshipList}) {
533 :			Trace("Building MetaData entry for $key relationship.") if T(4);
534 :			# Get the relationship's structure.
535 :			my $relationshipStructure = $relationshipList->{$key};
536 :			# Create the relationship header.
537 :			my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
538 :	parrello	1.45	$retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
539 :	parrello	1.10	# Get the entity names.
540 :			my $fromEntity = $relationshipStructure->{from};
541 :			my $toEntity = $relationshipStructure->{to};
542 :			# Describe the relationship arity. Note there's a bit of trickiness involving recursive
543 :			# many-to-many relationships. In a normal many-to-many we use two sentences to describe
544 :			# the arity (one for each direction). This is a bad idea for a recursive relationship,
545 :			# since both sentences will say the same thing.
546 :			my $arity = $relationshipStructure->{arity};
547 :			if ($arity eq "11") {
548 :	parrello	1.45	$retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
549 :	parrello	1.10	} else {
550 :	parrello	1.45	$retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
551 :	parrello	1.10	if ($arity eq "MM" && $fromEntity ne $toEntity) {
552 :	parrello	1.45	$retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
553 :	parrello	1.10	}
554 :			}
555 :	parrello	1.45	$retVal .= "</p>\n";
556 :	parrello	1.10	# If there are notes on this relationship, display them.
557 :			if (my $notes = $relationshipStructure->{Notes}) {
558 :	parrello	1.45	$retVal .= "<p>" . _HTMLNote($notes->{content}) . "</p>\n";
559 :	parrello	1.10	}
560 :			# Generate the relationship's relation table.
561 :			my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
562 :	parrello	1.45	$retVal .= $htmlString;
563 :	parrello	1.10	}
564 :			Trace("Building MetaData join table.") if T(4);
565 :			# Denote we're starting the join table.
566 :	parrello	1.45	$retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
567 :	parrello	1.10	# Create a table header.
568 :	parrello	1.45	$retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
569 :	parrello	1.10	# Loop through the joins.
570 :			my $joinTable = $metadata->{Joins};
571 :			my @joinKeys = keys %{$joinTable};
572 :			for my $joinKey (sort @joinKeys) {
573 :			# Separate out the source, the target, and the join clause.
574 :			$joinKey =~ m!^([^/]+)/(.+)$!;
575 :			my ($sourceRelation, $targetRelation) = ($1, $2);
576 :	parrello	1.30	Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
577 :	parrello	1.10	my $source = $self->ComputeObjectSentence($sourceRelation);
578 :			my $target = $self->ComputeObjectSentence($targetRelation);
579 :			my $clause = $joinTable->{$joinKey};
580 :			# Display them in a table row.
581 :	parrello	1.45	$retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
582 :	parrello	1.10	}
583 :			# Close the table.
584 :	parrello	1.45	$retVal .= _CloseTable();
585 :			Trace("Built MetaData HTML.") if T(3);
586 :			# Return the HTML.
587 :			return $retVal;
588 :	parrello	1.1	}
589 :
590 :			=head3 DumpMetaData
591 :
592 :	parrello	1.18	C<< $erdb->DumpMetaData(); >>
593 :	parrello	1.1
594 :			Return a dump of the metadata structure.
595 :
596 :			=cut
597 :
598 :			sub DumpMetaData {
599 :	parrello	1.10	# Get the parameters.
600 :			my ($self) = @_;
601 :			# Dump the meta-data.
602 :			return Data::Dumper::Dumper($self->{_metaData});
603 :	parrello	1.1	}
604 :
605 :			=head3 CreateTables
606 :
607 :	parrello	1.18	C<< $erdb->CreateTables(); >>
608 :	parrello	1.1
609 :			This method creates the tables for the database from the metadata structure loaded by the
610 :			constructor. It is expected this function will only be used on rare occasions, when the
611 :	parrello	1.2	user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
612 :	parrello	1.1	used by itself with the truncate flag turned on.
613 :
614 :			=cut
615 :
616 :			sub CreateTables {
617 :	parrello	1.10	# Get the parameters.
618 :			my ($self) = @_;
619 :	parrello	1.23	# Get the relation names.
620 :			my @relNames = $self->GetTableNames();
621 :			# Loop through the relations.
622 :			for my $relationName (@relNames) {
623 :			# Create a table for this relation.
624 :			$self->CreateTable($relationName);
625 :			Trace("Relation $relationName created.") if T(2);
626 :	parrello	1.10	}
627 :	parrello	1.1	}
628 :
629 :			=head3 CreateTable
630 :
631 :	parrello	1.18	C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
632 :	parrello	1.1
633 :			Create the table for a relation and optionally create its indexes.
634 :
635 :			=over 4
636 :
637 :			=item relationName
638 :
639 :			Name of the relation (which will also be the table name).
640 :
641 :	parrello	1.18	=item indexFlag
642 :	parrello	1.1
643 :			TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
644 :			L</CreateIndexes> must be called later to bring the indexes into existence.
645 :
646 :	parrello	1.18	=item estimatedRows (optional)
647 :
648 :			If specified, the estimated maximum number of rows for the relation. This
649 :			information allows the creation of tables using storage engines that are
650 :			faster but require size estimates, such as MyISAM.
651 :
652 :	parrello	1.1	=back
653 :
654 :			=cut
655 :
656 :			sub CreateTable {
657 :	parrello	1.10	# Get the parameters.
658 :	parrello	1.18	my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
659 :	parrello	1.10	# Get the database handle.
660 :			my $dbh = $self->{_dbh};
661 :			# Get the relation data and determine whether or not the relation is primary.
662 :			my $relationData = $self->_FindRelation($relationName);
663 :			my $rootFlag = $self->_IsPrimary($relationName);
664 :			# Create a list of the field data.
665 :			my @fieldList;
666 :			for my $fieldData (@{$relationData->{Fields}}) {
667 :			# Assemble the field name and type.
668 :			my $fieldName = _FixName($fieldData->{name});
669 :			my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
670 :			# Push the result into the field list.
671 :			push @fieldList, $fieldString;
672 :			}
673 :			# If this is a root table, add the "new_record" flag. It defaults to 0, so
674 :			if ($rootFlag) {
675 :			push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
676 :			}
677 :			# Convert the field list into a comma-delimited string.
678 :			my $fieldThing = join(', ', @fieldList);
679 :			# Insure the table is not already there.
680 :			$dbh->drop_table(tbl => $relationName);
681 :			Trace("Table $relationName dropped.") if T(2);
682 :	parrello	1.18	# If there are estimated rows, create an estimate so we can take advantage of
683 :			# faster DB technologies.
684 :			my $estimation = undef;
685 :			if ($estimatedRows) {
686 :			$estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
687 :			}
688 :	parrello	1.10	# Create the table.
689 :			Trace("Creating table $relationName: $fieldThing") if T(2);
690 :	parrello	1.18	$dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
691 :	parrello	1.10	Trace("Relation $relationName created in database.") if T(2);
692 :			# If we want to build the indexes, we do it here.
693 :			if ($indexFlag) {
694 :			$self->CreateIndex($relationName);
695 :			}
696 :	parrello	1.1	}
697 :
698 :	parrello	1.31	=head3 VerifyFields
699 :
700 :			C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
701 :
702 :			Run through the list of proposed field values, insuring that all the character fields are
703 :			below the maximum length. If any fields are too long, they will be truncated in place.
704 :
705 :			=over 4
706 :
707 :			=item relName
708 :
709 :			Name of the relation for which the specified fields are destined.
710 :
711 :			=item fieldList
712 :
713 :			Reference to a list, in order, of the fields to be put into the relation.
714 :
715 :			=item RETURN
716 :
717 :			Returns the number of fields truncated.
718 :
719 :			=back
720 :
721 :			=cut
722 :
723 :			sub VerifyFields {
724 :			# Get the parameters.
725 :			my ($self, $relName, $fieldList) = @_;
726 :			# Initialize the return value.
727 :			my $retVal = 0;
728 :			# Get the relation definition.
729 :			my $relData = $self->_FindRelation($relName);
730 :			# Get the list of field descriptors.
731 :			my $fieldTypes = $relData->{Fields};
732 :			my $fieldCount = scalar @{$fieldTypes};
733 :			# Loop through the two lists.
734 :			for (my $i = 0; $i < $fieldCount; $i++) {
735 :			# Get the type of the current field.
736 :			my $fieldType = $fieldTypes->[$i]->{type};
737 :			# If it's a character field, verify the length.
738 :			if ($fieldType =~ /string/) {
739 :			my $maxLen = $TypeTable{$fieldType}->{maxLen};
740 :			my $oldString = $fieldList->[$i];
741 :			if (length($oldString) > $maxLen) {
742 :			# Here it's too big, so we truncate it.
743 :			Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
744 :			$fieldList->[$i] = substr $oldString, 0, $maxLen;
745 :			$retVal++;
746 :			}
747 :			}
748 :			}
749 :			# Return the truncation count.
750 :			return $retVal;
751 :			}
752 :
753 :	parrello	1.42	=head3 DigestFields
754 :
755 :			C<< $erdb->DigestFields($relName, $fieldList); >>
756 :
757 :			Digest the strings in the field list that correspond to data type C<hash-string> in the
758 :			specified relation.
759 :
760 :			=over 4
761 :
762 :			=item relName
763 :
764 :			Name of the relation to which the fields belong.
765 :
766 :			=item fieldList
767 :
768 :			List of field contents to be loaded into the relation.
769 :
770 :			=back
771 :
772 :			=cut
773 :			#: Return Type ;
774 :			sub DigestFields {
775 :			# Get the parameters.
776 :			my ($self, $relName, $fieldList) = @_;
777 :			# Get the relation definition.
778 :			my $relData = $self->_FindRelation($relName);
779 :			# Get the list of field descriptors.
780 :			my $fieldTypes = $relData->{Fields};
781 :			my $fieldCount = scalar @{$fieldTypes};
782 :			# Loop through the two lists.
783 :			for (my $i = 0; $i < $fieldCount; $i++) {
784 :			# Get the type of the current field.
785 :			my $fieldType = $fieldTypes->[$i]->{type};
786 :			# If it's a hash string, digest it in place.
787 :			if ($fieldType eq 'hash-string') {
788 :	parrello	1.46	$fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
789 :	parrello	1.42	}
790 :			}
791 :			}
792 :
793 :	parrello	1.46	=head3 DigestKey
794 :
795 :			C<< my $digested = $erdb->DigestKey($keyValue); >>
796 :
797 :			Return the digested value of a symbolic key. The digested value can then be plugged into a
798 :			key-based search into a table with key-type hash-string.
799 :
800 :			Currently the digesting process is independent of the database structure, but that may not
801 :			always be the case, so this is an instance method instead of a static method.
802 :
803 :			=over 4
804 :
805 :			=item keyValue
806 :
807 :			Key value to digest.
808 :
809 :			=item RETURN
810 :
811 :	parrello	1.56	Digested value of the key.
812 :	parrello	1.46
813 :			=back
814 :
815 :			=cut
816 :
817 :			sub DigestKey {
818 :			# Get the parameters.
819 :			my ($self, $keyValue) = @_;
820 :			# Compute the digest.
821 :			my $retVal = md5_base64($keyValue);
822 :			# Return the result.
823 :			return $retVal;
824 :			}
825 :
826 :	parrello	1.1	=head3 CreateIndex
827 :
828 :	parrello	1.18	C<< $erdb->CreateIndex($relationName); >>
829 :	parrello	1.1
830 :			Create the indexes for a relation. If a table is being loaded from a large source file (as
831 :	parrello	1.12	is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
832 :			If that is the case, then L</CreateTable> should be called with the index flag set to
833 :			FALSE, and this method used after the load to create the indexes for the table.
834 :	parrello	1.1
835 :			=cut
836 :
837 :			sub CreateIndex {
838 :	parrello	1.10	# Get the parameters.
839 :			my ($self, $relationName) = @_;
840 :			# Get the relation's descriptor.
841 :			my $relationData = $self->_FindRelation($relationName);
842 :			# Get the database handle.
843 :			my $dbh = $self->{_dbh};
844 :			# Now we need to create this relation's indexes. We do this by looping through its index table.
845 :			my $indexHash = $relationData->{Indexes};
846 :			for my $indexName (keys %{$indexHash}) {
847 :			my $indexData = $indexHash->{$indexName};
848 :			# Get the index's field list.
849 :			my @fieldList = _FixNames(@{$indexData->{IndexFields}});
850 :			my $flds = join(', ', @fieldList);
851 :			# Get the index's uniqueness flag.
852 :			my $unique = (exists $indexData->{Unique} ? $indexData->{Unique} : 'false');
853 :			# Create the index.
854 :	parrello	1.24	my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
855 :			flds => $flds, unique => $unique);
856 :			if ($rv) {
857 :			Trace("Index created: $indexName for $relationName ($flds)") if T(1);
858 :			} else {
859 :			Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
860 :			}
861 :	parrello	1.10	}
862 :	parrello	1.1	}
863 :
864 :			=head3 LoadTables
865 :
866 :	parrello	1.18	C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
867 :	parrello	1.1
868 :			This method will load the database tables from a directory. The tables must already have been created
869 :			in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
870 :			all of the relations to be loaded must have a file in the directory with the same name as the relation
871 :			(optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
872 :			line of the file will be loaded as a row of the target relation table. The field values should be in
873 :			the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
874 :			erased before the new data is loaded in.
875 :
876 :			A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
877 :			tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
878 :			be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
879 :
880 :			=over 4
881 :
882 :			=item directoryName
883 :
884 :			Name of the directory containing the relation files to be loaded.
885 :
886 :			=item rebuild
887 :
888 :			TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
889 :			only way to erase existing data in the tables, since the TRUNCATE command is not supported
890 :			by all of the DB engines we use.
891 :
892 :			=item RETURN
893 :
894 :			Returns a statistical object describing the number of records read and a list of the error messages.
895 :
896 :			=back
897 :
898 :			=cut
899 :
900 :			sub LoadTables {
901 :	parrello	1.10	# Get the parameters.
902 :			my ($self, $directoryName, $rebuild) = @_;
903 :			# Start the timer.
904 :			my $startTime = gettimeofday;
905 :			# Clean any trailing slash from the directory name.
906 :			$directoryName =~ s!/\\$!!;
907 :			# Declare the return variable.
908 :			my $retVal = Stats->new();
909 :	parrello	1.23	# Get the relation names.
910 :			my @relNames = $self->GetTableNames();
911 :			for my $relationName (@relNames) {
912 :			# Try to load this relation.
913 :			my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
914 :	parrello	1.10	# Accumulate the statistics.
915 :			$retVal->Accumulate($result);
916 :			}
917 :			# Add the duration of the load to the statistical object.
918 :			$retVal->Add('duration', gettimeofday - $startTime);
919 :			# Return the accumulated statistics.
920 :			return $retVal;
921 :	parrello	1.1	}
922 :
923 :	parrello	1.23
924 :	parrello	1.1	=head3 GetTableNames
925 :
926 :	parrello	1.18	C<< my @names = $erdb->GetTableNames; >>
927 :	parrello	1.1
928 :			Return a list of the relations required to implement this database.
929 :
930 :			=cut
931 :
932 :			sub GetTableNames {
933 :	parrello	1.10	# Get the parameters.
934 :			my ($self) = @_;
935 :			# Get the relation list from the metadata.
936 :			my $relationTable = $self->{_metaData}->{RelationTable};
937 :			# Return the relation names.
938 :			return keys %{$relationTable};
939 :	parrello	1.1	}
940 :
941 :			=head3 GetEntityTypes
942 :
943 :	parrello	1.18	C<< my @names = $erdb->GetEntityTypes; >>
944 :	parrello	1.1
945 :			Return a list of the entity type names.
946 :
947 :			=cut
948 :
949 :			sub GetEntityTypes {
950 :	parrello	1.10	# Get the database object.
951 :			my ($self) = @_;
952 :			# Get the entity list from the metadata object.
953 :			my $entityList = $self->{_metaData}->{Entities};
954 :			# Return the list of entity names in alphabetical order.
955 :			return sort keys %{$entityList};
956 :	parrello	1.1	}
957 :
958 :	parrello	1.20	=head3 IsEntity
959 :
960 :			C<< my $flag = $erdb->IsEntity($entityName); >>
961 :
962 :			Return TRUE if the parameter is an entity name, else FALSE.
963 :
964 :			=over 4
965 :
966 :			=item entityName
967 :
968 :			Object name to be tested.
969 :
970 :			=item RETURN
971 :
972 :			Returns TRUE if the specified string is an entity name, else FALSE.
973 :
974 :			=back
975 :
976 :			=cut
977 :
978 :			sub IsEntity {
979 :			# Get the parameters.
980 :			my ($self, $entityName) = @_;
981 :			# Test to see if it's an entity.
982 :			return exists $self->{_metaData}->{Entities}->{$entityName};
983 :			}
984 :
985 :	parrello	1.1	=head3 Get
986 :
987 :	parrello	1.45	C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
988 :	parrello	1.1
989 :			This method returns a query object for entities of a specified type using a specified filter.
990 :			The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
991 :			field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
992 :			following call requests all B<Genome> objects for the genus specified in the variable
993 :			$genus.
994 :
995 :	parrello	1.45	C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
996 :	parrello	1.1
997 :			The WHERE clause contains a single question mark, so there is a single additional
998 :			parameter representing the parameter value. It would also be possible to code
999 :
1000 :	parrello	1.18	C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1001 :	parrello	1.1
1002 :			however, this version of the call would generate a syntax error if there were any quote
1003 :			characters inside the variable C<$genus>.
1004 :
1005 :			The use of the strange parenthesized notation for field names enables us to distinguish
1006 :			hyphens contained within field names from minus signs that participate in the computation
1007 :			of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1008 :
1009 :			It is possible to specify multiple entity and relationship names in order to retrieve more than
1010 :			one object's data at the same time, which allows highly complex joined queries. For example,
1011 :
1012 :	parrello	1.45	C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1013 :	parrello	1.1
1014 :			If multiple names are specified, then the query processor will automatically determine a
1015 :			join path between the entities and relationships. The algorithm used is very simplistic.
1016 :	parrello	1.39	In particular, if a relationship is recursive, the path is determined by the order in which
1017 :			the entity and the relationship appear. For example, consider a recursive relationship
1018 :			B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1019 :	parrello	1.1	coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1020 :			the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1021 :
1022 :	parrello	1.39	If an entity or relationship is mentioned twice, the name for the second occurrence will
1023 :			be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1024 :			for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1025 :			B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1026 :			the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1027 :
1028 :	parrello	1.1	=over 4
1029 :
1030 :			=item objectNames
1031 :
1032 :			List containing the names of the entity and relationship objects to be retrieved.
1033 :
1034 :			=item filterClause
1035 :
1036 :			WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1037 :			be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1038 :			specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1039 :			in the filter clause should be added to the parameter list as additional parameters. The
1040 :			fields in a filter clause can come from primary entity relations, relationship relations,
1041 :			or secondary entity relations; however, all of the entities and relationships involved must
1042 :			be included in the list of object names.
1043 :
1044 :			The filter clause can also specify a sort order. To do this, simply follow the filter string
1045 :			with an ORDER BY clause. For example, the following filter string gets all genomes for a
1046 :			particular genus and sorts them by species name.
1047 :
1048 :			C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1049 :
1050 :	parrello	1.30	Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1051 :			be processed. The idea is to make it less likely to find the verb by accident.
1052 :
1053 :	parrello	1.1	The rules for field references in a sort order are the same as those for field references in the
1054 :			filter clause in general; however, odd things may happen if a sort field is from a secondary
1055 :			relation.
1056 :
1057 :	parrello	1.39	Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1058 :			be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1059 :			a positive number. So, for example
1060 :
1061 :			C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1062 :
1063 :			will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1064 :			required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1065 :			use
1066 :
1067 :			C<< "LIMIT 10" >>
1068 :
1069 :	parrello	1.45	=item params
1070 :	parrello	1.1
1071 :	parrello	1.45	Reference to a list of parameter values to be substituted into the filter clause.
1072 :	parrello	1.1
1073 :			=item RETURN
1074 :
1075 :			Returns a B<DBQuery> that can be used to iterate through all of the results.
1076 :
1077 :			=back
1078 :
1079 :			=cut
1080 :
1081 :			sub Get {
1082 :	parrello	1.10	# Get the parameters.
1083 :	parrello	1.45	my ($self, $objectNames, $filterClause, $params) = @_;
1084 :			# Process the SQL stuff.
1085 :			my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1086 :			$self->_SetupSQL($objectNames, $filterClause);
1087 :			# Create the query.
1088 :			my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1089 :			".* $suffix";
1090 :			my $sth = $self->_GetStatementHandle($command, $params);
1091 :	parrello	1.39	# Now we create the relation map, which enables DBQuery to determine the order, name
1092 :			# and mapped name for each object in the query.
1093 :			my @relationMap = ();
1094 :	parrello	1.45	for my $mappedName (@{$mappedNameListRef}) {
1095 :			push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1096 :	parrello	1.39	}
1097 :	parrello	1.10	# Return the statement object.
1098 :	parrello	1.39	my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1099 :	parrello	1.10	return $retVal;
1100 :	parrello	1.1	}
1101 :
1102 :	parrello	1.45	=head3 GetFlat
1103 :
1104 :			C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1105 :
1106 :			This is a variation of L</GetAll> that asks for only a single field per record and
1107 :			returns a single flattened list.
1108 :
1109 :			=over 4
1110 :
1111 :			=item objectNames
1112 :
1113 :			List containing the names of the entity and relationship objects to be retrieved.
1114 :
1115 :			=item filterClause
1116 :
1117 :			WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1118 :			be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1119 :			B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1120 :			parameter list as additional parameters. The fields in a filter clause can come from primary
1121 :			entity relations, relationship relations, or secondary entity relations; however, all of the
1122 :			entities and relationships involved must be included in the list of object names.
1123 :
1124 :			=item parameterList
1125 :
1126 :			List of the parameters to be substituted in for the parameters marks in the filter clause.
1127 :
1128 :			=item field
1129 :
1130 :			Name of the field to be used to get the elements of the list returned.
1131 :
1132 :			=item RETURN
1133 :
1134 :			Returns a list of values.
1135 :
1136 :			=back
1137 :
1138 :			=cut
1139 :			#: Return Type @;
1140 :			sub GetFlat {
1141 :			# Get the parameters.
1142 :			my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1143 :			# Construct the query.
1144 :			my $query = $self->Get($objectNames, $filterClause, $parameterList);
1145 :			# Create the result list.
1146 :			my @retVal = ();
1147 :			# Loop through the records, adding the field values found to the result list.
1148 :			while (my $row = $query->Fetch()) {
1149 :			push @retVal, $row->Value($field);
1150 :			}
1151 :			# Return the list created.
1152 :			return @retVal;
1153 :			}
1154 :
1155 :	parrello	1.32	=head3 Delete
1156 :
1157 :			C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1158 :
1159 :			Delete an entity instance from the database. The instance is deleted along with all entity and
1160 :			relationship instances dependent on it. The idea of dependence here is recursive. An object is
1161 :			always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1162 :			relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1163 :			dependent relationship.
1164 :
1165 :			=over 4
1166 :
1167 :			=item entityName
1168 :
1169 :			Name of the entity type for the instance being deleted.
1170 :
1171 :			=item objectID
1172 :
1173 :			ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1174 :			then it is presumed to by a LIKE pattern.
1175 :
1176 :			=item testFlag
1177 :
1178 :			If TRUE, the delete statements will be traced without being executed.
1179 :
1180 :			=item RETURN
1181 :
1182 :			Returns a statistics object indicating how many records of each particular table were
1183 :			deleted.
1184 :
1185 :			=back
1186 :
1187 :			=cut
1188 :			#: Return Type $%;
1189 :			sub Delete {
1190 :			# Get the parameters.
1191 :			my ($self, $entityName, $objectID, $testFlag) = @_;
1192 :			# Declare the return variable.
1193 :			my $retVal = Stats->new();
1194 :			# Get the DBKernel object.
1195 :			my $db = $self->{_dbh};
1196 :			# We're going to generate all the paths branching out from the starting entity. One of
1197 :			# the things we have to be careful about is preventing loops. We'll use a hash to
1198 :			# determine if we've hit a loop.
1199 :			my %alreadyFound = ();
1200 :	parrello	1.33	# These next lists will serve as our result stack. We start by pushing object lists onto
1201 :	parrello	1.32	# the stack, and then popping them off to do the deletes. This means the deletes will
1202 :			# start with the longer paths before getting to the shorter ones. That, in turn, makes
1203 :			# sure we don't delete records that might be needed to forge relationships back to the
1204 :	parrello	1.33	# original item. We have two lists-- one for TO-relationships, and one for
1205 :			# FROM-relationships and entities.
1206 :			my @fromPathList = ();
1207 :			my @toPathList = ();
1208 :	parrello	1.32	# This final hash is used to remember what work still needs to be done. We push paths
1209 :			# onto the list, then pop them off to extend the paths. We prime it with the starting
1210 :			# point. Note that we will work hard to insure that the last item on a path in the
1211 :			# TODO list is always an entity.
1212 :			my @todoList = ([$entityName]);
1213 :			while (@todoList) {
1214 :			# Get the current path.
1215 :			my $current = pop @todoList;
1216 :			# Copy it into a list.
1217 :			my @stackedPath = @{$current};
1218 :			# Pull off the last item on the path. It will always be an entity.
1219 :			my $entityName = pop @stackedPath;
1220 :			# Add it to the alreadyFound list.
1221 :			$alreadyFound{$entityName} = 1;
1222 :			# Get the entity data.
1223 :			my $entityData = $self->_GetStructure($entityName);
1224 :			# The first task is to loop through the entity's relation. A DELETE command will
1225 :			# be needed for each of them.
1226 :			my $relations = $entityData->{Relations};
1227 :			for my $relation (keys %{$relations}) {
1228 :			my @augmentedList = (@stackedPath, $relation);
1229 :	parrello	1.33	push @fromPathList, \@augmentedList;
1230 :	parrello	1.32	}
1231 :			# Now we need to look for relationships connected to this entity.
1232 :			my $relationshipList = $self->{_metaData}->{Relationships};
1233 :			for my $relationshipName (keys %{$relationshipList}) {
1234 :			my $relationship = $relationshipList->{$relationshipName};
1235 :			# Check the FROM field. We're only interested if it's us.
1236 :			if ($relationship->{from} eq $entityName) {
1237 :			# Add the path to this relationship.
1238 :			my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1239 :	parrello	1.33	push @fromPathList, \@augmentedList;
1240 :	parrello	1.32	# Check the arity. If it's MM we're done. If it's 1M
1241 :			# and the target hasn't been seen yet, we want to
1242 :			# stack the entity for future processing.
1243 :			if ($relationship->{arity} eq '1M') {
1244 :			my $toEntity = $relationship->{to};
1245 :			if (! exists $alreadyFound{$toEntity}) {
1246 :			# Here we have a new entity that's dependent on
1247 :			# the current entity, so we need to stack it.
1248 :			my @stackList = (@augmentedList, $toEntity);
1249 :	parrello	1.33	push @fromPathList, \@stackList;
1250 :	parrello	1.34	} else {
1251 :			Trace("$toEntity ignored because it occurred previously.") if T(4);
1252 :	parrello	1.32	}
1253 :			}
1254 :			}
1255 :			# Now check the TO field. In this case only the relationship needs
1256 :	parrello	1.33	# deletion.
1257 :	parrello	1.32	if ($relationship->{to} eq $entityName) {
1258 :			my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1259 :	parrello	1.33	push @toPathList, \@augmentedList;
1260 :	parrello	1.32	}
1261 :			}
1262 :			}
1263 :			# Create the first qualifier for the WHERE clause. This selects the
1264 :			# keys of the primary entity records to be deleted. When we're deleting
1265 :			# from a dependent table, we construct a join page from the first qualifier
1266 :			# to the table containing the dependent records to delete.
1267 :			my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1268 :	parrello	1.33	# We need to make two passes. The first is through the to-list, and
1269 :			# the second through the from-list. The from-list is second because
1270 :			# the to-list may need to pass through some of the entities the
1271 :			# from-list would delete.
1272 :			my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1273 :			# Now it's time to do the deletes. We do it in two passes.
1274 :			for my $keyName ('to_link', 'from_link') {
1275 :			# Get the list for this key.
1276 :			my @pathList = @{$stackList{$keyName}};
1277 :	parrello	1.34	Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1278 :	parrello	1.33	# Loop through this list.
1279 :			while (my $path = pop @pathList) {
1280 :			# Get the table whose rows are to be deleted.
1281 :			my @pathTables = @{$path};
1282 :	parrello	1.37	# Start the DELETE statement. We need to call DBKernel because the
1283 :			# syntax of a DELETE-USING varies among DBMSs.
1284 :	parrello	1.33	my $target = $pathTables[$#pathTables];
1285 :	parrello	1.37	my $stmt = $db->SetUsing(@pathTables);
1286 :	parrello	1.33	# Now start the WHERE. The first thing is the ID field from the starting table. That
1287 :			# starting table will either be the entity relation or one of the entity's
1288 :			# sub-relations.
1289 :			$stmt .= " WHERE $pathTables[0].id $qualifier";
1290 :			# Now we run through the remaining entities in the path, connecting them up.
1291 :			for (my $i = 1; $i <= $#pathTables; $i += 2) {
1292 :			# Connect the current relationship to the preceding entity.
1293 :			my ($entity, $rel) = @pathTables[$i-1,$i];
1294 :			# The style of connection depends on the direction of the relationship.
1295 :	parrello	1.35	$stmt .= " AND $entity.id = $rel.$keyName";
1296 :	parrello	1.32	if ($i + 1 <= $#pathTables) {
1297 :			# Here there's a next entity, so connect that to the relationship's
1298 :			# to-link.
1299 :			my $entity2 = $pathTables[$i+1];
1300 :	parrello	1.35	$stmt .= " AND $rel.to_link = $entity2.id";
1301 :	parrello	1.32	}
1302 :			}
1303 :	parrello	1.33	# Now we have our desired DELETE statement.
1304 :			if ($testFlag) {
1305 :			# Here the user wants to trace without executing.
1306 :			Trace($stmt) if T(0);
1307 :			} else {
1308 :			# Here we can delete. Note that the SQL method dies with a confessing
1309 :			# if an error occurs, so we just go ahead and do it.
1310 :	parrello	1.36	Trace("Executing delete from $target using '$objectID'.") if T(3);
1311 :			my $rv = $db->SQL($stmt, 0, $objectID);
1312 :	parrello	1.33	# Accumulate the statistics for this delete. The only rows deleted
1313 :			# are from the target table, so we use its name to record the
1314 :			# statistic.
1315 :			$retVal->Add($target, $rv);
1316 :			}
1317 :	parrello	1.32	}
1318 :			}
1319 :			# Return the result.
1320 :			return $retVal;
1321 :			}
1322 :
1323 :	parrello	1.6	=head3 GetList
1324 :
1325 :	parrello	1.45	C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1326 :	parrello	1.6
1327 :			Return a list of object descriptors for the specified objects as determined by the
1328 :			specified filter clause.
1329 :
1330 :			This method is essentially the same as L</Get> except it returns a list of objects rather
1331 :	parrello	1.7	than a query object that can be used to get the results one record at a time.
1332 :	parrello	1.6
1333 :			=over 4
1334 :
1335 :			=item objectNames
1336 :
1337 :			List containing the names of the entity and relationship objects to be retrieved.
1338 :
1339 :			=item filterClause
1340 :
1341 :			WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1342 :			be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1343 :			specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1344 :			in the filter clause should be added to the parameter list as additional parameters. The
1345 :			fields in a filter clause can come from primary entity relations, relationship relations,
1346 :			or secondary entity relations; however, all of the entities and relationships involved must
1347 :			be included in the list of object names.
1348 :
1349 :			The filter clause can also specify a sort order. To do this, simply follow the filter string
1350 :			with an ORDER BY clause. For example, the following filter string gets all genomes for a
1351 :			particular genus and sorts them by species name.
1352 :
1353 :			C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1354 :
1355 :			The rules for field references in a sort order are the same as those for field references in the
1356 :			filter clause in general; however, odd things may happen if a sort field is from a secondary
1357 :			relation.
1358 :
1359 :	parrello	1.45	=item params
1360 :	parrello	1.6
1361 :	parrello	1.45	Reference to a list of parameter values to be substituted into the filter clause.
1362 :	parrello	1.6
1363 :			=item RETURN
1364 :
1365 :			Returns a list of B<DBObject>s that satisfy the query conditions.
1366 :
1367 :			=back
1368 :
1369 :			=cut
1370 :			#: Return Type @%
1371 :			sub GetList {
1372 :			# Get the parameters.
1373 :	parrello	1.45	my ($self, $objectNames, $filterClause, $params) = @_;
1374 :	parrello	1.10	# Declare the return variable.
1375 :			my @retVal = ();
1376 :			# Perform the query.
1377 :	parrello	1.45	my $query = $self->Get($objectNames, $filterClause, $params);
1378 :	parrello	1.10	# Loop through the results.
1379 :			while (my $object = $query->Fetch) {
1380 :			push @retVal, $object;
1381 :			}
1382 :	parrello	1.6	# Return the result.
1383 :			return @retVal;
1384 :			}
1385 :
1386 :	parrello	1.45	=head3 GetCount
1387 :
1388 :			C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1389 :
1390 :			Return the number of rows found by a specified query. This method would
1391 :			normally be used to count the records in a single table. For example, in a
1392 :			genetics database
1393 :
1394 :			my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1395 :
1396 :			would return the number of genomes for the genus I<homo>. It is conceivable, however,
1397 :			to use it to return records based on a join. For example,
1398 :
1399 :	parrello	1.47	my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1400 :	parrello	1.45	['homo %']);
1401 :
1402 :			would return the number of features for genomes in the genus I<homo>. Note that
1403 :			only the rows from the first table are counted. If the above command were
1404 :
1405 :			my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1406 :			['homo %']);
1407 :
1408 :			it would return the number of genomes, not the number of genome/feature pairs.
1409 :
1410 :			=over 4
1411 :
1412 :			=item objectNames
1413 :
1414 :			Reference to a list of the objects (entities and relationships) included in the
1415 :			query.
1416 :
1417 :			=item filter
1418 :
1419 :			A filter clause for restricting the query. The rules are the same as for the L</Get>
1420 :			method.
1421 :
1422 :			=item params
1423 :
1424 :			Reference to a list of the parameter values to be substituted for the parameter marks
1425 :			in the filter.
1426 :
1427 :			=item RETURN
1428 :
1429 :			Returns a count of the number of records in the first table that would satisfy
1430 :			the query.
1431 :
1432 :			=back
1433 :
1434 :			=cut
1435 :
1436 :			sub GetCount {
1437 :			# Get the parameters.
1438 :			my ($self, $objectNames, $filter, $params) = @_;
1439 :			# Declare the return variable.
1440 :			my $retVal;
1441 :	parrello	1.47	# Find out if we're counting an entity or a relationship.
1442 :			my $countedField;
1443 :			if ($self->IsEntity($objectNames->[0])) {
1444 :			$countedField = "id";
1445 :			} else {
1446 :			# For a relationship we count the to-link because it's usually more
1447 :			# numerous. Note we're automatically converting to the SQL form
1448 :			# of the field name (to_link vs. to-link).
1449 :			$countedField = "to_link";
1450 :			}
1451 :	parrello	1.45	# Create the SQL command suffix to get the desired records.
1452 :			my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
1453 :			$filter);
1454 :			# Prefix it with text telling it we want a record count.
1455 :			my $firstObject = $mappedNameListRef->[0];
1456 :	parrello	1.47	my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
1457 :	parrello	1.45	# Prepare and execute the command.
1458 :			my $sth = $self->_GetStatementHandle($command, $params);
1459 :			# Get the count value.
1460 :			($retVal) = $sth->fetchrow_array();
1461 :			# Check for a problem.
1462 :			if (! defined($retVal)) {
1463 :			if ($sth->err) {
1464 :			# Here we had an SQL error.
1465 :			Confess("Error retrieving row count: " . $sth->errstr());
1466 :			} else {
1467 :			# Here we have no result.
1468 :			Confess("No result attempting to retrieve row count.");
1469 :			}
1470 :			}
1471 :			# Return the result.
1472 :			return $retVal;
1473 :			}
1474 :
1475 :	parrello	1.1	=head3 ComputeObjectSentence
1476 :
1477 :	parrello	1.18	C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
1478 :	parrello	1.1
1479 :			Check an object name, and if it is a relationship convert it to a relationship sentence.
1480 :
1481 :			=over 4
1482 :
1483 :			=item objectName
1484 :
1485 :			Name of the entity or relationship.
1486 :
1487 :			=item RETURN
1488 :
1489 :			Returns a string containing the entity name or a relationship sentence.
1490 :
1491 :			=back
1492 :
1493 :			=cut
1494 :
1495 :			sub ComputeObjectSentence {
1496 :	parrello	1.10	# Get the parameters.
1497 :			my ($self, $objectName) = @_;
1498 :			# Set the default return value.
1499 :			my $retVal = $objectName;
1500 :			# Look for the object as a relationship.
1501 :			my $relTable = $self->{_metaData}->{Relationships};
1502 :			if (exists $relTable->{$objectName}) {
1503 :			# Get the relationship sentence.
1504 :			$retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
1505 :			}
1506 :			# Return the result.
1507 :			return $retVal;
1508 :	parrello	1.1	}
1509 :
1510 :			=head3 DumpRelations
1511 :
1512 :	parrello	1.18	C<< $erdb->DumpRelations($outputDirectory); >>
1513 :	parrello	1.1
1514 :			Write the contents of all the relations to tab-delimited files in the specified directory.
1515 :			Each file will have the same name as the relation dumped, with an extension of DTX.
1516 :
1517 :			=over 4
1518 :
1519 :			=item outputDirectory
1520 :
1521 :			Name of the directory into which the relation files should be dumped.
1522 :
1523 :			=back
1524 :
1525 :			=cut
1526 :
1527 :			sub DumpRelations {
1528 :	parrello	1.10	# Get the parameters.
1529 :			my ($self, $outputDirectory) = @_;
1530 :			# Now we need to run through all the relations. First, we loop through the entities.
1531 :			my $metaData = $self->{_metaData};
1532 :			my $entities = $metaData->{Entities};
1533 :			for my $entityName (keys %{$entities}) {
1534 :			my $entityStructure = $entities->{$entityName};
1535 :			# Get the entity's relations.
1536 :			my $relationList = $entityStructure->{Relations};
1537 :			# Loop through the relations, dumping them.
1538 :			for my $relationName (keys %{$relationList}) {
1539 :			my $relation = $relationList->{$relationName};
1540 :			$self->_DumpRelation($outputDirectory, $relationName, $relation);
1541 :			}
1542 :			}
1543 :			# Next, we loop through the relationships.
1544 :			my $relationships = $metaData->{Relationships};
1545 :			for my $relationshipName (keys %{$relationships}) {
1546 :			my $relationshipStructure = $relationships->{$relationshipName};
1547 :			# Dump this relationship's relation.
1548 :			$self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
1549 :			}
1550 :	parrello	1.1	}
1551 :
1552 :	parrello	1.51	=head3 InsertValue
1553 :
1554 :			C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
1555 :
1556 :			This method will insert a new value into the database. The value must be one
1557 :			associated with a secondary relation, since primary values cannot be inserted:
1558 :			they occur exactly once. Secondary values, on the other hand, can be missing
1559 :			or multiply-occurring.
1560 :
1561 :			=over 4
1562 :
1563 :			=item entityID
1564 :
1565 :			ID of the object that is to receive the new value.
1566 :
1567 :			=item fieldName
1568 :
1569 :			Field name for the new value-- this includes the entity name, since
1570 :			field names are of the format I<objectName>C<(>I<fieldName>C<)>.
1571 :
1572 :			=item value
1573 :
1574 :			New value to be put in the field.
1575 :
1576 :			=back
1577 :
1578 :			=cut
1579 :
1580 :			sub InsertValue {
1581 :			# Get the parameters.
1582 :			my ($self, $entityID, $fieldName, $value) = @_;
1583 :			# Parse the entity name and the real field name.
1584 :			if ($fieldName =~ /^([^(]+)$([^)]+)$/) {
1585 :			my $entityName = $1;
1586 :			my $fieldTitle = $2;
1587 :			# Get its descriptor.
1588 :			if (!$self->IsEntity($entityName)) {
1589 :			Confess("$entityName is not a valid entity.");
1590 :			} else {
1591 :			my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1592 :			# Find the relation containing this field.
1593 :			my $fieldHash = $entityData->{Fields};
1594 :	parrello	1.52	if (! exists $fieldHash->{$fieldTitle}) {
1595 :	parrello	1.51	Confess("$fieldTitle not found in $entityName.");
1596 :			} else {
1597 :			my $relation = $fieldHash->{$fieldTitle}->{relation};
1598 :			if ($relation eq $entityName) {
1599 :			Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
1600 :			} else {
1601 :			# Now we can create an INSERT statement.
1602 :			my $dbh = $self->{_dbh};
1603 :			my $fixedName = _FixName($fieldTitle);
1604 :	parrello	1.53	my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
1605 :	parrello	1.51	# Execute the command.
1606 :			$dbh->SQL($statement, 0, $entityID, $value);
1607 :			}
1608 :			}
1609 :			}
1610 :			} else {
1611 :			Confess("$fieldName is not a valid field name.");
1612 :			}
1613 :			}
1614 :
1615 :	parrello	1.1	=head3 InsertObject
1616 :
1617 :	parrello	1.18	C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
1618 :	parrello	1.1
1619 :			Insert an object into the database. The object is defined by a type name and then a hash
1620 :			of field names to values. Field values in the primary relation are represented by scalars.
1621 :			(Note that for relationships, the primary relation is the B<only> relation.)
1622 :			Field values for the other relations comprising the entity are always list references. For
1623 :			example, the following line inserts an inactive PEG feature named C<fig\|188.1.peg.1> with aliases
1624 :			C<ZP_00210270.1> and C<gi\|46206278>.
1625 :
1626 :	parrello	1.18	C<< $erdb->InsertObject('Feature', { id => 'fig\|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi\|46206278']}); >>
1627 :	parrello	1.1
1628 :			The next statement inserts a C<HasProperty> relationship between feature C<fig\|158879.1.peg.1> and
1629 :			property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
1630 :
1631 :	parrello	1.57	C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig\|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1632 :	parrello	1.1
1633 :			=over 4
1634 :
1635 :			=item newObjectType
1636 :
1637 :			Type name of the object to insert.
1638 :
1639 :			=item fieldHash
1640 :
1641 :			Hash of field names to values.
1642 :
1643 :			=item RETURN
1644 :
1645 :			Returns 1 if successful, 0 if an error occurred.
1646 :
1647 :			=back
1648 :
1649 :			=cut
1650 :
1651 :			sub InsertObject {
1652 :	parrello	1.10	# Get the parameters.
1653 :			my ($self, $newObjectType, $fieldHash) = @_;
1654 :			# Denote that so far we appear successful.
1655 :			my $retVal = 1;
1656 :			# Get the database handle.
1657 :			my $dbh = $self->{_dbh};
1658 :			# Get the relation list.
1659 :			my $relationTable = $self->_GetRelationTable($newObjectType);
1660 :			# Loop through the relations. We'll build insert statements for each one. If a relation is
1661 :			# secondary, we may end up generating multiple insert statements. If an error occurs, we
1662 :			# stop the loop.
1663 :			my @relationList = keys %{$relationTable};
1664 :			for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
1665 :			my $relationName = $relationList[$i];
1666 :			my $relationDefinition = $relationTable->{$relationName};
1667 :			# Get the relation's fields. For each field we will collect a value in the corresponding
1668 :			# position of the @valueList array. If one of the fields is missing, we will add it to the
1669 :			# @missing list.
1670 :			my @fieldList = @{$relationDefinition->{Fields}};
1671 :			my @fieldNameList = ();
1672 :			my @valueList = ();
1673 :			my @missing = ();
1674 :			my $recordCount = 1;
1675 :			for my $fieldDescriptor (@fieldList) {
1676 :			# Get the field name and save it. Note we need to fix it up so the hyphens
1677 :			# are converted to underscores.
1678 :			my $fieldName = $fieldDescriptor->{name};
1679 :			push @fieldNameList, _FixName($fieldName);
1680 :			# Look for the named field in the incoming structure. Note that we are looking
1681 :			# for the real field name, not the fixed-up one!
1682 :			if (exists $fieldHash->{$fieldName}) {
1683 :			# Here we found the field. Stash it in the value list.
1684 :			my $value = $fieldHash->{$fieldName};
1685 :			push @valueList, $value;
1686 :			# If the value is a list, we may need to increment the record count.
1687 :			if (ref $value eq "ARRAY") {
1688 :			my $thisCount = @{$value};
1689 :			if ($recordCount == 1) {
1690 :			# Here we have our first list, so we save its count.
1691 :			$recordCount = $thisCount;
1692 :			} elsif ($recordCount != $thisCount) {
1693 :			# Here we have a second list, so its length has to match the
1694 :			# previous lists.
1695 :			Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
1696 :			$retVal = 0;
1697 :			}
1698 :			}
1699 :			} else {
1700 :			# Here the field is not present. Flag it as missing.
1701 :			push @missing, $fieldName;
1702 :			}
1703 :			}
1704 :			# If we are the primary relation, add the new-record flag.
1705 :			if ($relationName eq $newObjectType) {
1706 :			push @valueList, 1;
1707 :			push @fieldNameList, "new_record";
1708 :			}
1709 :			# Only proceed if there are no missing fields.
1710 :			if (@missing > 0) {
1711 :			Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
1712 :			join(' ', @missing)) if T(1);
1713 :			} else {
1714 :			# Build the INSERT statement.
1715 :			my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
1716 :			") VALUES (";
1717 :			# Create a marker list of the proper size and put it in the statement.
1718 :			my @markers = ();
1719 :			while (@markers < @fieldNameList) { push @markers, '?'; }
1720 :			$statement .= join(', ', @markers) . ")";
1721 :			# We have the insert statement, so prepare it.
1722 :			my $sth = $dbh->prepare_command($statement);
1723 :			Trace("Insert statement prepared: $statement") if T(3);
1724 :			# Now we loop through the values. If a value is scalar, we use it unmodified. If it's
1725 :			# a list, we use the current element. The values are stored in the @parameterList array.
1726 :			my $done = 0;
1727 :			for (my $i = 0; $i < $recordCount; $i++) {
1728 :			# Clear the parameter list array.
1729 :			my @parameterList = ();
1730 :			# Loop through the values.
1731 :			for my $value (@valueList) {
1732 :			# Check to see if this is a scalar value.
1733 :			if (ref $value eq "ARRAY") {
1734 :			# Here we have a list value. Pull the current entry.
1735 :			push @parameterList, $value->[$i];
1736 :			} else {
1737 :			# Here we have a scalar value. Use it unmodified.
1738 :			push @parameterList, $value;
1739 :			}
1740 :			}
1741 :			# Execute the INSERT statement with the specified parameter list.
1742 :			$retVal = $sth->execute(@parameterList);
1743 :			if (!$retVal) {
1744 :			my $errorString = $sth->errstr();
1745 :			Trace("Insert error: $errorString.") if T(0);
1746 :			}
1747 :			}
1748 :			}
1749 :			}
1750 :			# Return the success indicator.
1751 :			return $retVal;
1752 :	parrello	1.1	}
1753 :
1754 :			=head3 LoadTable
1755 :
1756 :	parrello	1.18	C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
1757 :	parrello	1.1
1758 :	parrello	1.9	Load data from a tab-delimited file into a specified table, optionally re-creating the table
1759 :			first.
1760 :	parrello	1.1
1761 :			=over 4
1762 :
1763 :			=item fileName
1764 :
1765 :			Name of the file from which the table data should be loaded.
1766 :
1767 :			=item relationName
1768 :
1769 :			Name of the relation to be loaded. This is the same as the table name.
1770 :
1771 :			=item truncateFlag
1772 :
1773 :			TRUE if the table should be dropped and re-created, else FALSE
1774 :
1775 :			=item RETURN
1776 :
1777 :	parrello	1.28	Returns a statistical object containing a list of the error messages.
1778 :	parrello	1.1
1779 :			=back
1780 :
1781 :			=cut
1782 :			sub LoadTable {
1783 :	parrello	1.10	# Get the parameters.
1784 :			my ($self, $fileName, $relationName, $truncateFlag) = @_;
1785 :			# Create the statistical return object.
1786 :			my $retVal = _GetLoadStats();
1787 :			# Trace the fact of the load.
1788 :			Trace("Loading table $relationName from $fileName") if T(2);
1789 :			# Get the database handle.
1790 :			my $dbh = $self->{_dbh};
1791 :	parrello	1.22	# Get the input file size.
1792 :			my $fileSize = -s $fileName;
1793 :	parrello	1.10	# Get the relation data.
1794 :			my $relation = $self->_FindRelation($relationName);
1795 :			# Check the truncation flag.
1796 :			if ($truncateFlag) {
1797 :			Trace("Creating table $relationName") if T(2);
1798 :	parrello	1.19	# Compute the row count estimate. We take the size of the load file,
1799 :			# divide it by the estimated row size, and then multiply by 1.5 to
1800 :			# leave extra room. We postulate a minimum row count of 1000 to
1801 :			# prevent problems with incoming empty load files.
1802 :			my $rowSize = $self->EstimateRowSize($relationName);
1803 :			my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
1804 :	parrello	1.10	# Re-create the table without its index.
1805 :	parrello	1.19	$self->CreateTable($relationName, 0, $estimate);
1806 :	parrello	1.10	# If this is a pre-index DBMS, create the index here.
1807 :			if ($dbh->{_preIndex}) {
1808 :			eval {
1809 :			$self->CreateIndex($relationName);
1810 :			};
1811 :			if ($@) {
1812 :			$retVal->AddMessage($@);
1813 :			}
1814 :			}
1815 :			}
1816 :	parrello	1.3	# Load the table.
1817 :	parrello	1.10	my $rv;
1818 :			eval {
1819 :	parrello	1.20	$rv = $dbh->load_table(file => $fileName, tbl => $relationName);
1820 :	parrello	1.10	};
1821 :			if (!defined $rv) {
1822 :	parrello	1.3	$retVal->AddMessage($@) if ($@);
1823 :	parrello	1.20	$retVal->AddMessage("Table load failed for $relationName using $fileName.");
1824 :	parrello	1.10	Trace("Table load failed for $relationName.") if T(1);
1825 :			} else {
1826 :	parrello	1.22	# Here we successfully loaded the table.
1827 :			$retVal->Add("tables");
1828 :			my $size = -s $fileName;
1829 :			Trace("$size bytes loaded into $relationName.") if T(2);
1830 :	parrello	1.10	# If we're rebuilding, we need to create the table indexes.
1831 :			if ($truncateFlag && ! $dbh->{_preIndex}) {
1832 :			eval {
1833 :			$self->CreateIndex($relationName);
1834 :			};
1835 :			if ($@) {
1836 :			$retVal->AddMessage($@);
1837 :			}
1838 :			}
1839 :			}
1840 :	parrello	1.20	# Analyze the table to improve performance.
1841 :	parrello	1.61	Trace("Analyzing and compacting $relationName.") if T(3);
1842 :	olson	1.16	$dbh->vacuum_it($relationName);
1843 :	parrello	1.61	Trace("$relationName load completed.") if T(3);
1844 :	parrello	1.10	# Return the statistics.
1845 :			return $retVal;
1846 :	parrello	1.1	}
1847 :
1848 :			=head3 GenerateEntity
1849 :
1850 :	parrello	1.18	C<< my $fieldHash = $erdb->GenerateEntity($id, $type, \%values); >>
1851 :	parrello	1.1
1852 :			Generate the data for a new entity instance. This method creates a field hash suitable for
1853 :			passing as a parameter to L</InsertObject>. The ID is specified by the callr, but the rest
1854 :			of the fields are generated using information in the database schema.
1855 :
1856 :			Each data type has a default algorithm for generating random test data. This can be overridden
1857 :			by including a B<DataGen> element in the field. If this happens, the content of the element is
1858 :			executed as a PERL program in the context of this module. The element may make use of a C<$this>
1859 :			variable which contains the field hash as it has been built up to the current point. If any
1860 :			fields are dependent on other fields, the C<pass> attribute can be used to control the order
1861 :			in which the fields are generated. A field with a high data pass number will be generated after
1862 :			a field with a lower one. If any external values are needed, they should be passed in via the
1863 :			optional third parameter, which will be available to the data generation script under the name
1864 :			C<$value>. Several useful utility methods are provided for generating random values, including
1865 :			L</IntGen>, L</StringGen>, L</FloatGen>, and L</DateGen>. Note that dates are stored and generated
1866 :			in the form of a timestamp number rather than a string.
1867 :
1868 :			=over 4
1869 :
1870 :			=item id
1871 :
1872 :			ID to assign to the new entity.
1873 :
1874 :			=item type
1875 :
1876 :			Type name for the new entity.
1877 :
1878 :			=item values
1879 :
1880 :			Hash containing additional values that might be needed by the data generation methods (optional).
1881 :
1882 :			=back
1883 :
1884 :			=cut
1885 :
1886 :			sub GenerateEntity {
1887 :	parrello	1.10	# Get the parameters.
1888 :			my ($self, $id, $type, $values) = @_;
1889 :			# Create the return hash.
1890 :			my $this = { id => $id };
1891 :			# Get the metadata structure.
1892 :			my $metadata = $self->{_metaData};
1893 :			# Get this entity's list of fields.
1894 :			if (!exists $metadata->{Entities}->{$type}) {
1895 :			Confess("Unrecognized entity type $type in GenerateEntity.");
1896 :			} else {
1897 :			my $entity = $metadata->{Entities}->{$type};
1898 :			my $fields = $entity->{Fields};
1899 :			# Generate data from the fields.
1900 :			_GenerateFields($this, $fields, $type, $values);
1901 :			}
1902 :			# Return the hash created.
1903 :			return $this;
1904 :	parrello	1.1	}
1905 :
1906 :	parrello	1.6	=head3 GetEntity
1907 :
1908 :	parrello	1.18	C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
1909 :	parrello	1.6
1910 :			Return an object describing the entity instance with a specified ID.
1911 :
1912 :			=over 4
1913 :
1914 :			=item entityType
1915 :
1916 :			Entity type name.
1917 :
1918 :			=item ID
1919 :
1920 :			ID of the desired entity.
1921 :
1922 :			=item RETURN
1923 :
1924 :			Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
1925 :			instance is found with the specified key.
1926 :
1927 :			=back
1928 :
1929 :			=cut
1930 :
1931 :			sub GetEntity {
1932 :	parrello	1.10	# Get the parameters.
1933 :			my ($self, $entityType, $ID) = @_;
1934 :			# Create a query.
1935 :	parrello	1.45	my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
1936 :	parrello	1.10	# Get the first (and only) object.
1937 :			my $retVal = $query->Fetch();
1938 :			# Return the result.
1939 :			return $retVal;
1940 :	parrello	1.6	}
1941 :
1942 :			=head3 GetEntityValues
1943 :
1944 :	parrello	1.18	C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
1945 :	parrello	1.6
1946 :			Return a list of values from a specified entity instance.
1947 :
1948 :			=over 4
1949 :
1950 :			=item entityType
1951 :
1952 :			Entity type name.
1953 :
1954 :			=item ID
1955 :
1956 :			ID of the desired entity.
1957 :
1958 :			=item fields
1959 :
1960 :			List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
1961 :
1962 :			=item RETURN
1963 :
1964 :			Returns a flattened list of the values of the specified fields for the specified entity.
1965 :
1966 :			=back
1967 :
1968 :			=cut
1969 :
1970 :			sub GetEntityValues {
1971 :	parrello	1.10	# Get the parameters.
1972 :			my ($self, $entityType, $ID, $fields) = @_;
1973 :			# Get the specified entity.
1974 :			my $entity = $self->GetEntity($entityType, $ID);
1975 :			# Declare the return list.
1976 :			my @retVal = ();
1977 :			# If we found the entity, push the values into the return list.
1978 :			if ($entity) {
1979 :			push @retVal, $entity->Values($fields);
1980 :			}
1981 :			# Return the result.
1982 :			return @retVal;
1983 :	parrello	1.6	}
1984 :	parrello	1.1
1985 :	parrello	1.7	=head3 GetAll
1986 :
1987 :	parrello	1.18	C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
1988 :	parrello	1.7
1989 :			Return a list of values taken from the objects returned by a query. The first three
1990 :			parameters correspond to the parameters of the L</Get> method. The final parameter is
1991 :			a list of the fields desired from each record found by the query. The field name
1992 :			syntax is the standard syntax used for fields in the B<ERDB> system--
1993 :			B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
1994 :			or relationship and I<fieldName> is the name of the field.
1995 :
1996 :			The list returned will be a list of lists. Each element of the list will contain
1997 :			the values returned for the fields specified in the fourth parameter. If one of the
1998 :			fields specified returns multiple values, they are flattened in with the rest. For
1999 :			example, the following call will return a list of the features in a particular
2000 :			spreadsheet cell, and each feature will be represented by a list containing the
2001 :			feature ID followed by all of its aliases.
2002 :
2003 :	parrello	1.18	C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2004 :	parrello	1.7
2005 :			=over 4
2006 :
2007 :			=item objectNames
2008 :
2009 :			List containing the names of the entity and relationship objects to be retrieved.
2010 :
2011 :			=item filterClause
2012 :
2013 :			WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2014 :			be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2015 :			B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2016 :			parameter list as additional parameters. The fields in a filter clause can come from primary
2017 :			entity relations, relationship relations, or secondary entity relations; however, all of the
2018 :			entities and relationships involved must be included in the list of object names.
2019 :
2020 :			=item parameterList
2021 :
2022 :			List of the parameters to be substituted in for the parameters marks in the filter clause.
2023 :
2024 :			=item fields
2025 :
2026 :			List of the fields to be returned in each element of the list returned.
2027 :
2028 :			=item count
2029 :
2030 :			Maximum number of records to return. If omitted or 0, all available records will be returned.
2031 :
2032 :			=item RETURN
2033 :
2034 :			Returns a list of list references. Each element of the return list contains the values for the
2035 :			fields specified in the B<fields> parameter.
2036 :
2037 :			=back
2038 :
2039 :			=cut
2040 :			#: Return Type @@;
2041 :			sub GetAll {
2042 :	parrello	1.10	# Get the parameters.
2043 :			my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2044 :			# Translate the parameters from a list reference to a list. If the parameter
2045 :			# list is a scalar we convert it into a singleton list.
2046 :			my @parmList = ();
2047 :			if (ref $parameterList eq "ARRAY") {
2048 :	parrello	1.45	Trace("GetAll parm list is an array.") if T(4);
2049 :	parrello	1.10	@parmList = @{$parameterList};
2050 :			} else {
2051 :	parrello	1.45	Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2052 :	parrello	1.10	push @parmList, $parameterList;
2053 :			}
2054 :	parrello	1.30	# Insure the counter has a value.
2055 :			if (!defined $count) {
2056 :			$count = 0;
2057 :			}
2058 :			# Add the row limit to the filter clause.
2059 :			if ($count > 0) {
2060 :			$filterClause .= " LIMIT $count";
2061 :			}
2062 :	parrello	1.10	# Create the query.
2063 :	parrello	1.45	my $query = $self->Get($objectNames, $filterClause, \@parmList);
2064 :	parrello	1.10	# Set up a counter of the number of records read.
2065 :			my $fetched = 0;
2066 :			# Loop through the records returned, extracting the fields. Note that if the
2067 :			# counter is non-zero, we stop when the number of records read hits the count.
2068 :			my @retVal = ();
2069 :			while (($count == 0 \|\| $fetched < $count) && (my $row = $query->Fetch())) {
2070 :			my @rowData = $row->Values($fields);
2071 :			push @retVal, \@rowData;
2072 :			$fetched++;
2073 :			}
2074 :	parrello	1.54	Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2075 :	parrello	1.10	# Return the resulting list.
2076 :			return @retVal;
2077 :	parrello	1.7	}
2078 :
2079 :	parrello	1.55	=head3 Exists
2080 :
2081 :			C<< my $found = $sprout->Exists($entityName, $entityID); >>
2082 :
2083 :			Return TRUE if an entity exists, else FALSE.
2084 :
2085 :			=over 4
2086 :
2087 :			=item entityName
2088 :
2089 :			Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2090 :
2091 :			=item entityID
2092 :
2093 :			ID of the entity instance whose existence is to be checked.
2094 :
2095 :			=item RETURN
2096 :
2097 :			Returns TRUE if the entity instance exists, else FALSE.
2098 :
2099 :			=back
2100 :
2101 :			=cut
2102 :			#: Return Type $;
2103 :			sub Exists {
2104 :			# Get the parameters.
2105 :			my ($self, $entityName, $entityID) = @_;
2106 :			# Check for the entity instance.
2107 :			Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2108 :			my $testInstance = $self->GetEntity($entityName, $entityID);
2109 :			# Return an existence indicator.
2110 :			my $retVal = ($testInstance ? 1 : 0);
2111 :			return $retVal;
2112 :			}
2113 :
2114 :	parrello	1.18	=head3 EstimateRowSize
2115 :
2116 :			C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2117 :
2118 :			Estimate the row size of the specified relation. The estimated row size is computed by adding
2119 :			up the average length for each data type.
2120 :
2121 :			=over 4
2122 :
2123 :			=item relName
2124 :
2125 :			Name of the relation whose estimated row size is desired.
2126 :
2127 :			=item RETURN
2128 :
2129 :			Returns an estimate of the row size for the specified relation.
2130 :
2131 :			=back
2132 :
2133 :			=cut
2134 :			#: Return Type $;
2135 :			sub EstimateRowSize {
2136 :			# Get the parameters.
2137 :			my ($self, $relName) = @_;
2138 :			# Declare the return variable.
2139 :			my $retVal = 0;
2140 :			# Find the relation descriptor.
2141 :			my $relation = $self->_FindRelation($relName);
2142 :			# Get the list of fields.
2143 :			for my $fieldData (@{$relation->{Fields}}) {
2144 :			# Get the field type and add its length.
2145 :			my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2146 :			$retVal += $fieldLen;
2147 :			}
2148 :			# Return the result.
2149 :			return $retVal;
2150 :			}
2151 :
2152 :	parrello	1.38	=head3 GetFieldTable
2153 :
2154 :			C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2155 :
2156 :			Get the field structure for a specified entity or relationship.
2157 :
2158 :			=over 4
2159 :
2160 :			=item objectName
2161 :
2162 :			Name of the desired entity or relationship.
2163 :
2164 :			=item RETURN
2165 :
2166 :			The table containing the field descriptors for the specified object.
2167 :
2168 :			=back
2169 :
2170 :			=cut
2171 :
2172 :			sub GetFieldTable {
2173 :			# Get the parameters.
2174 :			my ($self, $objectName) = @_;
2175 :			# Get the descriptor from the metadata.
2176 :			my $objectData = $self->_GetStructure($objectName);
2177 :			# Return the object's field table.
2178 :			return $objectData->{Fields};
2179 :			}
2180 :
2181 :	parrello	1.48	=head2 Data Mining Methods
2182 :
2183 :	parrello	1.38	=head3 GetUsefulCrossValues
2184 :
2185 :			C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
2186 :
2187 :			Return a list of the useful attributes that would be returned by a B<Cross> call
2188 :			from an entity of the source entity type through the specified relationship. This
2189 :			means it will return the fields of the target entity type and the intersection data
2190 :			fields in the relationship. Only primary table fields are returned. In other words,
2191 :			the field names returned will be for fields where there is always one and only one
2192 :			value.
2193 :
2194 :			=over 4
2195 :
2196 :			=item sourceEntity
2197 :
2198 :			Name of the entity from which the relationship crossing will start.
2199 :
2200 :			=item relationship
2201 :
2202 :			Name of the relationship being crossed.
2203 :
2204 :			=item RETURN
2205 :
2206 :			Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
2207 :
2208 :			=back
2209 :
2210 :			=cut
2211 :			#: Return Type @;
2212 :			sub GetUsefulCrossValues {
2213 :			# Get the parameters.
2214 :			my ($self, $sourceEntity, $relationship) = @_;
2215 :			# Declare the return variable.
2216 :			my @retVal = ();
2217 :			# Determine the target entity for the relationship. This is whichever entity is not
2218 :			# the source entity. So, if the source entity is the FROM, we'll get the name of
2219 :			# the TO, and vice versa.
2220 :			my $relStructure = $self->_GetStructure($relationship);
2221 :			my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
2222 :			my $targetEntity = $relStructure->{$targetEntityType};
2223 :			# Get the field table for the entity.
2224 :			my $entityFields = $self->GetFieldTable($targetEntity);
2225 :			# The field table is a hash. The hash key is the field name. The hash value is a structure.
2226 :			# For the entity fields, the key aspect of the target structure is that the {relation} value
2227 :			# must match the entity name.
2228 :			my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
2229 :			keys %{$entityFields};
2230 :			# Push the fields found onto the return variable.
2231 :			push @retVal, sort @fieldList;
2232 :			# Get the field table for the relationship.
2233 :			my $relationshipFields = $self->GetFieldTable($relationship);
2234 :			# Here we have a different rule. We want all the fields other than "from-link" and "to-link".
2235 :			# This may end up being an empty set.
2236 :			my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
2237 :			keys %{$relationshipFields};
2238 :			# Push these onto the return list.
2239 :			push @retVal, sort @fieldList2;
2240 :			# Return the result.
2241 :			return @retVal;
2242 :			}
2243 :
2244 :	parrello	1.48	=head3 FindColumn
2245 :
2246 :			C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
2247 :
2248 :			Return the location a desired column in a data mining header line. The data
2249 :			mining header line is a tab-separated list of column names. The column
2250 :			identifier is either the numerical index of a column or the actual column
2251 :			name.
2252 :
2253 :			=over 4
2254 :
2255 :			=item headerLine
2256 :
2257 :			The header line from a data mining command, which consists of a tab-separated
2258 :			list of column names.
2259 :
2260 :			=item columnIdentifier
2261 :
2262 :			Either the ordinal number of the desired column (1-based), or the name of the
2263 :			desired column.
2264 :
2265 :			=item RETURN
2266 :
2267 :			Returns the array index (0-based) of the desired column.
2268 :
2269 :			=back
2270 :
2271 :			=cut
2272 :
2273 :			sub FindColumn {
2274 :			# Get the parameters.
2275 :			my ($headerLine, $columnIdentifier) = @_;
2276 :			# Declare the return variable.
2277 :			my $retVal;
2278 :			# Split the header line into column names.
2279 :			my @headers = ParseColumns($headerLine);
2280 :			# Determine whether we have a number or a name.
2281 :			if ($columnIdentifier =~ /^\d+$/) {
2282 :			# Here we have a number. Subtract 1 and validate the result.
2283 :			$retVal = $columnIdentifier - 1;
2284 :			if ($retVal < 0 \|\| $retVal > $#headers) {
2285 :			Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
2286 :			}
2287 :			} else {
2288 :			# Here we have a name. We need to find it in the list.
2289 :			for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
2290 :			if ($headers[$i] eq $columnIdentifier) {
2291 :			$retVal = $i;
2292 :			}
2293 :			}
2294 :			if (! defined($retVal)) {
2295 :			Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
2296 :			}
2297 :			}
2298 :			# Return the result.
2299 :			return $retVal;
2300 :			}
2301 :
2302 :			=head3 ParseColumns
2303 :
2304 :	parrello	1.50	C<< my @columns = ERDB::ParseColumns($line); >>
2305 :	parrello	1.48
2306 :			Convert the specified data line to a list of columns.
2307 :
2308 :			=over 4
2309 :
2310 :			=item line
2311 :
2312 :			A data mining input, consisting of a tab-separated list of columns terminated by a
2313 :			new-line.
2314 :
2315 :			=item RETURN
2316 :
2317 :			Returns a list consisting of the column values.
2318 :
2319 :			=back
2320 :
2321 :			=cut
2322 :
2323 :			sub ParseColumns {
2324 :			# Get the parameters.
2325 :	parrello	1.50	my ($line) = @_;
2326 :	parrello	1.48	# Chop off the line-end.
2327 :			chomp $line;
2328 :			# Split it into a list.
2329 :			my @retVal = split(/\t/, $line);
2330 :			# Return the result.
2331 :			return @retVal;
2332 :			}
2333 :
2334 :	parrello	1.1	=head2 Internal Utility Methods
2335 :
2336 :	parrello	1.45	=head3 SetupSQL
2337 :
2338 :			Process a list of object names and a filter clause so that they can be used to
2339 :			build an SQL statement. This method takes in a reference to a list of object names
2340 :			and a filter clause. It will return a corrected filter clause, a list of mapped
2341 :			names and the mapped name hash.
2342 :
2343 :			This is an instance method.
2344 :
2345 :			=over 4
2346 :
2347 :			=item objectNames
2348 :
2349 :			Reference to a list of the object names to be included in the query.
2350 :
2351 :			=item filterClause
2352 :
2353 :			A string containing the WHERE clause for the query (without the C<WHERE>) and also
2354 :			optionally the C<ORDER BY> and C<LIMIT> clauses.
2355 :
2356 :			=item RETURN
2357 :
2358 :			Returns a three-element list. The first element is the SQL statement suffix, beginning
2359 :			with the FROM clause. The second element is a reference to a list of the names to be
2360 :			used in retrieving the fields. The third element is a hash mapping the names to the
2361 :			objects they represent.
2362 :
2363 :			=back
2364 :
2365 :			=cut
2366 :
2367 :			sub _SetupSQL {
2368 :			my ($self, $objectNames, $filterClause) = @_;
2369 :			# Adjust the list of object names to account for multiple occurrences of the
2370 :			# same object. We start with a hash table keyed on object name that will
2371 :			# return the object suffix. The first time an object is encountered it will
2372 :			# not be found in the hash. The next time the hash will map the object name
2373 :			# to 2, then 3, and so forth.
2374 :			my %objectHash = ();
2375 :			# This list will contain the object names as they are to appear in the
2376 :			# FROM list.
2377 :			my @fromList = ();
2378 :			# This list contains the suffixed object name for each object. It is exactly
2379 :			# parallel to the list in the $objectNames parameter.
2380 :			my @mappedNameList = ();
2381 :			# Finally, this hash translates from a mapped name to its original object name.
2382 :			my %mappedNameHash = ();
2383 :			# Now we create the lists. Note that for every single name we push something into
2384 :			# @fromList and @mappedNameList. This insures that those two arrays are exactly
2385 :			# parallel to $objectNames.
2386 :			for my $objectName (@{$objectNames}) {
2387 :			# Get the next suffix for this object.
2388 :			my $suffix = $objectHash{$objectName};
2389 :			if (! $suffix) {
2390 :			# Here we are seeing the object for the first time. The object name
2391 :			# is used as is.
2392 :			push @mappedNameList, $objectName;
2393 :			push @fromList, $objectName;
2394 :			$mappedNameHash{$objectName} = $objectName;
2395 :			# Denote the next suffix will be 2.
2396 :			$objectHash{$objectName} = 2;
2397 :			} else {
2398 :			# Here we've seen the object before. We construct a new name using
2399 :			# the suffix from the hash and update the hash.
2400 :			my $mappedName = "$objectName$suffix";
2401 :			$objectHash{$objectName} = $suffix + 1;
2402 :			# The FROM list has the object name followed by the mapped name. This
2403 :			# tells SQL it's still the same table, but we're using a different name
2404 :			# for it to avoid confusion.
2405 :			push @fromList, "$objectName $mappedName";
2406 :			# The mapped-name list contains the real mapped name.
2407 :			push @mappedNameList, $mappedName;
2408 :			# Finally, enable us to get back from the mapped name to the object name.
2409 :			$mappedNameHash{$mappedName} = $objectName;
2410 :			}
2411 :			}
2412 :			# Begin the SELECT suffix. It starts with
2413 :			#
2414 :			# FROM name1, name2, ... nameN
2415 :			#
2416 :			my $suffix = "FROM " . join(', ', @fromList);
2417 :			# Check for a filter clause.
2418 :			if ($filterClause) {
2419 :			# Here we have one, so we convert its field names and add it to the query. First,
2420 :			# We create a copy of the filter string we can work with.
2421 :			my $filterString = $filterClause;
2422 :			# Next, we sort the object names by length. This helps protect us from finding
2423 :			# object names inside other object names when we're doing our search and replace.
2424 :			my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
2425 :			# We will also keep a list of conditions to add to the WHERE clause in order to link
2426 :			# entities and relationships as well as primary relations to secondary ones.
2427 :			my @joinWhere = ();
2428 :			# The final preparatory step is to create a hash table of relation names. The
2429 :			# table begins with the relation names already in the SELECT command. We may
2430 :			# need to add relations later if there is filtering on a field in a secondary
2431 :			# relation. The secondary relations are the ones that contain multiply-
2432 :			# occurring or optional fields.
2433 :			my %fromNames = map { $_ => 1 } @sortedNames;
2434 :			# We are ready to begin. We loop through the object names, replacing each
2435 :			# object name's field references by the corresponding SQL field reference.
2436 :			# Along the way, if we find a secondary relation, we will need to add it
2437 :			# to the FROM clause.
2438 :			for my $mappedName (@sortedNames) {
2439 :			# Get the length of the object name plus 2. This is the value we add to the
2440 :			# size of the field name to determine the size of the field reference as a
2441 :			# whole.
2442 :			my $nameLength = 2 + length $mappedName;
2443 :			# Get the real object name for this mapped name.
2444 :			my $objectName = $mappedNameHash{$mappedName};
2445 :			Trace("Processing $mappedName for object $objectName.") if T(4);
2446 :			# Get the object's field list.
2447 :			my $fieldList = $self->GetFieldTable($objectName);
2448 :			# Find the field references for this object.
2449 :			while ($filterString =~ m/$mappedName$([^)]*)$/g) {
2450 :			# At this point, $1 contains the field name, and the current position
2451 :			# is set immediately after the final parenthesis. We pull out the name of
2452 :			# the field and the position and length of the field reference as a whole.
2453 :			my $fieldName = $1;
2454 :			my $len = $nameLength + length $fieldName;
2455 :			my $pos = pos($filterString) - $len;
2456 :			# Insure the field exists.
2457 :			if (!exists $fieldList->{$fieldName}) {
2458 :			Confess("Field $fieldName not found for object $objectName.");
2459 :			} else {
2460 :			Trace("Processing $fieldName at position $pos.") if T(4);
2461 :			# Get the field's relation.
2462 :			my $relationName = $fieldList->{$fieldName}->{relation};
2463 :			# Now we have a secondary relation. We need to insure it matches the
2464 :			# mapped name of the primary relation. First we peel off the suffix
2465 :			# from the mapped name.
2466 :			my $mappingSuffix = substr $mappedName, length($objectName);
2467 :			# Put the mapping suffix onto the relation name to get the
2468 :			# mapped relation name.
2469 :			my $mappedRelationName = "$relationName$mappingSuffix";
2470 :			# Insure the relation is in the FROM clause.
2471 :			if (!exists $fromNames{$mappedRelationName}) {
2472 :			# Add the relation to the FROM clause.
2473 :			if ($mappedRelationName eq $relationName) {
2474 :			# The name is un-mapped, so we add it without
2475 :			# any frills.
2476 :			$suffix .= ", $relationName";
2477 :			push @joinWhere, "$objectName.id = $relationName.id";
2478 :			} else {
2479 :			# Here we have a mapping situation.
2480 :			$suffix .= ", $relationName $mappedRelationName";
2481 :			push @joinWhere, "$mappedRelationName.id = $mappedName.id";
2482 :			}
2483 :			# Denote we have this relation available for future fields.
2484 :			$fromNames{$mappedRelationName} = 1;
2485 :			}
2486 :			# Form an SQL field reference from the relation name and the field name.
2487 :			my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
2488 :			# Put it into the filter string in place of the old value.
2489 :			substr($filterString, $pos, $len) = $sqlReference;
2490 :			# Reposition the search.
2491 :			pos $filterString = $pos + length $sqlReference;
2492 :			}
2493 :			}
2494 :			}
2495 :			# The next step is to join the objects together. We only need to do this if there
2496 :			# is more than one object in the object list. We start with the first object and
2497 :			# run through the objects after it. Note also that we make a safety copy of the
2498 :			# list before running through it.
2499 :			my @mappedObjectList = @mappedNameList;
2500 :			my $lastMappedObject = shift @mappedObjectList;
2501 :			# Get the join table.
2502 :			my $joinTable = $self->{_metaData}->{Joins};
2503 :			# Loop through the object list.
2504 :			for my $thisMappedObject (@mappedObjectList) {
2505 :			# Look for a join using the real object names.
2506 :			my $lastObject = $mappedNameHash{$lastMappedObject};
2507 :			my $thisObject = $mappedNameHash{$thisMappedObject};
2508 :			my $joinKey = "$lastObject/$thisObject";
2509 :			if (!exists $joinTable->{$joinKey}) {
2510 :			# Here there's no join, so we throw an error.
2511 :			Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
2512 :			} else {
2513 :			# Get the join clause.
2514 :			my $unMappedJoin = $joinTable->{$joinKey};
2515 :			# Fix the names.
2516 :			$unMappedJoin =~ s/$lastObject/$lastMappedObject/;
2517 :			$unMappedJoin =~ s/$thisObject/$thisMappedObject/;
2518 :			push @joinWhere, $unMappedJoin;
2519 :			# Save this object as the last object for the next iteration.
2520 :			$lastMappedObject = $thisMappedObject;
2521 :			}
2522 :			}
2523 :			# Now we need to handle the whole ORDER BY / LIMIT thing. The important part
2524 :			# here is we want the filter clause to be empty if there's no WHERE filter.
2525 :			# We'll put the ORDER BY / LIMIT clauses in the following variable.
2526 :			my $orderClause = "";
2527 :			# Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
2528 :			# operator so that we find the first occurrence of either verb.
2529 :			if ($filterString =~ m/^(.?)\s(ORDER BY\|LIMIT)/g) {
2530 :			# Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
2531 :			my $pos = pos $filterString;
2532 :			$orderClause = $2 . substr($filterString, $pos);
2533 :			$filterString = $1;
2534 :			}
2535 :			# Add the filter and the join clauses (if any) to the SELECT command.
2536 :			if ($filterString) {
2537 :			Trace("Filter string is \"$filterString\".") if T(4);
2538 :			push @joinWhere, "($filterString)";
2539 :			}
2540 :			if (@joinWhere) {
2541 :			$suffix .= " WHERE " . join(' AND ', @joinWhere);
2542 :			}
2543 :			# Add the sort or limit clause (if any) to the SELECT command.
2544 :			if ($orderClause) {
2545 :			$suffix .= " $orderClause";
2546 :			}
2547 :			}
2548 :			# Return the suffix, the mapped name list, and the mapped name hash.
2549 :			return ($suffix, \@mappedNameList, \%mappedNameHash);
2550 :			}
2551 :
2552 :			=head3 GetStatementHandle
2553 :
2554 :			This method will prepare and execute an SQL query, returning the statement handle.
2555 :			The main reason for doing this here is so that everybody who does SQL queries gets
2556 :			the benefit of tracing.
2557 :
2558 :			This is an instance method.
2559 :
2560 :			=over 4
2561 :
2562 :			=item command
2563 :
2564 :			Command to prepare and execute.
2565 :
2566 :			=item params
2567 :
2568 :			Reference to a list of the values to be substituted in for the parameter marks.
2569 :
2570 :			=item RETURN
2571 :
2572 :			Returns a prepared and executed statement handle from which the caller can extract
2573 :			results.
2574 :
2575 :			=back
2576 :
2577 :			=cut
2578 :
2579 :			sub _GetStatementHandle {
2580 :			# Get the parameters.
2581 :			my ($self, $command, $params) = @_;
2582 :			# Trace the query.
2583 :			Trace("SQL query: $command") if T(SQL => 3);
2584 :			Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
2585 :			# Get the database handle.
2586 :			my $dbh = $self->{_dbh};
2587 :			# Prepare the command.
2588 :			my $sth = $dbh->prepare_command($command);
2589 :			# Execute it with the parameters bound in.
2590 :			$sth->execute(@{$params}) \|\| Confess("SELECT error" . $sth->errstr());
2591 :			# Return the statement handle.
2592 :			return $sth;
2593 :			}
2594 :
2595 :	parrello	1.1	=head3 GetLoadStats
2596 :
2597 :			Return a blank statistics object for use by the load methods.
2598 :
2599 :			This is a static method.
2600 :
2601 :			=cut
2602 :
2603 :	parrello	1.29	sub _GetLoadStats{
2604 :	parrello	1.28	return Stats->new();
2605 :	parrello	1.1	}
2606 :
2607 :			=head3 GenerateFields
2608 :
2609 :			Generate field values from a field structure and store in a specified table. The field names
2610 :			are first sorted by pass count, certain pre-defined fields are removed from the list, and
2611 :			then we rip through them evaluation the data generation string. Fields in the primary relation
2612 :			are stored as scalars; fields in secondary relations are stored as value lists.
2613 :
2614 :			This is a static method.
2615 :
2616 :			=over 4
2617 :
2618 :			=item this
2619 :
2620 :			Hash table into which the field values should be placed.
2621 :
2622 :			=item fields
2623 :
2624 :			Field structure from which the field descriptors should be taken.
2625 :
2626 :			=item type
2627 :
2628 :			Type name of the object whose fields are being generated.
2629 :
2630 :			=item values (optional)
2631 :
2632 :			Reference to a value structure from which additional values can be taken.
2633 :
2634 :			=item from (optiona)
2635 :
2636 :			Reference to the source entity instance if relationship data is being generated.
2637 :
2638 :			=item to (optional)
2639 :
2640 :			Reference to the target entity instance if relationship data is being generated.
2641 :
2642 :			=back
2643 :
2644 :			=cut
2645 :
2646 :			sub _GenerateFields {
2647 :	parrello	1.10	# Get the parameters.
2648 :			my ($this, $fields, $type, $values, $from, $to) = @_;
2649 :			# Sort the field names by pass number.
2650 :			my @fieldNames = sort { $fields->{$a}->{DataGen}->{pass} <=> $fields->{$b}->{DataGen}->{pass} } keys %{$fields};
2651 :			# Loop through the field names, generating data.
2652 :			for my $name (@fieldNames) {
2653 :			# Only proceed if this field needs to be generated.
2654 :			if (!exists $this->{$name}) {
2655 :			# Get this field's data generation descriptor.
2656 :			my $fieldDescriptor = $fields->{$name};
2657 :			my $data = $fieldDescriptor->{DataGen};
2658 :			# Get the code to generate the field value.
2659 :			my $codeString = $data->{content};
2660 :			# Determine whether or not this field is in the primary relation.
2661 :			if ($fieldDescriptor->{relation} eq $type) {
2662 :			# Here we have a primary relation field. Store the field value as
2663 :			# a scalar.
2664 :			$this->{$name} = eval($codeString);
2665 :			} else {
2666 :			# Here we have a secondary relation field. Create a null list
2667 :			# and push the desired number of field values onto it.
2668 :			my @fieldValues = ();
2669 :			my $count = IntGen(0,$data->{testCount});
2670 :			for (my $i = 0; $i < $count; $i++) {
2671 :			my $newValue = eval($codeString);
2672 :			push @fieldValues, $newValue;
2673 :			}
2674 :			# Store the value list in the main hash.
2675 :			$this->{$name} = \@fieldValues;
2676 :			}
2677 :			}
2678 :			}
2679 :	parrello	1.1	}
2680 :
2681 :			=head3 DumpRelation
2682 :
2683 :			Dump the specified relation's to the specified output file in tab-delimited format.
2684 :
2685 :			This is an instance method.
2686 :
2687 :			=over 4
2688 :
2689 :			=item outputDirectory
2690 :
2691 :			Directory to contain the output file.
2692 :
2693 :			=item relationName
2694 :
2695 :			Name of the relation to dump.
2696 :
2697 :			=item relation
2698 :
2699 :			Structure describing the relation to be dumped.
2700 :
2701 :			=back
2702 :
2703 :			=cut
2704 :
2705 :			sub _DumpRelation {
2706 :	parrello	1.10	# Get the parameters.
2707 :			my ($self, $outputDirectory, $relationName, $relation) = @_;
2708 :			# Open the output file.
2709 :			my $fileName = "$outputDirectory/$relationName.dtx";
2710 :			open(DTXOUT, ">$fileName") \|\| Confess("Could not open dump file $fileName: $!");
2711 :			# Create a query for the specified relation.
2712 :			my $dbh = $self->{_dbh};
2713 :			my $query = $dbh->prepare_command("SELECT * FROM $relationName");
2714 :			# Execute the query.
2715 :			$query->execute() \|\| Confess("SELECT error dumping $relationName.");
2716 :			# Loop through the results.
2717 :			while (my @row = $query->fetchrow) {
2718 :			# Escape any tabs or new-lines in the row text.
2719 :			for my $field (@row) {
2720 :			$field =~ s/\n/\\n/g;
2721 :			$field =~ s/\t/\\t/g;
2722 :			}
2723 :			# Tab-join the row and write it to the output file.
2724 :			my $rowText = join("\t", @row);
2725 :			print DTXOUT "$rowText\n";
2726 :			}
2727 :			# Close the output file.
2728 :			close DTXOUT;
2729 :	parrello	1.1	}
2730 :
2731 :			=head3 GetStructure
2732 :
2733 :			Get the data structure for a specified entity or relationship.
2734 :
2735 :			This is an instance method.
2736 :
2737 :			=over 4
2738 :
2739 :			=item objectName
2740 :
2741 :			Name of the desired entity or relationship.
2742 :
2743 :			=item RETURN
2744 :
2745 :			The descriptor for the specified object.
2746 :
2747 :			=back
2748 :
2749 :			=cut
2750 :
2751 :			sub _GetStructure {
2752 :	parrello	1.10	# Get the parameters.
2753 :			my ($self, $objectName) = @_;
2754 :			# Get the metadata structure.
2755 :			my $metadata = $self->{_metaData};
2756 :			# Declare the variable to receive the descriptor.
2757 :			my $retVal;
2758 :			# Get the descriptor from the metadata.
2759 :			if (exists $metadata->{Entities}->{$objectName}) {
2760 :			$retVal = $metadata->{Entities}->{$objectName};
2761 :			} elsif (exists $metadata->{Relationships}->{$objectName}) {
2762 :			$retVal = $metadata->{Relationships}->{$objectName};
2763 :			} else {
2764 :			Confess("Object $objectName not found in database.");
2765 :			}
2766 :			# Return the descriptor.
2767 :			return $retVal;
2768 :	parrello	1.1	}
2769 :
2770 :			=head3 GetRelationTable
2771 :
2772 :			Get the list of relations for a specified entity or relationship.
2773 :
2774 :			This is an instance method.
2775 :
2776 :			=over 4
2777 :
2778 :			=item objectName
2779 :
2780 :			Name of the desired entity or relationship.
2781 :
2782 :			=item RETURN
2783 :
2784 :			A table containing the relations for the specified object.
2785 :
2786 :			=back
2787 :
2788 :			=cut
2789 :
2790 :			sub _GetRelationTable {
2791 :	parrello	1.10	# Get the parameters.
2792 :			my ($self, $objectName) = @_;
2793 :			# Get the descriptor from the metadata.
2794 :			my $objectData = $self->_GetStructure($objectName);
2795 :			# Return the object's relation list.
2796 :			return $objectData->{Relations};
2797 :	parrello	1.1	}
2798 :
2799 :			=head3 ValidateFieldNames
2800 :
2801 :			Determine whether or not the field names are valid. A description of the problems with the names
2802 :			will be written to the standard error output. If there is an error, this method will abort. This is
2803 :			a static method.
2804 :
2805 :			=over 4
2806 :
2807 :			=item metadata
2808 :
2809 :			Metadata structure loaded from the XML data definition.
2810 :
2811 :			=back
2812 :
2813 :			=cut
2814 :
2815 :			sub _ValidateFieldNames {
2816 :	parrello	1.10	# Get the object.
2817 :			my ($metadata) = @_;
2818 :			# Declare the return value. We assume success.
2819 :			my $retVal = 1;
2820 :			# Loop through the sections of the database definition.
2821 :			for my $section ('Entities', 'Relationships') {
2822 :			# Loop through the objects in this section.
2823 :			for my $object (values %{$metadata->{$section}}) {
2824 :			# Loop through the object's fields.
2825 :			for my $fieldName (keys %{$object->{Fields}}) {
2826 :			# Now we make some initial validations.
2827 :			if ($fieldName =~ /--/) {
2828 :			# Here we have a doubled minus sign.
2829 :			print STDERR "Field name $fieldName has a doubled hyphen.\n";
2830 :			$retVal = 0;
2831 :			} elsif ($fieldName !~ /^[A-Za-z]/) {
2832 :			# Here the field name is missing the initial letter.
2833 :			print STDERR "Field name $fieldName does not begin with a letter.\n";
2834 :			$retVal = 0;
2835 :			} else {
2836 :			# Strip out the minus signs. Everything remaining must be a letter
2837 :			# or digit.
2838 :			my $strippedName = $fieldName;
2839 :			$strippedName =~ s/-//g;
2840 :			if ($strippedName !~ /^[A-Za-z0-9]+$/) {
2841 :			print STDERR "Field name $fieldName contains illegal characters.\n";
2842 :			$retVal = 0;
2843 :			}
2844 :			}
2845 :			}
2846 :			}
2847 :			}
2848 :			# If an error was found, fail.
2849 :			if ($retVal == 0) {
2850 :			Confess("Errors found in field names.");
2851 :			}
2852 :	parrello	1.1	}
2853 :
2854 :			=head3 LoadRelation
2855 :
2856 :			Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
2857 :			file with the same name as the relation exists in the specified directory.
2858 :
2859 :			This is an instance method.
2860 :
2861 :			=over 4
2862 :
2863 :			=item dbh
2864 :
2865 :			DBKernel object for accessing the database.
2866 :
2867 :			=item directoryName
2868 :
2869 :			Name of the directory containing the tab-delimited data files.
2870 :
2871 :			=item relationName
2872 :
2873 :			Name of the relation to load.
2874 :
2875 :			=item rebuild
2876 :
2877 :			TRUE if the table should be dropped and re-created before loading.
2878 :
2879 :			=item RETURN
2880 :
2881 :			Returns a statistical object describing the number of records read and a list of error messages.
2882 :
2883 :			=back
2884 :
2885 :			=cut
2886 :
2887 :			sub _LoadRelation {
2888 :	parrello	1.10	# Get the parameters.
2889 :			my ($self, $directoryName, $relationName, $rebuild) = @_;
2890 :			# Create the file name.
2891 :			my $fileName = "$directoryName/$relationName";
2892 :			# If the file doesn't exist, try adding the .dtx suffix.
2893 :			if (! -e $fileName) {
2894 :			$fileName .= ".dtx";
2895 :			if (! -e $fileName) {
2896 :			$fileName = "";
2897 :			}
2898 :			}
2899 :			# Create the return object.
2900 :			my $retVal = _GetLoadStats();
2901 :			# If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
2902 :			# be a null string.
2903 :			if ($fileName ne "") {
2904 :			# Load the relation from the file.
2905 :			$retVal = $self->LoadTable($fileName, $relationName, $rebuild);
2906 :			} elsif ($rebuild) {
2907 :			# Here we are rebuilding, but no file exists, so we just re-create the table.
2908 :			$self->CreateTable($relationName, 1);
2909 :			}
2910 :			# Return the statistics from the load.
2911 :			return $retVal;
2912 :	parrello	1.1	}
2913 :
2914 :			=head3 LoadMetaData
2915 :
2916 :			This method loads the data describing this database from an XML file into a metadata structure.
2917 :			The resulting structure is a set of nested hash tables containing all the information needed to
2918 :			load or use the database. The schema for the XML file is F<ERDatabase.xml>.
2919 :
2920 :			This is a static method.
2921 :
2922 :			=over 4
2923 :
2924 :			=item filename
2925 :
2926 :			Name of the file containing the database definition.
2927 :
2928 :			=item RETURN
2929 :
2930 :			Returns a structure describing the database.
2931 :
2932 :			=back
2933 :
2934 :			=cut
2935 :
2936 :			sub _LoadMetaData {
2937 :	parrello	1.10	# Get the parameters.
2938 :			my ($filename) = @_;
2939 :	parrello	1.15	Trace("Reading Sprout DBD from $filename.") if T(2);
2940 :	parrello	1.10	# Slurp the XML file into a variable. Extensive use of options is used to insure we
2941 :			# get the exact structure we want.
2942 :			my $metadata = XML::Simple::XMLin($filename,
2943 :			GroupTags => { Relationships => 'Relationship',
2944 :			Entities => 'Entity',
2945 :			Fields => 'Field',
2946 :			Indexes => 'Index',
2947 :			IndexFields => 'IndexField'},
2948 :			KeyAttr => { Relationship => 'name',
2949 :			Entity => 'name',
2950 :			Field => 'name'},
2951 :			ForceArray => ['Field', 'Index', 'IndexField'],
2952 :			ForceContent => 1,
2953 :			NormalizeSpace => 2
2954 :			);
2955 :			Trace("XML metadata loaded from file $filename.") if T(1);
2956 :			# Before we go any farther, we need to validate the field and object names. If an error is found,
2957 :			# the method below will fail.
2958 :			_ValidateFieldNames($metadata);
2959 :			# Next we need to create a hash table for finding relations. The entities and relationships are
2960 :			# implemented as one or more database relations.
2961 :			my %masterRelationTable = ();
2962 :			# Loop through the entities.
2963 :			my $entityList = $metadata->{Entities};
2964 :			for my $entityName (keys %{$entityList}) {
2965 :			my $entityStructure = $entityList->{$entityName};
2966 :			#
2967 :	parrello	1.12	# The first step is to create all the entity's default values. For C<Field> elements,
2968 :	parrello	1.10	# the relation name must be added where it is not specified. For relationships,
2969 :			# the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
2970 :			# field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
2971 :			# added that can be used to pull the implicit fields to the top when displaying the field
2972 :			# documentation. The PrettySort values are 1-based and indicate in which pass through a
2973 :			# relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
2974 :			# and so on.
2975 :			#
2976 :			# Fix up this entity.
2977 :			_FixupFields($entityStructure, $entityName, 2, 3);
2978 :			# Add the ID field.
2979 :			_AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
2980 :			relation => $entityName,
2981 :			Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
2982 :			PrettySort => 1});
2983 :			#
2984 :			# The current field list enables us to quickly find the relation containing a particular field.
2985 :			# We also need a list that tells us the fields in each relation. We do this by creating a
2986 :			# Relations structure in the entity structure and collating the fields into it based on their
2987 :			# C<relation> property. There is one tricky bit, which is that every relation has to have the
2988 :			# C<id> field in it. Note also that the field list is put into a C<Fields> member of the
2989 :			# relation's structure so that it looks more like the entity and relationship structures.
2990 :			#
2991 :			# First we need to create the relations list.
2992 :			my $relationTable = { };
2993 :			# Loop through the fields. We use a list of field names to prevent a problem with
2994 :			# the hash table cursor losing its place during the loop.
2995 :			my $fieldList = $entityStructure->{Fields};
2996 :			my @fieldNames = keys %{$fieldList};
2997 :			for my $fieldName (@fieldNames) {
2998 :			my $fieldData = $fieldList->{$fieldName};
2999 :			# Get the current field's relation name.
3000 :			my $relationName = $fieldData->{relation};
3001 :			# Insure the relation exists.
3002 :			if (!exists $relationTable->{$relationName}) {
3003 :			$relationTable->{$relationName} = { Fields => { } };
3004 :			}
3005 :			# Add the field to the relation's field structure.
3006 :			$relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
3007 :			}
3008 :			# Now that we've organized all our fields by relation name we need to do some serious
3009 :			# housekeeping. We must add the C<id> field to every relation and convert each relation
3010 :			# to a list of fields. First, we need the ID field itself.
3011 :			my $idField = $fieldList->{id};
3012 :			# Loop through the relations.
3013 :			for my $relationName (keys %{$relationTable}) {
3014 :			my $relation = $relationTable->{$relationName};
3015 :			# Get the relation's field list.
3016 :			my $relationFieldList = $relation->{Fields};
3017 :			# Add the ID field to it. If the field's already there, it will not make any
3018 :			# difference.
3019 :			$relationFieldList->{id} = $idField;
3020 :			# Convert the field set from a hash into a list using the pretty-sort number.
3021 :			$relation->{Fields} = _ReOrderRelationTable($relationFieldList);
3022 :			# Add the relation to the master table.
3023 :			$masterRelationTable{$relationName} = $relation;
3024 :			}
3025 :			# The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
3026 :			# The other relations must have at least one index that begins with the ID field. In addition, the
3027 :			# metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
3028 :			# get the entity's field list and index list.
3029 :			my $indexList = $entityStructure->{Indexes};
3030 :			# Loop through the indexes.
3031 :			for my $indexData (@{$indexList}) {
3032 :			# We need to find this index's fields. All of them should belong to the same relation.
3033 :			# The ID field is an exception, since it's in all relations.
3034 :			my $relationName = '0';
3035 :			for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
3036 :			# Get this field's name.
3037 :			my $fieldName = $fieldDescriptor->{name};
3038 :			# Only proceed if it is NOT the ID field.
3039 :			if ($fieldName ne 'id') {
3040 :			# Find the relation containing the current index field.
3041 :			my $thisName = $fieldList->{$fieldName}->{relation};
3042 :			if ($relationName eq '0') {
3043 :			# Here we're looking at the first field, so we save its relation name.
3044 :			$relationName = $thisName;
3045 :			} elsif ($relationName ne $thisName) {
3046 :			# Here we have a field mismatch.
3047 :			Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
3048 :			}
3049 :			}
3050 :			}
3051 :			# Now $relationName is the name of the relation that contains this index. Add the index structure
3052 :			# to the relation.
3053 :			push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
3054 :			}
3055 :			# Now each index has been put in a relation. We need to add the primary index for the primary
3056 :			# relation.
3057 :			push @{$relationTable->{$entityName}->{Indexes}},
3058 :			{ IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
3059 :			Notes => { content => "Primary index for $entityName." }
3060 :			};
3061 :			# The next step is to insure that each relation has at least one index that begins with the ID field.
3062 :			# After that, we convert each relation's index list to an index table. We first need to loop through
3063 :			# the relations.
3064 :			for my $relationName (keys %{$relationTable}) {
3065 :			my $relation = $relationTable->{$relationName};
3066 :			# Get the relation's index list.
3067 :			my $indexList = $relation->{Indexes};
3068 :			# Insure this relation has an ID index.
3069 :			my $found = 0;
3070 :			for my $index (@{$indexList}) {
3071 :			if ($index->{IndexFields}->[0]->{name} eq "id") {
3072 :			$found = 1;
3073 :			}
3074 :			}
3075 :			if ($found == 0) {
3076 :			push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
3077 :			}
3078 :			# Now we need to convert the relation's index list to an index table. We begin by creating
3079 :			# an empty table in the relation structure.
3080 :			$relation->{Indexes} = { };
3081 :			# Loop through the indexes.
3082 :			my $count = 0;
3083 :			for my $index (@{$indexList}) {
3084 :			# Add this index to the index table.
3085 :			_AddIndex("idx$relationName$count", $relation, $index);
3086 :			# Increment the counter so that the next index has a different name.
3087 :			$count++;
3088 :			}
3089 :			}
3090 :			# Finally, we add the relation structure to the entity.
3091 :			$entityStructure->{Relations} = $relationTable;
3092 :			}
3093 :			# Loop through the relationships. Relationships actually turn out to be much simpler than entities.
3094 :			# For one thing, there is only a single constituent relation.
3095 :			my $relationshipList = $metadata->{Relationships};
3096 :			for my $relationshipName (keys %{$relationshipList}) {
3097 :			my $relationshipStructure = $relationshipList->{$relationshipName};
3098 :			# Fix up this relationship.
3099 :			_FixupFields($relationshipStructure, $relationshipName, 2, 3);
3100 :			# Format a description for the FROM field.
3101 :			my $fromEntity = $relationshipStructure->{from};
3102 :			my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
3103 :			# Get the FROM entity's key type.
3104 :			my $fromType = $entityList->{$fromEntity}->{keyType};
3105 :			# Add the FROM field.
3106 :			_AddField($relationshipStructure, 'from-link', { type => $fromType,
3107 :			relation => $relationshipName,
3108 :			Notes => { content => $fromComment },
3109 :			PrettySort => 1});
3110 :			# Format a description for the TO field.
3111 :			my $toEntity = $relationshipStructure->{to};
3112 :			my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
3113 :			# Get the TO entity's key type.
3114 :			my $toType = $entityList->{$toEntity}->{keyType};
3115 :			# Add the TO field.
3116 :			_AddField($relationshipStructure, 'to-link', { type=> $toType,
3117 :			relation => $relationshipName,
3118 :			Notes => { content => $toComment },
3119 :			PrettySort => 1});
3120 :			# Create an index-free relation from the fields.
3121 :			my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
3122 :			Indexes => { } };
3123 :			$relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
3124 :			# Create the FROM and TO indexes.
3125 :			_CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
3126 :			_CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
3127 :			# Add the relation to the master table.
3128 :			$masterRelationTable{$relationshipName} = $thisRelation;
3129 :			}
3130 :			# Now store the master relation table in the metadata structure.
3131 :			$metadata->{RelationTable} = \%masterRelationTable;
3132 :			# Our final task is to create the join table. The join table is a hash that describes all
3133 :			# the join clauses for traveling through the relationships. The join clause is an equality
3134 :			# condition that can be put into a WHERE clause in order to join two objects. Two relationships
3135 :			# can be joined if they share an entity in common; and an entity can be joined to a relationship
3136 :			# if the entity is at either end of the relationship.
3137 :			my %joinTable = ();
3138 :			# Loop through the entities.
3139 :			for my $entityName (keys %{$entityList}) {
3140 :			# Build three lists of the relationships connected to this entity. One will be
3141 :			# for relationships from the entity, one for relationships to the entity, and
3142 :			# one for recursive relationships.
3143 :			my @fromList = ();
3144 :			my @toList = ();
3145 :			my @bothList = ();
3146 :	parrello	1.21	Trace("Join table build for $entityName.") if T(metadata => 4);
3147 :	parrello	1.10	for my $relationshipName (keys %{$relationshipList}) {
3148 :			my $relationship = $relationshipList->{$relationshipName};
3149 :			# Determine if this relationship has our entity in one of its link fields.
3150 :			my $fromEntity = $relationship->{from};
3151 :			my $toEntity = $relationship->{to};
3152 :	parrello	1.41	Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
3153 :	parrello	1.10	if ($fromEntity eq $entityName) {
3154 :			if ($toEntity eq $entityName) {
3155 :			# Here the relationship is recursive.
3156 :			push @bothList, $relationshipName;
3157 :	parrello	1.21	Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
3158 :	parrello	1.10	} else {
3159 :			# Here the relationship comes from the entity.
3160 :			push @fromList, $relationshipName;
3161 :	parrello	1.21	Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
3162 :	parrello	1.10	}
3163 :			} elsif ($toEntity eq $entityName) {
3164 :			# Here the relationship goes to the entity.
3165 :			push @toList, $relationshipName;
3166 :	parrello	1.21	Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
3167 :	parrello	1.10	}
3168 :			}
3169 :			# Create the nonrecursive joins. Note that we build two hashes for running
3170 :			# through the nonrecursive relationships since we'll have an outer loop
3171 :			# and an inner loop, and we can't do two "each" iterations on the same
3172 :			# hash table at the same time.
3173 :			my %directRelationships = ( from => \@fromList, to => \@toList );
3174 :			my %otherRelationships = ( from => \@fromList, to => \@toList );
3175 :			for my $linkType (keys %directRelationships) {
3176 :			my $relationships = $directRelationships{$linkType};
3177 :			# Loop through all the relationships.
3178 :			for my $relationshipName (@{$relationships}) {
3179 :			# Create joins between the entity and this relationship.
3180 :			my $linkField = "$relationshipName.${linkType}_link";
3181 :			my $joinClause = "$entityName.id = $linkField";
3182 :	parrello	1.21	Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
3183 :	parrello	1.10	$joinTable{"$entityName/$relationshipName"} = $joinClause;
3184 :			$joinTable{"$relationshipName/$entityName"} = $joinClause;
3185 :			# Create joins between this relationship and the other relationships.
3186 :			for my $otherType (keys %otherRelationships) {
3187 :			my $otherships = $otherRelationships{$otherType};
3188 :			for my $otherName (@{$otherships}) {
3189 :			# Get the key for this join.
3190 :			my $joinKey = "$otherName/$relationshipName";
3191 :			# Check for a duplicate or a self-join.
3192 :			if (exists $joinTable{$joinKey}) {
3193 :			# Here we have a duplicate, which means that the join
3194 :			# path is ambiguous. We delete the join from the join
3195 :			# table to prevent it from being used.
3196 :			delete $joinTable{$joinKey};
3197 :			Trace("Deleting ambiguous join $joinKey.") if T(4);
3198 :			} elsif ($otherName ne $relationshipName) {
3199 :			# Here we have a valid join. Note that joins between a
3200 :			# relationship and itself are prohibited.
3201 :			my $relJoinClause = "$otherName.${otherType}_link = $linkField";
3202 :			$joinTable{$joinKey} = $relJoinClause;
3203 :	parrello	1.21	Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
3204 :	parrello	1.10	}
3205 :			}
3206 :			}
3207 :			# Create joins between this relationship and the recursive relationships.
3208 :			# We don't need to check for ambiguous joins here, because a recursive
3209 :			# relationship can only be ambiguous with another recursive relationship,
3210 :			# and the incoming relationship from the outer loop is never recursive.
3211 :			for my $otherName (@bothList) {
3212 :	parrello	1.21	Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
3213 :	parrello	1.10	# Join from the left.
3214 :			$joinTable{"$relationshipName/$otherName"} =
3215 :			"$linkField = $otherName.from_link";
3216 :			# Join from the right.
3217 :			$joinTable{"$otherName/$relationshipName"} =
3218 :			"$otherName.to_link = $linkField";
3219 :			}
3220 :			}
3221 :			}
3222 :			# Create entity joins for the recursive relationships. Unlike the non-recursive
3223 :			# joins, the direction makes a difference with the recursive joins. This can give
3224 :			# rise to situations where we can't create the path we want; however, it is always
3225 :			# possible to get the same effect using multiple queries.
3226 :			for my $relationshipName (@bothList) {
3227 :	parrello	1.21	Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
3228 :	parrello	1.10	# Join to the entity from each direction.
3229 :			$joinTable{"$entityName/$relationshipName"} =
3230 :			"$entityName.id = $relationshipName.from_link";
3231 :			$joinTable{"$relationshipName/$entityName"} =
3232 :			"$relationshipName.to_link = $entityName.id";
3233 :			}
3234 :			}
3235 :			# Add the join table to the structure.
3236 :			$metadata->{Joins} = \%joinTable;
3237 :			# Return the slurped and fixed-up structure.
3238 :			return $metadata;
3239 :	parrello	1.1	}
3240 :
3241 :	parrello	1.42	=head3 SortNeeded
3242 :
3243 :	parrello	1.60	C<< my $parms = $erdb->SortNeeded($relationName); >>
3244 :
3245 :			Return the pipe command for the sort that should be applied to the specified
3246 :			relation when creating the load file.
3247 :
3248 :			For example, if the load file should be sorted ascending by the first
3249 :			field with duplicates removed, this method would return
3250 :	parrello	1.42
3251 :	parrello	1.60	sort -k 1 -u -t "\t"
3252 :
3253 :			If the first field is numeric and duplicates are okay, the method would
3254 :			return
3255 :
3256 :			sort -k 1n -t "\t"
3257 :	parrello	1.42
3258 :			=over 4
3259 :
3260 :			=item relationName
3261 :
3262 :			Name of the relation to be examined.
3263 :
3264 :	parrello	1.60	=item
3265 :	parrello	1.42
3266 :	parrello	1.60	Returns the sort command to use for sorting the relation, suitable for piping.
3267 :	parrello	1.42
3268 :			=back
3269 :
3270 :			=cut
3271 :			#: Return Type $;
3272 :			sub SortNeeded {
3273 :			# Get the parameters.
3274 :			my ($self, $relationName) = @_;
3275 :	parrello	1.60	# Declare a descriptor to hold the names of the key fields.
3276 :			my @keyNames = ();
3277 :			# Declare a flag for indicating uniqueness.
3278 :			my $unique;
3279 :			# Get the relation structure.
3280 :			my $relationData = $self->_FindRelation($relationName);
3281 :			# Find out if the relation is a primary entity relation,
3282 :			# a relationship relation, or a secondary entity relation.
3283 :	parrello	1.43	my $entityTable = $self->{_metaData}->{Entities};
3284 :	parrello	1.60	my $relationshipTable = $self->{_metaData}->{Relationships};
3285 :	parrello	1.42	if (exists $entityTable->{$relationName}) {
3286 :	parrello	1.60	# Here we have a primary entity relation, so we have a unique sort on the
3287 :			# ID field.
3288 :			$unique = "-u ";
3289 :			push @keyNames, "id";
3290 :			} elsif (exists $relationshipTable->{$relationName}) {
3291 :			# Here we have a relationship. We sort using the FROM index.
3292 :			$unique = "";
3293 :			my $relationshipData = $relationshipTable->{$relationName};
3294 :			my $index = $relationData->{Indexes}->{"idx${relationName}From"};
3295 :			push @keyNames, @{$index->{IndexFields}};
3296 :			} else {
3297 :			# Here we have a secondary entity relation, so we have a non-unique sort on
3298 :			# the ID field.
3299 :			$unique = "";
3300 :			push @keyNames, "id";
3301 :			}
3302 :			# Now we parse the key names into sort parameters. First, we prime the return
3303 :			# string.
3304 :	parrello	1.64	my $retVal = "sort -t \"\t\" $unique";
3305 :	parrello	1.60	# Get the relation's field list.
3306 :			my @fields = @{$relationData->{Fields}};
3307 :			# Loop through the keys.
3308 :			for my $keyData (@keyNames) {
3309 :			# Get the key and the ordering.
3310 :			my ($keyName, $ordering);
3311 :			if ($keyData =~ /^([^ ]+) DESC/) {
3312 :			($keyName, $ordering) = ($1, "descending");
3313 :			} else {
3314 :			($keyName, $ordering) = ($keyData, "ascending");
3315 :			}
3316 :			# Find the key's position and type.
3317 :			my $fieldSpec;
3318 :			for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
3319 :			my $thisField = $fields[$i];
3320 :			if ($thisField->{name} eq $keyName) {
3321 :			# Get the sort modifier for this field type. The modifier
3322 :			# decides whether we're using a character, numeric, or
3323 :			# floating-point sort.
3324 :			my $modifier = $TypeTable{$thisField->{type}}->{sort};
3325 :			# If the index is descending for this field, denote we want
3326 :			# to reverse the sort order on this field.
3327 :			if ($ordering eq 'descending') {
3328 :			$modifier .= "r";
3329 :			}
3330 :			# Store the position and modifier into the field spec, which
3331 :	parrello	1.62	# will stop the inner loop. Note that the field number is
3332 :			# 1-based in the sort command, so we have to increment the
3333 :			# index.
3334 :			$fieldSpec = ($i + 1) . $modifier;
3335 :	parrello	1.60	}
3336 :			}
3337 :			# Add this field to the sort command.
3338 :			$retVal .= " -k $fieldSpec";
3339 :	parrello	1.42	}
3340 :			# Return the result.
3341 :			return $retVal;
3342 :			}
3343 :
3344 :	parrello	1.1	=head3 CreateRelationshipIndex
3345 :
3346 :			Create an index for a relationship's relation.
3347 :
3348 :			This is a static method.
3349 :
3350 :			=over 4
3351 :
3352 :			=item indexKey
3353 :
3354 :			Type of index: either C<"From"> or C<"To">.
3355 :
3356 :			=item relationshipName
3357 :
3358 :			Name of the relationship.
3359 :
3360 :			=item relationshipStructure
3361 :
3362 :			Structure describing the relationship that the index will sort.
3363 :
3364 :			=back
3365 :
3366 :			=cut
3367 :
3368 :			sub _CreateRelationshipIndex {
3369 :	parrello	1.10	# Get the parameters.
3370 :			my ($indexKey, $relationshipName, $relationshipStructure) = @_;
3371 :			# Get the target relation.
3372 :			my $relationStructure = $relationshipStructure->{Relations}->{$relationshipName};
3373 :			# Create a descriptor for the link field that goes at the beginning of this index.
3374 :			my $firstField = { name => lcfirst $indexKey . '-link', order => 'ascending' };
3375 :			# Get the target index descriptor.
3376 :			my $newIndex = $relationshipStructure->{$indexKey . "Index"};
3377 :			# Add the first field to the index's field list. Due to the craziness of PERL, if the
3378 :			# index descriptor does not exist, it will be created automatically so we can add
3379 :			# the field to it.
3380 :			unshift @{$newIndex->{IndexFields}}, $firstField;
3381 :	parrello	1.12	# If this is a one-to-many relationship, the "To" index is unique.
3382 :			if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
3383 :			$newIndex->{Unique} = 'true';
3384 :			}
3385 :	parrello	1.10	# Add the index to the relation.
3386 :			_AddIndex("idx$relationshipName$indexKey", $relationStructure, $newIndex);
3387 :	parrello	1.1	}
3388 :
3389 :			=head3 AddIndex
3390 :
3391 :			Add an index to a relation structure.
3392 :
3393 :			This is a static method.
3394 :
3395 :			=over 4
3396 :
3397 :			=item indexName
3398 :
3399 :			Name to give to the new index.
3400 :
3401 :			=item relationStructure
3402 :
3403 :			Relation structure to which the new index should be added.
3404 :
3405 :			=item newIndex
3406 :
3407 :			New index to add.
3408 :
3409 :			=back
3410 :
3411 :			=cut
3412 :
3413 :			sub _AddIndex {
3414 :	parrello	1.10	# Get the parameters.
3415 :			my ($indexName, $relationStructure, $newIndex) = @_;
3416 :			# We want to re-do the index's field list. Instead of an object for each field,
3417 :			# we want a string consisting of the field name optionally followed by the token DESC.
3418 :			my @fieldList = ( );
3419 :			for my $field (@{$newIndex->{IndexFields}}) {
3420 :			# Create a string containing the field name.
3421 :			my $fieldString = $field->{name};
3422 :			# Add the ordering token if needed.
3423 :			if ($field->{order} eq "descending") {
3424 :			$fieldString .= " DESC";
3425 :			}
3426 :			# Push the result onto the field list.
3427 :			push @fieldList, $fieldString;
3428 :			}
3429 :			# Store the field list just created as the new index field list.
3430 :			$newIndex->{IndexFields} = \@fieldList;
3431 :			# Add the index to the relation's index list.
3432 :			$relationStructure->{Indexes}->{$indexName} = $newIndex;
3433 :	parrello	1.1	}
3434 :
3435 :			=head3 FixupFields
3436 :
3437 :			This method fixes the field list for an entity or relationship. It will add the caller-specified
3438 :			relation name to fields that do not have a name and set the C<PrettySort> value as specified.
3439 :
3440 :			This is a static method.
3441 :
3442 :			=over 4
3443 :
3444 :			=item structure
3445 :
3446 :			Entity or relationship structure to be fixed up.
3447 :
3448 :			=item defaultRelationName
3449 :
3450 :			Default relation name to be added to the fields.
3451 :
3452 :			=item prettySortValue
3453 :
3454 :			C<PrettySort> value for the relation's normal fields.
3455 :
3456 :			=item textPrettySortValue
3457 :
3458 :			C<PrettySort> value for the relation's text fields. This value can be set to one greater than the
3459 :			normal pretty sort value so that text fields go at the end of each relation.
3460 :
3461 :			=back
3462 :
3463 :			=cut
3464 :
3465 :			sub _FixupFields {
3466 :	parrello	1.10	# Get the parameters.
3467 :			my ($structure, $defaultRelationName, $prettySortValue, $textPrettySortValue) = @_;
3468 :			# Insure the structure has a field list.
3469 :			if (!exists $structure->{Fields}) {
3470 :			# Here it doesn't, so we create a new one.
3471 :			$structure->{Fields} = { };
3472 :			} else {
3473 :			# Here we have a field list. Loop through its fields.
3474 :			my $fieldStructures = $structure->{Fields};
3475 :			for my $fieldName (keys %{$fieldStructures}) {
3476 :	parrello	1.8	Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
3477 :	parrello	1.10	my $fieldData = $fieldStructures->{$fieldName};
3478 :			# Get the field type.
3479 :			my $type = $fieldData->{type};
3480 :			# Plug in a relation name if it is needed.
3481 :			Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
3482 :			# Plug in a data generator if we need one.
3483 :			if (!exists $fieldData->{DataGen}) {
3484 :			# The data generator will use the default for the field's type.
3485 :			$fieldData->{DataGen} = { content => $TypeTable{$type}->{dataGen} };
3486 :			}
3487 :			# Plug in the defaults for the optional data generation parameters.
3488 :			Tracer::MergeOptions($fieldData->{DataGen}, { testCount => 1, pass => 0 });
3489 :			# Add the PrettySortValue.
3490 :			$fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
3491 :			}
3492 :			}
3493 :	parrello	1.1	}
3494 :
3495 :			=head3 FixName
3496 :
3497 :			Fix the incoming field name so that it is a legal SQL column name.
3498 :
3499 :			This is a static method.
3500 :
3501 :			=over 4
3502 :
3503 :			=item fieldName
3504 :
3505 :			Field name to fix.
3506 :
3507 :			=item RETURN
3508 :
3509 :			Returns the fixed-up field name.
3510 :
3511 :			=back
3512 :
3513 :			=cut
3514 :
3515 :			sub _FixName {
3516 :	parrello	1.10	# Get the parameter.
3517 :			my ($fieldName) = @_;
3518 :			# Replace its minus signs with underscores.
3519 :			$fieldName =~ s/-/_/g;
3520 :			# Return the result.
3521 :			return $fieldName;
3522 :	parrello	1.1	}
3523 :
3524 :			=head3 FixNames
3525 :
3526 :			Fix all the field names in a list.
3527 :
3528 :			This is a static method.
3529 :
3530 :			=over 4
3531 :
3532 :			=item field1, field2, field3, ... fieldn
3533 :
3534 :			List of field names to fix.
3535 :
3536 :			=item RETURN
3537 :
3538 :			Returns a list of fixed-up versions of the incoming field names.
3539 :
3540 :			=back
3541 :
3542 :			=cut
3543 :
3544 :			sub _FixNames {
3545 :	parrello	1.10	# Create the result list.
3546 :			my @result = ( );
3547 :			# Loop through the incoming parameters.
3548 :			for my $field (@_) {
3549 :			push @result, _FixName($field);
3550 :			}
3551 :			# Return the result.
3552 :			return @result;
3553 :	parrello	1.1	}
3554 :
3555 :			=head3 AddField
3556 :
3557 :			Add a field to a field list.
3558 :
3559 :			This is a static method.
3560 :
3561 :			=over 4
3562 :
3563 :			=item structure
3564 :
3565 :			Structure (usually an entity or relationship) that is to contain the field.
3566 :
3567 :			=item fieldName
3568 :
3569 :			Name of the new field.
3570 :
3571 :			=item fieldData
3572 :
3573 :			Structure containing the data to put in the field.
3574 :
3575 :			=back
3576 :
3577 :			=cut
3578 :
3579 :			sub _AddField {
3580 :	parrello	1.10	# Get the parameters.
3581 :			my ($structure, $fieldName, $fieldData) = @_;
3582 :			# Create the field structure by copying the incoming data.
3583 :			my $fieldStructure = {%{$fieldData}};
3584 :			# Get a reference to the field list itself.
3585 :			my $fieldList = $structure->{Fields};
3586 :			# Add the field to the field list.
3587 :			$fieldList->{$fieldName} = $fieldStructure;
3588 :	parrello	1.1	}
3589 :
3590 :			=head3 ReOrderRelationTable
3591 :
3592 :			This method will take a relation table and re-sort it according to the implicit ordering of the
3593 :			C<PrettySort> property. Instead of a hash based on field names, it will return a list of fields.
3594 :			This requires creating a new hash that contains the field name in the C<name> property but doesn't
3595 :			have the C<PrettySort> property, and then inserting that new hash into the field list.
3596 :
3597 :			This is a static method.
3598 :
3599 :			=over 4
3600 :
3601 :			=item relationTable
3602 :
3603 :			Relation hash to be reformatted into a list.
3604 :
3605 :			=item RETURN
3606 :
3607 :			A list of field hashes.
3608 :
3609 :			=back
3610 :
3611 :			=cut
3612 :
3613 :			sub _ReOrderRelationTable {
3614 :	parrello	1.10	# Get the parameters.
3615 :			my ($relationTable) = @_;
3616 :			# Create the return list.
3617 :			my @resultList;
3618 :			# Rather than copy all the fields in a single pass, we make multiple passes and only copy
3619 :			# fields whose PrettySort value matches the current pass number. This process continues
3620 :			# until we process all the fields in the relation.
3621 :			my $fieldsLeft = (values %{$relationTable});
3622 :			for (my $sortPass = 1; $fieldsLeft > 0; $sortPass++) {
3623 :			# Loop through the fields. Note that we lexically sort the fields. This makes field name
3624 :			# secondary to pretty-sort number in the final ordering.
3625 :			for my $fieldName (sort keys %{$relationTable}) {
3626 :			# Get this field's data.
3627 :			my $fieldData = $relationTable->{$fieldName};
3628 :			# Verify the sort pass.
3629 :			if ($fieldData->{PrettySort} == $sortPass) {
3630 :			# Here we're in the correct pass. Denote we've found a field.
3631 :			$fieldsLeft--;
3632 :			# The next step is to create the field structure. This done by copying all
3633 :			# of the field elements except PrettySort and adding the name.
3634 :			my %thisField;
3635 :			for my $property (keys %{$fieldData}) {
3636 :			if ($property ne 'PrettySort') {
3637 :			$thisField{$property} = $fieldData->{$property};
3638 :			}
3639 :			}
3640 :			$thisField{name} = $fieldName;
3641 :			# Now we add this field to the end of the result list.
3642 :			push @resultList, \%thisField;
3643 :			}
3644 :			}
3645 :			}
3646 :			# Return a reference to the result list.
3647 :			return \@resultList;
3648 :	parrello	1.1
3649 :			}
3650 :
3651 :			=head3 IsPrimary
3652 :
3653 :			Return TRUE if a specified relation is a primary relation, else FALSE. A relation is primary
3654 :			if it has the same name as an entity or relationship.
3655 :
3656 :			This is an instance method.
3657 :
3658 :			=over 4
3659 :
3660 :			=item relationName
3661 :
3662 :			Name of the relevant relation.
3663 :
3664 :			=item RETURN
3665 :
3666 :			Returns TRUE for a primary relation, else FALSE.
3667 :
3668 :			=back
3669 :
3670 :			=cut
3671 :
3672 :			sub _IsPrimary {
3673 :	parrello	1.10	# Get the parameters.
3674 :			my ($self, $relationName) = @_;
3675 :			# Check for the relation in the entity table.
3676 :			my $entityTable = $self->{_metaData}->{Entities};
3677 :			my $retVal = exists $entityTable->{$relationName};
3678 :			if (! $retVal) {
3679 :			# Check for it in the relationship table.
3680 :			my $relationshipTable = $self->{_metaData}->{Relationships};
3681 :			$retVal = exists $relationshipTable->{$relationName};
3682 :			}
3683 :			# Return the determination indicator.
3684 :			return $retVal;
3685 :	parrello	1.1	}
3686 :
3687 :			=head3 FindRelation
3688 :
3689 :			Return the descriptor for the specified relation.
3690 :
3691 :			This is an instance method.
3692 :
3693 :			=over 4
3694 :
3695 :			=item relationName
3696 :
3697 :			Name of the relation whose descriptor is to be returned.
3698 :
3699 :			=item RETURN
3700 :
3701 :			Returns the object that describes the relation's indexes and fields.
3702 :
3703 :			=back
3704 :
3705 :			=cut
3706 :			sub _FindRelation {
3707 :	parrello	1.10	# Get the parameters.
3708 :			my ($self, $relationName) = @_;
3709 :			# Get the relation's structure from the master relation table in the metadata structure.
3710 :			my $metaData = $self->{_metaData};
3711 :			my $retVal = $metaData->{RelationTable}->{$relationName};
3712 :			# Return it to the caller.
3713 :			return $retVal;
3714 :	parrello	1.1	}
3715 :
3716 :			=head2 HTML Documentation Utility Methods
3717 :
3718 :			=head3 ComputeRelationshipSentence
3719 :
3720 :			The relationship sentence consists of the relationship name between the names of the
3721 :			two related entities and an arity indicator.
3722 :
3723 :			This is a static method.
3724 :
3725 :			=over 4
3726 :
3727 :			=item relationshipName
3728 :
3729 :			Name of the relationship.
3730 :
3731 :			=item relationshipStructure
3732 :
3733 :			Relationship structure containing the relationship's description and properties.
3734 :
3735 :			=item RETURN
3736 :
3737 :			Returns a string containing the entity names on either side of the relationship name and an
3738 :			indicator of the arity.
3739 :
3740 :			=back
3741 :
3742 :			=cut
3743 :
3744 :			sub _ComputeRelationshipSentence {
3745 :	parrello	1.10	# Get the parameters.
3746 :			my ($relationshipName, $relationshipStructure) = @_;
3747 :			# Format the relationship sentence.
3748 :			my $result = "$relationshipStructure->{from} <b>$relationshipName</b> $relationshipStructure->{to}";
3749 :			# Compute the arity.
3750 :			my $arityCode = $relationshipStructure->{arity};
3751 :			my $arity = $ArityTable{$arityCode};
3752 :			$result .= " ($arity)";
3753 :			return $result;
3754 :	parrello	1.1	}
3755 :
3756 :			=head3 ComputeRelationshipHeading
3757 :
3758 :			The relationship heading is the L<relationship sentence\|/ComputeRelationshipSentence> with the entity
3759 :			names hyperlinked to the appropriate entity sections of the document.
3760 :
3761 :			This is a static method.
3762 :
3763 :			=over 4
3764 :
3765 :			=item relationshipName
3766 :
3767 :			Name of the relationship.
3768 :
3769 :			=item relationshipStructure
3770 :
3771 :			Relationship structure containing the relationship's description and properties.
3772 :
3773 :			=item RETURN
3774 :
3775 :			Returns a string containing the entity names on either side of the relationship name with the entity
3776 :			names hyperlinked.
3777 :
3778 :			=back
3779 :
3780 :			=cut
3781 :
3782 :			sub _ComputeRelationshipHeading {
3783 :	parrello	1.10	# Get the parameters.
3784 :			my ($relationshipName, $relationshipStructure) = @_;
3785 :			# Get the FROM and TO entity names.
3786 :			my $fromEntity = $relationshipStructure->{from};
3787 :			my $toEntity = $relationshipStructure->{to};
3788 :			# Format a relationship sentence with hyperlinks in it.
3789 :			my $result = "<a href=\"#$fromEntity\">$fromEntity</a> $relationshipName <a href=\"#$toEntity\">$toEntity</a>";
3790 :			return $result;
3791 :	parrello	1.1	}
3792 :
3793 :			=head3 ShowRelationTable
3794 :
3795 :			Generate the HTML string for a particular relation. The relation's data will be formatted as an HTML
3796 :			table with three columns-- the field name, the field type, and the field description.
3797 :
3798 :			This is a static method.
3799 :
3800 :			=over 4
3801 :
3802 :			=item relationName
3803 :
3804 :			Name of the relation being formatted.
3805 :
3806 :			=item relationData
3807 :
3808 :			Hash containing the relation's fields and indexes.
3809 :
3810 :			=item RETURN
3811 :
3812 :			Returns an HTML string that can be used to display the relation name and all of its fields.
3813 :
3814 :			=back
3815 :
3816 :			=cut
3817 :
3818 :			sub _ShowRelationTable {
3819 :	parrello	1.10	# Get the parameters.
3820 :			my ($relationName, $relationData) = @_;
3821 :			# Start the relation's field table.
3822 :			my $htmlString = _OpenFieldTable($relationName);
3823 :			# Loop through the fields.
3824 :			for my $field (@{$relationData->{Fields}}) {
3825 :			$htmlString .= _ShowField($field);
3826 :			}
3827 :			# Close this relation's field table.
3828 :			$htmlString .= &_CloseTable;
3829 :			# Now we show the relation's indexes.
3830 :			$htmlString .= "<ul>\n";
3831 :			my $indexTable = $relationData->{Indexes};
3832 :			for my $indexName (sort keys %{$indexTable}) {
3833 :			my $indexData = $indexTable->{$indexName};
3834 :			# Determine whether or not the index is unique.
3835 :			my $fullName = $indexName;
3836 :			if (exists $indexData->{Unique} && $indexData->{Unique} eq "true") {
3837 :			$fullName .= " (unique)";
3838 :			}
3839 :			# Start an HTML list item for this index.
3840 :			$htmlString .= "<li><b>Index $fullName</b>\n<ul>\n";
3841 :			# Add any note text.
3842 :			if (my $note = $indexData->{Notes}) {
3843 :			$htmlString .= "<li>" . _HTMLNote($note->{content}) . "</li>\n";
3844 :			}
3845 :			# Add the fiield list.
3846 :			$htmlString .= "<li><i>" . join(', ', @{$indexData->{IndexFields}}) . "</i></li>\n";
3847 :			# Close this entry.
3848 :			$htmlString .= "</ul></li>\n";
3849 :			}
3850 :			# Close off the index list.
3851 :			$htmlString .= "</ul>\n";
3852 :	parrello	1.1	}
3853 :
3854 :			=head3 OpenFieldTable
3855 :
3856 :			This method creates the header string for the field table generated by L</ShowMetaData>.
3857 :
3858 :			This is a static method.
3859 :
3860 :			=over 4
3861 :
3862 :			=item tablename
3863 :
3864 :			Name of the table whose fields will be displayed.
3865 :
3866 :			=item RETURN
3867 :
3868 :			Returns a string containing the HTML for a field table's header.
3869 :
3870 :			=back
3871 :
3872 :			=cut
3873 :
3874 :			sub _OpenFieldTable {
3875 :	parrello	1.10	my ($tablename) = @_;
3876 :			return _OpenTable($tablename, 'Field', 'Type', 'Description');
3877 :	parrello	1.1	}
3878 :
3879 :			=head3 OpenTable
3880 :
3881 :			This method creates the header string for an HTML table.
3882 :
3883 :			This is a static method.
3884 :
3885 :			=over 4
3886 :
3887 :			=item tablename
3888 :
3889 :			Title of the table.
3890 :
3891 :			=item colName1, colName2, ..., colNameN
3892 :
3893 :			List of column names.
3894 :
3895 :			=item RETURN
3896 :
3897 :			Returns a string containing the HTML for the desired table's header.
3898 :
3899 :			=back
3900 :
3901 :			=cut
3902 :
3903 :			sub _OpenTable {
3904 :	parrello	1.10	# Get the parameters.
3905 :			my ($tablename, @colNames) = @_;
3906 :			# Compute the number of columns.
3907 :			my $colCount = @colNames;
3908 :			# Generate the title row.
3909 :			my $htmlString = "<p><table border=\"2\"><tr><td colspan=\"$colCount\" align=\"center\">$tablename</td></tr>\n";
3910 :			# Loop through the columns, adding the column header rows.
3911 :			$htmlString .= "<tr>";
3912 :			for my $colName (@colNames) {
3913 :			$htmlString .= "<th>$colName</th>";
3914 :			}
3915 :			$htmlString .= "</tr>\n";
3916 :			return $htmlString;
3917 :	parrello	1.1	}
3918 :
3919 :			=head3 CloseTable
3920 :
3921 :			This method returns the HTML for closing a table.
3922 :
3923 :			This is a static method.
3924 :
3925 :			=cut
3926 :
3927 :			sub _CloseTable {
3928 :	parrello	1.10	return "</table></p>\n";
3929 :	parrello	1.1	}
3930 :
3931 :			=head3 ShowField
3932 :
3933 :			This method returns the HTML for displaying a row of field information in a field table.
3934 :
3935 :			This is a static method.
3936 :
3937 :			=over 4
3938 :
3939 :			=item fieldData
3940 :
3941 :			Table of data about the field.
3942 :
3943 :			=item RETURN
3944 :
3945 :			Returns an HTML string for a table row that shows the field's name, type, and description.
3946 :
3947 :			=back
3948 :
3949 :			=cut
3950 :
3951 :			sub _ShowField {
3952 :	parrello	1.10	# Get the parameters.
3953 :			my ($fieldData) = @_;
3954 :			# Create the HTML string.
3955 :			my $htmlString = "<tr><th align=\"left\">$fieldData->{name}</th><td>$fieldData->{type}</td>";
3956 :			# If we have content, add it as a third column.
3957 :			if (exists $fieldData->{Notes}) {
3958 :			$htmlString .= "<td>" . _HTMLNote($fieldData->{Notes}->{content}) . "</td>";
3959 :			}
3960 :			# Close off the row.
3961 :			$htmlString .= "</tr>\n";
3962 :			# Return the result.
3963 :			return $htmlString;
3964 :	parrello	1.1	}
3965 :
3966 :			=head3 HTMLNote
3967 :
3968 :			Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3969 :			supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3970 :			Except for C<[p]>, all the codes are closed by slash-codes. So, for
3971 :			example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3972 :
3973 :			This is a static method.
3974 :
3975 :			=over 4
3976 :
3977 :			=item dataString
3978 :
3979 :			String to convert to HTML.
3980 :
3981 :			=item RETURN
3982 :
3983 :			An HTML string derived from the input string.
3984 :
3985 :			=back
3986 :
3987 :			=cut
3988 :
3989 :			sub _HTMLNote {
3990 :	parrello	1.10	# Get the parameter.
3991 :			my ($dataString) = @_;
3992 :			# Substitute the codes.
3993 :			$dataString =~ s!\[(/?[bi])\]!<$1>!g;
3994 :			$dataString =~ s!\[p\]!</p><p>!g;
3995 :			# Return the result.
3996 :			return $dataString;
3997 :	parrello	1.1	}
3998 :
3999 :			=head2 Data Generation Utilities
4000 :
4001 :			=head3 IntGen
4002 :
4003 :			C<< my $integer = IntGen($min, $max); >>
4004 :
4005 :			Returns a random number between the specified minimum and maximum (inclusive).
4006 :
4007 :			=over 4
4008 :
4009 :			=item min
4010 :
4011 :			Minimum permissible return value.
4012 :
4013 :			=item max
4014 :
4015 :			Maximum permissible return value.
4016 :
4017 :			=item RETURN
4018 :
4019 :			Returns a value no lower than the minimum and no greater than the maximum.
4020 :
4021 :			=back
4022 :
4023 :			=cut
4024 :
4025 :			sub IntGen {
4026 :	parrello	1.10	# Get the parameters.
4027 :			my ($min, $max) = @_;
4028 :			# Determine the range of possible values. Note we put some space well above the
4029 :			# maximum value to give it a fighting chance of apppearing in the list.
4030 :			my $span = $max + 0.99 - $min;
4031 :			# Create an integer in the range.
4032 :			my $retVal = $min + int(rand($span));
4033 :			# Return the result.
4034 :			return $retVal;
4035 :	parrello	1.1	}
4036 :
4037 :			=head3 RandChar
4038 :
4039 :			C<< my $char = RandChar($sourceString); >>
4040 :
4041 :			Select a random character from a string.
4042 :
4043 :			=over 4
4044 :
4045 :			=item sourceString
4046 :
4047 :			String from which the random character should be selected.
4048 :
4049 :			=item RETURN
4050 :
4051 :			Returns a single character from the incoming string.
4052 :
4053 :			=back
4054 :
4055 :			=cut
4056 :
4057 :			sub RandChar {
4058 :	parrello	1.10	# Get the parameter.
4059 :			my ($sourceString) = @_;
4060 :			# Select a random character.
4061 :			my $retVal = IntGen(0, (length $sourceString) - 1);
4062 :			# Return it.
4063 :			return substr($sourceString, $retVal, 1);
4064 :	parrello	1.1	}
4065 :
4066 :			=head3 RandChars
4067 :
4068 :			C<< my $string = RandChars($sourceString, $length); >>
4069 :
4070 :			Create a string from characters taken from a source string.
4071 :
4072 :			=over 4
4073 :
4074 :			=item sourceString
4075 :
4076 :			String from which the random characters should be selected.
4077 :
4078 :			=item length
4079 :
4080 :			Number of characters to put in the output string.
4081 :
4082 :			=item RETURN
4083 :
4084 :			Returns a string of the specified length consisting of characters taken from the
4085 :			source string.
4086 :
4087 :			=back
4088 :
4089 :			=cut
4090 :
4091 :			sub RandChars {
4092 :	parrello	1.10	# Get the parameters.
4093 :			my ($sourceString, $length) = @_;
4094 :			# Call RandChar repeatedly to generate the string.
4095 :			my $retVal = "";
4096 :			for (my $i = 0; $i < $length; $i++) {
4097 :			$retVal .= RandChar($sourceString);
4098 :			}
4099 :			# Return the result.
4100 :			return $retVal;
4101 :	parrello	1.1	}
4102 :
4103 :			=head3 RandParam
4104 :
4105 :			C<< my $value = RandParam($parm1, $parm2, ... $parmN); >>
4106 :
4107 :			Return a randomly-selected value from the parameter list.
4108 :
4109 :			=over 4
4110 :
4111 :			=item parm1, parm2, ... parmN
4112 :
4113 :			List of values of which one will be selected.
4114 :
4115 :			=item RETURN
4116 :
4117 :			Returns a randomly-chosen value from the specified list.
4118 :
4119 :			=back
4120 :
4121 :			=cut
4122 :
4123 :			sub RandParam {
4124 :	parrello	1.10	# Get the parameter.
4125 :			my @parms = @_;
4126 :			# Choose a random parameter from the list.
4127 :			my $chosenIndex = IntGen(0, $#parms);
4128 :			return $parms[$chosenIndex];
4129 :	parrello	1.1	}
4130 :
4131 :			=head3 StringGen
4132 :
4133 :			C<< my $string = StringGen($pattern1, $pattern2, ... $patternN); >>
4134 :
4135 :			Returns a random string derived from a randomly-chosen format pattern. The pattern
4136 :			can either be a number (indicating the number of characters desired, or the letter
4137 :			C<P> followed by a picture. The picture should contain C<A> when a letter is desired,
4138 :			C<9> when a digit is desired, C<V> when a vowel is desired, C<K> when a consonant is
4139 :			desired, and C<X> when a letter or a digit is desired. Any other character will be
4140 :			translated as a literal.
4141 :
4142 :			=over 4
4143 :
4144 :			=item pattern1, pattern2, ... patternN
4145 :
4146 :			List of patterns to be used to generate string values.
4147 :
4148 :			=item RETURN
4149 :
4150 :			A single string generated from a pattern.
4151 :
4152 :			=back
4153 :
4154 :			=cut
4155 :
4156 :			sub StringGen {
4157 :	parrello	1.10	# Get the parameters.
4158 :			my @patterns = @_;
4159 :			# Choose the appropriate pattern.
4160 :			my $chosenPattern = RandParam(@patterns);
4161 :			# Declare the return variable.
4162 :			my $retVal = "";
4163 :			# Determine whether this is a count or a picture pattern.
4164 :			if ($chosenPattern =~ m/^\d+/) {
4165 :			# Here we have a count. Get the string of source characters.
4166 :			my $letterString = $PictureTable{'X'};
4167 :			my $stringLen = length $letterString;
4168 :			# Save the number of characters we have to generate.
4169 :			my $charsLeft = $chosenPattern;
4170 :			# Loop until the return variable is full.
4171 :			while ($charsLeft > 0) {
4172 :			# Generate a random position in the soruce string.
4173 :			my $stringIndex = IntGen(0, $stringLen - 1);
4174 :			# Compute the number of characters to pull out of the source string.
4175 :			my $chunkSize = $stringLen - $stringIndex;
4176 :			if ($chunkSize > $charsLeft) { $chunkSize = $charsLeft; }
4177 :			# Stuff this chunk into the return value.
4178 :			$retVal .= substr($letterString, $stringIndex, $chunkSize);
4179 :			# Record the data moved.
4180 :			$charsLeft -= $chunkSize;
4181 :			}
4182 :			} elsif ($chosenPattern =~ m/^P/) {
4183 :			# Here we have a picture string. We will move through the picture one
4184 :			# character at a time generating data.
4185 :			for (my $i = 1; $i < length $chosenPattern; $i++) {
4186 :			# Get this picture character.
4187 :			my $chr = substr($chosenPattern, $i, 1);
4188 :			# Check to see if the picture char is one we recognize.
4189 :			if (exists $PictureTable{$chr}) {
4190 :			# Choose a random character from the available values for this
4191 :			# picture character.
4192 :			$retVal .= RandChar($PictureTable{$chr});
4193 :			} else {
4194 :			# Copy in the picture character as a literal.
4195 :			$retVal .= $chr;
4196 :			}
4197 :			}
4198 :			} else {
4199 :			# Here we have neither a picture string or a letter count, so we treat
4200 :			# the string as a literal.
4201 :			$retVal = $chosenPattern;
4202 :			}
4203 :			# Return the string formed.
4204 :			return $retVal;
4205 :	parrello	1.1	}
4206 :
4207 :			=head3 DateGen
4208 :
4209 :			C<< my $date = DateGen($startDayOffset, $endDayOffset, $minutes); >>
4210 :
4211 :			Return a numeric timestamp within the specified range of days with the specified minute
4212 :			value. The range of days is specified relevant to the current day. Thus, the call
4213 :
4214 :			C<< my $date = DateGen(-1, 5, 720); >>
4215 :
4216 :			will return a timestamp at noon (72 minutes past midnight) sometime during the week that
4217 :			began on the preceding day. If you want a random minute of the day, simply combine with
4218 :			a call to L</IntGen>, as follows.
4219 :
4220 :			C<< my $date = DateGen(-1, 5, IntGen(0, 1439)); >>
4221 :
4222 :			=over 4
4223 :
4224 :			=item startDayOffset
4225 :
4226 :			The earliest day that can be returned, relative to the current day.
4227 :
4228 :			=item endDayOffset
4229 :
4230 :			The latest day that can be returned, related to the current day.
4231 :
4232 :			=item minutes
4233 :
4234 :			Number of minutes into the selected day that should be used.
4235 :
4236 :			=back
4237 :
4238 :			=cut
4239 :
4240 :			sub DateGen {
4241 :	parrello	1.10	# Get the parameters.
4242 :			my ($startDayOffset, $endDayOffset, $minutes) = @_;
4243 :			# Get midnight of the current day.
4244 :			my $now = time();
4245 :			my ($sec, $min, $hour) = localtime($now);
4246 :			my $today = $now - (($hour * 60 + $min) * 60 + $sec);
4247 :			# Compute the day we want.
4248 :			my $newDay = IntGen($startDayOffset, $endDayOffset) * 86400 + $today;
4249 :			# Add the minutes.
4250 :			my $retVal = $newDay + $minutes * 60;
4251 :			# Return the result.
4252 :			return $retVal;
4253 :	parrello	1.1	}
4254 :
4255 :			=head3 FloatGen
4256 :
4257 :			C<< my $number = FloatGen($min, $max); >>
4258 :
4259 :			Return a random floating-point number greater than or equal to the specified minimum and
4260 :			less than the specified maximum.
4261 :
4262 :			=over 4
4263 :
4264 :			=item min
4265 :
4266 :			Minimum permissible value for the number returned.
4267 :
4268 :			=item max
4269 :
4270 :			Maximum permissible value for the number returned.
4271 :
4272 :			=item RETURN
4273 :
4274 :			Returns a floating-point number anywhere in the specified range.
4275 :
4276 :			=back
4277 :
4278 :			=cut
4279 :
4280 :			sub FloatGen {
4281 :	parrello	1.10	# Get the parameters.
4282 :			my ($min, $max) = @_;
4283 :			# Generate the result.
4284 :			my $retVal = rand($max - $min) + $min;
4285 :			return $retVal;
4286 :	parrello	1.1	}
4287 :
4288 :			=head3 ListGen
4289 :
4290 :			C<< my @list = ListGen($pattern, $count); >>
4291 :
4292 :			Return a list containing a fixed number of randomly-generated strings.
4293 :
4294 :			=over 4
4295 :
4296 :			=item pattern
4297 :
4298 :			A pattern (in the form expected by L</StringGen>) that should be used to generate the
4299 :			strings in the list.
4300 :
4301 :			=item count
4302 :
4303 :			The number of list entries to generate.
4304 :
4305 :			=item RETURN
4306 :
4307 :			Returns a list consisting of the specified number of strings.
4308 :
4309 :			=back
4310 :
4311 :			=cut
4312 :
4313 :			sub ListGen {
4314 :	parrello	1.10	# Get the parameters.
4315 :			my ($pattern, $count) = @_;
4316 :			# Generate the list.
4317 :			my @retVal = ();
4318 :			for (my $i = 0; $i < $count; $i++) {
4319 :			push @retVal, StringGen($pattern);
4320 :			}
4321 :			# Return it.
4322 :			return @retVal;
4323 :	parrello	1.1	}
4324 :
4325 :	overbeek	1.11	1;

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