Annotation of /Sprout/ERDB.pm

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1 :	parrello	1.1	package ERDB;
2 :
3 :	parrello	1.10	use strict;
4 :			use Tracer;
5 :	olson	1.14	use DBrtns;
6 :	parrello	1.10	use Data::Dumper;
7 :			use XML::Simple;
8 :			use DBQuery;
9 :			use DBObject;
10 :			use Stats;
11 :			use Time::HiRes qw(gettimeofday);
12 :	parrello	1.42	use Digest::MD5 qw(md5_base64);
13 :	parrello	1.19	use FIG;
14 :	parrello	1.73	use CGI;
15 :	parrello	1.1
16 :			=head1 Entity-Relationship Database Package
17 :
18 :			=head2 Introduction
19 :
20 :			The Entity-Relationship Database Package allows the client to create an easily-configurable
21 :			database of Entities connected by Relationships. Each entity is represented by one or more
22 :			relations in an underlying SQL database. Each relationship is represented by a single
23 :			relation that connects two entities.
24 :
25 :			Although this package is designed for general use, all examples are derived from the
26 :			Sprout database, which is the first database implemented using this package.
27 :
28 :			Each entity has at least one relation, the I<primary relation>, that has the same name as
29 :			the entity. The primary relation contains a field named C<id> that contains the unique
30 :			identifier of each entity instance. An entity may have additional relations that contain
31 :			fields which are optional or can occur more than once. For example, the B<FEATURE> entity
32 :			has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
33 :			is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
34 :			however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
35 :			relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36 :			The B<FEATURE> entity also contains an optional virulence number. This is implemented
37 :			as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38 :	parrello	1.8	(C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39 :			the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40 :			number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41 :			C<FeatureVirulence>.
42 :	parrello	1.1
43 :			Entities are connected by binary relationships implemented using single relations possessing the
44 :			same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
45 :			or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
46 :			ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
47 :			of the relationship is generally a verb phrase with the source entity as the subject and the
48 :			target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
49 :			and B<SOURCE> entities, and indicates that a particular source organization participated in the
50 :			mapping of the genome. A source organization frequently participates in the mapping
51 :			of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
52 :			this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
53 :			relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
54 :			and C<to-link>, which contains a source ID.
55 :
56 :			A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
57 :			are implemented as additional fields in the relationship's relation. So, for example, the
58 :			B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
59 :			to determine which sequences make up a contig. The relationship has as an attribute the
60 :			B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61 :			is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62 :
63 :	parrello	1.73	The database itself is described by an XML file. In addition to all the data required to define
64 :			the entities, relationships, and attributes, the schema provides space for notes describing
65 :			the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66 :			for the database.
67 :
68 :			Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69 :			in which case it will be used to generate a text search index in which the user searches for words
70 :			in the field instead of a particular field value.
71 :	parrello	1.1
72 :			Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73 :			is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74 :			was inserted by the L</InsertObject> method.
75 :
76 :	parrello	1.8	=head2 XML Database Description
77 :
78 :			=head3 Data Types
79 :
80 :			The ERDB system supports the following data types. Note that there are numerous string
81 :			types depending on the maximum length. Some database packages limit the total number of
82 :			characters you have in an index key; to insure the database works in all environments,
83 :			the type of string should be the shortest one possible that supports all the known values.
84 :
85 :			=over 4
86 :
87 :			=item char
88 :
89 :			single ASCII character
90 :
91 :			=item int
92 :
93 :			32-bit signed integer
94 :
95 :	parrello	1.60	=item counter
96 :
97 :			32-bit unsigned integer
98 :
99 :	parrello	1.8	=item date
100 :
101 :			64-bit unsigned integer, representing a PERL date/time value
102 :
103 :			=item text
104 :
105 :			long string; Text fields cannot be used in indexes or sorting and do not support the
106 :			normal syntax of filter clauses, but can be up to a billion character in length
107 :
108 :			=item float
109 :
110 :			double-precision floating-point number
111 :
112 :			=item boolean
113 :
114 :			single-bit numeric value; The value is stored as a 16-bit signed integer (for
115 :			compatability with certain database packages), but the only values supported are
116 :			0 and 1.
117 :
118 :	parrello	1.44	=item id-string
119 :
120 :			variable-length string, maximum 25 characters
121 :
122 :	parrello	1.8	=item key-string
123 :
124 :			variable-length string, maximum 40 characters
125 :
126 :			=item name-string
127 :
128 :			variable-length string, maximum 80 characters
129 :
130 :			=item medium-string
131 :
132 :			variable-length string, maximum 160 characters
133 :
134 :			=item string
135 :
136 :			variable-length string, maximum 255 characters
137 :
138 :	parrello	1.42	=item hash-string
139 :
140 :			variable-length string, maximum 22 characters
141 :
142 :	parrello	1.8	=back
143 :
144 :	parrello	1.42	The hash-string data type has a special meaning. The actual key passed into the loader will
145 :			be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146 :			MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147 :			digest. Therefore, it is presumed the keys will be unique. When the database is actually
148 :			in use, the hashed keys will be presented rather than the original values. For this reason,
149 :			they should not be used for entities where the key is meaningful.
150 :
151 :	parrello	1.8	=head3 Global Tags
152 :
153 :			The entire database definition must be inside a B<Database> tag. The display name of
154 :			the database is given by the text associated with the B<Title> tag. The display name
155 :			is only used in the automated documentation. It has no other effect. The entities and
156 :			relationships are listed inside the B<Entities> and B<Relationships> tags,
157 :			respectively. None of these tags have attributes.
158 :
159 :	parrello	1.10	<Database>
160 :			<Title>... display title here...</Title>
161 :			<Entities>
162 :			... entity definitions here ...
163 :			</Entities>
164 :			<Relationships>
165 :			... relationship definitions here...
166 :			</Relationships>
167 :			</Database>
168 :	parrello	1.8
169 :			Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170 :			The text inside the B<Notes> tag contains comments that will appear when the database
171 :			documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172 :			italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173 :
174 :			=head3 Fields
175 :
176 :			Both entities and relationships have fields described by B<Field> tags. A B<Field>
177 :			tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178 :			object mus be inside B<Fields> tags.
179 :
180 :	parrello	1.10	<Entity ... >
181 :			<Fields>
182 :			... Field tags ...
183 :			</Fields>
184 :			</Entity>
185 :	parrello	1.8
186 :			The attributes for the B<Field> tag are as follows.
187 :
188 :			=over 4
189 :
190 :			=item name
191 :
192 :			Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193 :			and the first character should be a letter. Most underlying databases are case-insensitive
194 :	parrello	1.70	with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195 :			the name C<search-relevance> has special meaning for full-text searches and should not be
196 :			used as a field name.
197 :	parrello	1.8
198 :			=item type
199 :
200 :			Data type of the field. The legal data types are given above.
201 :
202 :			=item relation
203 :
204 :			Name of the relation containing the field. This should only be specified for entity
205 :			fields. The ERDB system does not support optional fields or multi-occurring fields
206 :			in the primary relation of an entity. Instead, they are put into secondary relations.
207 :			So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208 :			grouping used to select a subset of the genomes. A given genome may not be in any
209 :			groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210 :			value. The relation name specified must be a valid table name. By convention, it is
211 :			usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212 :			entity, the fields without a relation attribute are said to belong to the
213 :			I<primary relation>. This relation has the same name as the entity itself.
214 :
215 :	parrello	1.70	=item searchable
216 :
217 :			If specified, then the field is a candidate for full-text searching. A single full-text
218 :			index will be created for each relation with at least one searchable field in it.
219 :			For best results, this option should only be used for string or text fields.
220 :
221 :	parrello	1.73	=item special
222 :
223 :			This attribute allows the subclass to assign special meaning for certain fields.
224 :			The interpretation is up to the subclass itself. Currently, only entity fields
225 :			can have this attribute.
226 :
227 :	parrello	1.8	=back
228 :
229 :			=head3 Indexes
230 :
231 :			An entity can have multiple alternate indexes associated with it. The fields must
232 :	parrello	1.74	all be from the same relation. The alternate indexes assist in ordering results
233 :	parrello	1.8	from a query. A relationship can have up to two indexes-- a I<to-index> and a
234 :			I<from-index>. These order the results when crossing the relationship. For
235 :			example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236 :			from-index would order the contigs of a ganome, and the to-index would order
237 :			the genomes of a contig. A relationship's index must specify only fields in
238 :			the relationship.
239 :
240 :			The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
241 :			of a relationship is specified using the B<FromIndex> tag; the to-index is specified
242 :			using the B<ToIndex> tag.
243 :
244 :			Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245 :			tag containing the B<IndexField> tags. These specify, in order, the fields used in
246 :			the index. The attributes of an B<IndexField> tag are as follows.
247 :
248 :			=over 4
249 :
250 :			=item name
251 :
252 :			Name of the field.
253 :
254 :			=item order
255 :
256 :			Sort order of the field-- C<ascending> or C<descending>.
257 :
258 :			=back
259 :
260 :			The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
261 :
262 :			=head3 Object and Field Names
263 :
264 :			By convention entity and relationship names use capital casing (e.g. C<Genome> or
265 :			C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
266 :			with respect to relation names, converting them internally to all-upper case or
267 :			all-lower case.
268 :
269 :			If syntax or parsing errors occur when you try to load or use an ERDB database, the
270 :			most likely reason is that one of your objects has an SQL reserved word as its name.
271 :			The list of SQL reserved words keeps increasing; however, most are unlikely to show
272 :			up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
273 :			C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
274 :			C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
275 :
276 :			Every entity has a field called C<id> that acts as its primary key. Every relationship
277 :			has fields called C<from-link> and C<to-link> that contain copies of the relevant
278 :			entity IDs. These are essentially ERDB's reserved words, and should not be used
279 :			for user-defined field names.
280 :
281 :			=head3 Entities
282 :
283 :			An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
284 :			B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
285 :			containing one or more fields. The attributes of the B<Entity> tag are as follows.
286 :
287 :			=over 4
288 :
289 :			=item name
290 :
291 :			Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
292 :			or C<GroupBlock>) and should be a noun or noun phrase.
293 :
294 :			=item keyType
295 :
296 :			Data type of the primary key. The primary key is always named C<id>.
297 :
298 :			=back
299 :
300 :			=head3 Relationships
301 :
302 :			A relationship is described by the C<Relationship> tag. Within a relationship,
303 :			there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
304 :			fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
305 :			the to-index.
306 :
307 :			The C<Relationship> tag has the following attributes.
308 :
309 :			=over 4
310 :
311 :			=item name
312 :
313 :			Name of the relationship. The relationship name, by convention, uses capital casing
314 :			(e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
315 :			phrase, designed to fit between the from-entity and the to-entity (e.g.
316 :			Block C<ContainsRegionIn> Genome).
317 :
318 :			=item from
319 :
320 :			Name of the entity from which the relationship starts.
321 :
322 :			=item to
323 :
324 :			Name of the entity to which the relationship proceeds.
325 :
326 :			=item arity
327 :
328 :			Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
329 :
330 :			=back
331 :
332 :	parrello	1.1	=cut
333 :
334 :			# GLOBALS
335 :
336 :			# Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
337 :			# "maxLen" is the maximum permissible length of the incoming string data used to populate a field
338 :	parrello	1.73	# of the specified type. "avgLen" is the average byte length for estimating
339 :	parrello	1.75	# record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
340 :			# and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
341 :			# index
342 :	parrello	1.73	my %TypeTable = ( char => { sqlType => 'CHAR(1)', maxLen => 1, avgLen => 1, sort => "",
343 :	parrello	1.75	indexMod => 0, notes => "single ASCII character"},
344 :	parrello	1.73	int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n",
345 :	parrello	1.75	indexMod => 0, notes => "signed 32-bit integer"},
346 :	parrello	1.73	counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n",
347 :	parrello	1.75	indexMod => 0, notes => "unsigned 32-bit integer"},
348 :	parrello	1.73	string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "",
349 :	parrello	1.75	indexMod => 0, notes => "character string, 0 to 255 characters"},
350 :	parrello	1.73	text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "",
351 :	parrello	1.75	indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
352 :	parrello	1.73	date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n",
353 :	parrello	1.75	indexMod => 0, notes => "signed, 64-bit integer"},
354 :	parrello	1.73	float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g",
355 :	parrello	1.75	indexMod => 0, notes => "64-bit double precision floating-point number"},
356 :	parrello	1.73	boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n",
357 :	parrello	1.75	indexMod => 0, notes => "boolean value: 0 if false, 1 if true"},
358 :	parrello	1.42	'hash-string' =>
359 :	parrello	1.73	{ sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "",
360 :	parrello	1.75	indexMod => 0, notes => "string stored in digested form, used for certain types of key fields"},
361 :	parrello	1.44	'id-string' =>
362 :	parrello	1.73	{ sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "",
363 :	parrello	1.75	indexMod => 0, notes => "character string, 0 to 25 characters"},
364 :	parrello	1.10	'key-string' =>
365 :	parrello	1.73	{ sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "",
366 :	parrello	1.75	indexMod => 0, notes => "character string, 0 to 40 characters"},
367 :	parrello	1.10	'name-string' =>
368 :	parrello	1.73	{ sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "",
369 :	parrello	1.75	indexMod => 0, notes => "character string, 0 to 80 characters"},
370 :	parrello	1.10	'medium-string' =>
371 :	parrello	1.73	{ sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "",
372 :	parrello	1.75	indexMod => 0, notes => "character string, 0 to 160 characters"},
373 :	parrello	1.10	);
374 :	parrello	1.1
375 :			# Table translating arities into natural language.
376 :			my %ArityTable = ( '11' => 'one-to-one',
377 :	parrello	1.10	'1M' => 'one-to-many',
378 :			'MM' => 'many-to-many'
379 :			);
380 :	parrello	1.1
381 :	parrello	1.73	# Options for XML input and output.
382 :
383 :			my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
384 :			Entities => 'Entity',
385 :			Fields => 'Field',
386 :			Indexes => 'Index',
387 :			IndexFields => 'IndexField'
388 :			},
389 :			KeyAttr => { Relationship => 'name',
390 :			Entity => 'name',
391 :			Field => 'name'
392 :			},
393 :			SuppressEmpty => 1,
394 :			);
395 :
396 :			my %XmlInOpts = (
397 :			ForceArray => ['Field', 'Index', 'IndexField'],
398 :			ForceContent => 1,
399 :			NormalizeSpace => 2,
400 :			);
401 :			my %XmlOutOpts = (
402 :			RootName => 'Database',
403 :			XMLDecl => 1,
404 :			);
405 :	parrello	1.1
406 :
407 :			=head2 Public Methods
408 :
409 :			=head3 new
410 :
411 :	parrello	1.5	C<< my $database = ERDB->new($dbh, $metaFileName); >>
412 :	parrello	1.1
413 :			Create a new ERDB object.
414 :
415 :			=over 4
416 :
417 :			=item dbh
418 :
419 :			DBKernel database object for the target database.
420 :
421 :			=item metaFileName
422 :
423 :			Name of the XML file containing the metadata.
424 :
425 :			=back
426 :
427 :			=cut
428 :
429 :			sub new {
430 :	parrello	1.10	# Get the parameters.
431 :			my ($class, $dbh, $metaFileName, $options) = @_;
432 :			# Load the meta-data.
433 :			my $metaData = _LoadMetaData($metaFileName);
434 :			# Create the object.
435 :			my $self = { _dbh => $dbh,
436 :			_metaData => $metaData
437 :			};
438 :			# Bless and return it.
439 :			bless $self, $class;
440 :			return $self;
441 :	parrello	1.1	}
442 :
443 :			=head3 ShowMetaData
444 :
445 :	parrello	1.18	C<< $erdb->ShowMetaData($fileName); >>
446 :	parrello	1.1
447 :			This method outputs a description of the database. This description can be used to help users create
448 :			the data to be loaded into the relations.
449 :
450 :			=over 4
451 :
452 :			=item filename
453 :
454 :			The name of the output file.
455 :
456 :			=back
457 :
458 :			=cut
459 :
460 :			sub ShowMetaData {
461 :	parrello	1.10	# Get the parameters.
462 :			my ($self, $filename) = @_;
463 :			# Get the metadata and the title string.
464 :			my $metadata = $self->{_metaData};
465 :			# Get the title string.
466 :			my $title = $metadata->{Title};
467 :			# Get the entity and relationship lists.
468 :			my $entityList = $metadata->{Entities};
469 :			my $relationshipList = $metadata->{Relationships};
470 :			# Open the output file.
471 :			open(HTMLOUT, ">$filename") \|\| Confess("Could not open MetaData display file $filename: $!");
472 :			Trace("Building MetaData table of contents.") if T(4);
473 :			# Write the HTML heading stuff.
474 :			print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
475 :			print HTMLOUT "</head>\n<body>\n";
476 :	parrello	1.45	# Write the documentation.
477 :			print HTMLOUT $self->DisplayMetaData();
478 :			# Close the document.
479 :			print HTMLOUT "</body>\n</html>\n";
480 :			# Close the file.
481 :			close HTMLOUT;
482 :			}
483 :
484 :			=head3 DisplayMetaData
485 :
486 :			C<< my $html = $erdb->DisplayMetaData(); >>
487 :
488 :			Return an HTML description of the database. This description can be used to help users create
489 :			the data to be loaded into the relations and form queries. The output is raw includable HTML
490 :			without any HEAD or BODY tags.
491 :
492 :			=over 4
493 :
494 :			=item filename
495 :
496 :			The name of the output file.
497 :
498 :			=back
499 :
500 :			=cut
501 :
502 :			sub DisplayMetaData {
503 :			# Get the parameters.
504 :			my ($self) = @_;
505 :			# Get the metadata and the title string.
506 :			my $metadata = $self->{_metaData};
507 :			# Get the title string.
508 :			my $title = $metadata->{Title};
509 :			# Get the entity and relationship lists.
510 :			my $entityList = $metadata->{Entities};
511 :			my $relationshipList = $metadata->{Relationships};
512 :			# Declare the return variable.
513 :			my $retVal = "";
514 :			# Open the output file.
515 :			Trace("Building MetaData table of contents.") if T(4);
516 :	parrello	1.10	# Here we do the table of contents. It starts as an unordered list of section names. Each
517 :			# section contains an ordered list of entity or relationship subsections.
518 :	parrello	1.45	$retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
519 :	parrello	1.10	# Loop through the Entities, displaying a list item for each.
520 :			foreach my $key (sort keys %{$entityList}) {
521 :			# Display this item.
522 :	parrello	1.45	$retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
523 :	parrello	1.10	}
524 :			# Close off the entity section and start the relationship section.
525 :	parrello	1.45	$retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
526 :	parrello	1.10	# Loop through the Relationships.
527 :			foreach my $key (sort keys %{$relationshipList}) {
528 :			# Display this item.
529 :			my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
530 :	parrello	1.45	$retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
531 :	parrello	1.10	}
532 :			# Close off the relationship section and list the join table section.
533 :	parrello	1.45	$retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
534 :	parrello	1.10	# Close off the table of contents itself.
535 :	parrello	1.45	$retVal .= "</ul>\n";
536 :	parrello	1.10	# Now we start with the actual data. Denote we're starting the entity section.
537 :	parrello	1.45	$retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
538 :	parrello	1.10	# Loop through the entities.
539 :			for my $key (sort keys %{$entityList}) {
540 :			Trace("Building MetaData entry for $key entity.") if T(4);
541 :			# Create the entity header. It contains a bookmark and the entity name.
542 :	parrello	1.45	$retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
543 :	parrello	1.10	# Get the entity data.
544 :			my $entityData = $entityList->{$key};
545 :			# If there's descriptive text, display it.
546 :			if (my $notes = $entityData->{Notes}) {
547 :	parrello	1.73	$retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
548 :	parrello	1.10	}
549 :			# Now we want a list of the entity's relationships. First, we set up the relationship subsection.
550 :	parrello	1.45	$retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
551 :	parrello	1.10	# Loop through the relationships.
552 :			for my $relationship (sort keys %{$relationshipList}) {
553 :			# Get the relationship data.
554 :			my $relationshipStructure = $relationshipList->{$relationship};
555 :			# Only use the relationship if if has this entity in its FROM or TO fields.
556 :			if ($relationshipStructure->{from} eq $key \|\| $relationshipStructure->{to} eq $key) {
557 :			# Get the relationship sentence and append the arity.
558 :			my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
559 :			# Display the relationship data.
560 :	parrello	1.45	$retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
561 :	parrello	1.10	}
562 :			}
563 :			# Close off the relationship list.
564 :	parrello	1.45	$retVal .= "</ul>\n";
565 :	parrello	1.10	# Get the entity's relations.
566 :			my $relationList = $entityData->{Relations};
567 :			# Create a header for the relation subsection.
568 :	parrello	1.45	$retVal .= "<h4>Relations for <b>$key</b></h4>\n";
569 :	parrello	1.10	# Loop through the relations, displaying them.
570 :			for my $relation (sort keys %{$relationList}) {
571 :			my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
572 :	parrello	1.45	$retVal .= $htmlString;
573 :	parrello	1.10	}
574 :			}
575 :			# Denote we're starting the relationship section.
576 :	parrello	1.45	$retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
577 :	parrello	1.10	# Loop through the relationships.
578 :			for my $key (sort keys %{$relationshipList}) {
579 :			Trace("Building MetaData entry for $key relationship.") if T(4);
580 :			# Get the relationship's structure.
581 :			my $relationshipStructure = $relationshipList->{$key};
582 :			# Create the relationship header.
583 :			my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
584 :	parrello	1.45	$retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
585 :	parrello	1.10	# Get the entity names.
586 :			my $fromEntity = $relationshipStructure->{from};
587 :			my $toEntity = $relationshipStructure->{to};
588 :			# Describe the relationship arity. Note there's a bit of trickiness involving recursive
589 :			# many-to-many relationships. In a normal many-to-many we use two sentences to describe
590 :			# the arity (one for each direction). This is a bad idea for a recursive relationship,
591 :			# since both sentences will say the same thing.
592 :			my $arity = $relationshipStructure->{arity};
593 :			if ($arity eq "11") {
594 :	parrello	1.45	$retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
595 :	parrello	1.10	} else {
596 :	parrello	1.45	$retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
597 :	parrello	1.10	if ($arity eq "MM" && $fromEntity ne $toEntity) {
598 :	parrello	1.45	$retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
599 :	parrello	1.10	}
600 :			}
601 :	parrello	1.45	$retVal .= "</p>\n";
602 :	parrello	1.10	# If there are notes on this relationship, display them.
603 :			if (my $notes = $relationshipStructure->{Notes}) {
604 :	parrello	1.73	$retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
605 :	parrello	1.10	}
606 :			# Generate the relationship's relation table.
607 :			my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
608 :	parrello	1.45	$retVal .= $htmlString;
609 :	parrello	1.10	}
610 :			Trace("Building MetaData join table.") if T(4);
611 :			# Denote we're starting the join table.
612 :	parrello	1.45	$retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
613 :	parrello	1.10	# Create a table header.
614 :	parrello	1.45	$retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
615 :	parrello	1.10	# Loop through the joins.
616 :			my $joinTable = $metadata->{Joins};
617 :			my @joinKeys = keys %{$joinTable};
618 :			for my $joinKey (sort @joinKeys) {
619 :			# Separate out the source, the target, and the join clause.
620 :			$joinKey =~ m!^([^/]+)/(.+)$!;
621 :			my ($sourceRelation, $targetRelation) = ($1, $2);
622 :	parrello	1.30	Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
623 :	parrello	1.10	my $source = $self->ComputeObjectSentence($sourceRelation);
624 :			my $target = $self->ComputeObjectSentence($targetRelation);
625 :			my $clause = $joinTable->{$joinKey};
626 :			# Display them in a table row.
627 :	parrello	1.45	$retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
628 :	parrello	1.10	}
629 :			# Close the table.
630 :	parrello	1.45	$retVal .= _CloseTable();
631 :			Trace("Built MetaData HTML.") if T(3);
632 :			# Return the HTML.
633 :			return $retVal;
634 :	parrello	1.1	}
635 :
636 :			=head3 DumpMetaData
637 :
638 :	parrello	1.18	C<< $erdb->DumpMetaData(); >>
639 :	parrello	1.1
640 :			Return a dump of the metadata structure.
641 :
642 :			=cut
643 :
644 :			sub DumpMetaData {
645 :	parrello	1.10	# Get the parameters.
646 :			my ($self) = @_;
647 :			# Dump the meta-data.
648 :			return Data::Dumper::Dumper($self->{_metaData});
649 :	parrello	1.1	}
650 :
651 :	parrello	1.74	=head3 FindIndexForEntity
652 :
653 :			C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
654 :
655 :			This method locates the entry in an entity's index list that begins with the
656 :			specified attribute name. If the entity has no index list, one will be
657 :			created. This method works on raw XML, not a live ERDB object.
658 :
659 :			=over 4
660 :
661 :			=item xml
662 :
663 :			The raw XML structure defining the database.
664 :
665 :			=item entityName
666 :
667 :			The name of the relevant entity.
668 :
669 :			=item attributeName
670 :
671 :			The name of the attribute relevant to the search.
672 :
673 :			=item RETURN
674 :
675 :			The numerical index in the index list of the index entry for the specified entity and
676 :			attribute, or C<undef> if no such index exists.
677 :
678 :			=back
679 :
680 :			=cut
681 :
682 :			sub FindIndexForEntity {
683 :			# Get the parameters.
684 :			my ($xml, $entityName, $attributeName) = @_;
685 :			# Declare the return variable.
686 :			my $retVal;
687 :			# Get the named entity.
688 :			my $entityData = $xml->{Entities}->{$entityName};
689 :			if (! $entityData) {
690 :			Confess("Entity $entityName not found in DBD structure.");
691 :			} else {
692 :			# Insure it has an index list.
693 :			if (! exists $entityData->{Indexes}) {
694 :			$entityData->{Indexes} = [];
695 :			} else {
696 :			# Search for the desired index.
697 :			my $indexList = $entityData->{Indexes};
698 :			my $n = scalar @{$indexList};
699 :			Trace("Searching $n indexes in index list for $entityName.") if T(2);
700 :			# We use an indexed FOR here because we're returning an
701 :			# index number instead of an object. We do THAT so we can
702 :			# delete the index from the list if needed.
703 :			for (my $i = 0; $i < $n && !defined($retVal); $i++) {
704 :			my $index = $indexList->[$i];
705 :			my $fields = $index->{IndexFields};
706 :			# Technically this IF should be safe (that is, we are guaranteed
707 :			# the existence of a "$fields->[0]"), because when we load the XML
708 :			# we have SuppressEmpty specified.
709 :			if ($fields->[0]->{name} eq $attributeName) {
710 :			$retVal = $i;
711 :			}
712 :			}
713 :			}
714 :			}
715 :			Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
716 :			Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
717 :			# Return the result.
718 :			return $retVal;
719 :			}
720 :
721 :	parrello	1.1	=head3 CreateTables
722 :
723 :	parrello	1.18	C<< $erdb->CreateTables(); >>
724 :	parrello	1.1
725 :			This method creates the tables for the database from the metadata structure loaded by the
726 :			constructor. It is expected this function will only be used on rare occasions, when the
727 :	parrello	1.2	user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
728 :	parrello	1.1	used by itself with the truncate flag turned on.
729 :
730 :			=cut
731 :
732 :			sub CreateTables {
733 :	parrello	1.10	# Get the parameters.
734 :			my ($self) = @_;
735 :	parrello	1.23	# Get the relation names.
736 :			my @relNames = $self->GetTableNames();
737 :			# Loop through the relations.
738 :			for my $relationName (@relNames) {
739 :			# Create a table for this relation.
740 :			$self->CreateTable($relationName);
741 :			Trace("Relation $relationName created.") if T(2);
742 :	parrello	1.10	}
743 :	parrello	1.1	}
744 :
745 :			=head3 CreateTable
746 :
747 :	parrello	1.18	C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
748 :	parrello	1.1
749 :			Create the table for a relation and optionally create its indexes.
750 :
751 :			=over 4
752 :
753 :			=item relationName
754 :
755 :			Name of the relation (which will also be the table name).
756 :
757 :	parrello	1.18	=item indexFlag
758 :	parrello	1.1
759 :			TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
760 :			L</CreateIndexes> must be called later to bring the indexes into existence.
761 :
762 :	parrello	1.18	=item estimatedRows (optional)
763 :
764 :			If specified, the estimated maximum number of rows for the relation. This
765 :			information allows the creation of tables using storage engines that are
766 :			faster but require size estimates, such as MyISAM.
767 :
768 :	parrello	1.1	=back
769 :
770 :			=cut
771 :
772 :			sub CreateTable {
773 :	parrello	1.10	# Get the parameters.
774 :	parrello	1.18	my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
775 :	parrello	1.10	# Get the database handle.
776 :			my $dbh = $self->{_dbh};
777 :			# Get the relation data and determine whether or not the relation is primary.
778 :			my $relationData = $self->_FindRelation($relationName);
779 :			my $rootFlag = $self->_IsPrimary($relationName);
780 :			# Create a list of the field data.
781 :			my @fieldList;
782 :			for my $fieldData (@{$relationData->{Fields}}) {
783 :			# Assemble the field name and type.
784 :			my $fieldName = _FixName($fieldData->{name});
785 :			my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
786 :			# Push the result into the field list.
787 :			push @fieldList, $fieldString;
788 :			}
789 :			# If this is a root table, add the "new_record" flag. It defaults to 0, so
790 :			if ($rootFlag) {
791 :			push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
792 :			}
793 :			# Convert the field list into a comma-delimited string.
794 :			my $fieldThing = join(', ', @fieldList);
795 :			# Insure the table is not already there.
796 :			$dbh->drop_table(tbl => $relationName);
797 :			Trace("Table $relationName dropped.") if T(2);
798 :	parrello	1.18	# If there are estimated rows, create an estimate so we can take advantage of
799 :			# faster DB technologies.
800 :			my $estimation = undef;
801 :			if ($estimatedRows) {
802 :			$estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
803 :			}
804 :	parrello	1.10	# Create the table.
805 :			Trace("Creating table $relationName: $fieldThing") if T(2);
806 :	parrello	1.18	$dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
807 :	parrello	1.10	Trace("Relation $relationName created in database.") if T(2);
808 :	parrello	1.70	# If we want to build the indexes, we do it here. Note that the full-text search
809 :			# index will not be built until the table has been loaded.
810 :	parrello	1.10	if ($indexFlag) {
811 :			$self->CreateIndex($relationName);
812 :			}
813 :	parrello	1.1	}
814 :
815 :	parrello	1.31	=head3 VerifyFields
816 :
817 :			C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
818 :
819 :			Run through the list of proposed field values, insuring that all the character fields are
820 :			below the maximum length. If any fields are too long, they will be truncated in place.
821 :
822 :			=over 4
823 :
824 :			=item relName
825 :
826 :			Name of the relation for which the specified fields are destined.
827 :
828 :			=item fieldList
829 :
830 :			Reference to a list, in order, of the fields to be put into the relation.
831 :
832 :			=item RETURN
833 :
834 :			Returns the number of fields truncated.
835 :
836 :			=back
837 :
838 :			=cut
839 :
840 :			sub VerifyFields {
841 :			# Get the parameters.
842 :			my ($self, $relName, $fieldList) = @_;
843 :			# Initialize the return value.
844 :			my $retVal = 0;
845 :			# Get the relation definition.
846 :			my $relData = $self->_FindRelation($relName);
847 :			# Get the list of field descriptors.
848 :			my $fieldTypes = $relData->{Fields};
849 :			my $fieldCount = scalar @{$fieldTypes};
850 :			# Loop through the two lists.
851 :			for (my $i = 0; $i < $fieldCount; $i++) {
852 :			# Get the type of the current field.
853 :			my $fieldType = $fieldTypes->[$i]->{type};
854 :			# If it's a character field, verify the length.
855 :			if ($fieldType =~ /string/) {
856 :			my $maxLen = $TypeTable{$fieldType}->{maxLen};
857 :			my $oldString = $fieldList->[$i];
858 :			if (length($oldString) > $maxLen) {
859 :			# Here it's too big, so we truncate it.
860 :			Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
861 :			$fieldList->[$i] = substr $oldString, 0, $maxLen;
862 :			$retVal++;
863 :			}
864 :			}
865 :			}
866 :			# Return the truncation count.
867 :			return $retVal;
868 :			}
869 :
870 :	parrello	1.42	=head3 DigestFields
871 :
872 :			C<< $erdb->DigestFields($relName, $fieldList); >>
873 :
874 :			Digest the strings in the field list that correspond to data type C<hash-string> in the
875 :			specified relation.
876 :
877 :			=over 4
878 :
879 :			=item relName
880 :
881 :			Name of the relation to which the fields belong.
882 :
883 :			=item fieldList
884 :
885 :			List of field contents to be loaded into the relation.
886 :
887 :			=back
888 :
889 :			=cut
890 :			#: Return Type ;
891 :			sub DigestFields {
892 :			# Get the parameters.
893 :			my ($self, $relName, $fieldList) = @_;
894 :			# Get the relation definition.
895 :			my $relData = $self->_FindRelation($relName);
896 :			# Get the list of field descriptors.
897 :			my $fieldTypes = $relData->{Fields};
898 :			my $fieldCount = scalar @{$fieldTypes};
899 :			# Loop through the two lists.
900 :			for (my $i = 0; $i < $fieldCount; $i++) {
901 :			# Get the type of the current field.
902 :			my $fieldType = $fieldTypes->[$i]->{type};
903 :			# If it's a hash string, digest it in place.
904 :			if ($fieldType eq 'hash-string') {
905 :	parrello	1.46	$fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
906 :	parrello	1.42	}
907 :			}
908 :			}
909 :
910 :	parrello	1.46	=head3 DigestKey
911 :
912 :			C<< my $digested = $erdb->DigestKey($keyValue); >>
913 :
914 :			Return the digested value of a symbolic key. The digested value can then be plugged into a
915 :			key-based search into a table with key-type hash-string.
916 :
917 :			Currently the digesting process is independent of the database structure, but that may not
918 :			always be the case, so this is an instance method instead of a static method.
919 :
920 :			=over 4
921 :
922 :			=item keyValue
923 :
924 :			Key value to digest.
925 :
926 :			=item RETURN
927 :
928 :	parrello	1.56	Digested value of the key.
929 :	parrello	1.46
930 :			=back
931 :
932 :			=cut
933 :
934 :			sub DigestKey {
935 :			# Get the parameters.
936 :			my ($self, $keyValue) = @_;
937 :			# Compute the digest.
938 :			my $retVal = md5_base64($keyValue);
939 :			# Return the result.
940 :			return $retVal;
941 :			}
942 :
943 :	parrello	1.1	=head3 CreateIndex
944 :
945 :	parrello	1.18	C<< $erdb->CreateIndex($relationName); >>
946 :	parrello	1.1
947 :			Create the indexes for a relation. If a table is being loaded from a large source file (as
948 :	parrello	1.12	is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
949 :			If that is the case, then L</CreateTable> should be called with the index flag set to
950 :			FALSE, and this method used after the load to create the indexes for the table.
951 :	parrello	1.1
952 :			=cut
953 :
954 :			sub CreateIndex {
955 :	parrello	1.10	# Get the parameters.
956 :			my ($self, $relationName) = @_;
957 :			# Get the relation's descriptor.
958 :			my $relationData = $self->_FindRelation($relationName);
959 :			# Get the database handle.
960 :			my $dbh = $self->{_dbh};
961 :			# Now we need to create this relation's indexes. We do this by looping through its index table.
962 :			my $indexHash = $relationData->{Indexes};
963 :			for my $indexName (keys %{$indexHash}) {
964 :			my $indexData = $indexHash->{$indexName};
965 :			# Get the index's field list.
966 :	parrello	1.75	my @rawFields = @{$indexData->{IndexFields}};
967 :			# Get a hash of the relation's field types.
968 :			my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
969 :			# We need to check for text fields. We need a append a length limitation for them. To do
970 :			# that, we need the relation's field list.
971 :			my $relFields = $relationData->{Fields};
972 :			for (my $i = 0; $i <= $#rawFields; $i++) {
973 :			# Get the field type.
974 :			my $field = $rawFields[$i];
975 :			my $type = $types{$field};
976 :			# Ask if it requires using prefix notation for the index.
977 :			my $mod = $TypeTable{$type}->{indexMod};
978 :			Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
979 :			if ($mod) {
980 :			# Append the prefix length to the field name,
981 :			$rawFields[$i] .= "($mod)";
982 :			}
983 :			}
984 :			my @fieldList = _FixNames(@rawFields);
985 :	parrello	1.10	my $flds = join(', ', @fieldList);
986 :			# Get the index's uniqueness flag.
987 :	parrello	1.70	my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
988 :	parrello	1.10	# Create the index.
989 :	parrello	1.24	my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
990 :	parrello	1.70	flds => $flds, kind => $unique);
991 :	parrello	1.24	if ($rv) {
992 :			Trace("Index created: $indexName for $relationName ($flds)") if T(1);
993 :			} else {
994 :			Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
995 :			}
996 :	parrello	1.10	}
997 :	parrello	1.1	}
998 :
999 :	parrello	1.75	=head3 GetSecondaryFields
1000 :
1001 :			C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1002 :
1003 :			This method will return a list of the name and type of each of the secondary
1004 :			fields for a specified entity. Secondary fields are stored in two-column tables
1005 :			in addition to the primary entity table. This enables the field to have no value
1006 :			or to have multiple values.
1007 :
1008 :			=over 4
1009 :
1010 :			=item entityName
1011 :
1012 :			Name of the entity whose secondary fields are desired.
1013 :
1014 :			=item RETURN
1015 :
1016 :			Returns a hash mapping the field names to their field types.
1017 :
1018 :			=back
1019 :
1020 :			=cut
1021 :
1022 :			sub GetSecondaryFields {
1023 :			# Get the parameters.
1024 :			my ($self, $entityName) = @_;
1025 :			# Declare the return variable.
1026 :			my %retVal = ();
1027 :			# Look for the entity.
1028 :			my $table = $self->GetFieldTable($entityName);
1029 :			# Loop through the fields, pulling out the secondaries.
1030 :			for my $field (sort keys %{$table}) {
1031 :			if ($table->{$field}->{relation} ne $entityName) {
1032 :			# Here we have a secondary field.
1033 :			$retVal{$field} = $table->{$field}->{type};
1034 :			}
1035 :			}
1036 :			# Return the result.
1037 :			return %retVal;
1038 :			}
1039 :
1040 :			=head3 GetFieldRelationName
1041 :
1042 :			C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1043 :
1044 :			Return the name of the relation containing a specified field.
1045 :
1046 :			=over 4
1047 :
1048 :			=item objectName
1049 :
1050 :			Name of the entity or relationship containing the field.
1051 :
1052 :			=item fieldName
1053 :
1054 :			Name of the relevant field in that entity or relationship.
1055 :
1056 :			=item RETURN
1057 :
1058 :			Returns the name of the database relation containing the field, or C<undef> if
1059 :			the field does not exist.
1060 :
1061 :			=back
1062 :
1063 :			=cut
1064 :
1065 :			sub GetFieldRelationName {
1066 :			# Get the parameters.
1067 :			my ($self, $objectName, $fieldName) = @_;
1068 :			# Declare the return variable.
1069 :			my $retVal;
1070 :			# Get the object field table.
1071 :			my $table = $self->GetFieldTable($objectName);
1072 :			# Only proceed if the field exists.
1073 :			if (exists $table->{$fieldName}) {
1074 :			# Determine the name of the relation that contains this field.
1075 :			$retVal = $table->{$fieldName}->{relation};
1076 :			}
1077 :			# Return the result.
1078 :			return $retVal;
1079 :			}
1080 :
1081 :			=head3 DeleteValue
1082 :
1083 :			C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1084 :
1085 :			Delete secondary field values from the database. This method can be used to delete all
1086 :			values of a specified field for a particular entity instance, or only a single value.
1087 :
1088 :			Secondary fields are stored in two-column relations separate from an entity's primary
1089 :			table, and as a result a secondary field can legitimately have no value or multiple
1090 :			values. Therefore, it makes sense to talk about deleting secondary fields where it
1091 :			would not make sense for primary fields.
1092 :
1093 :			=over 4
1094 :
1095 :			=item entityName
1096 :
1097 :			Name of the entity from which the fields are to be deleted.
1098 :
1099 :			=item id
1100 :
1101 :			ID of the entity instance to be processed. If the instance is not found, this
1102 :	parrello	1.76	method will have no effect. If C<undef> is specified, all values for all of
1103 :			the entity instances will be deleted.
1104 :	parrello	1.75
1105 :			=item fieldName
1106 :
1107 :			Name of the field whose values are to be deleted.
1108 :
1109 :			=item fieldValue (optional)
1110 :
1111 :			Value to be deleted. If not specified, then all values of the specified field
1112 :			will be deleted for the entity instance. If specified, then only the values which
1113 :			match this parameter will be deleted.
1114 :
1115 :			=item RETURN
1116 :
1117 :			Returns the number of rows deleted.
1118 :
1119 :			=back
1120 :
1121 :			=cut
1122 :
1123 :			sub DeleteValue {
1124 :			# Get the parameters.
1125 :			my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1126 :			# Declare the return value.
1127 :			my $retVal = 0;
1128 :			# We need to set up an SQL command to do the deletion. First, we
1129 :			# find the name of the field's relation.
1130 :			my $table = $self->GetFieldTable($entityName);
1131 :			my $field = $table->{$fieldName};
1132 :			my $relation = $field->{relation};
1133 :			# Make sure this is a secondary field.
1134 :			if ($relation eq $entityName) {
1135 :			Confess("Cannot delete values of $fieldName for $entityName.");
1136 :			} else {
1137 :			# Set up the SQL command to delete all values.
1138 :	parrello	1.76	my $sql = "DELETE FROM $relation";
1139 :			# Build the filter.
1140 :			my @filters = ();
1141 :			my @parms = ();
1142 :			# Check for a filter by ID.
1143 :			if (defined $id) {
1144 :			push @filters, "id = ?";
1145 :			push @parms, $id;
1146 :			}
1147 :			# Check for a filter by value.
1148 :	parrello	1.75	if (defined $fieldValue) {
1149 :	parrello	1.76	push @filters, "$fieldName = ?";
1150 :	parrello	1.75	push @parms, $fieldValue;
1151 :			}
1152 :	parrello	1.76	# Append the filters to the command.
1153 :			if (@filters) {
1154 :			$sql .= " WHERE " . join(" AND ", @filters);
1155 :			}
1156 :	parrello	1.75	# Execute the command.
1157 :			my $dbh = $self->{_dbh};
1158 :			$retVal = $dbh->SQL($sql, 0, @parms);
1159 :			}
1160 :			# Return the result.
1161 :			return $retVal;
1162 :			}
1163 :
1164 :	parrello	1.1	=head3 LoadTables
1165 :
1166 :	parrello	1.18	C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1167 :	parrello	1.1
1168 :			This method will load the database tables from a directory. The tables must already have been created
1169 :			in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1170 :			all of the relations to be loaded must have a file in the directory with the same name as the relation
1171 :			(optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1172 :			line of the file will be loaded as a row of the target relation table. The field values should be in
1173 :			the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1174 :			erased before the new data is loaded in.
1175 :
1176 :			A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1177 :			tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1178 :			be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1179 :
1180 :			=over 4
1181 :
1182 :			=item directoryName
1183 :
1184 :			Name of the directory containing the relation files to be loaded.
1185 :
1186 :			=item rebuild
1187 :
1188 :			TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1189 :			only way to erase existing data in the tables, since the TRUNCATE command is not supported
1190 :			by all of the DB engines we use.
1191 :
1192 :			=item RETURN
1193 :
1194 :			Returns a statistical object describing the number of records read and a list of the error messages.
1195 :
1196 :			=back
1197 :
1198 :			=cut
1199 :
1200 :			sub LoadTables {
1201 :	parrello	1.10	# Get the parameters.
1202 :			my ($self, $directoryName, $rebuild) = @_;
1203 :			# Start the timer.
1204 :			my $startTime = gettimeofday;
1205 :			# Clean any trailing slash from the directory name.
1206 :			$directoryName =~ s!/\\$!!;
1207 :			# Declare the return variable.
1208 :			my $retVal = Stats->new();
1209 :	parrello	1.23	# Get the relation names.
1210 :			my @relNames = $self->GetTableNames();
1211 :			for my $relationName (@relNames) {
1212 :			# Try to load this relation.
1213 :			my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1214 :	parrello	1.10	# Accumulate the statistics.
1215 :			$retVal->Accumulate($result);
1216 :			}
1217 :			# Add the duration of the load to the statistical object.
1218 :			$retVal->Add('duration', gettimeofday - $startTime);
1219 :			# Return the accumulated statistics.
1220 :			return $retVal;
1221 :	parrello	1.1	}
1222 :
1223 :	parrello	1.23
1224 :	parrello	1.1	=head3 GetTableNames
1225 :
1226 :	parrello	1.18	C<< my @names = $erdb->GetTableNames; >>
1227 :	parrello	1.1
1228 :			Return a list of the relations required to implement this database.
1229 :
1230 :			=cut
1231 :
1232 :			sub GetTableNames {
1233 :	parrello	1.10	# Get the parameters.
1234 :			my ($self) = @_;
1235 :			# Get the relation list from the metadata.
1236 :			my $relationTable = $self->{_metaData}->{RelationTable};
1237 :			# Return the relation names.
1238 :			return keys %{$relationTable};
1239 :	parrello	1.1	}
1240 :
1241 :			=head3 GetEntityTypes
1242 :
1243 :	parrello	1.18	C<< my @names = $erdb->GetEntityTypes; >>
1244 :	parrello	1.1
1245 :			Return a list of the entity type names.
1246 :
1247 :			=cut
1248 :
1249 :			sub GetEntityTypes {
1250 :	parrello	1.10	# Get the database object.
1251 :			my ($self) = @_;
1252 :			# Get the entity list from the metadata object.
1253 :			my $entityList = $self->{_metaData}->{Entities};
1254 :			# Return the list of entity names in alphabetical order.
1255 :			return sort keys %{$entityList};
1256 :	parrello	1.1	}
1257 :
1258 :	parrello	1.73	=head3 GetDataTypes
1259 :
1260 :			C<< my %types = ERDB::GetDataTypes(); >>
1261 :
1262 :			Return a table of ERDB data types. The table returned is a hash of hashes.
1263 :			The keys of the big hash are the datatypes. Each smaller hash has several
1264 :			values used to manage the data. The most interesting is the SQL type (key
1265 :			C<sqlType>) and the descriptive node (key C<notes>).
1266 :
1267 :			Note that changing the values in the smaller hashes will seriously break
1268 :			things, so this data should be treated as read-only.
1269 :
1270 :			=cut
1271 :
1272 :			sub GetDataTypes {
1273 :			return %TypeTable;
1274 :			}
1275 :
1276 :
1277 :	parrello	1.20	=head3 IsEntity
1278 :
1279 :			C<< my $flag = $erdb->IsEntity($entityName); >>
1280 :
1281 :			Return TRUE if the parameter is an entity name, else FALSE.
1282 :
1283 :			=over 4
1284 :
1285 :			=item entityName
1286 :
1287 :			Object name to be tested.
1288 :
1289 :			=item RETURN
1290 :
1291 :			Returns TRUE if the specified string is an entity name, else FALSE.
1292 :
1293 :			=back
1294 :
1295 :			=cut
1296 :
1297 :			sub IsEntity {
1298 :			# Get the parameters.
1299 :			my ($self, $entityName) = @_;
1300 :			# Test to see if it's an entity.
1301 :			return exists $self->{_metaData}->{Entities}->{$entityName};
1302 :			}
1303 :
1304 :	parrello	1.1	=head3 Get
1305 :
1306 :	parrello	1.45	C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1307 :	parrello	1.1
1308 :			This method returns a query object for entities of a specified type using a specified filter.
1309 :			The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1310 :			field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1311 :			following call requests all B<Genome> objects for the genus specified in the variable
1312 :			$genus.
1313 :
1314 :	parrello	1.45	C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1315 :	parrello	1.1
1316 :			The WHERE clause contains a single question mark, so there is a single additional
1317 :			parameter representing the parameter value. It would also be possible to code
1318 :
1319 :	parrello	1.18	C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1320 :	parrello	1.1
1321 :			however, this version of the call would generate a syntax error if there were any quote
1322 :			characters inside the variable C<$genus>.
1323 :
1324 :			The use of the strange parenthesized notation for field names enables us to distinguish
1325 :			hyphens contained within field names from minus signs that participate in the computation
1326 :			of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1327 :
1328 :			It is possible to specify multiple entity and relationship names in order to retrieve more than
1329 :			one object's data at the same time, which allows highly complex joined queries. For example,
1330 :
1331 :	parrello	1.45	C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1332 :	parrello	1.1
1333 :			If multiple names are specified, then the query processor will automatically determine a
1334 :			join path between the entities and relationships. The algorithm used is very simplistic.
1335 :	parrello	1.39	In particular, if a relationship is recursive, the path is determined by the order in which
1336 :			the entity and the relationship appear. For example, consider a recursive relationship
1337 :			B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1338 :	parrello	1.1	coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1339 :			the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1340 :
1341 :	parrello	1.39	If an entity or relationship is mentioned twice, the name for the second occurrence will
1342 :			be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1343 :			for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1344 :			B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1345 :			the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1346 :
1347 :	parrello	1.1	=over 4
1348 :
1349 :			=item objectNames
1350 :
1351 :			List containing the names of the entity and relationship objects to be retrieved.
1352 :
1353 :			=item filterClause
1354 :
1355 :			WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1356 :			be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1357 :			specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1358 :			in the filter clause should be added to the parameter list as additional parameters. The
1359 :			fields in a filter clause can come from primary entity relations, relationship relations,
1360 :			or secondary entity relations; however, all of the entities and relationships involved must
1361 :			be included in the list of object names.
1362 :
1363 :			The filter clause can also specify a sort order. To do this, simply follow the filter string
1364 :			with an ORDER BY clause. For example, the following filter string gets all genomes for a
1365 :			particular genus and sorts them by species name.
1366 :
1367 :			C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1368 :
1369 :	parrello	1.30	Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1370 :			be processed. The idea is to make it less likely to find the verb by accident.
1371 :
1372 :	parrello	1.1	The rules for field references in a sort order are the same as those for field references in the
1373 :			filter clause in general; however, odd things may happen if a sort field is from a secondary
1374 :			relation.
1375 :
1376 :	parrello	1.39	Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1377 :			be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1378 :			a positive number. So, for example
1379 :
1380 :			C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1381 :
1382 :			will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1383 :			required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1384 :			use
1385 :
1386 :			C<< "LIMIT 10" >>
1387 :
1388 :	parrello	1.45	=item params
1389 :	parrello	1.1
1390 :	parrello	1.45	Reference to a list of parameter values to be substituted into the filter clause.
1391 :	parrello	1.1
1392 :			=item RETURN
1393 :
1394 :			Returns a B<DBQuery> that can be used to iterate through all of the results.
1395 :
1396 :			=back
1397 :
1398 :			=cut
1399 :
1400 :			sub Get {
1401 :	parrello	1.10	# Get the parameters.
1402 :	parrello	1.45	my ($self, $objectNames, $filterClause, $params) = @_;
1403 :			# Process the SQL stuff.
1404 :			my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1405 :			$self->_SetupSQL($objectNames, $filterClause);
1406 :			# Create the query.
1407 :			my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1408 :			".* $suffix";
1409 :			my $sth = $self->_GetStatementHandle($command, $params);
1410 :	parrello	1.39	# Now we create the relation map, which enables DBQuery to determine the order, name
1411 :			# and mapped name for each object in the query.
1412 :			my @relationMap = ();
1413 :	parrello	1.45	for my $mappedName (@{$mappedNameListRef}) {
1414 :			push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1415 :	parrello	1.39	}
1416 :	parrello	1.10	# Return the statement object.
1417 :	parrello	1.39	my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1418 :	parrello	1.10	return $retVal;
1419 :	parrello	1.1	}
1420 :
1421 :	parrello	1.70	=head3 Search
1422 :
1423 :			C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1424 :
1425 :			Perform a full text search with filtering. The search will be against a specified object
1426 :			in the object name list. That object will get an extra field containing the search
1427 :			relevance. Note that except for the search expression, the parameters of this method are
1428 :			the same as those for L</Get> and follow the same rules.
1429 :
1430 :			=over 4
1431 :
1432 :			=item searchExpression
1433 :
1434 :	parrello	1.75	Boolean search expression for the text fields of the target object. The default mode for
1435 :			a Boolean search expression is OR, but we want the default to be AND, so we will
1436 :			add a C<+> operator to each word with no other operator before it.
1437 :	parrello	1.70
1438 :			=item idx
1439 :
1440 :			Index in the I<$objectNames> list of the table to be searched in full-text mode.
1441 :
1442 :			=item objectNames
1443 :
1444 :			List containing the names of the entity and relationship objects to be retrieved.
1445 :
1446 :			=item filterClause
1447 :
1448 :			WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1449 :			be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1450 :			specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1451 :			in the filter clause should be added to the parameter list as additional parameters. The
1452 :			fields in a filter clause can come from primary entity relations, relationship relations,
1453 :			or secondary entity relations; however, all of the entities and relationships involved must
1454 :			be included in the list of object names.
1455 :
1456 :			=item params
1457 :
1458 :			Reference to a list of parameter values to be substituted into the filter clause.
1459 :
1460 :			=item RETURN
1461 :
1462 :			Returns a query object for the specified search.
1463 :
1464 :			=back
1465 :
1466 :			=cut
1467 :
1468 :			sub Search {
1469 :			# Get the parameters.
1470 :			my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1471 :			# Declare the return variable.
1472 :			my $retVal;
1473 :	parrello	1.72	# Create a safety copy of the parameter list. Note we have to be careful to insure
1474 :			# a parameter list exists before we copy it.
1475 :			my @myParams = ();
1476 :			if (defined $params) {
1477 :			@myParams = @{$params};
1478 :			}
1479 :	parrello	1.70	# Get the first object's structure so we have access to the searchable fields.
1480 :			my $object1Name = $objectNames->[$idx];
1481 :			my $object1Structure = $self->_GetStructure($object1Name);
1482 :			# Get the field list.
1483 :			if (! exists $object1Structure->{searchFields}) {
1484 :			Confess("No searchable index for $object1Name.");
1485 :			} else {
1486 :			# Get the field list.
1487 :			my @fields = @{$object1Structure->{searchFields}};
1488 :	parrello	1.71	# Clean the search expression.
1489 :			my $actualKeywords = $self->CleanKeywords($searchExpression);
1490 :	parrello	1.75	# Prefix a "+" to each uncontrolled word. This converts the default
1491 :			# search mode from OR to AND.
1492 :			$actualKeywords =~ s/(^\|\s)(\w)/$1\+$2/g;
1493 :	parrello	1.72	Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1494 :	parrello	1.70	# We need two match expressions, one for the filter clause and one in the
1495 :			# query itself. Both will use a parameter mark, so we need to push the
1496 :			# search expression onto the front of the parameter list twice.
1497 :	parrello	1.71	unshift @myParams, $actualKeywords, $actualKeywords;
1498 :	parrello	1.70	# Build the match expression.
1499 :			my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1500 :			my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1501 :			# Process the SQL stuff.
1502 :			my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1503 :			$self->_SetupSQL($objectNames, $filterClause, $matchClause);
1504 :			# Create the query. Note that the match clause is inserted at the front of
1505 :			# the select fields.
1506 :			my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1507 :			".* $suffix";
1508 :			my $sth = $self->_GetStatementHandle($command, \@myParams);
1509 :			# Now we create the relation map, which enables DBQuery to determine the order, name
1510 :			# and mapped name for each object in the query.
1511 :			my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1512 :			# Return the statement object.
1513 :			$retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1514 :			}
1515 :			return $retVal;
1516 :			}
1517 :
1518 :	parrello	1.45	=head3 GetFlat
1519 :
1520 :			C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1521 :
1522 :			This is a variation of L</GetAll> that asks for only a single field per record and
1523 :			returns a single flattened list.
1524 :
1525 :			=over 4
1526 :
1527 :			=item objectNames
1528 :
1529 :			List containing the names of the entity and relationship objects to be retrieved.
1530 :
1531 :			=item filterClause
1532 :
1533 :			WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1534 :			be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1535 :			B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1536 :			parameter list as additional parameters. The fields in a filter clause can come from primary
1537 :			entity relations, relationship relations, or secondary entity relations; however, all of the
1538 :			entities and relationships involved must be included in the list of object names.
1539 :
1540 :			=item parameterList
1541 :
1542 :			List of the parameters to be substituted in for the parameters marks in the filter clause.
1543 :
1544 :			=item field
1545 :
1546 :			Name of the field to be used to get the elements of the list returned.
1547 :
1548 :			=item RETURN
1549 :
1550 :			Returns a list of values.
1551 :
1552 :			=back
1553 :
1554 :			=cut
1555 :			#: Return Type @;
1556 :			sub GetFlat {
1557 :			# Get the parameters.
1558 :			my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1559 :			# Construct the query.
1560 :			my $query = $self->Get($objectNames, $filterClause, $parameterList);
1561 :			# Create the result list.
1562 :			my @retVal = ();
1563 :			# Loop through the records, adding the field values found to the result list.
1564 :			while (my $row = $query->Fetch()) {
1565 :			push @retVal, $row->Value($field);
1566 :			}
1567 :			# Return the list created.
1568 :			return @retVal;
1569 :			}
1570 :
1571 :	parrello	1.73	=head3 SpecialFields
1572 :
1573 :			C<< my %specials = $erdb->SpecialFields($entityName); >>
1574 :
1575 :			Return a hash mapping special fields in the specified entity to the value of their
1576 :			C<special> attribute. This enables the subclass to get access to the special field
1577 :			attributes without needed to plumb the internal ERDB data structures.
1578 :
1579 :			=over 4
1580 :
1581 :			=item entityName
1582 :
1583 :			Name of the entity whose special fields are desired.
1584 :
1585 :			=item RETURN
1586 :
1587 :			Returns a hash. The keys of the hash are the special field names, and the values
1588 :			are the values from each special field's C<special> attribute.
1589 :
1590 :			=back
1591 :
1592 :			=cut
1593 :
1594 :			sub SpecialFields {
1595 :			# Get the parameters.
1596 :			my ($self, $entityName) = @_;
1597 :			# Declare the return variable.
1598 :			my %retVal = ();
1599 :			# Find the entity's data structure.
1600 :	parrello	1.75	my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1601 :	parrello	1.73	# Loop through its fields, adding each special field to the return hash.
1602 :			my $fieldHash = $entityData->{Fields};
1603 :			for my $fieldName (keys %{$fieldHash}) {
1604 :			my $fieldData = $fieldHash->{$fieldName};
1605 :			if (exists $fieldData->{special}) {
1606 :			$retVal{$fieldName} = $fieldData->{special};
1607 :			}
1608 :			}
1609 :			# Return the result.
1610 :			return %retVal;
1611 :			}
1612 :
1613 :	parrello	1.32	=head3 Delete
1614 :
1615 :			C<< my $stats = $erdb->Delete($entityName, $objectID); >>
1616 :
1617 :			Delete an entity instance from the database. The instance is deleted along with all entity and
1618 :			relationship instances dependent on it. The idea of dependence here is recursive. An object is
1619 :			always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1620 :			relationship connected to a dependent entity or the "to" entity connected to a 1-to-many
1621 :			dependent relationship.
1622 :
1623 :			=over 4
1624 :
1625 :			=item entityName
1626 :
1627 :			Name of the entity type for the instance being deleted.
1628 :
1629 :			=item objectID
1630 :
1631 :			ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1632 :			then it is presumed to by a LIKE pattern.
1633 :
1634 :			=item testFlag
1635 :
1636 :			If TRUE, the delete statements will be traced without being executed.
1637 :
1638 :			=item RETURN
1639 :
1640 :			Returns a statistics object indicating how many records of each particular table were
1641 :			deleted.
1642 :
1643 :			=back
1644 :
1645 :			=cut
1646 :			#: Return Type $%;
1647 :			sub Delete {
1648 :			# Get the parameters.
1649 :			my ($self, $entityName, $objectID, $testFlag) = @_;
1650 :			# Declare the return variable.
1651 :			my $retVal = Stats->new();
1652 :			# Get the DBKernel object.
1653 :			my $db = $self->{_dbh};
1654 :			# We're going to generate all the paths branching out from the starting entity. One of
1655 :			# the things we have to be careful about is preventing loops. We'll use a hash to
1656 :			# determine if we've hit a loop.
1657 :			my %alreadyFound = ();
1658 :	parrello	1.33	# These next lists will serve as our result stack. We start by pushing object lists onto
1659 :	parrello	1.32	# the stack, and then popping them off to do the deletes. This means the deletes will
1660 :			# start with the longer paths before getting to the shorter ones. That, in turn, makes
1661 :			# sure we don't delete records that might be needed to forge relationships back to the
1662 :	parrello	1.33	# original item. We have two lists-- one for TO-relationships, and one for
1663 :			# FROM-relationships and entities.
1664 :			my @fromPathList = ();
1665 :			my @toPathList = ();
1666 :	parrello	1.32	# This final hash is used to remember what work still needs to be done. We push paths
1667 :			# onto the list, then pop them off to extend the paths. We prime it with the starting
1668 :			# point. Note that we will work hard to insure that the last item on a path in the
1669 :	parrello	1.75	# to-do list is always an entity.
1670 :	parrello	1.32	my @todoList = ([$entityName]);
1671 :			while (@todoList) {
1672 :			# Get the current path.
1673 :			my $current = pop @todoList;
1674 :			# Copy it into a list.
1675 :			my @stackedPath = @{$current};
1676 :			# Pull off the last item on the path. It will always be an entity.
1677 :			my $entityName = pop @stackedPath;
1678 :			# Add it to the alreadyFound list.
1679 :			$alreadyFound{$entityName} = 1;
1680 :			# Get the entity data.
1681 :			my $entityData = $self->_GetStructure($entityName);
1682 :			# The first task is to loop through the entity's relation. A DELETE command will
1683 :			# be needed for each of them.
1684 :			my $relations = $entityData->{Relations};
1685 :			for my $relation (keys %{$relations}) {
1686 :			my @augmentedList = (@stackedPath, $relation);
1687 :	parrello	1.33	push @fromPathList, \@augmentedList;
1688 :	parrello	1.32	}
1689 :			# Now we need to look for relationships connected to this entity.
1690 :			my $relationshipList = $self->{_metaData}->{Relationships};
1691 :			for my $relationshipName (keys %{$relationshipList}) {
1692 :			my $relationship = $relationshipList->{$relationshipName};
1693 :			# Check the FROM field. We're only interested if it's us.
1694 :			if ($relationship->{from} eq $entityName) {
1695 :			# Add the path to this relationship.
1696 :			my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1697 :	parrello	1.33	push @fromPathList, \@augmentedList;
1698 :	parrello	1.32	# Check the arity. If it's MM we're done. If it's 1M
1699 :			# and the target hasn't been seen yet, we want to
1700 :			# stack the entity for future processing.
1701 :			if ($relationship->{arity} eq '1M') {
1702 :			my $toEntity = $relationship->{to};
1703 :			if (! exists $alreadyFound{$toEntity}) {
1704 :			# Here we have a new entity that's dependent on
1705 :			# the current entity, so we need to stack it.
1706 :			my @stackList = (@augmentedList, $toEntity);
1707 :	parrello	1.33	push @fromPathList, \@stackList;
1708 :	parrello	1.34	} else {
1709 :			Trace("$toEntity ignored because it occurred previously.") if T(4);
1710 :	parrello	1.32	}
1711 :			}
1712 :			}
1713 :			# Now check the TO field. In this case only the relationship needs
1714 :	parrello	1.33	# deletion.
1715 :	parrello	1.32	if ($relationship->{to} eq $entityName) {
1716 :			my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1717 :	parrello	1.33	push @toPathList, \@augmentedList;
1718 :	parrello	1.32	}
1719 :			}
1720 :			}
1721 :			# Create the first qualifier for the WHERE clause. This selects the
1722 :			# keys of the primary entity records to be deleted. When we're deleting
1723 :			# from a dependent table, we construct a join page from the first qualifier
1724 :			# to the table containing the dependent records to delete.
1725 :			my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1726 :	parrello	1.33	# We need to make two passes. The first is through the to-list, and
1727 :			# the second through the from-list. The from-list is second because
1728 :			# the to-list may need to pass through some of the entities the
1729 :			# from-list would delete.
1730 :			my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1731 :			# Now it's time to do the deletes. We do it in two passes.
1732 :			for my $keyName ('to_link', 'from_link') {
1733 :			# Get the list for this key.
1734 :			my @pathList = @{$stackList{$keyName}};
1735 :	parrello	1.34	Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1736 :	parrello	1.33	# Loop through this list.
1737 :			while (my $path = pop @pathList) {
1738 :			# Get the table whose rows are to be deleted.
1739 :			my @pathTables = @{$path};
1740 :	parrello	1.37	# Start the DELETE statement. We need to call DBKernel because the
1741 :			# syntax of a DELETE-USING varies among DBMSs.
1742 :	parrello	1.33	my $target = $pathTables[$#pathTables];
1743 :	parrello	1.37	my $stmt = $db->SetUsing(@pathTables);
1744 :	parrello	1.33	# Now start the WHERE. The first thing is the ID field from the starting table. That
1745 :			# starting table will either be the entity relation or one of the entity's
1746 :			# sub-relations.
1747 :			$stmt .= " WHERE $pathTables[0].id $qualifier";
1748 :			# Now we run through the remaining entities in the path, connecting them up.
1749 :			for (my $i = 1; $i <= $#pathTables; $i += 2) {
1750 :			# Connect the current relationship to the preceding entity.
1751 :			my ($entity, $rel) = @pathTables[$i-1,$i];
1752 :			# The style of connection depends on the direction of the relationship.
1753 :	parrello	1.35	$stmt .= " AND $entity.id = $rel.$keyName";
1754 :	parrello	1.32	if ($i + 1 <= $#pathTables) {
1755 :			# Here there's a next entity, so connect that to the relationship's
1756 :			# to-link.
1757 :			my $entity2 = $pathTables[$i+1];
1758 :	parrello	1.35	$stmt .= " AND $rel.to_link = $entity2.id";
1759 :	parrello	1.32	}
1760 :			}
1761 :	parrello	1.33	# Now we have our desired DELETE statement.
1762 :			if ($testFlag) {
1763 :			# Here the user wants to trace without executing.
1764 :			Trace($stmt) if T(0);
1765 :			} else {
1766 :			# Here we can delete. Note that the SQL method dies with a confessing
1767 :			# if an error occurs, so we just go ahead and do it.
1768 :	parrello	1.36	Trace("Executing delete from $target using '$objectID'.") if T(3);
1769 :			my $rv = $db->SQL($stmt, 0, $objectID);
1770 :	parrello	1.33	# Accumulate the statistics for this delete. The only rows deleted
1771 :			# are from the target table, so we use its name to record the
1772 :			# statistic.
1773 :			$retVal->Add($target, $rv);
1774 :			}
1775 :	parrello	1.32	}
1776 :			}
1777 :			# Return the result.
1778 :			return $retVal;
1779 :			}
1780 :
1781 :	parrello	1.70	=head3 SortNeeded
1782 :
1783 :			C<< my $parms = $erdb->SortNeeded($relationName); >>
1784 :
1785 :			Return the pipe command for the sort that should be applied to the specified
1786 :			relation when creating the load file.
1787 :
1788 :			For example, if the load file should be sorted ascending by the first
1789 :			field, this method would return
1790 :
1791 :			sort -k1 -t"\t"
1792 :
1793 :			If the first field is numeric, the method would return
1794 :
1795 :			sort -k1n -t"\t"
1796 :
1797 :			Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1798 :			keys using a sort.
1799 :
1800 :			=over 4
1801 :
1802 :			=item relationName
1803 :
1804 :			Name of the relation to be examined.
1805 :
1806 :			=item
1807 :
1808 :			Returns the sort command to use for sorting the relation, suitable for piping.
1809 :
1810 :			=back
1811 :
1812 :			=cut
1813 :			#: Return Type $;
1814 :			sub SortNeeded {
1815 :			# Get the parameters.
1816 :			my ($self, $relationName) = @_;
1817 :			# Declare a descriptor to hold the names of the key fields.
1818 :			my @keyNames = ();
1819 :			# Get the relation structure.
1820 :			my $relationData = $self->_FindRelation($relationName);
1821 :			# Find out if the relation is a primary entity relation,
1822 :			# a relationship relation, or a secondary entity relation.
1823 :			my $entityTable = $self->{_metaData}->{Entities};
1824 :			my $relationshipTable = $self->{_metaData}->{Relationships};
1825 :			if (exists $entityTable->{$relationName}) {
1826 :			# Here we have a primary entity relation.
1827 :			push @keyNames, "id";
1828 :			} elsif (exists $relationshipTable->{$relationName}) {
1829 :			# Here we have a relationship. We sort using the FROM index.
1830 :			my $relationshipData = $relationshipTable->{$relationName};
1831 :	parrello	1.75	my $index = $relationData->{Indexes}->{idxFrom};
1832 :	parrello	1.70	push @keyNames, @{$index->{IndexFields}};
1833 :			} else {
1834 :			# Here we have a secondary entity relation, so we have a sort on the ID field.
1835 :			push @keyNames, "id";
1836 :			}
1837 :			# Now we parse the key names into sort parameters. First, we prime the return
1838 :			# string.
1839 :			my $retVal = "sort -t\"\t\" ";
1840 :			# Get the relation's field list.
1841 :			my @fields = @{$relationData->{Fields}};
1842 :			# Loop through the keys.
1843 :			for my $keyData (@keyNames) {
1844 :			# Get the key and the ordering.
1845 :			my ($keyName, $ordering);
1846 :			if ($keyData =~ /^([^ ]+) DESC/) {
1847 :			($keyName, $ordering) = ($1, "descending");
1848 :			} else {
1849 :			($keyName, $ordering) = ($keyData, "ascending");
1850 :			}
1851 :			# Find the key's position and type.
1852 :			my $fieldSpec;
1853 :			for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1854 :			my $thisField = $fields[$i];
1855 :			if ($thisField->{name} eq $keyName) {
1856 :			# Get the sort modifier for this field type. The modifier
1857 :			# decides whether we're using a character, numeric, or
1858 :			# floating-point sort.
1859 :			my $modifier = $TypeTable{$thisField->{type}}->{sort};
1860 :			# If the index is descending for this field, denote we want
1861 :			# to reverse the sort order on this field.
1862 :			if ($ordering eq 'descending') {
1863 :			$modifier .= "r";
1864 :			}
1865 :			# Store the position and modifier into the field spec, which
1866 :			# will stop the inner loop. Note that the field number is
1867 :			# 1-based in the sort command, so we have to increment the
1868 :			# index.
1869 :			$fieldSpec = ($i + 1) . $modifier;
1870 :			}
1871 :			}
1872 :			# Add this field to the sort command.
1873 :			$retVal .= " -k$fieldSpec";
1874 :			}
1875 :			# Return the result.
1876 :			return $retVal;
1877 :			}
1878 :
1879 :	parrello	1.6	=head3 GetList
1880 :
1881 :	parrello	1.45	C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1882 :	parrello	1.6
1883 :			Return a list of object descriptors for the specified objects as determined by the
1884 :			specified filter clause.
1885 :
1886 :			This method is essentially the same as L</Get> except it returns a list of objects rather
1887 :	parrello	1.7	than a query object that can be used to get the results one record at a time.
1888 :	parrello	1.6
1889 :			=over 4
1890 :
1891 :			=item objectNames
1892 :
1893 :			List containing the names of the entity and relationship objects to be retrieved.
1894 :
1895 :			=item filterClause
1896 :
1897 :			WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1898 :			be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1899 :			specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1900 :			in the filter clause should be added to the parameter list as additional parameters. The
1901 :			fields in a filter clause can come from primary entity relations, relationship relations,
1902 :			or secondary entity relations; however, all of the entities and relationships involved must
1903 :			be included in the list of object names.
1904 :
1905 :			The filter clause can also specify a sort order. To do this, simply follow the filter string
1906 :			with an ORDER BY clause. For example, the following filter string gets all genomes for a
1907 :			particular genus and sorts them by species name.
1908 :
1909 :			C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1910 :
1911 :			The rules for field references in a sort order are the same as those for field references in the
1912 :			filter clause in general; however, odd things may happen if a sort field is from a secondary
1913 :			relation.
1914 :
1915 :	parrello	1.45	=item params
1916 :	parrello	1.6
1917 :	parrello	1.45	Reference to a list of parameter values to be substituted into the filter clause.
1918 :	parrello	1.6
1919 :			=item RETURN
1920 :
1921 :			Returns a list of B<DBObject>s that satisfy the query conditions.
1922 :
1923 :			=back
1924 :
1925 :			=cut
1926 :			#: Return Type @%
1927 :			sub GetList {
1928 :			# Get the parameters.
1929 :	parrello	1.45	my ($self, $objectNames, $filterClause, $params) = @_;
1930 :	parrello	1.10	# Declare the return variable.
1931 :			my @retVal = ();
1932 :			# Perform the query.
1933 :	parrello	1.45	my $query = $self->Get($objectNames, $filterClause, $params);
1934 :	parrello	1.10	# Loop through the results.
1935 :			while (my $object = $query->Fetch) {
1936 :			push @retVal, $object;
1937 :			}
1938 :	parrello	1.6	# Return the result.
1939 :			return @retVal;
1940 :			}
1941 :
1942 :	parrello	1.45	=head3 GetCount
1943 :
1944 :			C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1945 :
1946 :			Return the number of rows found by a specified query. This method would
1947 :			normally be used to count the records in a single table. For example, in a
1948 :			genetics database
1949 :
1950 :			my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1951 :
1952 :			would return the number of genomes for the genus I<homo>. It is conceivable, however,
1953 :			to use it to return records based on a join. For example,
1954 :
1955 :	parrello	1.47	my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1956 :	parrello	1.45	['homo %']);
1957 :
1958 :			would return the number of features for genomes in the genus I<homo>. Note that
1959 :			only the rows from the first table are counted. If the above command were
1960 :
1961 :			my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1962 :			['homo %']);
1963 :
1964 :			it would return the number of genomes, not the number of genome/feature pairs.
1965 :
1966 :			=over 4
1967 :
1968 :			=item objectNames
1969 :
1970 :			Reference to a list of the objects (entities and relationships) included in the
1971 :			query.
1972 :
1973 :			=item filter
1974 :
1975 :			A filter clause for restricting the query. The rules are the same as for the L</Get>
1976 :			method.
1977 :
1978 :			=item params
1979 :
1980 :			Reference to a list of the parameter values to be substituted for the parameter marks
1981 :			in the filter.
1982 :
1983 :			=item RETURN
1984 :
1985 :			Returns a count of the number of records in the first table that would satisfy
1986 :			the query.
1987 :
1988 :			=back
1989 :
1990 :			=cut
1991 :
1992 :			sub GetCount {
1993 :			# Get the parameters.
1994 :			my ($self, $objectNames, $filter, $params) = @_;
1995 :	parrello	1.66	# Insure the params argument is an array reference if the caller left it off.
1996 :			if (! defined($params)) {
1997 :			$params = [];
1998 :			}
1999 :	parrello	1.45	# Declare the return variable.
2000 :			my $retVal;
2001 :	parrello	1.47	# Find out if we're counting an entity or a relationship.
2002 :			my $countedField;
2003 :			if ($self->IsEntity($objectNames->[0])) {
2004 :			$countedField = "id";
2005 :			} else {
2006 :			# For a relationship we count the to-link because it's usually more
2007 :			# numerous. Note we're automatically converting to the SQL form
2008 :			# of the field name (to_link vs. to-link).
2009 :			$countedField = "to_link";
2010 :			}
2011 :	parrello	1.45	# Create the SQL command suffix to get the desired records.
2012 :			my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2013 :			$filter);
2014 :			# Prefix it with text telling it we want a record count.
2015 :			my $firstObject = $mappedNameListRef->[0];
2016 :	parrello	1.47	my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2017 :	parrello	1.45	# Prepare and execute the command.
2018 :			my $sth = $self->_GetStatementHandle($command, $params);
2019 :			# Get the count value.
2020 :			($retVal) = $sth->fetchrow_array();
2021 :			# Check for a problem.
2022 :			if (! defined($retVal)) {
2023 :			if ($sth->err) {
2024 :			# Here we had an SQL error.
2025 :			Confess("Error retrieving row count: " . $sth->errstr());
2026 :			} else {
2027 :			# Here we have no result.
2028 :			Confess("No result attempting to retrieve row count.");
2029 :			}
2030 :			}
2031 :			# Return the result.
2032 :			return $retVal;
2033 :			}
2034 :
2035 :	parrello	1.1	=head3 ComputeObjectSentence
2036 :
2037 :	parrello	1.18	C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2038 :	parrello	1.1
2039 :			Check an object name, and if it is a relationship convert it to a relationship sentence.
2040 :
2041 :			=over 4
2042 :
2043 :			=item objectName
2044 :
2045 :			Name of the entity or relationship.
2046 :
2047 :			=item RETURN
2048 :
2049 :			Returns a string containing the entity name or a relationship sentence.
2050 :
2051 :			=back
2052 :
2053 :			=cut
2054 :
2055 :			sub ComputeObjectSentence {
2056 :	parrello	1.10	# Get the parameters.
2057 :			my ($self, $objectName) = @_;
2058 :			# Set the default return value.
2059 :			my $retVal = $objectName;
2060 :			# Look for the object as a relationship.
2061 :			my $relTable = $self->{_metaData}->{Relationships};
2062 :			if (exists $relTable->{$objectName}) {
2063 :			# Get the relationship sentence.
2064 :			$retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2065 :			}
2066 :			# Return the result.
2067 :			return $retVal;
2068 :	parrello	1.1	}
2069 :
2070 :			=head3 DumpRelations
2071 :
2072 :	parrello	1.18	C<< $erdb->DumpRelations($outputDirectory); >>
2073 :	parrello	1.1
2074 :			Write the contents of all the relations to tab-delimited files in the specified directory.
2075 :			Each file will have the same name as the relation dumped, with an extension of DTX.
2076 :
2077 :			=over 4
2078 :
2079 :			=item outputDirectory
2080 :
2081 :			Name of the directory into which the relation files should be dumped.
2082 :
2083 :			=back
2084 :
2085 :			=cut
2086 :
2087 :			sub DumpRelations {
2088 :	parrello	1.10	# Get the parameters.
2089 :			my ($self, $outputDirectory) = @_;
2090 :			# Now we need to run through all the relations. First, we loop through the entities.
2091 :			my $metaData = $self->{_metaData};
2092 :			my $entities = $metaData->{Entities};
2093 :			for my $entityName (keys %{$entities}) {
2094 :			my $entityStructure = $entities->{$entityName};
2095 :			# Get the entity's relations.
2096 :			my $relationList = $entityStructure->{Relations};
2097 :			# Loop through the relations, dumping them.
2098 :			for my $relationName (keys %{$relationList}) {
2099 :			my $relation = $relationList->{$relationName};
2100 :			$self->_DumpRelation($outputDirectory, $relationName, $relation);
2101 :			}
2102 :			}
2103 :			# Next, we loop through the relationships.
2104 :			my $relationships = $metaData->{Relationships};
2105 :			for my $relationshipName (keys %{$relationships}) {
2106 :			my $relationshipStructure = $relationships->{$relationshipName};
2107 :			# Dump this relationship's relation.
2108 :			$self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2109 :			}
2110 :	parrello	1.1	}
2111 :
2112 :	parrello	1.51	=head3 InsertValue
2113 :
2114 :			C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2115 :
2116 :			This method will insert a new value into the database. The value must be one
2117 :			associated with a secondary relation, since primary values cannot be inserted:
2118 :			they occur exactly once. Secondary values, on the other hand, can be missing
2119 :			or multiply-occurring.
2120 :
2121 :			=over 4
2122 :
2123 :			=item entityID
2124 :
2125 :			ID of the object that is to receive the new value.
2126 :
2127 :			=item fieldName
2128 :
2129 :			Field name for the new value-- this includes the entity name, since
2130 :			field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2131 :
2132 :			=item value
2133 :
2134 :			New value to be put in the field.
2135 :
2136 :			=back
2137 :
2138 :			=cut
2139 :
2140 :			sub InsertValue {
2141 :			# Get the parameters.
2142 :			my ($self, $entityID, $fieldName, $value) = @_;
2143 :			# Parse the entity name and the real field name.
2144 :			if ($fieldName =~ /^([^(]+)$([^)]+)$/) {
2145 :			my $entityName = $1;
2146 :			my $fieldTitle = $2;
2147 :			# Get its descriptor.
2148 :			if (!$self->IsEntity($entityName)) {
2149 :			Confess("$entityName is not a valid entity.");
2150 :			} else {
2151 :			my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2152 :			# Find the relation containing this field.
2153 :			my $fieldHash = $entityData->{Fields};
2154 :	parrello	1.52	if (! exists $fieldHash->{$fieldTitle}) {
2155 :	parrello	1.51	Confess("$fieldTitle not found in $entityName.");
2156 :			} else {
2157 :			my $relation = $fieldHash->{$fieldTitle}->{relation};
2158 :			if ($relation eq $entityName) {
2159 :			Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2160 :			} else {
2161 :			# Now we can create an INSERT statement.
2162 :			my $dbh = $self->{_dbh};
2163 :			my $fixedName = _FixName($fieldTitle);
2164 :	parrello	1.53	my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2165 :	parrello	1.51	# Execute the command.
2166 :			$dbh->SQL($statement, 0, $entityID, $value);
2167 :			}
2168 :			}
2169 :			}
2170 :			} else {
2171 :			Confess("$fieldName is not a valid field name.");
2172 :			}
2173 :			}
2174 :
2175 :	parrello	1.1	=head3 InsertObject
2176 :
2177 :	parrello	1.18	C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2178 :	parrello	1.1
2179 :			Insert an object into the database. The object is defined by a type name and then a hash
2180 :			of field names to values. Field values in the primary relation are represented by scalars.
2181 :			(Note that for relationships, the primary relation is the B<only> relation.)
2182 :			Field values for the other relations comprising the entity are always list references. For
2183 :			example, the following line inserts an inactive PEG feature named C<fig\|188.1.peg.1> with aliases
2184 :			C<ZP_00210270.1> and C<gi\|46206278>.
2185 :
2186 :	parrello	1.18	C<< $erdb->InsertObject('Feature', { id => 'fig\|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi\|46206278']}); >>
2187 :	parrello	1.1
2188 :			The next statement inserts a C<HasProperty> relationship between feature C<fig\|158879.1.peg.1> and
2189 :			property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2190 :
2191 :	parrello	1.57	C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig\|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2192 :	parrello	1.1
2193 :			=over 4
2194 :
2195 :			=item newObjectType
2196 :
2197 :			Type name of the object to insert.
2198 :
2199 :			=item fieldHash
2200 :
2201 :			Hash of field names to values.
2202 :
2203 :			=item RETURN
2204 :
2205 :			Returns 1 if successful, 0 if an error occurred.
2206 :
2207 :			=back
2208 :
2209 :			=cut
2210 :
2211 :			sub InsertObject {
2212 :	parrello	1.10	# Get the parameters.
2213 :			my ($self, $newObjectType, $fieldHash) = @_;
2214 :			# Denote that so far we appear successful.
2215 :			my $retVal = 1;
2216 :			# Get the database handle.
2217 :			my $dbh = $self->{_dbh};
2218 :			# Get the relation list.
2219 :			my $relationTable = $self->_GetRelationTable($newObjectType);
2220 :			# Loop through the relations. We'll build insert statements for each one. If a relation is
2221 :			# secondary, we may end up generating multiple insert statements. If an error occurs, we
2222 :			# stop the loop.
2223 :			my @relationList = keys %{$relationTable};
2224 :			for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2225 :			my $relationName = $relationList[$i];
2226 :			my $relationDefinition = $relationTable->{$relationName};
2227 :			# Get the relation's fields. For each field we will collect a value in the corresponding
2228 :			# position of the @valueList array. If one of the fields is missing, we will add it to the
2229 :			# @missing list.
2230 :			my @fieldList = @{$relationDefinition->{Fields}};
2231 :			my @fieldNameList = ();
2232 :			my @valueList = ();
2233 :			my @missing = ();
2234 :			my $recordCount = 1;
2235 :			for my $fieldDescriptor (@fieldList) {
2236 :			# Get the field name and save it. Note we need to fix it up so the hyphens
2237 :			# are converted to underscores.
2238 :			my $fieldName = $fieldDescriptor->{name};
2239 :			push @fieldNameList, _FixName($fieldName);
2240 :			# Look for the named field in the incoming structure. Note that we are looking
2241 :			# for the real field name, not the fixed-up one!
2242 :			if (exists $fieldHash->{$fieldName}) {
2243 :			# Here we found the field. Stash it in the value list.
2244 :			my $value = $fieldHash->{$fieldName};
2245 :			push @valueList, $value;
2246 :			# If the value is a list, we may need to increment the record count.
2247 :			if (ref $value eq "ARRAY") {
2248 :			my $thisCount = @{$value};
2249 :			if ($recordCount == 1) {
2250 :			# Here we have our first list, so we save its count.
2251 :			$recordCount = $thisCount;
2252 :			} elsif ($recordCount != $thisCount) {
2253 :			# Here we have a second list, so its length has to match the
2254 :			# previous lists.
2255 :			Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2256 :			$retVal = 0;
2257 :			}
2258 :			}
2259 :			} else {
2260 :			# Here the field is not present. Flag it as missing.
2261 :			push @missing, $fieldName;
2262 :			}
2263 :			}
2264 :			# If we are the primary relation, add the new-record flag.
2265 :			if ($relationName eq $newObjectType) {
2266 :			push @valueList, 1;
2267 :			push @fieldNameList, "new_record";
2268 :			}
2269 :			# Only proceed if there are no missing fields.
2270 :			if (@missing > 0) {
2271 :			Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2272 :			join(' ', @missing)) if T(1);
2273 :			} else {
2274 :			# Build the INSERT statement.
2275 :			my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2276 :			") VALUES (";
2277 :			# Create a marker list of the proper size and put it in the statement.
2278 :			my @markers = ();
2279 :			while (@markers < @fieldNameList) { push @markers, '?'; }
2280 :			$statement .= join(', ', @markers) . ")";
2281 :			# We have the insert statement, so prepare it.
2282 :			my $sth = $dbh->prepare_command($statement);
2283 :			Trace("Insert statement prepared: $statement") if T(3);
2284 :			# Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2285 :			# a list, we use the current element. The values are stored in the @parameterList array.
2286 :			my $done = 0;
2287 :			for (my $i = 0; $i < $recordCount; $i++) {
2288 :			# Clear the parameter list array.
2289 :			my @parameterList = ();
2290 :			# Loop through the values.
2291 :			for my $value (@valueList) {
2292 :			# Check to see if this is a scalar value.
2293 :			if (ref $value eq "ARRAY") {
2294 :			# Here we have a list value. Pull the current entry.
2295 :			push @parameterList, $value->[$i];
2296 :			} else {
2297 :			# Here we have a scalar value. Use it unmodified.
2298 :			push @parameterList, $value;
2299 :			}
2300 :			}
2301 :			# Execute the INSERT statement with the specified parameter list.
2302 :			$retVal = $sth->execute(@parameterList);
2303 :			if (!$retVal) {
2304 :			my $errorString = $sth->errstr();
2305 :			Trace("Insert error: $errorString.") if T(0);
2306 :			}
2307 :			}
2308 :			}
2309 :			}
2310 :			# Return the success indicator.
2311 :			return $retVal;
2312 :	parrello	1.1	}
2313 :
2314 :			=head3 LoadTable
2315 :
2316 :	parrello	1.18	C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2317 :	parrello	1.1
2318 :	parrello	1.9	Load data from a tab-delimited file into a specified table, optionally re-creating the table
2319 :			first.
2320 :	parrello	1.1
2321 :			=over 4
2322 :
2323 :			=item fileName
2324 :
2325 :			Name of the file from which the table data should be loaded.
2326 :
2327 :			=item relationName
2328 :
2329 :			Name of the relation to be loaded. This is the same as the table name.
2330 :
2331 :			=item truncateFlag
2332 :
2333 :			TRUE if the table should be dropped and re-created, else FALSE
2334 :
2335 :			=item RETURN
2336 :
2337 :	parrello	1.28	Returns a statistical object containing a list of the error messages.
2338 :	parrello	1.1
2339 :			=back
2340 :
2341 :			=cut
2342 :			sub LoadTable {
2343 :	parrello	1.10	# Get the parameters.
2344 :			my ($self, $fileName, $relationName, $truncateFlag) = @_;
2345 :			# Create the statistical return object.
2346 :			my $retVal = _GetLoadStats();
2347 :			# Trace the fact of the load.
2348 :			Trace("Loading table $relationName from $fileName") if T(2);
2349 :			# Get the database handle.
2350 :			my $dbh = $self->{_dbh};
2351 :	parrello	1.22	# Get the input file size.
2352 :			my $fileSize = -s $fileName;
2353 :	parrello	1.10	# Get the relation data.
2354 :			my $relation = $self->_FindRelation($relationName);
2355 :			# Check the truncation flag.
2356 :			if ($truncateFlag) {
2357 :			Trace("Creating table $relationName") if T(2);
2358 :	parrello	1.19	# Compute the row count estimate. We take the size of the load file,
2359 :			# divide it by the estimated row size, and then multiply by 1.5 to
2360 :			# leave extra room. We postulate a minimum row count of 1000 to
2361 :			# prevent problems with incoming empty load files.
2362 :			my $rowSize = $self->EstimateRowSize($relationName);
2363 :			my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2364 :	parrello	1.10	# Re-create the table without its index.
2365 :	parrello	1.19	$self->CreateTable($relationName, 0, $estimate);
2366 :	parrello	1.10	# If this is a pre-index DBMS, create the index here.
2367 :			if ($dbh->{_preIndex}) {
2368 :			eval {
2369 :			$self->CreateIndex($relationName);
2370 :			};
2371 :			if ($@) {
2372 :			$retVal->AddMessage($@);
2373 :			}
2374 :			}
2375 :			}
2376 :	parrello	1.3	# Load the table.
2377 :	parrello	1.10	my $rv;
2378 :			eval {
2379 :	parrello	1.20	$rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2380 :	parrello	1.10	};
2381 :			if (!defined $rv) {
2382 :	parrello	1.3	$retVal->AddMessage($@) if ($@);
2383 :	parrello	1.73	$retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2384 :	parrello	1.10	Trace("Table load failed for $relationName.") if T(1);
2385 :			} else {
2386 :	parrello	1.22	# Here we successfully loaded the table.
2387 :			$retVal->Add("tables");
2388 :			my $size = -s $fileName;
2389 :			Trace("$size bytes loaded into $relationName.") if T(2);
2390 :	parrello	1.10	# If we're rebuilding, we need to create the table indexes.
2391 :	parrello	1.70	if ($truncateFlag) {
2392 :			# Indexes are created here for PostGres. For PostGres, indexes are
2393 :			# best built at the end. For MySQL, the reverse is true.
2394 :			if (! $dbh->{_preIndex}) {
2395 :			eval {
2396 :			$self->CreateIndex($relationName);
2397 :			};
2398 :			if ($@) {
2399 :			$retVal->AddMessage($@);
2400 :			}
2401 :			}
2402 :			# The full-text index (if any) is always built last, even for MySQL.
2403 :			# First we need to see if this table has a full-text index. Only
2404 :			# primary relations are allowed that privilege.
2405 :			if ($self->_IsPrimary($relationName)) {
2406 :			# Get the relation's entity/relationship structure.
2407 :			my $structure = $self->_GetStructure($relationName);
2408 :			# Check for a searchable fields list.
2409 :			if (exists $structure->{searchFields}) {
2410 :			# Here we know that we need to create a full-text search index.
2411 :			# Get an SQL-formatted field name list.
2412 :			my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2413 :			# Create the index.
2414 :	parrello	1.75	$dbh->create_index(tbl => $relationName, idx => "search_idx",
2415 :	parrello	1.70	flds => $fields, kind => 'fulltext');
2416 :			}
2417 :	parrello	1.10	}
2418 :			}
2419 :			}
2420 :	parrello	1.20	# Analyze the table to improve performance.
2421 :	parrello	1.61	Trace("Analyzing and compacting $relationName.") if T(3);
2422 :	olson	1.16	$dbh->vacuum_it($relationName);
2423 :	parrello	1.61	Trace("$relationName load completed.") if T(3);
2424 :	parrello	1.10	# Return the statistics.
2425 :			return $retVal;
2426 :	parrello	1.1	}
2427 :
2428 :	parrello	1.73	=head3 DropRelation
2429 :	parrello	1.1
2430 :	parrello	1.73	C<< $erdb->DropRelation($relationName); >>
2431 :	parrello	1.1
2432 :	parrello	1.73	Physically drop a relation from the database.
2433 :	parrello	1.1
2434 :			=over 4
2435 :
2436 :	parrello	1.73	=item relationName
2437 :	parrello	1.1
2438 :	parrello	1.73	Name of the relation to drop. If it does not exist, this method will have
2439 :			no effect.
2440 :	parrello	1.1
2441 :			=back
2442 :
2443 :			=cut
2444 :
2445 :	parrello	1.73	sub DropRelation {
2446 :	parrello	1.10	# Get the parameters.
2447 :	parrello	1.73	my ($self, $relationName) = @_;
2448 :			# Get the database handle.
2449 :			my $dbh = $self->{_dbh};
2450 :			# Drop the relation. The method used here has no effect if the relation
2451 :			# does not exist.
2452 :	parrello	1.74	Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2453 :			$dbh->drop_table(tbl => $relationName);
2454 :	parrello	1.1	}
2455 :
2456 :	parrello	1.6	=head3 GetEntity
2457 :
2458 :	parrello	1.18	C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2459 :	parrello	1.6
2460 :			Return an object describing the entity instance with a specified ID.
2461 :
2462 :			=over 4
2463 :
2464 :			=item entityType
2465 :
2466 :			Entity type name.
2467 :
2468 :			=item ID
2469 :
2470 :			ID of the desired entity.
2471 :
2472 :			=item RETURN
2473 :
2474 :			Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2475 :			instance is found with the specified key.
2476 :
2477 :			=back
2478 :
2479 :			=cut
2480 :
2481 :			sub GetEntity {
2482 :	parrello	1.10	# Get the parameters.
2483 :			my ($self, $entityType, $ID) = @_;
2484 :			# Create a query.
2485 :	parrello	1.45	my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2486 :	parrello	1.10	# Get the first (and only) object.
2487 :			my $retVal = $query->Fetch();
2488 :			# Return the result.
2489 :			return $retVal;
2490 :	parrello	1.6	}
2491 :
2492 :	parrello	1.69	=head3 GetChoices
2493 :
2494 :			C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2495 :
2496 :			Return a list of all the values for the specified field that are represented in the
2497 :			specified entity.
2498 :
2499 :			Note that if the field is not indexed, then this will be a very slow operation.
2500 :
2501 :			=over 4
2502 :
2503 :			=item entityName
2504 :
2505 :			Name of an entity in the database.
2506 :
2507 :			=item fieldName
2508 :
2509 :			Name of a field belonging to the entity. This is a raw field name without
2510 :			the standard parenthesized notation used in most calls.
2511 :
2512 :			=item RETURN
2513 :
2514 :			Returns a list of the distinct values for the specified field in the database.
2515 :
2516 :			=back
2517 :
2518 :			=cut
2519 :
2520 :			sub GetChoices {
2521 :			# Get the parameters.
2522 :			my ($self, $entityName, $fieldName) = @_;
2523 :			# Declare the return variable.
2524 :			my @retVal;
2525 :			# Get the entity data structure.
2526 :			my $entityData = $self->_GetStructure($entityName);
2527 :			# Get the field.
2528 :			my $fieldHash = $entityData->{Fields};
2529 :			if (! exists $fieldHash->{$fieldName}) {
2530 :			Confess("$fieldName not found in $entityName.");
2531 :			} else {
2532 :			# Get the name of the relation containing the field.
2533 :			my $relation = $fieldHash->{$fieldName}->{relation};
2534 :			# Fix up the field name.
2535 :			my $realName = _FixName($fieldName);
2536 :			# Get the database handle.
2537 :			my $dbh = $self->{_dbh};
2538 :			# Query the database.
2539 :			my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2540 :			# Clean the results. They are stored as a list of lists, and we just want the one list.
2541 :			@retVal = sort map { $_->[0] } @{$results};
2542 :			}
2543 :			# Return the result.
2544 :			return @retVal;
2545 :			}
2546 :
2547 :	parrello	1.6	=head3 GetEntityValues
2548 :
2549 :	parrello	1.18	C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2550 :	parrello	1.6
2551 :	parrello	1.68	Return a list of values from a specified entity instance. If the entity instance
2552 :			does not exist, an empty list is returned.
2553 :	parrello	1.6
2554 :			=over 4
2555 :
2556 :			=item entityType
2557 :
2558 :			Entity type name.
2559 :
2560 :			=item ID
2561 :
2562 :			ID of the desired entity.
2563 :
2564 :			=item fields
2565 :
2566 :			List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2567 :
2568 :			=item RETURN
2569 :
2570 :			Returns a flattened list of the values of the specified fields for the specified entity.
2571 :
2572 :			=back
2573 :
2574 :			=cut
2575 :
2576 :			sub GetEntityValues {
2577 :	parrello	1.10	# Get the parameters.
2578 :			my ($self, $entityType, $ID, $fields) = @_;
2579 :			# Get the specified entity.
2580 :			my $entity = $self->GetEntity($entityType, $ID);
2581 :			# Declare the return list.
2582 :			my @retVal = ();
2583 :			# If we found the entity, push the values into the return list.
2584 :			if ($entity) {
2585 :			push @retVal, $entity->Values($fields);
2586 :			}
2587 :			# Return the result.
2588 :			return @retVal;
2589 :	parrello	1.6	}
2590 :	parrello	1.1
2591 :	parrello	1.7	=head3 GetAll
2592 :
2593 :	parrello	1.18	C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2594 :	parrello	1.7
2595 :			Return a list of values taken from the objects returned by a query. The first three
2596 :			parameters correspond to the parameters of the L</Get> method. The final parameter is
2597 :			a list of the fields desired from each record found by the query. The field name
2598 :			syntax is the standard syntax used for fields in the B<ERDB> system--
2599 :			B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2600 :			or relationship and I<fieldName> is the name of the field.
2601 :
2602 :			The list returned will be a list of lists. Each element of the list will contain
2603 :			the values returned for the fields specified in the fourth parameter. If one of the
2604 :			fields specified returns multiple values, they are flattened in with the rest. For
2605 :			example, the following call will return a list of the features in a particular
2606 :			spreadsheet cell, and each feature will be represented by a list containing the
2607 :			feature ID followed by all of its aliases.
2608 :
2609 :	parrello	1.18	C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2610 :	parrello	1.7
2611 :			=over 4
2612 :
2613 :			=item objectNames
2614 :
2615 :			List containing the names of the entity and relationship objects to be retrieved.
2616 :
2617 :			=item filterClause
2618 :
2619 :			WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2620 :			be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2621 :			B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2622 :			parameter list as additional parameters. The fields in a filter clause can come from primary
2623 :			entity relations, relationship relations, or secondary entity relations; however, all of the
2624 :			entities and relationships involved must be included in the list of object names.
2625 :
2626 :			=item parameterList
2627 :
2628 :			List of the parameters to be substituted in for the parameters marks in the filter clause.
2629 :
2630 :			=item fields
2631 :
2632 :			List of the fields to be returned in each element of the list returned.
2633 :
2634 :			=item count
2635 :
2636 :			Maximum number of records to return. If omitted or 0, all available records will be returned.
2637 :
2638 :			=item RETURN
2639 :
2640 :			Returns a list of list references. Each element of the return list contains the values for the
2641 :			fields specified in the B<fields> parameter.
2642 :
2643 :			=back
2644 :
2645 :			=cut
2646 :			#: Return Type @@;
2647 :			sub GetAll {
2648 :	parrello	1.10	# Get the parameters.
2649 :			my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2650 :			# Translate the parameters from a list reference to a list. If the parameter
2651 :			# list is a scalar we convert it into a singleton list.
2652 :			my @parmList = ();
2653 :			if (ref $parameterList eq "ARRAY") {
2654 :	parrello	1.45	Trace("GetAll parm list is an array.") if T(4);
2655 :	parrello	1.10	@parmList = @{$parameterList};
2656 :			} else {
2657 :	parrello	1.45	Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2658 :	parrello	1.10	push @parmList, $parameterList;
2659 :			}
2660 :	parrello	1.30	# Insure the counter has a value.
2661 :			if (!defined $count) {
2662 :			$count = 0;
2663 :			}
2664 :			# Add the row limit to the filter clause.
2665 :			if ($count > 0) {
2666 :			$filterClause .= " LIMIT $count";
2667 :			}
2668 :	parrello	1.10	# Create the query.
2669 :	parrello	1.45	my $query = $self->Get($objectNames, $filterClause, \@parmList);
2670 :	parrello	1.10	# Set up a counter of the number of records read.
2671 :			my $fetched = 0;
2672 :			# Loop through the records returned, extracting the fields. Note that if the
2673 :			# counter is non-zero, we stop when the number of records read hits the count.
2674 :			my @retVal = ();
2675 :			while (($count == 0 \|\| $fetched < $count) && (my $row = $query->Fetch())) {
2676 :			my @rowData = $row->Values($fields);
2677 :			push @retVal, \@rowData;
2678 :			$fetched++;
2679 :			}
2680 :	parrello	1.54	Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2681 :	parrello	1.10	# Return the resulting list.
2682 :			return @retVal;
2683 :	parrello	1.7	}
2684 :
2685 :	parrello	1.55	=head3 Exists
2686 :
2687 :			C<< my $found = $sprout->Exists($entityName, $entityID); >>
2688 :
2689 :			Return TRUE if an entity exists, else FALSE.
2690 :
2691 :			=over 4
2692 :
2693 :			=item entityName
2694 :
2695 :			Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2696 :
2697 :			=item entityID
2698 :
2699 :			ID of the entity instance whose existence is to be checked.
2700 :
2701 :			=item RETURN
2702 :
2703 :			Returns TRUE if the entity instance exists, else FALSE.
2704 :
2705 :			=back
2706 :
2707 :			=cut
2708 :			#: Return Type $;
2709 :			sub Exists {
2710 :			# Get the parameters.
2711 :			my ($self, $entityName, $entityID) = @_;
2712 :			# Check for the entity instance.
2713 :			Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2714 :			my $testInstance = $self->GetEntity($entityName, $entityID);
2715 :			# Return an existence indicator.
2716 :			my $retVal = ($testInstance ? 1 : 0);
2717 :			return $retVal;
2718 :			}
2719 :
2720 :	parrello	1.18	=head3 EstimateRowSize
2721 :
2722 :			C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2723 :
2724 :			Estimate the row size of the specified relation. The estimated row size is computed by adding
2725 :			up the average length for each data type.
2726 :
2727 :			=over 4
2728 :
2729 :			=item relName
2730 :
2731 :			Name of the relation whose estimated row size is desired.
2732 :
2733 :			=item RETURN
2734 :
2735 :			Returns an estimate of the row size for the specified relation.
2736 :
2737 :			=back
2738 :
2739 :			=cut
2740 :			#: Return Type $;
2741 :			sub EstimateRowSize {
2742 :			# Get the parameters.
2743 :			my ($self, $relName) = @_;
2744 :			# Declare the return variable.
2745 :			my $retVal = 0;
2746 :			# Find the relation descriptor.
2747 :			my $relation = $self->_FindRelation($relName);
2748 :			# Get the list of fields.
2749 :			for my $fieldData (@{$relation->{Fields}}) {
2750 :			# Get the field type and add its length.
2751 :			my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2752 :			$retVal += $fieldLen;
2753 :			}
2754 :			# Return the result.
2755 :			return $retVal;
2756 :			}
2757 :
2758 :	parrello	1.38	=head3 GetFieldTable
2759 :
2760 :			C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2761 :
2762 :			Get the field structure for a specified entity or relationship.
2763 :
2764 :			=over 4
2765 :
2766 :			=item objectName
2767 :
2768 :			Name of the desired entity or relationship.
2769 :
2770 :			=item RETURN
2771 :
2772 :			The table containing the field descriptors for the specified object.
2773 :
2774 :			=back
2775 :
2776 :			=cut
2777 :
2778 :			sub GetFieldTable {
2779 :			# Get the parameters.
2780 :			my ($self, $objectName) = @_;
2781 :			# Get the descriptor from the metadata.
2782 :			my $objectData = $self->_GetStructure($objectName);
2783 :			# Return the object's field table.
2784 :			return $objectData->{Fields};
2785 :			}
2786 :
2787 :	parrello	1.73	=head3 SplitKeywords
2788 :
2789 :			C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2790 :
2791 :			This method returns a list of the positive keywords in the specified
2792 :			keyword string. All of the operators will have been stripped off,
2793 :			and if the keyword is preceded by a minus operator (C<->), it will
2794 :			not be in the list returned. The idea here is to get a list of the
2795 :			keywords the user wants to see. The list will be processed to remove
2796 :			duplicates.
2797 :
2798 :			It is possible to create a string that confuses this method. For example
2799 :
2800 :			frog toad -frog
2801 :
2802 :			would return both C<frog> and C<toad>. If this is a problem we can deal
2803 :			with it later.
2804 :
2805 :			=over 4
2806 :
2807 :			=item keywordString
2808 :
2809 :			The keyword string to be parsed.
2810 :
2811 :			=item RETURN
2812 :
2813 :			Returns a list of the words in the keyword string the user wants to
2814 :			see.
2815 :
2816 :			=back
2817 :
2818 :			=cut
2819 :
2820 :			sub SplitKeywords {
2821 :			# Get the parameters.
2822 :			my ($keywordString) = @_;
2823 :			# Make a safety copy of the string. (This helps during debugging.)
2824 :			my $workString = $keywordString;
2825 :			# Convert operators we don't care about to spaces.
2826 :			$workString =~ tr/+"()<>/ /;
2827 :			# Split the rest of the string along space boundaries. Note that we
2828 :			# eliminate any words that are zero length or begin with a minus sign.
2829 :			my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2830 :			# Use a hash to remove duplicates.
2831 :			my %words = map { $_ => 1 } @wordList;
2832 :			# Return the result.
2833 :			return sort keys %words;
2834 :			}
2835 :
2836 :			=head3 ValidateFieldName
2837 :
2838 :			C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2839 :
2840 :			Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2841 :			be hyphenated words subject to certain restrictions.
2842 :
2843 :			=over 4
2844 :
2845 :			=item fieldName
2846 :
2847 :			Field name to be validated.
2848 :
2849 :			=item RETURN
2850 :
2851 :			Returns TRUE if the field name is valid, else FALSE.
2852 :
2853 :			=back
2854 :
2855 :			=cut
2856 :
2857 :			sub ValidateFieldName {
2858 :			# Get the parameters.
2859 :			my ($fieldName) = @_;
2860 :			# Declare the return variable. The field name is valid until we hear
2861 :			# differently.
2862 :			my $retVal = 1;
2863 :			# Look for bad stuff in the name.
2864 :			if ($fieldName =~ /--/) {
2865 :			# Here we have a doubled minus sign.
2866 :			Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2867 :			$retVal = 0;
2868 :			} elsif ($fieldName !~ /^[A-Za-z]/) {
2869 :			# Here the field name is missing the initial letter.
2870 :			Trace("Field name $fieldName does not begin with a letter.") if T(1);
2871 :			$retVal = 0;
2872 :			} else {
2873 :	parrello	1.75	# Strip out the minus signs. Everything remaining must be a letter,
2874 :			# underscore, or digit.
2875 :	parrello	1.73	my $strippedName = $fieldName;
2876 :			$strippedName =~ s/-//g;
2877 :	parrello	1.75	if ($strippedName !~ /^(\w\|\d)+$/) {
2878 :	parrello	1.73	Trace("Field name $fieldName contains illegal characters.") if T(1);
2879 :			$retVal = 0;
2880 :			}
2881 :			}
2882 :			# Return the result.
2883 :			return $retVal;
2884 :			}
2885 :
2886 :			=head3 ReadMetaXML
2887 :
2888 :			C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2889 :
2890 :			This method reads a raw database definition XML file and returns it.
2891 :			Normally, the metadata used by the ERDB system has been processed and
2892 :			modified to make it easier to load and retrieve the data; however,
2893 :			this method can be used to get the data in its raw form.
2894 :
2895 :			=over 4
2896 :
2897 :			=item fileName
2898 :
2899 :			Name of the XML file to read.
2900 :
2901 :			=item RETURN
2902 :
2903 :			Returns a hash reference containing the raw XML data from the specified file.
2904 :
2905 :			=back
2906 :
2907 :			=cut
2908 :
2909 :			sub ReadMetaXML {
2910 :			# Get the parameters.
2911 :			my ($fileName) = @_;
2912 :			# Read the XML.
2913 :			my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2914 :			Trace("XML metadata loaded from file $fileName.") if T(1);
2915 :			# Return the result.
2916 :			return $retVal;
2917 :			}
2918 :
2919 :			=head3 GetEntityFieldHash
2920 :
2921 :			C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2922 :
2923 :			Get the field hash of the named entity in the specified raw XML structure.
2924 :			The field hash may not exist, in which case we need to create it.
2925 :
2926 :			=over 4
2927 :
2928 :			=item structure
2929 :
2930 :			Raw XML structure defininng the database. This is not the run-time XML used by
2931 :			an ERDB object, since that has all sorts of optimizations built-in.
2932 :
2933 :			=item entityName
2934 :
2935 :			Name of the entity whose field structure is desired.
2936 :
2937 :			=item RETURN
2938 :
2939 :			Returns the field hash used to define the entity's fields.
2940 :
2941 :			=back
2942 :
2943 :			=cut
2944 :
2945 :			sub GetEntityFieldHash {
2946 :			# Get the parameters.
2947 :			my ($structure, $entityName) = @_;
2948 :			# Get the entity structure.
2949 :			my $entityData = $structure->{Entities}->{$entityName};
2950 :			# Look for a field structure.
2951 :			my $retVal = $entityData->{Fields};
2952 :			# If it doesn't exist, create it.
2953 :			if (! defined($retVal)) {
2954 :			$entityData->{Fields} = {};
2955 :			$retVal = $entityData->{Fields};
2956 :			}
2957 :			# Return the result.
2958 :			return $retVal;
2959 :			}
2960 :
2961 :			=head3 WriteMetaXML
2962 :
2963 :			C<< ERDB::WriteMetaXML($structure, $fileName); >>
2964 :
2965 :			Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2966 :			used to update the database definition. It must be used with care, however, since it
2967 :			will only work on a raw structure, not on the processed structure created by an ERDB
2968 :			constructor.
2969 :
2970 :			=over 4
2971 :
2972 :			=item structure
2973 :
2974 :			XML structure to be written to the file.
2975 :
2976 :			=item fileName
2977 :
2978 :			Name of the output file to which the updated XML should be stored.
2979 :
2980 :			=back
2981 :
2982 :			=cut
2983 :
2984 :			sub WriteMetaXML {
2985 :			# Get the parameters.
2986 :			my ($structure, $fileName) = @_;
2987 :			# Compute the output.
2988 :			my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2989 :			# Write it to the file.
2990 :			my $xmlOut = Open(undef, ">$fileName");
2991 :			print $xmlOut $fileString;
2992 :			}
2993 :
2994 :
2995 :			=head3 HTMLNote
2996 :
2997 :			Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2998 :			supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
2999 :			Except for C<[p]>, all the codes are closed by slash-codes. So, for
3000 :			example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3001 :
3002 :			C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3003 :
3004 :			=over 4
3005 :
3006 :			=item dataString
3007 :
3008 :			String to convert to HTML.
3009 :
3010 :			=item RETURN
3011 :
3012 :			An HTML string derived from the input string.
3013 :
3014 :			=back
3015 :
3016 :			=cut
3017 :
3018 :			sub HTMLNote {
3019 :			# Get the parameter.
3020 :			my ($dataString) = @_;
3021 :			# HTML-escape the text.
3022 :			my $retVal = CGI::escapeHTML($dataString);
3023 :			# Substitute the bulletin board codes.
3024 :			$retVal =~ s!\[(/?[bi])\]!<$1>!g;
3025 :			$retVal =~ s!\[p\]!</p><p>!g;
3026 :			# Return the result.
3027 :			return $retVal;
3028 :			}
3029 :
3030 :
3031 :	parrello	1.48	=head2 Data Mining Methods
3032 :
3033 :	parrello	1.38	=head3 GetUsefulCrossValues
3034 :
3035 :			C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3036 :
3037 :			Return a list of the useful attributes that would be returned by a B<Cross> call
3038 :			from an entity of the source entity type through the specified relationship. This
3039 :			means it will return the fields of the target entity type and the intersection data
3040 :			fields in the relationship. Only primary table fields are returned. In other words,
3041 :			the field names returned will be for fields where there is always one and only one
3042 :			value.
3043 :
3044 :			=over 4
3045 :
3046 :			=item sourceEntity
3047 :
3048 :			Name of the entity from which the relationship crossing will start.
3049 :
3050 :			=item relationship
3051 :
3052 :			Name of the relationship being crossed.
3053 :
3054 :			=item RETURN
3055 :
3056 :			Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3057 :
3058 :			=back
3059 :
3060 :			=cut
3061 :			#: Return Type @;
3062 :			sub GetUsefulCrossValues {
3063 :			# Get the parameters.
3064 :			my ($self, $sourceEntity, $relationship) = @_;
3065 :			# Declare the return variable.
3066 :			my @retVal = ();
3067 :			# Determine the target entity for the relationship. This is whichever entity is not
3068 :			# the source entity. So, if the source entity is the FROM, we'll get the name of
3069 :			# the TO, and vice versa.
3070 :			my $relStructure = $self->_GetStructure($relationship);
3071 :			my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3072 :			my $targetEntity = $relStructure->{$targetEntityType};
3073 :			# Get the field table for the entity.
3074 :			my $entityFields = $self->GetFieldTable($targetEntity);
3075 :			# The field table is a hash. The hash key is the field name. The hash value is a structure.
3076 :			# For the entity fields, the key aspect of the target structure is that the {relation} value
3077 :			# must match the entity name.
3078 :			my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3079 :			keys %{$entityFields};
3080 :			# Push the fields found onto the return variable.
3081 :			push @retVal, sort @fieldList;
3082 :			# Get the field table for the relationship.
3083 :			my $relationshipFields = $self->GetFieldTable($relationship);
3084 :			# Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3085 :			# This may end up being an empty set.
3086 :			my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3087 :			keys %{$relationshipFields};
3088 :			# Push these onto the return list.
3089 :			push @retVal, sort @fieldList2;
3090 :			# Return the result.
3091 :			return @retVal;
3092 :			}
3093 :
3094 :	parrello	1.48	=head3 FindColumn
3095 :
3096 :			C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3097 :
3098 :			Return the location a desired column in a data mining header line. The data
3099 :			mining header line is a tab-separated list of column names. The column
3100 :			identifier is either the numerical index of a column or the actual column
3101 :			name.
3102 :
3103 :			=over 4
3104 :
3105 :			=item headerLine
3106 :
3107 :			The header line from a data mining command, which consists of a tab-separated
3108 :			list of column names.
3109 :
3110 :			=item columnIdentifier
3111 :
3112 :			Either the ordinal number of the desired column (1-based), or the name of the
3113 :			desired column.
3114 :
3115 :			=item RETURN
3116 :
3117 :			Returns the array index (0-based) of the desired column.
3118 :
3119 :			=back
3120 :
3121 :			=cut
3122 :
3123 :			sub FindColumn {
3124 :			# Get the parameters.
3125 :			my ($headerLine, $columnIdentifier) = @_;
3126 :			# Declare the return variable.
3127 :			my $retVal;
3128 :			# Split the header line into column names.
3129 :			my @headers = ParseColumns($headerLine);
3130 :			# Determine whether we have a number or a name.
3131 :			if ($columnIdentifier =~ /^\d+$/) {
3132 :			# Here we have a number. Subtract 1 and validate the result.
3133 :			$retVal = $columnIdentifier - 1;
3134 :			if ($retVal < 0 \|\| $retVal > $#headers) {
3135 :			Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3136 :			}
3137 :			} else {
3138 :			# Here we have a name. We need to find it in the list.
3139 :			for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3140 :			if ($headers[$i] eq $columnIdentifier) {
3141 :			$retVal = $i;
3142 :			}
3143 :			}
3144 :			if (! defined($retVal)) {
3145 :			Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3146 :			}
3147 :			}
3148 :			# Return the result.
3149 :			return $retVal;
3150 :			}
3151 :
3152 :			=head3 ParseColumns
3153 :
3154 :	parrello	1.50	C<< my @columns = ERDB::ParseColumns($line); >>
3155 :	parrello	1.48
3156 :			Convert the specified data line to a list of columns.
3157 :
3158 :			=over 4
3159 :
3160 :			=item line
3161 :
3162 :			A data mining input, consisting of a tab-separated list of columns terminated by a
3163 :			new-line.
3164 :
3165 :			=item RETURN
3166 :
3167 :			Returns a list consisting of the column values.
3168 :
3169 :			=back
3170 :
3171 :			=cut
3172 :
3173 :			sub ParseColumns {
3174 :			# Get the parameters.
3175 :	parrello	1.50	my ($line) = @_;
3176 :	parrello	1.48	# Chop off the line-end.
3177 :			chomp $line;
3178 :			# Split it into a list.
3179 :			my @retVal = split(/\t/, $line);
3180 :			# Return the result.
3181 :			return @retVal;
3182 :			}
3183 :
3184 :	parrello	1.71	=head2 Virtual Methods
3185 :
3186 :			=head3 CleanKeywords
3187 :
3188 :			C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3189 :
3190 :			Clean up a search expression or keyword list. This is a virtual method that may
3191 :			be overridden by the subclass. The base-class method removes extra spaces
3192 :			and converts everything to lower case.
3193 :
3194 :			=over 4
3195 :
3196 :			=item searchExpression
3197 :
3198 :			Search expression or keyword list to clean. Note that a search expression may
3199 :			contain boolean operators which need to be preserved. This includes leading
3200 :			minus signs.
3201 :
3202 :			=item RETURN
3203 :
3204 :			Cleaned expression or keyword list.
3205 :
3206 :			=back
3207 :
3208 :			=cut
3209 :
3210 :			sub CleanKeywords {
3211 :			# Get the parameters.
3212 :			my ($self, $searchExpression) = @_;
3213 :			# Lower-case the expression and copy it into the return variable. Note that we insure we
3214 :			# don't accidentally end up with an undefined value.
3215 :			my $retVal = lc($searchExpression \|\| "");
3216 :			# Remove extra spaces.
3217 :			$retVal =~ s/\s+/ /g;
3218 :			$retVal =~ s/(^\s+)\|(\s+$)//g;
3219 :			# Return the result.
3220 :			return $retVal;
3221 :			}
3222 :
3223 :	parrello	1.73	=head3 GetSourceObject
3224 :
3225 :			C<< my $source = $erdb->GetSourceObject($entityName); >>
3226 :
3227 :			Return the object to be used in loading special attributes of the specified entity. The
3228 :			algorithm for loading special attributes is stored in the C<DataGen> elements of the
3229 :			XML
3230 :
3231 :	parrello	1.1	=head2 Internal Utility Methods
3232 :
3233 :	parrello	1.70	=head3 _RelationMap
3234 :
3235 :			C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3236 :
3237 :			Create the relation map for an SQL query. The relation map is used by B<DBObject>
3238 :			to determine how to interpret the results of the query.
3239 :
3240 :			=over 4
3241 :
3242 :			=item mappedNameHashRef
3243 :
3244 :			Reference to a hash that maps modified object names to real object names.
3245 :
3246 :			=item mappedNameListRef
3247 :
3248 :			Reference to a list of modified object names in the order they appear in the
3249 :			SELECT list.
3250 :
3251 :			=item RETURN
3252 :
3253 :			Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3254 :			query followed by the actual name of that object. This enables the B<DBObject> to
3255 :			determine the order of the tables in the query and which object name belongs to each
3256 :			mapped object name. Most of the time these two values are the same; however, if a
3257 :			relation occurs twice in the query, the relation name in the field list and WHERE
3258 :			clause will use a mapped name (generally the actual relation name with a numeric
3259 :			suffix) that does not match the actual relation name.
3260 :
3261 :			=back
3262 :
3263 :			=cut
3264 :
3265 :			sub _RelationMap {
3266 :			# Get the parameters.
3267 :			my ($mappedNameHashRef, $mappedNameListRef) = @_;
3268 :			# Declare the return variable.
3269 :			my @retVal = ();
3270 :			# Build the map.
3271 :			for my $mappedName (@{$mappedNameListRef}) {
3272 :			push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3273 :			}
3274 :			# Return it.
3275 :			return @retVal;
3276 :			}
3277 :
3278 :
3279 :			=head3 _SetupSQL
3280 :	parrello	1.45
3281 :			Process a list of object names and a filter clause so that they can be used to
3282 :			build an SQL statement. This method takes in a reference to a list of object names
3283 :			and a filter clause. It will return a corrected filter clause, a list of mapped
3284 :			names and the mapped name hash.
3285 :
3286 :			This is an instance method.
3287 :
3288 :			=over 4
3289 :
3290 :			=item objectNames
3291 :
3292 :			Reference to a list of the object names to be included in the query.
3293 :
3294 :			=item filterClause
3295 :
3296 :			A string containing the WHERE clause for the query (without the C<WHERE>) and also
3297 :			optionally the C<ORDER BY> and C<LIMIT> clauses.
3298 :
3299 :	parrello	1.70	=item matchClause
3300 :
3301 :			An optional full-text search clause. If specified, it will be inserted at the
3302 :			front of the WHERE clause. It should already be SQL-formatted; that is, the
3303 :			field names should be in the form I<table>C<.>I<fieldName>.
3304 :
3305 :	parrello	1.45	=item RETURN
3306 :
3307 :			Returns a three-element list. The first element is the SQL statement suffix, beginning
3308 :			with the FROM clause. The second element is a reference to a list of the names to be
3309 :			used in retrieving the fields. The third element is a hash mapping the names to the
3310 :			objects they represent.
3311 :
3312 :			=back
3313 :
3314 :			=cut
3315 :
3316 :			sub _SetupSQL {
3317 :	parrello	1.70	my ($self, $objectNames, $filterClause, $matchClause) = @_;
3318 :	parrello	1.45	# Adjust the list of object names to account for multiple occurrences of the
3319 :			# same object. We start with a hash table keyed on object name that will
3320 :			# return the object suffix. The first time an object is encountered it will
3321 :			# not be found in the hash. The next time the hash will map the object name
3322 :			# to 2, then 3, and so forth.
3323 :			my %objectHash = ();
3324 :			# This list will contain the object names as they are to appear in the
3325 :			# FROM list.
3326 :			my @fromList = ();
3327 :			# This list contains the suffixed object name for each object. It is exactly
3328 :			# parallel to the list in the $objectNames parameter.
3329 :			my @mappedNameList = ();
3330 :			# Finally, this hash translates from a mapped name to its original object name.
3331 :			my %mappedNameHash = ();
3332 :			# Now we create the lists. Note that for every single name we push something into
3333 :			# @fromList and @mappedNameList. This insures that those two arrays are exactly
3334 :			# parallel to $objectNames.
3335 :			for my $objectName (@{$objectNames}) {
3336 :			# Get the next suffix for this object.
3337 :			my $suffix = $objectHash{$objectName};
3338 :			if (! $suffix) {
3339 :			# Here we are seeing the object for the first time. The object name
3340 :			# is used as is.
3341 :			push @mappedNameList, $objectName;
3342 :			push @fromList, $objectName;
3343 :			$mappedNameHash{$objectName} = $objectName;
3344 :			# Denote the next suffix will be 2.
3345 :			$objectHash{$objectName} = 2;
3346 :			} else {
3347 :			# Here we've seen the object before. We construct a new name using
3348 :			# the suffix from the hash and update the hash.
3349 :			my $mappedName = "$objectName$suffix";
3350 :			$objectHash{$objectName} = $suffix + 1;
3351 :			# The FROM list has the object name followed by the mapped name. This
3352 :			# tells SQL it's still the same table, but we're using a different name
3353 :			# for it to avoid confusion.
3354 :			push @fromList, "$objectName $mappedName";
3355 :			# The mapped-name list contains the real mapped name.
3356 :			push @mappedNameList, $mappedName;
3357 :			# Finally, enable us to get back from the mapped name to the object name.
3358 :			$mappedNameHash{$mappedName} = $objectName;
3359 :			}
3360 :			}
3361 :			# Begin the SELECT suffix. It starts with
3362 :			#
3363 :			# FROM name1, name2, ... nameN
3364 :			#
3365 :			my $suffix = "FROM " . join(', ', @fromList);
3366 :	parrello	1.70	# Now for the WHERE. First, we need a place for the filter string.
3367 :			my $filterString = "";
3368 :			# We will also keep a list of conditions to add to the WHERE clause in order to link
3369 :			# entities and relationships as well as primary relations to secondary ones.
3370 :			my @joinWhere = ();
3371 :	parrello	1.45	# Check for a filter clause.
3372 :			if ($filterClause) {
3373 :			# Here we have one, so we convert its field names and add it to the query. First,
3374 :			# We create a copy of the filter string we can work with.
3375 :	parrello	1.70	$filterString = $filterClause;
3376 :	parrello	1.45	# Next, we sort the object names by length. This helps protect us from finding
3377 :			# object names inside other object names when we're doing our search and replace.
3378 :			my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3379 :			# The final preparatory step is to create a hash table of relation names. The
3380 :			# table begins with the relation names already in the SELECT command. We may
3381 :			# need to add relations later if there is filtering on a field in a secondary
3382 :			# relation. The secondary relations are the ones that contain multiply-
3383 :			# occurring or optional fields.
3384 :			my %fromNames = map { $_ => 1 } @sortedNames;
3385 :			# We are ready to begin. We loop through the object names, replacing each
3386 :			# object name's field references by the corresponding SQL field reference.
3387 :			# Along the way, if we find a secondary relation, we will need to add it
3388 :			# to the FROM clause.
3389 :			for my $mappedName (@sortedNames) {
3390 :			# Get the length of the object name plus 2. This is the value we add to the
3391 :			# size of the field name to determine the size of the field reference as a
3392 :			# whole.
3393 :			my $nameLength = 2 + length $mappedName;
3394 :			# Get the real object name for this mapped name.
3395 :			my $objectName = $mappedNameHash{$mappedName};
3396 :			Trace("Processing $mappedName for object $objectName.") if T(4);
3397 :			# Get the object's field list.
3398 :			my $fieldList = $self->GetFieldTable($objectName);
3399 :			# Find the field references for this object.
3400 :			while ($filterString =~ m/$mappedName$([^)]*)$/g) {
3401 :			# At this point, $1 contains the field name, and the current position
3402 :			# is set immediately after the final parenthesis. We pull out the name of
3403 :			# the field and the position and length of the field reference as a whole.
3404 :			my $fieldName = $1;
3405 :			my $len = $nameLength + length $fieldName;
3406 :			my $pos = pos($filterString) - $len;
3407 :			# Insure the field exists.
3408 :			if (!exists $fieldList->{$fieldName}) {
3409 :			Confess("Field $fieldName not found for object $objectName.");
3410 :			} else {
3411 :			Trace("Processing $fieldName at position $pos.") if T(4);
3412 :			# Get the field's relation.
3413 :			my $relationName = $fieldList->{$fieldName}->{relation};
3414 :			# Now we have a secondary relation. We need to insure it matches the
3415 :			# mapped name of the primary relation. First we peel off the suffix
3416 :			# from the mapped name.
3417 :			my $mappingSuffix = substr $mappedName, length($objectName);
3418 :			# Put the mapping suffix onto the relation name to get the
3419 :			# mapped relation name.
3420 :			my $mappedRelationName = "$relationName$mappingSuffix";
3421 :			# Insure the relation is in the FROM clause.
3422 :			if (!exists $fromNames{$mappedRelationName}) {
3423 :			# Add the relation to the FROM clause.
3424 :			if ($mappedRelationName eq $relationName) {
3425 :			# The name is un-mapped, so we add it without
3426 :			# any frills.
3427 :			$suffix .= ", $relationName";
3428 :			push @joinWhere, "$objectName.id = $relationName.id";
3429 :			} else {
3430 :			# Here we have a mapping situation.
3431 :			$suffix .= ", $relationName $mappedRelationName";
3432 :			push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3433 :			}
3434 :			# Denote we have this relation available for future fields.
3435 :			$fromNames{$mappedRelationName} = 1;
3436 :			}
3437 :			# Form an SQL field reference from the relation name and the field name.
3438 :			my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3439 :			# Put it into the filter string in place of the old value.
3440 :			substr($filterString, $pos, $len) = $sqlReference;
3441 :			# Reposition the search.
3442 :			pos $filterString = $pos + length $sqlReference;
3443 :			}
3444 :			}
3445 :			}
3446 :	parrello	1.70	}
3447 :			# The next step is to join the objects together. We only need to do this if there
3448 :			# is more than one object in the object list. We start with the first object and
3449 :			# run through the objects after it. Note also that we make a safety copy of the
3450 :			# list before running through it, because we shift off the first object before
3451 :			# processing the rest.
3452 :			my @mappedObjectList = @mappedNameList;
3453 :			my $lastMappedObject = shift @mappedObjectList;
3454 :			# Get the join table.
3455 :			my $joinTable = $self->{_metaData}->{Joins};
3456 :			# Loop through the object list.
3457 :			for my $thisMappedObject (@mappedObjectList) {
3458 :			# Look for a join using the real object names.
3459 :			my $lastObject = $mappedNameHash{$lastMappedObject};
3460 :			my $thisObject = $mappedNameHash{$thisMappedObject};
3461 :			my $joinKey = "$lastObject/$thisObject";
3462 :			if (!exists $joinTable->{$joinKey}) {
3463 :			# Here there's no join, so we throw an error.
3464 :			Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3465 :			} else {
3466 :			# Get the join clause.
3467 :			my $unMappedJoin = $joinTable->{$joinKey};
3468 :			# Fix the names.
3469 :			$unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3470 :			$unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3471 :			push @joinWhere, $unMappedJoin;
3472 :			# Save this object as the last object for the next iteration.
3473 :			$lastMappedObject = $thisMappedObject;
3474 :			}
3475 :			}
3476 :			# Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3477 :			# here is we want the filter clause to be empty if there's no WHERE filter.
3478 :			# We'll put the ORDER BY / LIMIT clauses in the following variable.
3479 :			my $orderClause = "";
3480 :			# This is only necessary if we have a filter string in which the ORDER BY
3481 :			# and LIMIT clauses can live.
3482 :			if ($filterString) {
3483 :	parrello	1.45	# Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3484 :			# operator so that we find the first occurrence of either verb.
3485 :			if ($filterString =~ m/^(.?)\s(ORDER BY\|LIMIT)/g) {
3486 :			# Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3487 :			my $pos = pos $filterString;
3488 :			$orderClause = $2 . substr($filterString, $pos);
3489 :			$filterString = $1;
3490 :			}
3491 :	parrello	1.70	}
3492 :			# All the things that are supposed to be in the WHERE clause of the
3493 :			# SELECT command need to be put into @joinWhere so we can string them
3494 :			# together. We begin with the match clause. This is important,
3495 :			# because the match clause's parameter mark must precede any parameter
3496 :			# marks in the filter string.
3497 :			if ($matchClause) {
3498 :			push @joinWhere, $matchClause;
3499 :			}
3500 :			# Add the filter string. We put it in parentheses to avoid operator
3501 :			# precedence problems with the match clause or the joins.
3502 :			if ($filterString) {
3503 :			Trace("Filter string is \"$filterString\".") if T(4);
3504 :			push @joinWhere, "($filterString)";
3505 :			}
3506 :			# String it all together into a big filter clause.
3507 :			if (@joinWhere) {
3508 :			$suffix .= " WHERE " . join(' AND ', @joinWhere);
3509 :			}
3510 :			# Add the sort or limit clause (if any).
3511 :			if ($orderClause) {
3512 :			$suffix .= " $orderClause";
3513 :	parrello	1.45	}
3514 :			# Return the suffix, the mapped name list, and the mapped name hash.
3515 :			return ($suffix, \@mappedNameList, \%mappedNameHash);
3516 :			}
3517 :
3518 :	parrello	1.70	=head3 _GetStatementHandle
3519 :	parrello	1.45
3520 :			This method will prepare and execute an SQL query, returning the statement handle.
3521 :			The main reason for doing this here is so that everybody who does SQL queries gets
3522 :			the benefit of tracing.
3523 :
3524 :			This is an instance method.
3525 :
3526 :			=over 4
3527 :
3528 :			=item command
3529 :
3530 :			Command to prepare and execute.
3531 :
3532 :			=item params
3533 :
3534 :			Reference to a list of the values to be substituted in for the parameter marks.
3535 :
3536 :			=item RETURN
3537 :
3538 :			Returns a prepared and executed statement handle from which the caller can extract
3539 :			results.
3540 :
3541 :			=back
3542 :
3543 :			=cut
3544 :
3545 :			sub _GetStatementHandle {
3546 :			# Get the parameters.
3547 :			my ($self, $command, $params) = @_;
3548 :			# Trace the query.
3549 :			Trace("SQL query: $command") if T(SQL => 3);
3550 :			Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3551 :			# Get the database handle.
3552 :			my $dbh = $self->{_dbh};
3553 :			# Prepare the command.
3554 :			my $sth = $dbh->prepare_command($command);
3555 :			# Execute it with the parameters bound in.
3556 :	parrello	1.75	$sth->execute(@{$params}) \|\| Confess("SELECT error: " . $sth->errstr());
3557 :	parrello	1.45	# Return the statement handle.
3558 :			return $sth;
3559 :			}
3560 :
3561 :	parrello	1.70	=head3 _GetLoadStats
3562 :	parrello	1.1
3563 :			Return a blank statistics object for use by the load methods.
3564 :
3565 :			This is a static method.
3566 :
3567 :			=cut
3568 :
3569 :	parrello	1.29	sub _GetLoadStats{
3570 :	parrello	1.28	return Stats->new();
3571 :	parrello	1.1	}
3572 :
3573 :	parrello	1.70	=head3 _DumpRelation
3574 :	parrello	1.1
3575 :	parrello	1.73	Dump the specified relation to the specified output file in tab-delimited format.
3576 :	parrello	1.1
3577 :			This is an instance method.
3578 :
3579 :			=over 4
3580 :
3581 :			=item outputDirectory
3582 :
3583 :			Directory to contain the output file.
3584 :
3585 :			=item relationName
3586 :
3587 :			Name of the relation to dump.
3588 :
3589 :			=item relation
3590 :
3591 :			Structure describing the relation to be dumped.
3592 :
3593 :			=back
3594 :
3595 :			=cut
3596 :
3597 :			sub _DumpRelation {
3598 :	parrello	1.10	# Get the parameters.
3599 :			my ($self, $outputDirectory, $relationName, $relation) = @_;
3600 :			# Open the output file.
3601 :			my $fileName = "$outputDirectory/$relationName.dtx";
3602 :			open(DTXOUT, ">$fileName") \|\| Confess("Could not open dump file $fileName: $!");
3603 :			# Create a query for the specified relation.
3604 :			my $dbh = $self->{_dbh};
3605 :			my $query = $dbh->prepare_command("SELECT * FROM $relationName");
3606 :			# Execute the query.
3607 :			$query->execute() \|\| Confess("SELECT error dumping $relationName.");
3608 :			# Loop through the results.
3609 :			while (my @row = $query->fetchrow) {
3610 :			# Escape any tabs or new-lines in the row text.
3611 :			for my $field (@row) {
3612 :			$field =~ s/\n/\\n/g;
3613 :			$field =~ s/\t/\\t/g;
3614 :			}
3615 :			# Tab-join the row and write it to the output file.
3616 :			my $rowText = join("\t", @row);
3617 :			print DTXOUT "$rowText\n";
3618 :			}
3619 :			# Close the output file.
3620 :			close DTXOUT;
3621 :	parrello	1.1	}
3622 :
3623 :	parrello	1.70	=head3 _GetStructure
3624 :	parrello	1.1
3625 :			Get the data structure for a specified entity or relationship.
3626 :
3627 :			This is an instance method.
3628 :
3629 :			=over 4
3630 :
3631 :			=item objectName
3632 :
3633 :			Name of the desired entity or relationship.
3634 :
3635 :			=item RETURN
3636 :
3637 :			The descriptor for the specified object.
3638 :
3639 :			=back
3640 :
3641 :			=cut
3642 :
3643 :			sub _GetStructure {
3644 :	parrello	1.10	# Get the parameters.
3645 :			my ($self, $objectName) = @_;
3646 :			# Get the metadata structure.
3647 :			my $metadata = $self->{_metaData};
3648 :			# Declare the variable to receive the descriptor.
3649 :			my $retVal;
3650 :			# Get the descriptor from the metadata.
3651 :			if (exists $metadata->{Entities}->{$objectName}) {
3652 :			$retVal = $metadata->{Entities}->{$objectName};
3653 :			} elsif (exists $metadata->{Relationships}->{$objectName}) {
3654 :			$retVal = $metadata->{Relationships}->{$objectName};
3655 :			} else {
3656 :			Confess("Object $objectName not found in database.");
3657 :			}
3658 :			# Return the descriptor.
3659 :			return $retVal;
3660 :	parrello	1.1	}
3661 :
3662 :	parrello	1.70
3663 :
3664 :			=head3 _GetRelationTable
3665 :	parrello	1.1
3666 :			Get the list of relations for a specified entity or relationship.
3667 :
3668 :			This is an instance method.
3669 :
3670 :			=over 4
3671 :
3672 :			=item objectName
3673 :
3674 :			Name of the desired entity or relationship.
3675 :
3676 :			=item RETURN
3677 :
3678 :			A table containing the relations for the specified object.
3679 :
3680 :			=back
3681 :
3682 :			=cut
3683 :
3684 :			sub _GetRelationTable {
3685 :	parrello	1.10	# Get the parameters.
3686 :			my ($self, $objectName) = @_;
3687 :			# Get the descriptor from the metadata.
3688 :			my $objectData = $self->_GetStructure($objectName);
3689 :			# Return the object's relation list.
3690 :			return $objectData->{Relations};
3691 :	parrello	1.1	}
3692 :
3693 :	parrello	1.70	=head3 _ValidateFieldNames
3694 :	parrello	1.1
3695 :			Determine whether or not the field names are valid. A description of the problems with the names
3696 :			will be written to the standard error output. If there is an error, this method will abort. This is
3697 :			a static method.
3698 :
3699 :			=over 4
3700 :
3701 :			=item metadata
3702 :
3703 :			Metadata structure loaded from the XML data definition.
3704 :
3705 :			=back
3706 :
3707 :			=cut
3708 :
3709 :			sub _ValidateFieldNames {
3710 :	parrello	1.10	# Get the object.
3711 :			my ($metadata) = @_;
3712 :			# Declare the return value. We assume success.
3713 :			my $retVal = 1;
3714 :			# Loop through the sections of the database definition.
3715 :			for my $section ('Entities', 'Relationships') {
3716 :			# Loop through the objects in this section.
3717 :			for my $object (values %{$metadata->{$section}}) {
3718 :			# Loop through the object's fields.
3719 :			for my $fieldName (keys %{$object->{Fields}}) {
3720 :	parrello	1.73	# If this field name is invalid, set the return value to zero
3721 :			# so we know we encountered an error.
3722 :			if (! ValidateFieldName($fieldName)) {
3723 :	parrello	1.10	$retVal = 0;
3724 :			}
3725 :			}
3726 :			}
3727 :			}
3728 :			# If an error was found, fail.
3729 :			if ($retVal == 0) {
3730 :			Confess("Errors found in field names.");
3731 :			}
3732 :	parrello	1.1	}
3733 :
3734 :	parrello	1.70	=head3 _LoadRelation
3735 :	parrello	1.1
3736 :			Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
3737 :			file with the same name as the relation exists in the specified directory.
3738 :
3739 :			This is an instance method.
3740 :
3741 :			=over 4
3742 :
3743 :			=item dbh
3744 :
3745 :			DBKernel object for accessing the database.
3746 :
3747 :			=item directoryName
3748 :
3749 :			Name of the directory containing the tab-delimited data files.
3750 :
3751 :			=item relationName
3752 :
3753 :			Name of the relation to load.
3754 :
3755 :			=item rebuild
3756 :
3757 :			TRUE if the table should be dropped and re-created before loading.
3758 :
3759 :			=item RETURN
3760 :
3761 :			Returns a statistical object describing the number of records read and a list of error messages.
3762 :
3763 :			=back
3764 :
3765 :			=cut
3766 :
3767 :			sub _LoadRelation {
3768 :	parrello	1.10	# Get the parameters.
3769 :			my ($self, $directoryName, $relationName, $rebuild) = @_;
3770 :			# Create the file name.
3771 :			my $fileName = "$directoryName/$relationName";
3772 :			# If the file doesn't exist, try adding the .dtx suffix.
3773 :			if (! -e $fileName) {
3774 :			$fileName .= ".dtx";
3775 :			if (! -e $fileName) {
3776 :			$fileName = "";
3777 :			}
3778 :			}
3779 :			# Create the return object.
3780 :			my $retVal = _GetLoadStats();
3781 :			# If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
3782 :			# be a null string.
3783 :			if ($fileName ne "") {
3784 :			# Load the relation from the file.
3785 :			$retVal = $self->LoadTable($fileName, $relationName, $rebuild);
3786 :			} elsif ($rebuild) {
3787 :			# Here we are rebuilding, but no file exists, so we just re-create the table.
3788 :			$self->CreateTable($relationName, 1);
3789 :			}
3790 :			# Return the statistics from the load.
3791 :			return $retVal;
3792 :	parrello	1.1	}
3793 :
3794 :	parrello	1.73
3795 :	parrello	1.70	=head3 _LoadMetaData
3796 :	parrello	1.1
3797 :			This method loads the data describing this database from an XML file into a metadata structure.
3798 :			The resulting structure is a set of nested hash tables containing all the information needed to
3799 :			load or use the database. The schema for the XML file is F<ERDatabase.xml>.
3800 :
3801 :			This is a static method.
3802 :
3803 :			=over 4
3804 :
3805 :			=item filename
3806 :
3807 :			Name of the file containing the database definition.
3808 :
3809 :			=item RETURN
3810 :
3811 :			Returns a structure describing the database.
3812 :
3813 :			=back
3814 :
3815 :			=cut
3816 :
3817 :			sub _LoadMetaData {
3818 :	parrello	1.10	# Get the parameters.
3819 :			my ($filename) = @_;
3820 :	parrello	1.75	Trace("Reading DBD from $filename.") if T(2);
3821 :	parrello	1.10	# Slurp the XML file into a variable. Extensive use of options is used to insure we
3822 :			# get the exact structure we want.
3823 :	parrello	1.73	my $metadata = ReadMetaXML($filename);
3824 :	parrello	1.10	# Before we go any farther, we need to validate the field and object names. If an error is found,
3825 :			# the method below will fail.
3826 :			_ValidateFieldNames($metadata);
3827 :			# Next we need to create a hash table for finding relations. The entities and relationships are
3828 :			# implemented as one or more database relations.
3829 :			my %masterRelationTable = ();
3830 :			# Loop through the entities.
3831 :			my $entityList = $metadata->{Entities};
3832 :			for my $entityName (keys %{$entityList}) {
3833 :			my $entityStructure = $entityList->{$entityName};
3834 :			#
3835 :	parrello	1.12	# The first step is to create all the entity's default values. For C<Field> elements,
3836 :	parrello	1.10	# the relation name must be added where it is not specified. For relationships,
3837 :			# the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
3838 :			# field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
3839 :			# added that can be used to pull the implicit fields to the top when displaying the field
3840 :			# documentation. The PrettySort values are 1-based and indicate in which pass through a
3841 :			# relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
3842 :			# and so on.
3843 :			#
3844 :			# Fix up this entity.
3845 :			_FixupFields($entityStructure, $entityName, 2, 3);
3846 :			# Add the ID field.
3847 :			_AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
3848 :			relation => $entityName,
3849 :			Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
3850 :			PrettySort => 1});
3851 :			#
3852 :			# The current field list enables us to quickly find the relation containing a particular field.
3853 :			# We also need a list that tells us the fields in each relation. We do this by creating a
3854 :			# Relations structure in the entity structure and collating the fields into it based on their
3855 :			# C<relation> property. There is one tricky bit, which is that every relation has to have the
3856 :			# C<id> field in it. Note also that the field list is put into a C<Fields> member of the
3857 :			# relation's structure so that it looks more like the entity and relationship structures.
3858 :			#
3859 :			# First we need to create the relations list.
3860 :			my $relationTable = { };
3861 :			# Loop through the fields. We use a list of field names to prevent a problem with
3862 :			# the hash table cursor losing its place during the loop.
3863 :			my $fieldList = $entityStructure->{Fields};
3864 :			my @fieldNames = keys %{$fieldList};
3865 :			for my $fieldName (@fieldNames) {
3866 :			my $fieldData = $fieldList->{$fieldName};
3867 :			# Get the current field's relation name.
3868 :			my $relationName = $fieldData->{relation};
3869 :			# Insure the relation exists.
3870 :			if (!exists $relationTable->{$relationName}) {
3871 :			$relationTable->{$relationName} = { Fields => { } };
3872 :			}
3873 :			# Add the field to the relation's field structure.
3874 :			$relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
3875 :			}
3876 :			# Now that we've organized all our fields by relation name we need to do some serious
3877 :			# housekeeping. We must add the C<id> field to every relation and convert each relation
3878 :			# to a list of fields. First, we need the ID field itself.
3879 :			my $idField = $fieldList->{id};
3880 :			# Loop through the relations.
3881 :			for my $relationName (keys %{$relationTable}) {
3882 :			my $relation = $relationTable->{$relationName};
3883 :			# Get the relation's field list.
3884 :			my $relationFieldList = $relation->{Fields};
3885 :			# Add the ID field to it. If the field's already there, it will not make any
3886 :			# difference.
3887 :			$relationFieldList->{id} = $idField;
3888 :			# Convert the field set from a hash into a list using the pretty-sort number.
3889 :			$relation->{Fields} = _ReOrderRelationTable($relationFieldList);
3890 :			# Add the relation to the master table.
3891 :			$masterRelationTable{$relationName} = $relation;
3892 :			}
3893 :			# The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
3894 :			# The other relations must have at least one index that begins with the ID field. In addition, the
3895 :			# metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
3896 :			# get the entity's field list and index list.
3897 :			my $indexList = $entityStructure->{Indexes};
3898 :			# Loop through the indexes.
3899 :			for my $indexData (@{$indexList}) {
3900 :			# We need to find this index's fields. All of them should belong to the same relation.
3901 :			# The ID field is an exception, since it's in all relations.
3902 :			my $relationName = '0';
3903 :			for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
3904 :			# Get this field's name.
3905 :			my $fieldName = $fieldDescriptor->{name};
3906 :			# Only proceed if it is NOT the ID field.
3907 :			if ($fieldName ne 'id') {
3908 :			# Find the relation containing the current index field.
3909 :			my $thisName = $fieldList->{$fieldName}->{relation};
3910 :			if ($relationName eq '0') {
3911 :			# Here we're looking at the first field, so we save its relation name.
3912 :			$relationName = $thisName;
3913 :			} elsif ($relationName ne $thisName) {
3914 :			# Here we have a field mismatch.
3915 :			Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
3916 :			}
3917 :			}
3918 :			}
3919 :			# Now $relationName is the name of the relation that contains this index. Add the index structure
3920 :			# to the relation.
3921 :			push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
3922 :			}
3923 :			# Now each index has been put in a relation. We need to add the primary index for the primary
3924 :			# relation.
3925 :			push @{$relationTable->{$entityName}->{Indexes}},
3926 :			{ IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
3927 :			Notes => { content => "Primary index for $entityName." }
3928 :			};
3929 :			# The next step is to insure that each relation has at least one index that begins with the ID field.
3930 :			# After that, we convert each relation's index list to an index table. We first need to loop through
3931 :			# the relations.
3932 :			for my $relationName (keys %{$relationTable}) {
3933 :			my $relation = $relationTable->{$relationName};
3934 :			# Get the relation's index list.
3935 :			my $indexList = $relation->{Indexes};
3936 :			# Insure this relation has an ID index.
3937 :			my $found = 0;
3938 :			for my $index (@{$indexList}) {
3939 :			if ($index->{IndexFields}->[0]->{name} eq "id") {
3940 :			$found = 1;
3941 :			}
3942 :			}
3943 :			if ($found == 0) {
3944 :			push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
3945 :			}
3946 :			# Now we need to convert the relation's index list to an index table. We begin by creating
3947 :			# an empty table in the relation structure.
3948 :			$relation->{Indexes} = { };
3949 :			# Loop through the indexes.
3950 :			my $count = 0;
3951 :			for my $index (@{$indexList}) {
3952 :			# Add this index to the index table.
3953 :	parrello	1.75	_AddIndex("idx$count", $relation, $index);
3954 :	parrello	1.10	# Increment the counter so that the next index has a different name.
3955 :			$count++;
3956 :			}
3957 :			}
3958 :			# Finally, we add the relation structure to the entity.
3959 :			$entityStructure->{Relations} = $relationTable;
3960 :			}
3961 :			# Loop through the relationships. Relationships actually turn out to be much simpler than entities.
3962 :			# For one thing, there is only a single constituent relation.
3963 :			my $relationshipList = $metadata->{Relationships};
3964 :			for my $relationshipName (keys %{$relationshipList}) {
3965 :			my $relationshipStructure = $relationshipList->{$relationshipName};
3966 :			# Fix up this relationship.
3967 :			_FixupFields($relationshipStructure, $relationshipName, 2, 3);
3968 :			# Format a description for the FROM field.
3969 :			my $fromEntity = $relationshipStructure->{from};
3970 :			my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
3971 :			# Get the FROM entity's key type.
3972 :			my $fromType = $entityList->{$fromEntity}->{keyType};
3973 :			# Add the FROM field.
3974 :			_AddField($relationshipStructure, 'from-link', { type => $fromType,
3975 :			relation => $relationshipName,
3976 :			Notes => { content => $fromComment },
3977 :			PrettySort => 1});
3978 :			# Format a description for the TO field.
3979 :			my $toEntity = $relationshipStructure->{to};
3980 :			my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
3981 :			# Get the TO entity's key type.
3982 :			my $toType = $entityList->{$toEntity}->{keyType};
3983 :			# Add the TO field.
3984 :			_AddField($relationshipStructure, 'to-link', { type=> $toType,
3985 :			relation => $relationshipName,
3986 :			Notes => { content => $toComment },
3987 :			PrettySort => 1});
3988 :			# Create an index-free relation from the fields.
3989 :			my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
3990 :			Indexes => { } };
3991 :			$relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
3992 :			# Create the FROM and TO indexes.
3993 :			_CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
3994 :			_CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
3995 :			# Add the relation to the master table.
3996 :			$masterRelationTable{$relationshipName} = $thisRelation;
3997 :			}
3998 :			# Now store the master relation table in the metadata structure.
3999 :			$metadata->{RelationTable} = \%masterRelationTable;
4000 :			# Our final task is to create the join table. The join table is a hash that describes all
4001 :			# the join clauses for traveling through the relationships. The join clause is an equality
4002 :			# condition that can be put into a WHERE clause in order to join two objects. Two relationships
4003 :			# can be joined if they share an entity in common; and an entity can be joined to a relationship
4004 :			# if the entity is at either end of the relationship.
4005 :			my %joinTable = ();
4006 :			# Loop through the entities.
4007 :			for my $entityName (keys %{$entityList}) {
4008 :			# Build three lists of the relationships connected to this entity. One will be
4009 :			# for relationships from the entity, one for relationships to the entity, and
4010 :			# one for recursive relationships.
4011 :			my @fromList = ();
4012 :			my @toList = ();
4013 :			my @bothList = ();
4014 :	parrello	1.21	Trace("Join table build for $entityName.") if T(metadata => 4);
4015 :	parrello	1.10	for my $relationshipName (keys %{$relationshipList}) {
4016 :			my $relationship = $relationshipList->{$relationshipName};
4017 :			# Determine if this relationship has our entity in one of its link fields.
4018 :			my $fromEntity = $relationship->{from};
4019 :			my $toEntity = $relationship->{to};
4020 :	parrello	1.41	Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4021 :	parrello	1.10	if ($fromEntity eq $entityName) {
4022 :			if ($toEntity eq $entityName) {
4023 :			# Here the relationship is recursive.
4024 :			push @bothList, $relationshipName;
4025 :	parrello	1.21	Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
4026 :	parrello	1.10	} else {
4027 :			# Here the relationship comes from the entity.
4028 :			push @fromList, $relationshipName;
4029 :	parrello	1.21	Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
4030 :	parrello	1.10	}
4031 :			} elsif ($toEntity eq $entityName) {
4032 :			# Here the relationship goes to the entity.
4033 :			push @toList, $relationshipName;
4034 :	parrello	1.21	Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
4035 :	parrello	1.10	}
4036 :			}
4037 :			# Create the nonrecursive joins. Note that we build two hashes for running
4038 :			# through the nonrecursive relationships since we'll have an outer loop
4039 :			# and an inner loop, and we can't do two "each" iterations on the same
4040 :			# hash table at the same time.
4041 :			my %directRelationships = ( from => \@fromList, to => \@toList );
4042 :			my %otherRelationships = ( from => \@fromList, to => \@toList );
4043 :			for my $linkType (keys %directRelationships) {
4044 :			my $relationships = $directRelationships{$linkType};
4045 :			# Loop through all the relationships.
4046 :			for my $relationshipName (@{$relationships}) {
4047 :			# Create joins between the entity and this relationship.
4048 :			my $linkField = "$relationshipName.${linkType}_link";
4049 :			my $joinClause = "$entityName.id = $linkField";
4050 :	parrello	1.21	Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
4051 :	parrello	1.10	$joinTable{"$entityName/$relationshipName"} = $joinClause;
4052 :			$joinTable{"$relationshipName/$entityName"} = $joinClause;
4053 :			# Create joins between this relationship and the other relationships.
4054 :			for my $otherType (keys %otherRelationships) {
4055 :			my $otherships = $otherRelationships{$otherType};
4056 :			for my $otherName (@{$otherships}) {
4057 :			# Get the key for this join.
4058 :			my $joinKey = "$otherName/$relationshipName";
4059 :			# Check for a duplicate or a self-join.
4060 :			if (exists $joinTable{$joinKey}) {
4061 :			# Here we have a duplicate, which means that the join
4062 :			# path is ambiguous. We delete the join from the join
4063 :			# table to prevent it from being used.
4064 :			delete $joinTable{$joinKey};
4065 :			Trace("Deleting ambiguous join $joinKey.") if T(4);
4066 :			} elsif ($otherName ne $relationshipName) {
4067 :			# Here we have a valid join. Note that joins between a
4068 :			# relationship and itself are prohibited.
4069 :			my $relJoinClause = "$otherName.${otherType}_link = $linkField";
4070 :			$joinTable{$joinKey} = $relJoinClause;
4071 :	parrello	1.21	Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
4072 :	parrello	1.10	}
4073 :			}
4074 :			}
4075 :			# Create joins between this relationship and the recursive relationships.
4076 :			# We don't need to check for ambiguous joins here, because a recursive
4077 :			# relationship can only be ambiguous with another recursive relationship,
4078 :			# and the incoming relationship from the outer loop is never recursive.
4079 :			for my $otherName (@bothList) {
4080 :	parrello	1.21	Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
4081 :	parrello	1.10	# Join from the left.
4082 :			$joinTable{"$relationshipName/$otherName"} =
4083 :			"$linkField = $otherName.from_link";
4084 :			# Join from the right.
4085 :			$joinTable{"$otherName/$relationshipName"} =
4086 :			"$otherName.to_link = $linkField";
4087 :			}
4088 :			}
4089 :			}
4090 :			# Create entity joins for the recursive relationships. Unlike the non-recursive
4091 :			# joins, the direction makes a difference with the recursive joins. This can give
4092 :			# rise to situations where we can't create the path we want; however, it is always
4093 :			# possible to get the same effect using multiple queries.
4094 :			for my $relationshipName (@bothList) {
4095 :	parrello	1.21	Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
4096 :	parrello	1.10	# Join to the entity from each direction.
4097 :			$joinTable{"$entityName/$relationshipName"} =
4098 :			"$entityName.id = $relationshipName.from_link";
4099 :			$joinTable{"$relationshipName/$entityName"} =
4100 :			"$relationshipName.to_link = $entityName.id";
4101 :			}
4102 :			}
4103 :			# Add the join table to the structure.
4104 :			$metadata->{Joins} = \%joinTable;
4105 :			# Return the slurped and fixed-up structure.
4106 :			return $metadata;
4107 :	parrello	1.1	}
4108 :
4109 :	parrello	1.70	=head3 _CreateRelationshipIndex
4110 :	parrello	1.1
4111 :			Create an index for a relationship's relation.
4112 :
4113 :			This is a static method.
4114 :
4115 :			=over 4
4116 :
4117 :			=item indexKey
4118 :
4119 :			Type of index: either C<"From"> or C<"To">.
4120 :
4121 :			=item relationshipName
4122 :
4123 :			Name of the relationship.
4124 :
4125 :			=item relationshipStructure
4126 :
4127 :			Structure describing the relationship that the index will sort.
4128 :
4129 :			=back
4130 :
4131 :			=cut
4132 :
4133 :			sub _CreateRelationshipIndex {
4134 :	parrello	1.10	# Get the parameters.
4135 :			my ($indexKey, $relationshipName, $relationshipStructure) = @_;
4136 :			# Get the target relation.
4137 :			my $relationStructure = $relationshipStructure->{Relations}->{$relationshipName};
4138 :			# Create a descriptor for the link field that goes at the beginning of this index.
4139 :			my $firstField = { name => lcfirst $indexKey . '-link', order => 'ascending' };
4140 :			# Get the target index descriptor.
4141 :			my $newIndex = $relationshipStructure->{$indexKey . "Index"};
4142 :			# Add the first field to the index's field list. Due to the craziness of PERL, if the
4143 :			# index descriptor does not exist, it will be created automatically so we can add
4144 :			# the field to it.
4145 :			unshift @{$newIndex->{IndexFields}}, $firstField;
4146 :	parrello	1.12	# If this is a one-to-many relationship, the "To" index is unique.
4147 :			if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
4148 :			$newIndex->{Unique} = 'true';
4149 :			}
4150 :	parrello	1.10	# Add the index to the relation.
4151 :	parrello	1.75	_AddIndex("idx$indexKey", $relationStructure, $newIndex);
4152 :	parrello	1.1	}
4153 :
4154 :	parrello	1.70	=head3 _AddIndex
4155 :	parrello	1.1
4156 :			Add an index to a relation structure.
4157 :
4158 :			This is a static method.
4159 :
4160 :			=over 4
4161 :
4162 :			=item indexName
4163 :
4164 :			Name to give to the new index.
4165 :
4166 :			=item relationStructure
4167 :
4168 :			Relation structure to which the new index should be added.
4169 :
4170 :			=item newIndex
4171 :
4172 :			New index to add.
4173 :
4174 :			=back
4175 :
4176 :			=cut
4177 :
4178 :			sub _AddIndex {
4179 :	parrello	1.10	# Get the parameters.
4180 :			my ($indexName, $relationStructure, $newIndex) = @_;
4181 :			# We want to re-do the index's field list. Instead of an object for each field,
4182 :			# we want a string consisting of the field name optionally followed by the token DESC.
4183 :			my @fieldList = ( );
4184 :			for my $field (@{$newIndex->{IndexFields}}) {
4185 :			# Create a string containing the field name.
4186 :			my $fieldString = $field->{name};
4187 :			# Add the ordering token if needed.
4188 :			if ($field->{order} eq "descending") {
4189 :			$fieldString .= " DESC";
4190 :			}
4191 :			# Push the result onto the field list.
4192 :			push @fieldList, $fieldString;
4193 :			}
4194 :			# Store the field list just created as the new index field list.
4195 :			$newIndex->{IndexFields} = \@fieldList;
4196 :			# Add the index to the relation's index list.
4197 :			$relationStructure->{Indexes}->{$indexName} = $newIndex;
4198 :	parrello	1.1	}
4199 :
4200 :	parrello	1.70	=head3 _FixupFields
4201 :	parrello	1.1
4202 :			This method fixes the field list for an entity or relationship. It will add the caller-specified
4203 :			relation name to fields that do not have a name and set the C<PrettySort> value as specified.
4204 :
4205 :			This is a static method.
4206 :
4207 :			=over 4
4208 :
4209 :			=item structure
4210 :
4211 :			Entity or relationship structure to be fixed up.
4212 :
4213 :			=item defaultRelationName
4214 :
4215 :			Default relation name to be added to the fields.
4216 :
4217 :			=item prettySortValue
4218 :
4219 :			C<PrettySort> value for the relation's normal fields.
4220 :
4221 :			=item textPrettySortValue
4222 :
4223 :			C<PrettySort> value for the relation's text fields. This value can be set to one greater than the
4224 :			normal pretty sort value so that text fields go at the end of each relation.
4225 :
4226 :			=back
4227 :
4228 :			=cut
4229 :
4230 :			sub _FixupFields {
4231 :	parrello	1.10	# Get the parameters.
4232 :			my ($structure, $defaultRelationName, $prettySortValue, $textPrettySortValue) = @_;
4233 :			# Insure the structure has a field list.
4234 :			if (!exists $structure->{Fields}) {
4235 :			# Here it doesn't, so we create a new one.
4236 :			$structure->{Fields} = { };
4237 :			} else {
4238 :	parrello	1.70	# Here we have a field list. We need to track the searchable fields, so we
4239 :			# create a list for stashing them.
4240 :			my @textFields = ();
4241 :			# Loop through the fields.
4242 :	parrello	1.10	my $fieldStructures = $structure->{Fields};
4243 :			for my $fieldName (keys %{$fieldStructures}) {
4244 :	parrello	1.8	Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
4245 :	parrello	1.10	my $fieldData = $fieldStructures->{$fieldName};
4246 :			# Get the field type.
4247 :			my $type = $fieldData->{type};
4248 :			# Plug in a relation name if it is needed.
4249 :			Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4250 :	parrello	1.70	# Check for searchability.
4251 :			if ($fieldData->{searchable}) {
4252 :			# Only allow this for a primary relation.
4253 :			if ($fieldData->{relation} ne $defaultRelationName) {
4254 :			Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4255 :			} else {
4256 :			push @textFields, $fieldName;
4257 :			}
4258 :			}
4259 :	parrello	1.10	# Add the PrettySortValue.
4260 :			$fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4261 :			}
4262 :	parrello	1.70	# If there are searchable fields, remember the fact.
4263 :			if (@textFields) {
4264 :			$structure->{searchFields} = \@textFields;
4265 :			}
4266 :	parrello	1.10	}
4267 :	parrello	1.1	}
4268 :
4269 :	parrello	1.70	=head3 _FixName
4270 :	parrello	1.1
4271 :			Fix the incoming field name so that it is a legal SQL column name.
4272 :
4273 :			This is a static method.
4274 :
4275 :			=over 4
4276 :
4277 :			=item fieldName
4278 :
4279 :			Field name to fix.
4280 :
4281 :			=item RETURN
4282 :
4283 :			Returns the fixed-up field name.
4284 :
4285 :			=back
4286 :
4287 :			=cut
4288 :
4289 :			sub _FixName {
4290 :	parrello	1.10	# Get the parameter.
4291 :			my ($fieldName) = @_;
4292 :			# Replace its minus signs with underscores.
4293 :			$fieldName =~ s/-/_/g;
4294 :			# Return the result.
4295 :			return $fieldName;
4296 :	parrello	1.1	}
4297 :
4298 :	parrello	1.70	=head3 _FixNames
4299 :	parrello	1.1
4300 :			Fix all the field names in a list.
4301 :
4302 :			This is a static method.
4303 :
4304 :			=over 4
4305 :
4306 :			=item field1, field2, field3, ... fieldn
4307 :
4308 :			List of field names to fix.
4309 :
4310 :			=item RETURN
4311 :
4312 :			Returns a list of fixed-up versions of the incoming field names.
4313 :
4314 :			=back
4315 :
4316 :			=cut
4317 :
4318 :			sub _FixNames {
4319 :	parrello	1.10	# Create the result list.