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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 : parrello 1.88 use ERDBObject;
10 : parrello 1.10 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 : parrello 1.86 An entity can have multiple alternate indexes associated with it. The fields in an
232 :     index must all be from the same relation. The alternate indexes assist in searching
233 :     on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
234 :     I<from-index> that order the results when crossing the relationship. For
235 : parrello 1.8 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 : parrello 1.86 the genomes of a contig. In addition, it can have zero or more alternate
238 :     indexes. A relationship's index must specify only fields in
239 : parrello 1.8 the relationship.
240 :    
241 : parrello 1.86 The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
242 :     The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
243 :     specified using the B<ToIndex> tag.
244 : parrello 1.8
245 :     Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
246 :     tag containing the B<IndexField> tags. These specify, in order, the fields used in
247 :     the index. The attributes of an B<IndexField> tag are as follows.
248 :    
249 :     =over 4
250 :    
251 :     =item name
252 :    
253 :     Name of the field.
254 :    
255 :     =item order
256 :    
257 :     Sort order of the field-- C<ascending> or C<descending>.
258 :    
259 :     =back
260 :    
261 : parrello 1.78 The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
262 :     have a B<Unique> attribute. If specified, the index will be generated as a unique
263 :     index.
264 : parrello 1.8
265 :     =head3 Object and Field Names
266 :    
267 :     By convention entity and relationship names use capital casing (e.g. C<Genome> or
268 :     C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
269 :     with respect to relation names, converting them internally to all-upper case or
270 :     all-lower case.
271 :    
272 :     If syntax or parsing errors occur when you try to load or use an ERDB database, the
273 :     most likely reason is that one of your objects has an SQL reserved word as its name.
274 :     The list of SQL reserved words keeps increasing; however, most are unlikely to show
275 :     up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
276 :     C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
277 :     C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
278 :    
279 :     Every entity has a field called C<id> that acts as its primary key. Every relationship
280 :     has fields called C<from-link> and C<to-link> that contain copies of the relevant
281 :     entity IDs. These are essentially ERDB's reserved words, and should not be used
282 :     for user-defined field names.
283 :    
284 :     =head3 Entities
285 :    
286 :     An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
287 :     B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
288 :     containing one or more fields. The attributes of the B<Entity> tag are as follows.
289 :    
290 :     =over 4
291 :    
292 :     =item name
293 :    
294 :     Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
295 :     or C<GroupBlock>) and should be a noun or noun phrase.
296 :    
297 :     =item keyType
298 :    
299 :     Data type of the primary key. The primary key is always named C<id>.
300 :    
301 :     =back
302 :    
303 :     =head3 Relationships
304 :    
305 :     A relationship is described by the C<Relationship> tag. Within a relationship,
306 :     there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
307 : parrello 1.86 fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
308 :     the to-index, and an C<Indexes> tag containing the alternate indexes.
309 : parrello 1.8
310 :     The C<Relationship> tag has the following attributes.
311 :    
312 :     =over 4
313 :    
314 :     =item name
315 :    
316 :     Name of the relationship. The relationship name, by convention, uses capital casing
317 :     (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
318 :     phrase, designed to fit between the from-entity and the to-entity (e.g.
319 :     Block C<ContainsRegionIn> Genome).
320 :    
321 :     =item from
322 :    
323 :     Name of the entity from which the relationship starts.
324 :    
325 :     =item to
326 :    
327 :     Name of the entity to which the relationship proceeds.
328 :    
329 :     =item arity
330 :    
331 :     Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
332 :    
333 :     =back
334 :    
335 : parrello 1.1 =cut
336 :    
337 :     # GLOBALS
338 :    
339 :     # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
340 :     # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
341 : parrello 1.73 # of the specified type. "avgLen" is the average byte length for estimating
342 : parrello 1.75 # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
343 :     # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
344 :     # index
345 : parrello 1.73 my %TypeTable = ( char => { sqlType => 'CHAR(1)', maxLen => 1, avgLen => 1, sort => "",
346 : parrello 1.75 indexMod => 0, notes => "single ASCII character"},
347 : parrello 1.73 int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n",
348 : parrello 1.75 indexMod => 0, notes => "signed 32-bit integer"},
349 : parrello 1.73 counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n",
350 : parrello 1.75 indexMod => 0, notes => "unsigned 32-bit integer"},
351 : parrello 1.73 string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "",
352 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 255 characters"},
353 : parrello 1.73 text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "",
354 : parrello 1.75 indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
355 : parrello 1.73 date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n",
356 : parrello 1.75 indexMod => 0, notes => "signed, 64-bit integer"},
357 : parrello 1.73 float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g",
358 : parrello 1.75 indexMod => 0, notes => "64-bit double precision floating-point number"},
359 : parrello 1.73 boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n",
360 : parrello 1.75 indexMod => 0, notes => "boolean value: 0 if false, 1 if true"},
361 : parrello 1.42 'hash-string' =>
362 : parrello 1.73 { sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "",
363 : parrello 1.75 indexMod => 0, notes => "string stored in digested form, used for certain types of key fields"},
364 : parrello 1.44 'id-string' =>
365 : parrello 1.73 { sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "",
366 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 25 characters"},
367 : parrello 1.10 'key-string' =>
368 : parrello 1.73 { sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "",
369 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 40 characters"},
370 : parrello 1.10 'name-string' =>
371 : parrello 1.73 { sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "",
372 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 80 characters"},
373 : parrello 1.10 'medium-string' =>
374 : parrello 1.73 { sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "",
375 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 160 characters"},
376 : parrello 1.10 );
377 : parrello 1.1
378 :     # Table translating arities into natural language.
379 :     my %ArityTable = ( '11' => 'one-to-one',
380 : parrello 1.10 '1M' => 'one-to-many',
381 :     'MM' => 'many-to-many'
382 :     );
383 : parrello 1.1
384 : parrello 1.73 # Options for XML input and output.
385 :    
386 :     my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
387 :     Entities => 'Entity',
388 :     Fields => 'Field',
389 :     Indexes => 'Index',
390 :     IndexFields => 'IndexField'
391 :     },
392 :     KeyAttr => { Relationship => 'name',
393 :     Entity => 'name',
394 :     Field => 'name'
395 :     },
396 :     SuppressEmpty => 1,
397 :     );
398 :    
399 :     my %XmlInOpts = (
400 : parrello 1.78 ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
401 : parrello 1.73 ForceContent => 1,
402 :     NormalizeSpace => 2,
403 :     );
404 :     my %XmlOutOpts = (
405 :     RootName => 'Database',
406 :     XMLDecl => 1,
407 :     );
408 : parrello 1.1
409 :    
410 :     =head2 Public Methods
411 :    
412 :     =head3 new
413 :    
414 : parrello 1.5 C<< my $database = ERDB->new($dbh, $metaFileName); >>
415 : parrello 1.1
416 :     Create a new ERDB object.
417 :    
418 :     =over 4
419 :    
420 :     =item dbh
421 :    
422 :     DBKernel database object for the target database.
423 :    
424 :     =item metaFileName
425 :    
426 :     Name of the XML file containing the metadata.
427 :    
428 :     =back
429 :    
430 :     =cut
431 :    
432 :     sub new {
433 : parrello 1.10 # Get the parameters.
434 :     my ($class, $dbh, $metaFileName, $options) = @_;
435 :     # Load the meta-data.
436 :     my $metaData = _LoadMetaData($metaFileName);
437 :     # Create the object.
438 :     my $self = { _dbh => $dbh,
439 :     _metaData => $metaData
440 :     };
441 :     # Bless and return it.
442 :     bless $self, $class;
443 :     return $self;
444 : parrello 1.1 }
445 :    
446 :     =head3 ShowMetaData
447 :    
448 : parrello 1.18 C<< $erdb->ShowMetaData($fileName); >>
449 : parrello 1.1
450 :     This method outputs a description of the database. This description can be used to help users create
451 :     the data to be loaded into the relations.
452 :    
453 :     =over 4
454 :    
455 :     =item filename
456 :    
457 :     The name of the output file.
458 :    
459 :     =back
460 :    
461 :     =cut
462 :    
463 :     sub ShowMetaData {
464 : parrello 1.10 # Get the parameters.
465 :     my ($self, $filename) = @_;
466 :     # Get the metadata and the title string.
467 :     my $metadata = $self->{_metaData};
468 :     # Get the title string.
469 :     my $title = $metadata->{Title};
470 :     # Get the entity and relationship lists.
471 :     my $entityList = $metadata->{Entities};
472 :     my $relationshipList = $metadata->{Relationships};
473 :     # Open the output file.
474 :     open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
475 :     Trace("Building MetaData table of contents.") if T(4);
476 :     # Write the HTML heading stuff.
477 :     print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
478 :     print HTMLOUT "</head>\n<body>\n";
479 : parrello 1.45 # Write the documentation.
480 :     print HTMLOUT $self->DisplayMetaData();
481 :     # Close the document.
482 :     print HTMLOUT "</body>\n</html>\n";
483 :     # Close the file.
484 :     close HTMLOUT;
485 :     }
486 :    
487 :     =head3 DisplayMetaData
488 :    
489 :     C<< my $html = $erdb->DisplayMetaData(); >>
490 :    
491 :     Return an HTML description of the database. This description can be used to help users create
492 :     the data to be loaded into the relations and form queries. The output is raw includable HTML
493 :     without any HEAD or BODY tags.
494 :    
495 :     =over 4
496 :    
497 :     =item filename
498 :    
499 :     The name of the output file.
500 :    
501 :     =back
502 :    
503 :     =cut
504 :    
505 :     sub DisplayMetaData {
506 :     # Get the parameters.
507 :     my ($self) = @_;
508 :     # Get the metadata and the title string.
509 :     my $metadata = $self->{_metaData};
510 :     # Get the title string.
511 :     my $title = $metadata->{Title};
512 :     # Get the entity and relationship lists.
513 :     my $entityList = $metadata->{Entities};
514 :     my $relationshipList = $metadata->{Relationships};
515 :     # Declare the return variable.
516 :     my $retVal = "";
517 :     # Open the output file.
518 :     Trace("Building MetaData table of contents.") if T(4);
519 : parrello 1.10 # Here we do the table of contents. It starts as an unordered list of section names. Each
520 :     # section contains an ordered list of entity or relationship subsections.
521 : parrello 1.45 $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
522 : parrello 1.10 # Loop through the Entities, displaying a list item for each.
523 :     foreach my $key (sort keys %{$entityList}) {
524 :     # Display this item.
525 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
526 : parrello 1.10 }
527 :     # Close off the entity section and start the relationship section.
528 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
529 : parrello 1.10 # Loop through the Relationships.
530 :     foreach my $key (sort keys %{$relationshipList}) {
531 :     # Display this item.
532 :     my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
533 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
534 : parrello 1.10 }
535 :     # Close off the relationship section and list the join table section.
536 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
537 : parrello 1.10 # Close off the table of contents itself.
538 : parrello 1.45 $retVal .= "</ul>\n";
539 : parrello 1.10 # Now we start with the actual data. Denote we're starting the entity section.
540 : parrello 1.45 $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
541 : parrello 1.10 # Loop through the entities.
542 :     for my $key (sort keys %{$entityList}) {
543 :     Trace("Building MetaData entry for $key entity.") if T(4);
544 :     # Create the entity header. It contains a bookmark and the entity name.
545 : parrello 1.45 $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
546 : parrello 1.10 # Get the entity data.
547 :     my $entityData = $entityList->{$key};
548 :     # If there's descriptive text, display it.
549 :     if (my $notes = $entityData->{Notes}) {
550 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
551 : parrello 1.10 }
552 : parrello 1.83 # See if we need a list of the entity's relationships.
553 :     my $relCount = keys %{$relationshipList};
554 :     if ($relCount > 0) {
555 :     # First, we set up the relationship subsection.
556 :     $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
557 :     # Loop through the relationships.
558 :     for my $relationship (sort keys %{$relationshipList}) {
559 :     # Get the relationship data.
560 :     my $relationshipStructure = $relationshipList->{$relationship};
561 :     # Only use the relationship if if has this entity in its FROM or TO fields.
562 :     if ($relationshipStructure->{from} eq $key || $relationshipStructure->{to} eq $key) {
563 :     # Get the relationship sentence and append the arity.
564 :     my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
565 :     # Display the relationship data.
566 :     $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
567 :     }
568 : parrello 1.10 }
569 : parrello 1.83 # Close off the relationship list.
570 :     $retVal .= "</ul>\n";
571 : parrello 1.10 }
572 :     # Get the entity's relations.
573 :     my $relationList = $entityData->{Relations};
574 :     # Create a header for the relation subsection.
575 : parrello 1.45 $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
576 : parrello 1.10 # Loop through the relations, displaying them.
577 :     for my $relation (sort keys %{$relationList}) {
578 :     my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
579 : parrello 1.45 $retVal .= $htmlString;
580 : parrello 1.10 }
581 :     }
582 :     # Denote we're starting the relationship section.
583 : parrello 1.45 $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
584 : parrello 1.10 # Loop through the relationships.
585 :     for my $key (sort keys %{$relationshipList}) {
586 :     Trace("Building MetaData entry for $key relationship.") if T(4);
587 :     # Get the relationship's structure.
588 :     my $relationshipStructure = $relationshipList->{$key};
589 :     # Create the relationship header.
590 :     my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
591 : parrello 1.45 $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
592 : parrello 1.10 # Get the entity names.
593 :     my $fromEntity = $relationshipStructure->{from};
594 :     my $toEntity = $relationshipStructure->{to};
595 :     # Describe the relationship arity. Note there's a bit of trickiness involving recursive
596 :     # many-to-many relationships. In a normal many-to-many we use two sentences to describe
597 :     # the arity (one for each direction). This is a bad idea for a recursive relationship,
598 :     # since both sentences will say the same thing.
599 :     my $arity = $relationshipStructure->{arity};
600 :     if ($arity eq "11") {
601 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
602 : parrello 1.10 } else {
603 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
604 : parrello 1.10 if ($arity eq "MM" && $fromEntity ne $toEntity) {
605 : parrello 1.45 $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
606 : parrello 1.10 }
607 :     }
608 : parrello 1.45 $retVal .= "</p>\n";
609 : parrello 1.10 # If there are notes on this relationship, display them.
610 :     if (my $notes = $relationshipStructure->{Notes}) {
611 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
612 : parrello 1.10 }
613 :     # Generate the relationship's relation table.
614 :     my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
615 : parrello 1.45 $retVal .= $htmlString;
616 : parrello 1.10 }
617 :     Trace("Building MetaData join table.") if T(4);
618 :     # Denote we're starting the join table.
619 : parrello 1.45 $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
620 : parrello 1.10 # Create a table header.
621 : parrello 1.45 $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
622 : parrello 1.10 # Loop through the joins.
623 :     my $joinTable = $metadata->{Joins};
624 :     my @joinKeys = keys %{$joinTable};
625 :     for my $joinKey (sort @joinKeys) {
626 :     # Separate out the source, the target, and the join clause.
627 :     $joinKey =~ m!^([^/]+)/(.+)$!;
628 :     my ($sourceRelation, $targetRelation) = ($1, $2);
629 : parrello 1.30 Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
630 : parrello 1.10 my $source = $self->ComputeObjectSentence($sourceRelation);
631 :     my $target = $self->ComputeObjectSentence($targetRelation);
632 :     my $clause = $joinTable->{$joinKey};
633 :     # Display them in a table row.
634 : parrello 1.45 $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
635 : parrello 1.10 }
636 :     # Close the table.
637 : parrello 1.45 $retVal .= _CloseTable();
638 :     Trace("Built MetaData HTML.") if T(3);
639 :     # Return the HTML.
640 :     return $retVal;
641 : parrello 1.1 }
642 :    
643 :     =head3 DumpMetaData
644 :    
645 : parrello 1.18 C<< $erdb->DumpMetaData(); >>
646 : parrello 1.1
647 :     Return a dump of the metadata structure.
648 :    
649 :     =cut
650 :    
651 :     sub DumpMetaData {
652 : parrello 1.10 # Get the parameters.
653 :     my ($self) = @_;
654 :     # Dump the meta-data.
655 :     return Data::Dumper::Dumper($self->{_metaData});
656 : parrello 1.1 }
657 :    
658 : parrello 1.89 =head3 CreatePPO
659 :    
660 :     C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
661 :    
662 :     Create a PPO XML file from an ERDB data definition XML file. At the
663 :     current time, the PPO XML file can be used to create a database with
664 :     similar functionality. Eventually, the PPO will be able to use the
665 :     created XML to access the live ERDB database.
666 :    
667 :     =over 4
668 :    
669 :     =item erdbXMLFile
670 :    
671 :     Name of the XML data definition file for the ERDB database. This
672 :     file must exist.
673 :    
674 :     =item ppoXMLFile
675 :    
676 :     Output file for the PPO XML definition. If this file exists, it
677 :     will be overwritten.
678 :    
679 :     =back
680 :    
681 :     =cut
682 :    
683 :     sub CreatePPO {
684 :     # Get the parameters.
685 :     my ($erdbXMLFile, $ppoXMLFile) = @_;
686 :     # First, we want to slurp in the ERDB XML file in its raw form.
687 :     my $xml = ReadMetaXML($erdbXMLFile);
688 :     # Create a variable to hold all of the objects in the PPO project.
689 :     my @objects = ();
690 :     # Get the relationship hash.
691 :     my $relationships = $xml->{Relationships};
692 :     # Loop through the entities.
693 :     my $entities = $xml->{Entities};
694 :     for my $entityName (keys %{$entities}) {
695 :     # Get the entity's data structures.
696 :     my $entityObject = $entities->{$entityName};
697 :     # We put the object's fields in here, according to their type.
698 :     my (@object_refs, @scalars, @indexes, @arrays);
699 :     # Create the ID field for the entity. We get the key type from the
700 :     # entity object and compute the corresponding SQL type.
701 :     my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
702 :     push @scalars, { label => 'id', type => $type };
703 :     # Loop through the entity fields.
704 :     for my $fieldName ( keys %{$entityObject->{Fields}} ) {
705 :     # Get the field object.
706 :     my $fieldObject = $entityObject->{Fields}->{$fieldName};
707 :     # Convert it to a scalar tag.
708 :     my $scalar = _CreatePPOField($fieldName, $fieldObject);
709 :     # If we have a relation, this field is stored in an array.
710 :     # otherwise, it is a scalar. The array tag has scalars
711 :     # stored as an XML array. In ERDB, there is only ever one,
712 :     # but PPO can have more.
713 :     my $relation = $fieldObject->{relation};
714 :     if ($relation) {
715 :     push @arrays, { scalar => [$scalar] };
716 :     } else {
717 :     push @scalars, $scalar;
718 :     }
719 :     }
720 :     # Loop through the relationships. If this entity is the to-entity
721 :     # on a relationship of 1M arity, then it is implemented as a PPO
722 :     # object reference.
723 :     for my $relationshipName (keys %{$relationships}) {
724 :     # Get the relationship data.
725 :     my $relationshipData = $relationships->{$relationshipName};
726 :     # If we have a from for this entity and an arity of 1M, we
727 :     # have an object reference.
728 :     if ($relationshipData->{to} eq $entityName &&
729 :     $relationshipData->{arity} eq '1M') {
730 :     # Build the object reference tag.
731 :     push @object_refs, { label => $relationshipName,
732 :     type => $relationshipData->{from} };
733 :     }
734 :     }
735 :     # Create the indexes.
736 :     my $indexList = $entityObject->{Indexes};
737 :     push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
738 :     # Build the object XML tree.
739 :     my $object = { label => $entityName,
740 :     object_ref => \@object_refs,
741 :     scalar => \@scalars,
742 :     index => \@indexes,
743 :     array => \@arrays
744 :     };
745 :     # Push the object onto the objects list.
746 :     push @objects, $object;
747 :     }
748 :     # Loop through the relationships, searching for MMs. The 1Ms were
749 :     # already handled by the entity search above.
750 :     for my $relationshipName (keys %{$relationships}) {
751 :     # Get this relationship's object.
752 :     my $relationshipObject = $relationships->{$relationshipName};
753 :     # Only proceed if it's many-to-many.
754 :     if ($relationshipObject->{arity} eq 'MM') {
755 :     # Create the tag lists for the relationship object.
756 :     my (@object_refs, @scalars, @indexes);
757 :     # The relationship will be created as an object with object
758 :     # references for its links to the participating entities.
759 :     my %links = ( from => $relationshipObject->{from},
760 :     to => $relationshipObject->{to} );
761 :     for my $link (keys %links) {
762 :     # Create an object_ref tag for this piece of the
763 :     # relationship (from or to).
764 :     my $object_ref = { label => $link,
765 :     type => $links{$link} };
766 :     push @object_refs, $object_ref;
767 :     }
768 :     # Loop through the intersection data fields, creating scalar tags.
769 :     # There are no fancy array tags in a relationship.
770 :     for my $fieldName (keys %{$relationshipObject->{Fields}}) {
771 :     my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
772 :     push @scalars, _CreatePPOField($fieldName, $fieldObject);
773 :     }
774 :     # Finally, the indexes: currently we cannot support the to-index and
775 :     # from-index in PPO, so we just process the alternate indexes.
776 :     my $indexList = $relationshipObject->{Indexes};
777 :     push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
778 :     # Wrap up all the stuff about this relationship.
779 :     my $object = { label => $relationshipName,
780 :     scalar => \@scalars,
781 :     object_ref => \@object_refs,
782 :     index => \@indexes
783 :     };
784 :     # Push it into the object list.
785 :     push @objects, $object;
786 :     }
787 :     }
788 :     # Compute a title.
789 :     my $title;
790 :     if ($erdbXMLFile =~ /\/([^\/]+)DBD\.xml/) {
791 :     # Here we have a standard file name we can use for a title.
792 :     $title = $1;
793 :     } else {
794 :     # Here the file name is non-standard, so we carve up the
795 :     # database title.
796 :     $title = $xml->{Title}->{content};
797 :     $title =~ s/\s\.,//g;
798 :     }
799 :     # Wrap up the XML as a project.
800 :     my $ppoXML = { project => { label => $title,
801 :     object => \@objects }};
802 :     # Write out the results.
803 :     my $ppoString = XML::Simple::XMLout($ppoXML,
804 :     AttrIndent => 1,
805 :     KeepRoot => 1);
806 :     Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
807 :     }
808 :    
809 :    
810 :    
811 : parrello 1.74 =head3 FindIndexForEntity
812 :    
813 :     C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
814 :    
815 :     This method locates the entry in an entity's index list that begins with the
816 :     specified attribute name. If the entity has no index list, one will be
817 :     created. This method works on raw XML, not a live ERDB object.
818 :    
819 :     =over 4
820 :    
821 :     =item xml
822 :    
823 :     The raw XML structure defining the database.
824 :    
825 :     =item entityName
826 :    
827 :     The name of the relevant entity.
828 :    
829 :     =item attributeName
830 :    
831 :     The name of the attribute relevant to the search.
832 :    
833 :     =item RETURN
834 :    
835 :     The numerical index in the index list of the index entry for the specified entity and
836 :     attribute, or C<undef> if no such index exists.
837 :    
838 :     =back
839 :    
840 :     =cut
841 :    
842 :     sub FindIndexForEntity {
843 :     # Get the parameters.
844 :     my ($xml, $entityName, $attributeName) = @_;
845 :     # Declare the return variable.
846 :     my $retVal;
847 :     # Get the named entity.
848 :     my $entityData = $xml->{Entities}->{$entityName};
849 :     if (! $entityData) {
850 :     Confess("Entity $entityName not found in DBD structure.");
851 :     } else {
852 :     # Insure it has an index list.
853 :     if (! exists $entityData->{Indexes}) {
854 :     $entityData->{Indexes} = [];
855 :     } else {
856 :     # Search for the desired index.
857 :     my $indexList = $entityData->{Indexes};
858 :     my $n = scalar @{$indexList};
859 :     Trace("Searching $n indexes in index list for $entityName.") if T(2);
860 :     # We use an indexed FOR here because we're returning an
861 :     # index number instead of an object. We do THAT so we can
862 :     # delete the index from the list if needed.
863 :     for (my $i = 0; $i < $n && !defined($retVal); $i++) {
864 :     my $index = $indexList->[$i];
865 :     my $fields = $index->{IndexFields};
866 :     # Technically this IF should be safe (that is, we are guaranteed
867 :     # the existence of a "$fields->[0]"), because when we load the XML
868 :     # we have SuppressEmpty specified.
869 :     if ($fields->[0]->{name} eq $attributeName) {
870 :     $retVal = $i;
871 :     }
872 :     }
873 :     }
874 :     }
875 :     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
876 :     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
877 :     # Return the result.
878 :     return $retVal;
879 :     }
880 :    
881 : parrello 1.1 =head3 CreateTables
882 :    
883 : parrello 1.18 C<< $erdb->CreateTables(); >>
884 : parrello 1.1
885 :     This method creates the tables for the database from the metadata structure loaded by the
886 :     constructor. It is expected this function will only be used on rare occasions, when the
887 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
888 : parrello 1.1 used by itself with the truncate flag turned on.
889 :    
890 :     =cut
891 :    
892 :     sub CreateTables {
893 : parrello 1.10 # Get the parameters.
894 :     my ($self) = @_;
895 : parrello 1.23 # Get the relation names.
896 :     my @relNames = $self->GetTableNames();
897 :     # Loop through the relations.
898 :     for my $relationName (@relNames) {
899 :     # Create a table for this relation.
900 : parrello 1.87 $self->CreateTable($relationName, 1);
901 : parrello 1.23 Trace("Relation $relationName created.") if T(2);
902 : parrello 1.10 }
903 : parrello 1.1 }
904 :    
905 :     =head3 CreateTable
906 :    
907 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
908 : parrello 1.1
909 :     Create the table for a relation and optionally create its indexes.
910 :    
911 :     =over 4
912 :    
913 :     =item relationName
914 :    
915 :     Name of the relation (which will also be the table name).
916 :    
917 : parrello 1.18 =item indexFlag
918 : parrello 1.1
919 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
920 :     L</CreateIndexes> must be called later to bring the indexes into existence.
921 :    
922 : parrello 1.18 =item estimatedRows (optional)
923 :    
924 :     If specified, the estimated maximum number of rows for the relation. This
925 :     information allows the creation of tables using storage engines that are
926 :     faster but require size estimates, such as MyISAM.
927 :    
928 : parrello 1.1 =back
929 :    
930 :     =cut
931 :    
932 :     sub CreateTable {
933 : parrello 1.10 # Get the parameters.
934 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
935 : parrello 1.10 # Get the database handle.
936 :     my $dbh = $self->{_dbh};
937 :     # Get the relation data and determine whether or not the relation is primary.
938 :     my $relationData = $self->_FindRelation($relationName);
939 :     my $rootFlag = $self->_IsPrimary($relationName);
940 :     # Create a list of the field data.
941 :     my @fieldList;
942 :     for my $fieldData (@{$relationData->{Fields}}) {
943 :     # Assemble the field name and type.
944 :     my $fieldName = _FixName($fieldData->{name});
945 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
946 :     # Push the result into the field list.
947 :     push @fieldList, $fieldString;
948 :     }
949 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
950 :     if ($rootFlag) {
951 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
952 :     }
953 :     # Convert the field list into a comma-delimited string.
954 :     my $fieldThing = join(', ', @fieldList);
955 :     # Insure the table is not already there.
956 :     $dbh->drop_table(tbl => $relationName);
957 :     Trace("Table $relationName dropped.") if T(2);
958 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
959 :     # faster DB technologies.
960 :     my $estimation = undef;
961 :     if ($estimatedRows) {
962 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
963 :     }
964 : parrello 1.10 # Create the table.
965 :     Trace("Creating table $relationName: $fieldThing") if T(2);
966 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
967 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
968 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
969 :     # index will not be built until the table has been loaded.
970 : parrello 1.10 if ($indexFlag) {
971 :     $self->CreateIndex($relationName);
972 :     }
973 : parrello 1.1 }
974 :    
975 : parrello 1.31 =head3 VerifyFields
976 :    
977 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
978 :    
979 :     Run through the list of proposed field values, insuring that all the character fields are
980 :     below the maximum length. If any fields are too long, they will be truncated in place.
981 :    
982 :     =over 4
983 :    
984 :     =item relName
985 :    
986 :     Name of the relation for which the specified fields are destined.
987 :    
988 :     =item fieldList
989 :    
990 :     Reference to a list, in order, of the fields to be put into the relation.
991 :    
992 :     =item RETURN
993 :    
994 :     Returns the number of fields truncated.
995 :    
996 :     =back
997 :    
998 :     =cut
999 :    
1000 :     sub VerifyFields {
1001 :     # Get the parameters.
1002 :     my ($self, $relName, $fieldList) = @_;
1003 :     # Initialize the return value.
1004 :     my $retVal = 0;
1005 :     # Get the relation definition.
1006 :     my $relData = $self->_FindRelation($relName);
1007 :     # Get the list of field descriptors.
1008 :     my $fieldTypes = $relData->{Fields};
1009 :     my $fieldCount = scalar @{$fieldTypes};
1010 :     # Loop through the two lists.
1011 :     for (my $i = 0; $i < $fieldCount; $i++) {
1012 :     # Get the type of the current field.
1013 :     my $fieldType = $fieldTypes->[$i]->{type};
1014 :     # If it's a character field, verify the length.
1015 :     if ($fieldType =~ /string/) {
1016 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
1017 :     my $oldString = $fieldList->[$i];
1018 :     if (length($oldString) > $maxLen) {
1019 :     # Here it's too big, so we truncate it.
1020 :     Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1021 :     $fieldList->[$i] = substr $oldString, 0, $maxLen;
1022 :     $retVal++;
1023 :     }
1024 :     }
1025 :     }
1026 :     # Return the truncation count.
1027 :     return $retVal;
1028 :     }
1029 :    
1030 : parrello 1.42 =head3 DigestFields
1031 :    
1032 :     C<< $erdb->DigestFields($relName, $fieldList); >>
1033 :    
1034 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
1035 :     specified relation.
1036 :    
1037 :     =over 4
1038 :    
1039 :     =item relName
1040 :    
1041 :     Name of the relation to which the fields belong.
1042 :    
1043 :     =item fieldList
1044 :    
1045 :     List of field contents to be loaded into the relation.
1046 :    
1047 :     =back
1048 :    
1049 :     =cut
1050 :     #: Return Type ;
1051 :     sub DigestFields {
1052 :     # Get the parameters.
1053 :     my ($self, $relName, $fieldList) = @_;
1054 :     # Get the relation definition.
1055 :     my $relData = $self->_FindRelation($relName);
1056 :     # Get the list of field descriptors.
1057 :     my $fieldTypes = $relData->{Fields};
1058 :     my $fieldCount = scalar @{$fieldTypes};
1059 :     # Loop through the two lists.
1060 :     for (my $i = 0; $i < $fieldCount; $i++) {
1061 :     # Get the type of the current field.
1062 :     my $fieldType = $fieldTypes->[$i]->{type};
1063 :     # If it's a hash string, digest it in place.
1064 :     if ($fieldType eq 'hash-string') {
1065 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1066 : parrello 1.42 }
1067 :     }
1068 :     }
1069 :    
1070 : parrello 1.46 =head3 DigestKey
1071 :    
1072 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
1073 :    
1074 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
1075 :     key-based search into a table with key-type hash-string.
1076 :    
1077 :     Currently the digesting process is independent of the database structure, but that may not
1078 :     always be the case, so this is an instance method instead of a static method.
1079 :    
1080 :     =over 4
1081 :    
1082 :     =item keyValue
1083 :    
1084 :     Key value to digest.
1085 :    
1086 :     =item RETURN
1087 :    
1088 : parrello 1.56 Digested value of the key.
1089 : parrello 1.46
1090 :     =back
1091 :    
1092 :     =cut
1093 :    
1094 :     sub DigestKey {
1095 :     # Get the parameters.
1096 :     my ($self, $keyValue) = @_;
1097 :     # Compute the digest.
1098 :     my $retVal = md5_base64($keyValue);
1099 :     # Return the result.
1100 :     return $retVal;
1101 :     }
1102 :    
1103 : parrello 1.1 =head3 CreateIndex
1104 :    
1105 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
1106 : parrello 1.1
1107 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
1108 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
1109 :     If that is the case, then L</CreateTable> should be called with the index flag set to
1110 :     FALSE, and this method used after the load to create the indexes for the table.
1111 : parrello 1.1
1112 :     =cut
1113 :    
1114 :     sub CreateIndex {
1115 : parrello 1.10 # Get the parameters.
1116 :     my ($self, $relationName) = @_;
1117 :     # Get the relation's descriptor.
1118 :     my $relationData = $self->_FindRelation($relationName);
1119 :     # Get the database handle.
1120 :     my $dbh = $self->{_dbh};
1121 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
1122 :     my $indexHash = $relationData->{Indexes};
1123 :     for my $indexName (keys %{$indexHash}) {
1124 :     my $indexData = $indexHash->{$indexName};
1125 :     # Get the index's field list.
1126 : parrello 1.75 my @rawFields = @{$indexData->{IndexFields}};
1127 :     # Get a hash of the relation's field types.
1128 :     my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1129 : parrello 1.78 # We need to check for text fields so we can append a length limitation for them. To do
1130 : parrello 1.75 # that, we need the relation's field list.
1131 :     my $relFields = $relationData->{Fields};
1132 :     for (my $i = 0; $i <= $#rawFields; $i++) {
1133 :     # Get the field type.
1134 :     my $field = $rawFields[$i];
1135 :     my $type = $types{$field};
1136 :     # Ask if it requires using prefix notation for the index.
1137 :     my $mod = $TypeTable{$type}->{indexMod};
1138 :     Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1139 :     if ($mod) {
1140 :     # Append the prefix length to the field name,
1141 :     $rawFields[$i] .= "($mod)";
1142 :     }
1143 :     }
1144 :     my @fieldList = _FixNames(@rawFields);
1145 : parrello 1.10 my $flds = join(', ', @fieldList);
1146 :     # Get the index's uniqueness flag.
1147 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1148 : parrello 1.10 # Create the index.
1149 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1150 : parrello 1.70 flds => $flds, kind => $unique);
1151 : parrello 1.24 if ($rv) {
1152 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1153 :     } else {
1154 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
1155 :     }
1156 : parrello 1.10 }
1157 : parrello 1.1 }
1158 :    
1159 : parrello 1.75 =head3 GetSecondaryFields
1160 :    
1161 :     C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1162 :    
1163 :     This method will return a list of the name and type of each of the secondary
1164 :     fields for a specified entity. Secondary fields are stored in two-column tables
1165 :     in addition to the primary entity table. This enables the field to have no value
1166 :     or to have multiple values.
1167 :    
1168 :     =over 4
1169 :    
1170 :     =item entityName
1171 :    
1172 :     Name of the entity whose secondary fields are desired.
1173 :    
1174 :     =item RETURN
1175 :    
1176 :     Returns a hash mapping the field names to their field types.
1177 :    
1178 :     =back
1179 :    
1180 :     =cut
1181 :    
1182 :     sub GetSecondaryFields {
1183 :     # Get the parameters.
1184 :     my ($self, $entityName) = @_;
1185 :     # Declare the return variable.
1186 :     my %retVal = ();
1187 :     # Look for the entity.
1188 :     my $table = $self->GetFieldTable($entityName);
1189 :     # Loop through the fields, pulling out the secondaries.
1190 :     for my $field (sort keys %{$table}) {
1191 :     if ($table->{$field}->{relation} ne $entityName) {
1192 :     # Here we have a secondary field.
1193 :     $retVal{$field} = $table->{$field}->{type};
1194 :     }
1195 :     }
1196 :     # Return the result.
1197 :     return %retVal;
1198 :     }
1199 :    
1200 :     =head3 GetFieldRelationName
1201 :    
1202 :     C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1203 :    
1204 :     Return the name of the relation containing a specified field.
1205 :    
1206 :     =over 4
1207 :    
1208 :     =item objectName
1209 :    
1210 :     Name of the entity or relationship containing the field.
1211 :    
1212 :     =item fieldName
1213 :    
1214 :     Name of the relevant field in that entity or relationship.
1215 :    
1216 :     =item RETURN
1217 :    
1218 :     Returns the name of the database relation containing the field, or C<undef> if
1219 :     the field does not exist.
1220 :    
1221 :     =back
1222 :    
1223 :     =cut
1224 :    
1225 :     sub GetFieldRelationName {
1226 :     # Get the parameters.
1227 :     my ($self, $objectName, $fieldName) = @_;
1228 :     # Declare the return variable.
1229 :     my $retVal;
1230 :     # Get the object field table.
1231 :     my $table = $self->GetFieldTable($objectName);
1232 :     # Only proceed if the field exists.
1233 :     if (exists $table->{$fieldName}) {
1234 :     # Determine the name of the relation that contains this field.
1235 :     $retVal = $table->{$fieldName}->{relation};
1236 :     }
1237 :     # Return the result.
1238 :     return $retVal;
1239 :     }
1240 :    
1241 :     =head3 DeleteValue
1242 :    
1243 :     C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1244 :    
1245 :     Delete secondary field values from the database. This method can be used to delete all
1246 :     values of a specified field for a particular entity instance, or only a single value.
1247 :    
1248 :     Secondary fields are stored in two-column relations separate from an entity's primary
1249 :     table, and as a result a secondary field can legitimately have no value or multiple
1250 :     values. Therefore, it makes sense to talk about deleting secondary fields where it
1251 :     would not make sense for primary fields.
1252 :    
1253 :     =over 4
1254 :    
1255 :     =item entityName
1256 :    
1257 :     Name of the entity from which the fields are to be deleted.
1258 :    
1259 :     =item id
1260 :    
1261 :     ID of the entity instance to be processed. If the instance is not found, this
1262 : parrello 1.76 method will have no effect. If C<undef> is specified, all values for all of
1263 :     the entity instances will be deleted.
1264 : parrello 1.75
1265 :     =item fieldName
1266 :    
1267 :     Name of the field whose values are to be deleted.
1268 :    
1269 :     =item fieldValue (optional)
1270 :    
1271 :     Value to be deleted. If not specified, then all values of the specified field
1272 :     will be deleted for the entity instance. If specified, then only the values which
1273 :     match this parameter will be deleted.
1274 :    
1275 :     =item RETURN
1276 :    
1277 :     Returns the number of rows deleted.
1278 :    
1279 :     =back
1280 :    
1281 :     =cut
1282 :    
1283 :     sub DeleteValue {
1284 :     # Get the parameters.
1285 :     my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1286 :     # Declare the return value.
1287 :     my $retVal = 0;
1288 :     # We need to set up an SQL command to do the deletion. First, we
1289 :     # find the name of the field's relation.
1290 :     my $table = $self->GetFieldTable($entityName);
1291 :     my $field = $table->{$fieldName};
1292 :     my $relation = $field->{relation};
1293 :     # Make sure this is a secondary field.
1294 :     if ($relation eq $entityName) {
1295 :     Confess("Cannot delete values of $fieldName for $entityName.");
1296 :     } else {
1297 :     # Set up the SQL command to delete all values.
1298 : parrello 1.76 my $sql = "DELETE FROM $relation";
1299 :     # Build the filter.
1300 :     my @filters = ();
1301 :     my @parms = ();
1302 :     # Check for a filter by ID.
1303 :     if (defined $id) {
1304 :     push @filters, "id = ?";
1305 :     push @parms, $id;
1306 :     }
1307 :     # Check for a filter by value.
1308 : parrello 1.75 if (defined $fieldValue) {
1309 : parrello 1.76 push @filters, "$fieldName = ?";
1310 : parrello 1.75 push @parms, $fieldValue;
1311 :     }
1312 : parrello 1.76 # Append the filters to the command.
1313 :     if (@filters) {
1314 :     $sql .= " WHERE " . join(" AND ", @filters);
1315 :     }
1316 : parrello 1.75 # Execute the command.
1317 :     my $dbh = $self->{_dbh};
1318 :     $retVal = $dbh->SQL($sql, 0, @parms);
1319 :     }
1320 :     # Return the result.
1321 :     return $retVal;
1322 :     }
1323 :    
1324 : parrello 1.1 =head3 LoadTables
1325 :    
1326 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1327 : parrello 1.1
1328 :     This method will load the database tables from a directory. The tables must already have been created
1329 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1330 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
1331 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1332 :     line of the file will be loaded as a row of the target relation table. The field values should be in
1333 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1334 :     erased before the new data is loaded in.
1335 :    
1336 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1337 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1338 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1339 :    
1340 :     =over 4
1341 :    
1342 :     =item directoryName
1343 :    
1344 :     Name of the directory containing the relation files to be loaded.
1345 :    
1346 :     =item rebuild
1347 :    
1348 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1349 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
1350 :     by all of the DB engines we use.
1351 :    
1352 :     =item RETURN
1353 :    
1354 :     Returns a statistical object describing the number of records read and a list of the error messages.
1355 :    
1356 :     =back
1357 :    
1358 :     =cut
1359 :    
1360 :     sub LoadTables {
1361 : parrello 1.10 # Get the parameters.
1362 :     my ($self, $directoryName, $rebuild) = @_;
1363 :     # Start the timer.
1364 :     my $startTime = gettimeofday;
1365 :     # Clean any trailing slash from the directory name.
1366 :     $directoryName =~ s!/\\$!!;
1367 :     # Declare the return variable.
1368 :     my $retVal = Stats->new();
1369 : parrello 1.23 # Get the relation names.
1370 :     my @relNames = $self->GetTableNames();
1371 :     for my $relationName (@relNames) {
1372 :     # Try to load this relation.
1373 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1374 : parrello 1.10 # Accumulate the statistics.
1375 :     $retVal->Accumulate($result);
1376 :     }
1377 :     # Add the duration of the load to the statistical object.
1378 :     $retVal->Add('duration', gettimeofday - $startTime);
1379 :     # Return the accumulated statistics.
1380 :     return $retVal;
1381 : parrello 1.1 }
1382 :    
1383 : parrello 1.23
1384 : parrello 1.1 =head3 GetTableNames
1385 :    
1386 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
1387 : parrello 1.1
1388 :     Return a list of the relations required to implement this database.
1389 :    
1390 :     =cut
1391 :    
1392 :     sub GetTableNames {
1393 : parrello 1.10 # Get the parameters.
1394 :     my ($self) = @_;
1395 :     # Get the relation list from the metadata.
1396 :     my $relationTable = $self->{_metaData}->{RelationTable};
1397 :     # Return the relation names.
1398 :     return keys %{$relationTable};
1399 : parrello 1.1 }
1400 :    
1401 :     =head3 GetEntityTypes
1402 :    
1403 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
1404 : parrello 1.1
1405 :     Return a list of the entity type names.
1406 :    
1407 :     =cut
1408 :    
1409 :     sub GetEntityTypes {
1410 : parrello 1.10 # Get the database object.
1411 :     my ($self) = @_;
1412 :     # Get the entity list from the metadata object.
1413 :     my $entityList = $self->{_metaData}->{Entities};
1414 :     # Return the list of entity names in alphabetical order.
1415 :     return sort keys %{$entityList};
1416 : parrello 1.1 }
1417 :    
1418 : parrello 1.73 =head3 GetDataTypes
1419 :    
1420 :     C<< my %types = ERDB::GetDataTypes(); >>
1421 :    
1422 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1423 :     The keys of the big hash are the datatypes. Each smaller hash has several
1424 :     values used to manage the data. The most interesting is the SQL type (key
1425 :     C<sqlType>) and the descriptive node (key C<notes>).
1426 :    
1427 :     Note that changing the values in the smaller hashes will seriously break
1428 :     things, so this data should be treated as read-only.
1429 :    
1430 :     =cut
1431 :    
1432 :     sub GetDataTypes {
1433 :     return %TypeTable;
1434 :     }
1435 :    
1436 :    
1437 : parrello 1.20 =head3 IsEntity
1438 :    
1439 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1440 :    
1441 :     Return TRUE if the parameter is an entity name, else FALSE.
1442 :    
1443 :     =over 4
1444 :    
1445 :     =item entityName
1446 :    
1447 :     Object name to be tested.
1448 :    
1449 :     =item RETURN
1450 :    
1451 :     Returns TRUE if the specified string is an entity name, else FALSE.
1452 :    
1453 :     =back
1454 :    
1455 :     =cut
1456 :    
1457 :     sub IsEntity {
1458 :     # Get the parameters.
1459 :     my ($self, $entityName) = @_;
1460 :     # Test to see if it's an entity.
1461 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1462 :     }
1463 :    
1464 : parrello 1.1 =head3 Get
1465 :    
1466 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1467 : parrello 1.1
1468 :     This method returns a query object for entities of a specified type using a specified filter.
1469 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1470 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1471 :     following call requests all B<Genome> objects for the genus specified in the variable
1472 :     $genus.
1473 :    
1474 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1475 : parrello 1.1
1476 :     The WHERE clause contains a single question mark, so there is a single additional
1477 :     parameter representing the parameter value. It would also be possible to code
1478 :    
1479 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1480 : parrello 1.1
1481 :     however, this version of the call would generate a syntax error if there were any quote
1482 :     characters inside the variable C<$genus>.
1483 :    
1484 :     The use of the strange parenthesized notation for field names enables us to distinguish
1485 :     hyphens contained within field names from minus signs that participate in the computation
1486 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1487 :    
1488 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1489 :     one object's data at the same time, which allows highly complex joined queries. For example,
1490 :    
1491 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1492 : parrello 1.1
1493 :     If multiple names are specified, then the query processor will automatically determine a
1494 :     join path between the entities and relationships. The algorithm used is very simplistic.
1495 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1496 :     the entity and the relationship appear. For example, consider a recursive relationship
1497 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1498 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1499 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1500 :    
1501 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1502 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1503 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1504 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1505 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1506 :    
1507 : parrello 1.1 =over 4
1508 :    
1509 :     =item objectNames
1510 :    
1511 :     List containing the names of the entity and relationship objects to be retrieved.
1512 :    
1513 :     =item filterClause
1514 :    
1515 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1516 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1517 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1518 :     in the filter clause should be added to the parameter list as additional parameters. The
1519 :     fields in a filter clause can come from primary entity relations, relationship relations,
1520 :     or secondary entity relations; however, all of the entities and relationships involved must
1521 :     be included in the list of object names.
1522 :    
1523 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1524 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1525 :     particular genus and sorts them by species name.
1526 :    
1527 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1528 :    
1529 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1530 :     be processed. The idea is to make it less likely to find the verb by accident.
1531 :    
1532 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1533 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1534 :     relation.
1535 :    
1536 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1537 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1538 :     a positive number. So, for example
1539 :    
1540 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1541 :    
1542 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1543 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1544 :     use
1545 :    
1546 :     C<< "LIMIT 10" >>
1547 :    
1548 : parrello 1.45 =item params
1549 : parrello 1.1
1550 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1551 : parrello 1.1
1552 :     =item RETURN
1553 :    
1554 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1555 :    
1556 :     =back
1557 :    
1558 :     =cut
1559 :    
1560 :     sub Get {
1561 : parrello 1.10 # Get the parameters.
1562 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1563 :     # Process the SQL stuff.
1564 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1565 :     $self->_SetupSQL($objectNames, $filterClause);
1566 :     # Create the query.
1567 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1568 :     ".* $suffix";
1569 :     my $sth = $self->_GetStatementHandle($command, $params);
1570 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1571 :     # and mapped name for each object in the query.
1572 :     my @relationMap = ();
1573 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1574 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1575 : parrello 1.39 }
1576 : parrello 1.10 # Return the statement object.
1577 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1578 : parrello 1.10 return $retVal;
1579 : parrello 1.1 }
1580 :    
1581 : parrello 1.78
1582 :    
1583 : parrello 1.70 =head3 Search
1584 :    
1585 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1586 :    
1587 :     Perform a full text search with filtering. The search will be against a specified object
1588 :     in the object name list. That object will get an extra field containing the search
1589 :     relevance. Note that except for the search expression, the parameters of this method are
1590 :     the same as those for L</Get> and follow the same rules.
1591 :    
1592 :     =over 4
1593 :    
1594 :     =item searchExpression
1595 :    
1596 : parrello 1.75 Boolean search expression for the text fields of the target object. The default mode for
1597 :     a Boolean search expression is OR, but we want the default to be AND, so we will
1598 :     add a C<+> operator to each word with no other operator before it.
1599 : parrello 1.70
1600 :     =item idx
1601 :    
1602 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1603 :    
1604 :     =item objectNames
1605 :    
1606 :     List containing the names of the entity and relationship objects to be retrieved.
1607 :    
1608 :     =item filterClause
1609 :    
1610 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1611 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1612 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1613 :     in the filter clause should be added to the parameter list as additional parameters. The
1614 :     fields in a filter clause can come from primary entity relations, relationship relations,
1615 :     or secondary entity relations; however, all of the entities and relationships involved must
1616 :     be included in the list of object names.
1617 :    
1618 :     =item params
1619 :    
1620 :     Reference to a list of parameter values to be substituted into the filter clause.
1621 :    
1622 :     =item RETURN
1623 :    
1624 :     Returns a query object for the specified search.
1625 :    
1626 :     =back
1627 :    
1628 :     =cut
1629 :    
1630 :     sub Search {
1631 :     # Get the parameters.
1632 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1633 :     # Declare the return variable.
1634 :     my $retVal;
1635 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1636 :     # a parameter list exists before we copy it.
1637 :     my @myParams = ();
1638 :     if (defined $params) {
1639 :     @myParams = @{$params};
1640 :     }
1641 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1642 :     my $object1Name = $objectNames->[$idx];
1643 :     my $object1Structure = $self->_GetStructure($object1Name);
1644 :     # Get the field list.
1645 :     if (! exists $object1Structure->{searchFields}) {
1646 :     Confess("No searchable index for $object1Name.");
1647 :     } else {
1648 :     # Get the field list.
1649 :     my @fields = @{$object1Structure->{searchFields}};
1650 : parrello 1.71 # Clean the search expression.
1651 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1652 : parrello 1.75 # Prefix a "+" to each uncontrolled word. This converts the default
1653 :     # search mode from OR to AND.
1654 : parrello 1.80 $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1655 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1656 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1657 :     # query itself. Both will use a parameter mark, so we need to push the
1658 :     # search expression onto the front of the parameter list twice.
1659 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1660 : parrello 1.70 # Build the match expression.
1661 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1662 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1663 :     # Process the SQL stuff.
1664 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1665 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1666 :     # Create the query. Note that the match clause is inserted at the front of
1667 :     # the select fields.
1668 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1669 :     ".* $suffix";
1670 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1671 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1672 :     # and mapped name for each object in the query.
1673 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1674 :     # Return the statement object.
1675 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1676 :     }
1677 :     return $retVal;
1678 :     }
1679 :    
1680 : parrello 1.45 =head3 GetFlat
1681 :    
1682 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1683 :    
1684 :     This is a variation of L</GetAll> that asks for only a single field per record and
1685 :     returns a single flattened list.
1686 :    
1687 :     =over 4
1688 :    
1689 :     =item objectNames
1690 :    
1691 :     List containing the names of the entity and relationship objects to be retrieved.
1692 :    
1693 :     =item filterClause
1694 :    
1695 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1696 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1697 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1698 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1699 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1700 :     entities and relationships involved must be included in the list of object names.
1701 :    
1702 :     =item parameterList
1703 :    
1704 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1705 :    
1706 :     =item field
1707 :    
1708 :     Name of the field to be used to get the elements of the list returned.
1709 :    
1710 :     =item RETURN
1711 :    
1712 :     Returns a list of values.
1713 :    
1714 :     =back
1715 :    
1716 :     =cut
1717 :     #: Return Type @;
1718 :     sub GetFlat {
1719 :     # Get the parameters.
1720 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1721 :     # Construct the query.
1722 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1723 :     # Create the result list.
1724 :     my @retVal = ();
1725 :     # Loop through the records, adding the field values found to the result list.
1726 :     while (my $row = $query->Fetch()) {
1727 :     push @retVal, $row->Value($field);
1728 :     }
1729 :     # Return the list created.
1730 :     return @retVal;
1731 :     }
1732 :    
1733 : parrello 1.73 =head3 SpecialFields
1734 :    
1735 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1736 :    
1737 :     Return a hash mapping special fields in the specified entity to the value of their
1738 :     C<special> attribute. This enables the subclass to get access to the special field
1739 :     attributes without needed to plumb the internal ERDB data structures.
1740 :    
1741 :     =over 4
1742 :    
1743 :     =item entityName
1744 :    
1745 :     Name of the entity whose special fields are desired.
1746 :    
1747 :     =item RETURN
1748 :    
1749 :     Returns a hash. The keys of the hash are the special field names, and the values
1750 :     are the values from each special field's C<special> attribute.
1751 :    
1752 :     =back
1753 :    
1754 :     =cut
1755 :    
1756 :     sub SpecialFields {
1757 :     # Get the parameters.
1758 :     my ($self, $entityName) = @_;
1759 :     # Declare the return variable.
1760 :     my %retVal = ();
1761 :     # Find the entity's data structure.
1762 : parrello 1.75 my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1763 : parrello 1.73 # Loop through its fields, adding each special field to the return hash.
1764 :     my $fieldHash = $entityData->{Fields};
1765 :     for my $fieldName (keys %{$fieldHash}) {
1766 :     my $fieldData = $fieldHash->{$fieldName};
1767 :     if (exists $fieldData->{special}) {
1768 :     $retVal{$fieldName} = $fieldData->{special};
1769 :     }
1770 :     }
1771 :     # Return the result.
1772 :     return %retVal;
1773 :     }
1774 :    
1775 : parrello 1.32 =head3 Delete
1776 :    
1777 : parrello 1.78 C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1778 : parrello 1.32
1779 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1780 : parrello 1.77 relationship instances dependent on it. The definition of I<dependence> is recursive.
1781 :    
1782 :     An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1783 :     relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1784 : parrello 1.32 dependent relationship.
1785 :    
1786 :     =over 4
1787 :    
1788 :     =item entityName
1789 :    
1790 :     Name of the entity type for the instance being deleted.
1791 :    
1792 :     =item objectID
1793 :    
1794 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1795 :     then it is presumed to by a LIKE pattern.
1796 :    
1797 : parrello 1.78 =item options
1798 : parrello 1.32
1799 : parrello 1.78 A hash detailing the options for this delete operation.
1800 : parrello 1.32
1801 :     =item RETURN
1802 :    
1803 :     Returns a statistics object indicating how many records of each particular table were
1804 :     deleted.
1805 :    
1806 :     =back
1807 :    
1808 : parrello 1.78 The permissible options for this method are as follows.
1809 :    
1810 :     =over 4
1811 :    
1812 :     =item testMode
1813 :    
1814 :     If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1815 :    
1816 :     =item keepRoot
1817 :    
1818 :     If TRUE, then the entity instances will not be deleted, only the dependent records.
1819 :    
1820 :     =back
1821 :    
1822 : parrello 1.32 =cut
1823 :     #: Return Type $%;
1824 :     sub Delete {
1825 :     # Get the parameters.
1826 : parrello 1.78 my ($self, $entityName, $objectID, %options) = @_;
1827 : parrello 1.32 # Declare the return variable.
1828 :     my $retVal = Stats->new();
1829 :     # Get the DBKernel object.
1830 :     my $db = $self->{_dbh};
1831 :     # We're going to generate all the paths branching out from the starting entity. One of
1832 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1833 :     # determine if we've hit a loop.
1834 :     my %alreadyFound = ();
1835 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1836 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1837 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1838 :     # sure we don't delete records that might be needed to forge relationships back to the
1839 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1840 :     # FROM-relationships and entities.
1841 :     my @fromPathList = ();
1842 :     my @toPathList = ();
1843 : parrello 1.78 # This final list is used to remember what work still needs to be done. We push paths
1844 : parrello 1.32 # onto the list, then pop them off to extend the paths. We prime it with the starting
1845 :     # point. Note that we will work hard to insure that the last item on a path in the
1846 : parrello 1.75 # to-do list is always an entity.
1847 : parrello 1.32 my @todoList = ([$entityName]);
1848 :     while (@todoList) {
1849 :     # Get the current path.
1850 :     my $current = pop @todoList;
1851 :     # Copy it into a list.
1852 :     my @stackedPath = @{$current};
1853 :     # Pull off the last item on the path. It will always be an entity.
1854 : parrello 1.78 my $myEntityName = pop @stackedPath;
1855 : parrello 1.32 # Add it to the alreadyFound list.
1856 : parrello 1.78 $alreadyFound{$myEntityName} = 1;
1857 :     # Figure out if we need to delete this entity.
1858 :     if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1859 :     # Get the entity data.
1860 :     my $entityData = $self->_GetStructure($myEntityName);
1861 :     # Loop through the entity's relations. A DELETE command will be needed for each of them.
1862 :     my $relations = $entityData->{Relations};
1863 :     for my $relation (keys %{$relations}) {
1864 :     my @augmentedList = (@stackedPath, $relation);
1865 :     push @fromPathList, \@augmentedList;
1866 :     }
1867 : parrello 1.32 }
1868 :     # Now we need to look for relationships connected to this entity.
1869 :     my $relationshipList = $self->{_metaData}->{Relationships};
1870 :     for my $relationshipName (keys %{$relationshipList}) {
1871 :     my $relationship = $relationshipList->{$relationshipName};
1872 :     # Check the FROM field. We're only interested if it's us.
1873 : parrello 1.78 if ($relationship->{from} eq $myEntityName) {
1874 : parrello 1.32 # Add the path to this relationship.
1875 : parrello 1.78 my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1876 : parrello 1.33 push @fromPathList, \@augmentedList;
1877 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1878 :     # and the target hasn't been seen yet, we want to
1879 :     # stack the entity for future processing.
1880 :     if ($relationship->{arity} eq '1M') {
1881 :     my $toEntity = $relationship->{to};
1882 :     if (! exists $alreadyFound{$toEntity}) {
1883 :     # Here we have a new entity that's dependent on
1884 :     # the current entity, so we need to stack it.
1885 :     my @stackList = (@augmentedList, $toEntity);
1886 : parrello 1.33 push @fromPathList, \@stackList;
1887 : parrello 1.34 } else {
1888 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1889 : parrello 1.32 }
1890 :     }
1891 :     }
1892 :     # Now check the TO field. In this case only the relationship needs
1893 : parrello 1.33 # deletion.
1894 : parrello 1.78 if ($relationship->{to} eq $myEntityName) {
1895 :     my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1896 : parrello 1.33 push @toPathList, \@augmentedList;
1897 : parrello 1.32 }
1898 :     }
1899 :     }
1900 :     # Create the first qualifier for the WHERE clause. This selects the
1901 :     # keys of the primary entity records to be deleted. When we're deleting
1902 : parrello 1.78 # from a dependent table, we construct a join path from the first qualifier
1903 : parrello 1.32 # to the table containing the dependent records to delete.
1904 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1905 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1906 :     # the second through the from-list. The from-list is second because
1907 :     # the to-list may need to pass through some of the entities the
1908 :     # from-list would delete.
1909 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1910 :     # Now it's time to do the deletes. We do it in two passes.
1911 :     for my $keyName ('to_link', 'from_link') {
1912 :     # Get the list for this key.
1913 :     my @pathList = @{$stackList{$keyName}};
1914 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1915 : parrello 1.33 # Loop through this list.
1916 :     while (my $path = pop @pathList) {
1917 :     # Get the table whose rows are to be deleted.
1918 :     my @pathTables = @{$path};
1919 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1920 :     # syntax of a DELETE-USING varies among DBMSs.
1921 : parrello 1.33 my $target = $pathTables[$#pathTables];
1922 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1923 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1924 :     # starting table will either be the entity relation or one of the entity's
1925 :     # sub-relations.
1926 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1927 :     # Now we run through the remaining entities in the path, connecting them up.
1928 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1929 :     # Connect the current relationship to the preceding entity.
1930 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1931 :     # The style of connection depends on the direction of the relationship.
1932 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1933 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1934 :     # Here there's a next entity, so connect that to the relationship's
1935 :     # to-link.
1936 :     my $entity2 = $pathTables[$i+1];
1937 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1938 : parrello 1.32 }
1939 :     }
1940 : parrello 1.33 # Now we have our desired DELETE statement.
1941 : parrello 1.78 if ($options{testMode}) {
1942 : parrello 1.33 # Here the user wants to trace without executing.
1943 :     Trace($stmt) if T(0);
1944 :     } else {
1945 : parrello 1.77 # Here we can delete. Note that the SQL method dies with a confession
1946 : parrello 1.33 # if an error occurs, so we just go ahead and do it.
1947 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1948 :     my $rv = $db->SQL($stmt, 0, $objectID);
1949 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1950 :     # are from the target table, so we use its name to record the
1951 :     # statistic.
1952 :     $retVal->Add($target, $rv);
1953 :     }
1954 : parrello 1.32 }
1955 :     }
1956 :     # Return the result.
1957 :     return $retVal;
1958 :     }
1959 :    
1960 : parrello 1.78 =head3 Disconnect
1961 :    
1962 :     C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1963 :    
1964 :     Disconnect an entity instance from all the objects to which it is related. This
1965 :     will delete each relationship instance that connects to the specified entity.
1966 :    
1967 :     =over 4
1968 :    
1969 :     =item relationshipName
1970 :    
1971 :     Name of the relationship whose instances are to be deleted.
1972 :    
1973 :     =item originEntityName
1974 :    
1975 :     Name of the entity that is to be disconnected.
1976 :    
1977 :     =item originEntityID
1978 :    
1979 :     ID of the entity that is to be disconnected.
1980 :    
1981 :     =back
1982 :    
1983 :     =cut
1984 :    
1985 :     sub Disconnect {
1986 :     # Get the parameters.
1987 :     my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1988 :     # Get the relationship descriptor.
1989 :     my $structure = $self->_GetStructure($relationshipName);
1990 :     # Insure we have a relationship.
1991 :     if (! exists $structure->{from}) {
1992 :     Confess("$relationshipName is not a relationship in the database.");
1993 :     } else {
1994 :     # Get the database handle.
1995 :     my $dbh = $self->{_dbh};
1996 :     # We'll set this value to 1 if we find our entity.
1997 :     my $found = 0;
1998 :     # Loop through the ends of the relationship.
1999 :     for my $dir ('from', 'to') {
2000 :     if ($structure->{$dir} eq $originEntityName) {
2001 :     # Delete all relationship instances on this side of the entity instance.
2002 : parrello 1.84 Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2003 : parrello 1.78 $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2004 :     $found = 1;
2005 :     }
2006 :     }
2007 :     # Insure we found the entity on at least one end.
2008 :     if (! $found) {
2009 :     Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2010 :     }
2011 :     }
2012 :     }
2013 :    
2014 : parrello 1.79 =head3 DeleteRow
2015 :    
2016 :     C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
2017 :    
2018 :     Delete a row from a relationship. In most cases, only the from-link and to-link are
2019 :     needed; however, for relationships with intersection data values can be specified
2020 :     for the other fields using a hash.
2021 :    
2022 :     =over 4
2023 :    
2024 :     =item relationshipName
2025 :    
2026 :     Name of the relationship from which the row is to be deleted.
2027 :    
2028 :     =item fromLink
2029 :    
2030 :     ID of the entity instance in the From direction.
2031 :    
2032 :     =item toLink
2033 :    
2034 :     ID of the entity instance in the To direction.
2035 :    
2036 :     =item values
2037 :    
2038 :     Reference to a hash of other values to be used for filtering the delete.
2039 :    
2040 :     =back
2041 :    
2042 :     =cut
2043 :    
2044 :     sub DeleteRow {
2045 :     # Get the parameters.
2046 :     my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2047 :     # Create a hash of all the filter information.
2048 :     my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2049 :     if (defined $values) {
2050 :     for my $key (keys %{$values}) {
2051 :     $filter{$key} = $values->{$key};
2052 :     }
2053 :     }
2054 :     # Build an SQL statement out of the hash.
2055 :     my @filters = ();
2056 :     my @parms = ();
2057 :     for my $key (keys %filter) {
2058 :     push @filters, _FixName($key) . " = ?";
2059 :     push @parms, $filter{$key};
2060 :     }
2061 :     Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2062 :     my $command = "DELETE FROM $relationshipName WHERE " .
2063 :     join(" AND ", @filters);
2064 :     # Execute it.
2065 :     my $dbh = $self->{_dbh};
2066 :     $dbh->SQL($command, undef, @parms);
2067 :     }
2068 :    
2069 : parrello 1.70 =head3 SortNeeded
2070 :    
2071 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
2072 :    
2073 :     Return the pipe command for the sort that should be applied to the specified
2074 :     relation when creating the load file.
2075 :    
2076 :     For example, if the load file should be sorted ascending by the first
2077 :     field, this method would return
2078 :    
2079 :     sort -k1 -t"\t"
2080 :    
2081 :     If the first field is numeric, the method would return
2082 :    
2083 :     sort -k1n -t"\t"
2084 :    
2085 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2086 :     keys using a sort.
2087 :    
2088 :     =over 4
2089 :    
2090 :     =item relationName
2091 :    
2092 :     Name of the relation to be examined.
2093 :    
2094 :     =item
2095 :    
2096 :     Returns the sort command to use for sorting the relation, suitable for piping.
2097 :    
2098 :     =back
2099 :    
2100 :     =cut
2101 :     #: Return Type $;
2102 :     sub SortNeeded {
2103 :     # Get the parameters.
2104 :     my ($self, $relationName) = @_;
2105 :     # Declare a descriptor to hold the names of the key fields.
2106 :     my @keyNames = ();
2107 :     # Get the relation structure.
2108 :     my $relationData = $self->_FindRelation($relationName);
2109 :     # Find out if the relation is a primary entity relation,
2110 :     # a relationship relation, or a secondary entity relation.
2111 :     my $entityTable = $self->{_metaData}->{Entities};
2112 :     my $relationshipTable = $self->{_metaData}->{Relationships};
2113 :     if (exists $entityTable->{$relationName}) {
2114 :     # Here we have a primary entity relation.
2115 :     push @keyNames, "id";
2116 :     } elsif (exists $relationshipTable->{$relationName}) {
2117 :     # Here we have a relationship. We sort using the FROM index.
2118 :     my $relationshipData = $relationshipTable->{$relationName};
2119 : parrello 1.75 my $index = $relationData->{Indexes}->{idxFrom};
2120 : parrello 1.70 push @keyNames, @{$index->{IndexFields}};
2121 :     } else {
2122 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
2123 :     push @keyNames, "id";
2124 :     }
2125 :     # Now we parse the key names into sort parameters. First, we prime the return
2126 :     # string.
2127 :     my $retVal = "sort -t\"\t\" ";
2128 :     # Get the relation's field list.
2129 :     my @fields = @{$relationData->{Fields}};
2130 :     # Loop through the keys.
2131 :     for my $keyData (@keyNames) {
2132 :     # Get the key and the ordering.
2133 :     my ($keyName, $ordering);
2134 :     if ($keyData =~ /^([^ ]+) DESC/) {
2135 :     ($keyName, $ordering) = ($1, "descending");
2136 :     } else {
2137 :     ($keyName, $ordering) = ($keyData, "ascending");
2138 :     }
2139 :     # Find the key's position and type.
2140 :     my $fieldSpec;
2141 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2142 :     my $thisField = $fields[$i];
2143 :     if ($thisField->{name} eq $keyName) {
2144 :     # Get the sort modifier for this field type. The modifier
2145 :     # decides whether we're using a character, numeric, or
2146 :     # floating-point sort.
2147 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
2148 :     # If the index is descending for this field, denote we want
2149 :     # to reverse the sort order on this field.
2150 :     if ($ordering eq 'descending') {
2151 :     $modifier .= "r";
2152 :     }
2153 :     # Store the position and modifier into the field spec, which
2154 :     # will stop the inner loop. Note that the field number is
2155 :     # 1-based in the sort command, so we have to increment the
2156 :     # index.
2157 :     $fieldSpec = ($i + 1) . $modifier;
2158 :     }
2159 :     }
2160 :     # Add this field to the sort command.
2161 :     $retVal .= " -k$fieldSpec";
2162 :     }
2163 :     # Return the result.
2164 :     return $retVal;
2165 :     }
2166 :    
2167 : parrello 1.6 =head3 GetList
2168 :    
2169 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2170 : parrello 1.6
2171 :     Return a list of object descriptors for the specified objects as determined by the
2172 :     specified filter clause.
2173 :    
2174 :     This method is essentially the same as L</Get> except it returns a list of objects rather
2175 : parrello 1.7 than a query object that can be used to get the results one record at a time.
2176 : parrello 1.6
2177 :     =over 4
2178 :    
2179 :     =item objectNames
2180 :    
2181 :     List containing the names of the entity and relationship objects to be retrieved.
2182 :    
2183 :     =item filterClause
2184 :    
2185 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2186 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2187 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2188 :     in the filter clause should be added to the parameter list as additional parameters. The
2189 :     fields in a filter clause can come from primary entity relations, relationship relations,
2190 :     or secondary entity relations; however, all of the entities and relationships involved must
2191 :     be included in the list of object names.
2192 :    
2193 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
2194 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
2195 :     particular genus and sorts them by species name.
2196 :    
2197 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2198 :    
2199 :     The rules for field references in a sort order are the same as those for field references in the
2200 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
2201 :     relation.
2202 :    
2203 : parrello 1.45 =item params
2204 : parrello 1.6
2205 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
2206 : parrello 1.6
2207 :     =item RETURN
2208 :    
2209 : parrello 1.88 Returns a list of B<ERDBObject>s that satisfy the query conditions.
2210 : parrello 1.6
2211 :     =back
2212 :    
2213 :     =cut
2214 :     #: Return Type @%
2215 :     sub GetList {
2216 :     # Get the parameters.
2217 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
2218 : parrello 1.10 # Declare the return variable.
2219 :     my @retVal = ();
2220 :     # Perform the query.
2221 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
2222 : parrello 1.10 # Loop through the results.
2223 :     while (my $object = $query->Fetch) {
2224 :     push @retVal, $object;
2225 :     }
2226 : parrello 1.6 # Return the result.
2227 :     return @retVal;
2228 :     }
2229 :    
2230 : parrello 1.45 =head3 GetCount
2231 :    
2232 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2233 :    
2234 :     Return the number of rows found by a specified query. This method would
2235 :     normally be used to count the records in a single table. For example, in a
2236 :     genetics database
2237 :    
2238 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2239 :    
2240 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
2241 :     to use it to return records based on a join. For example,
2242 :    
2243 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2244 : parrello 1.45 ['homo %']);
2245 :    
2246 :     would return the number of features for genomes in the genus I<homo>. Note that
2247 :     only the rows from the first table are counted. If the above command were
2248 :    
2249 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2250 :     ['homo %']);
2251 :    
2252 :     it would return the number of genomes, not the number of genome/feature pairs.
2253 :    
2254 :     =over 4
2255 :    
2256 :     =item objectNames
2257 :    
2258 :     Reference to a list of the objects (entities and relationships) included in the
2259 :     query.
2260 :    
2261 :     =item filter
2262 :    
2263 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
2264 :     method.
2265 :    
2266 :     =item params
2267 :    
2268 :     Reference to a list of the parameter values to be substituted for the parameter marks
2269 :     in the filter.
2270 :    
2271 :     =item RETURN
2272 :    
2273 :     Returns a count of the number of records in the first table that would satisfy
2274 :     the query.
2275 :    
2276 :     =back
2277 :    
2278 :     =cut
2279 :    
2280 :     sub GetCount {
2281 :     # Get the parameters.
2282 :     my ($self, $objectNames, $filter, $params) = @_;
2283 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
2284 :     if (! defined($params)) {
2285 :     $params = [];
2286 :     }
2287 : parrello 1.45 # Declare the return variable.
2288 :     my $retVal;
2289 : parrello 1.47 # Find out if we're counting an entity or a relationship.
2290 :     my $countedField;
2291 :     if ($self->IsEntity($objectNames->[0])) {
2292 :     $countedField = "id";
2293 :     } else {
2294 :     # For a relationship we count the to-link because it's usually more
2295 :     # numerous. Note we're automatically converting to the SQL form
2296 :     # of the field name (to_link vs. to-link).
2297 :     $countedField = "to_link";
2298 :     }
2299 : parrello 1.45 # Create the SQL command suffix to get the desired records.
2300 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2301 :     $filter);
2302 :     # Prefix it with text telling it we want a record count.
2303 :     my $firstObject = $mappedNameListRef->[0];
2304 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2305 : parrello 1.45 # Prepare and execute the command.
2306 :     my $sth = $self->_GetStatementHandle($command, $params);
2307 :     # Get the count value.
2308 :     ($retVal) = $sth->fetchrow_array();
2309 :     # Check for a problem.
2310 :     if (! defined($retVal)) {
2311 :     if ($sth->err) {
2312 :     # Here we had an SQL error.
2313 :     Confess("Error retrieving row count: " . $sth->errstr());
2314 :     } else {
2315 :     # Here we have no result.
2316 :     Confess("No result attempting to retrieve row count.");
2317 :     }
2318 :     }
2319 :     # Return the result.
2320 :     return $retVal;
2321 :     }
2322 :    
2323 : parrello 1.1 =head3 ComputeObjectSentence
2324 :    
2325 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2326 : parrello 1.1
2327 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
2328 :    
2329 :     =over 4
2330 :    
2331 :     =item objectName
2332 :    
2333 :     Name of the entity or relationship.
2334 :    
2335 :     =item RETURN
2336 :    
2337 :     Returns a string containing the entity name or a relationship sentence.
2338 :    
2339 :     =back
2340 :    
2341 :     =cut
2342 :    
2343 :     sub ComputeObjectSentence {
2344 : parrello 1.10 # Get the parameters.
2345 :     my ($self, $objectName) = @_;
2346 :     # Set the default return value.
2347 :     my $retVal = $objectName;
2348 :     # Look for the object as a relationship.
2349 :     my $relTable = $self->{_metaData}->{Relationships};
2350 :     if (exists $relTable->{$objectName}) {
2351 :     # Get the relationship sentence.
2352 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2353 :     }
2354 :     # Return the result.
2355 :     return $retVal;
2356 : parrello 1.1 }
2357 :    
2358 :     =head3 DumpRelations
2359 :    
2360 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
2361 : parrello 1.1
2362 :     Write the contents of all the relations to tab-delimited files in the specified directory.
2363 :     Each file will have the same name as the relation dumped, with an extension of DTX.
2364 :    
2365 :     =over 4
2366 :    
2367 :     =item outputDirectory
2368 :    
2369 :     Name of the directory into which the relation files should be dumped.
2370 :    
2371 :     =back
2372 :    
2373 :     =cut
2374 :    
2375 :     sub DumpRelations {
2376 : parrello 1.10 # Get the parameters.
2377 :     my ($self, $outputDirectory) = @_;
2378 :     # Now we need to run through all the relations. First, we loop through the entities.
2379 :     my $metaData = $self->{_metaData};
2380 :     my $entities = $metaData->{Entities};
2381 :     for my $entityName (keys %{$entities}) {
2382 :     my $entityStructure = $entities->{$entityName};
2383 :     # Get the entity's relations.
2384 :     my $relationList = $entityStructure->{Relations};
2385 :     # Loop through the relations, dumping them.
2386 :     for my $relationName (keys %{$relationList}) {
2387 :     my $relation = $relationList->{$relationName};
2388 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
2389 :     }
2390 :     }
2391 :     # Next, we loop through the relationships.
2392 :     my $relationships = $metaData->{Relationships};
2393 :     for my $relationshipName (keys %{$relationships}) {
2394 :     my $relationshipStructure = $relationships->{$relationshipName};
2395 :     # Dump this relationship's relation.
2396 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2397 :     }
2398 : parrello 1.1 }
2399 :    
2400 : parrello 1.51 =head3 InsertValue
2401 :    
2402 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2403 :    
2404 :     This method will insert a new value into the database. The value must be one
2405 :     associated with a secondary relation, since primary values cannot be inserted:
2406 :     they occur exactly once. Secondary values, on the other hand, can be missing
2407 :     or multiply-occurring.
2408 :    
2409 :     =over 4
2410 :    
2411 :     =item entityID
2412 :    
2413 :     ID of the object that is to receive the new value.
2414 :    
2415 :     =item fieldName
2416 :    
2417 :     Field name for the new value-- this includes the entity name, since
2418 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2419 :    
2420 :     =item value
2421 :    
2422 :     New value to be put in the field.
2423 :    
2424 :     =back
2425 :    
2426 :     =cut
2427 :    
2428 :     sub InsertValue {
2429 :     # Get the parameters.
2430 :     my ($self, $entityID, $fieldName, $value) = @_;
2431 :     # Parse the entity name and the real field name.
2432 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2433 :     my $entityName = $1;
2434 :     my $fieldTitle = $2;
2435 :     # Get its descriptor.
2436 :     if (!$self->IsEntity($entityName)) {
2437 :     Confess("$entityName is not a valid entity.");
2438 :     } else {
2439 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2440 :     # Find the relation containing this field.
2441 :     my $fieldHash = $entityData->{Fields};
2442 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
2443 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
2444 :     } else {
2445 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
2446 :     if ($relation eq $entityName) {
2447 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2448 :     } else {
2449 :     # Now we can create an INSERT statement.
2450 :     my $dbh = $self->{_dbh};
2451 :     my $fixedName = _FixName($fieldTitle);
2452 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2453 : parrello 1.51 # Execute the command.
2454 :     $dbh->SQL($statement, 0, $entityID, $value);
2455 :     }
2456 :     }
2457 :     }
2458 :     } else {
2459 :     Confess("$fieldName is not a valid field name.");
2460 :     }
2461 :     }
2462 :    
2463 : parrello 1.1 =head3 InsertObject
2464 :    
2465 : parrello 1.78 C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2466 : parrello 1.1
2467 :     Insert an object into the database. The object is defined by a type name and then a hash
2468 :     of field names to values. Field values in the primary relation are represented by scalars.
2469 :     (Note that for relationships, the primary relation is the B<only> relation.)
2470 :     Field values for the other relations comprising the entity are always list references. For
2471 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2472 :     C<ZP_00210270.1> and C<gi|46206278>.
2473 :    
2474 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2475 : parrello 1.1
2476 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2477 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2478 :    
2479 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2480 : parrello 1.1
2481 :     =over 4
2482 :    
2483 :     =item newObjectType
2484 :    
2485 :     Type name of the object to insert.
2486 :    
2487 :     =item fieldHash
2488 :    
2489 :     Hash of field names to values.
2490 :    
2491 :     =back
2492 :    
2493 :     =cut
2494 :    
2495 :     sub InsertObject {
2496 : parrello 1.10 # Get the parameters.
2497 :     my ($self, $newObjectType, $fieldHash) = @_;
2498 :     # Denote that so far we appear successful.
2499 :     my $retVal = 1;
2500 :     # Get the database handle.
2501 :     my $dbh = $self->{_dbh};
2502 :     # Get the relation list.
2503 :     my $relationTable = $self->_GetRelationTable($newObjectType);
2504 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
2505 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
2506 :     # stop the loop.
2507 :     my @relationList = keys %{$relationTable};
2508 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2509 :     my $relationName = $relationList[$i];
2510 :     my $relationDefinition = $relationTable->{$relationName};
2511 :     # Get the relation's fields. For each field we will collect a value in the corresponding
2512 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
2513 :     # @missing list.
2514 :     my @fieldList = @{$relationDefinition->{Fields}};
2515 :     my @fieldNameList = ();
2516 :     my @valueList = ();
2517 :     my @missing = ();
2518 :     my $recordCount = 1;
2519 :     for my $fieldDescriptor (@fieldList) {
2520 :     # Get the field name and save it. Note we need to fix it up so the hyphens
2521 :     # are converted to underscores.
2522 :     my $fieldName = $fieldDescriptor->{name};
2523 :     push @fieldNameList, _FixName($fieldName);
2524 :     # Look for the named field in the incoming structure. Note that we are looking
2525 :     # for the real field name, not the fixed-up one!
2526 :     if (exists $fieldHash->{$fieldName}) {
2527 :     # Here we found the field. Stash it in the value list.
2528 :     my $value = $fieldHash->{$fieldName};
2529 :     push @valueList, $value;
2530 :     # If the value is a list, we may need to increment the record count.
2531 :     if (ref $value eq "ARRAY") {
2532 :     my $thisCount = @{$value};
2533 :     if ($recordCount == 1) {
2534 :     # Here we have our first list, so we save its count.
2535 :     $recordCount = $thisCount;
2536 :     } elsif ($recordCount != $thisCount) {
2537 :     # Here we have a second list, so its length has to match the
2538 :     # previous lists.
2539 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2540 :     $retVal = 0;
2541 :     }
2542 :     }
2543 :     } else {
2544 :     # Here the field is not present. Flag it as missing.
2545 :     push @missing, $fieldName;
2546 :     }
2547 :     }
2548 :     # If we are the primary relation, add the new-record flag.
2549 :     if ($relationName eq $newObjectType) {
2550 :     push @valueList, 1;
2551 :     push @fieldNameList, "new_record";
2552 :     }
2553 :     # Only proceed if there are no missing fields.
2554 :     if (@missing > 0) {
2555 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2556 :     join(' ', @missing)) if T(1);
2557 :     } else {
2558 :     # Build the INSERT statement.
2559 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2560 :     ") VALUES (";
2561 :     # Create a marker list of the proper size and put it in the statement.
2562 :     my @markers = ();
2563 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2564 :     $statement .= join(', ', @markers) . ")";
2565 :     # We have the insert statement, so prepare it.
2566 :     my $sth = $dbh->prepare_command($statement);
2567 :     Trace("Insert statement prepared: $statement") if T(3);
2568 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2569 :     # a list, we use the current element. The values are stored in the @parameterList array.
2570 :     my $done = 0;
2571 :     for (my $i = 0; $i < $recordCount; $i++) {
2572 :     # Clear the parameter list array.
2573 :     my @parameterList = ();
2574 :     # Loop through the values.
2575 :     for my $value (@valueList) {
2576 :     # Check to see if this is a scalar value.
2577 :     if (ref $value eq "ARRAY") {
2578 :     # Here we have a list value. Pull the current entry.
2579 :     push @parameterList, $value->[$i];
2580 :     } else {
2581 :     # Here we have a scalar value. Use it unmodified.
2582 :     push @parameterList, $value;
2583 :     }
2584 :     }
2585 :     # Execute the INSERT statement with the specified parameter list.
2586 :     $retVal = $sth->execute(@parameterList);
2587 :     if (!$retVal) {
2588 :     my $errorString = $sth->errstr();
2589 : parrello 1.78 Confess("Error inserting into $relationName: $errorString");
2590 : parrello 1.85 } else {
2591 :     Trace("Insert successful using $parameterList[0].") if T(3);
2592 : parrello 1.10 }
2593 :     }
2594 :     }
2595 :     }
2596 : parrello 1.78 # Return a 1 for backward compatability.
2597 :     return 1;
2598 :     }
2599 :    
2600 :     =head3 UpdateEntity
2601 :    
2602 :     C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2603 :    
2604 :     Update the values of an entity. This is an unprotected update, so it should only be
2605 :     done if the database resides on a database server.
2606 :    
2607 :     =over 4
2608 :    
2609 :     =item entityName
2610 :    
2611 :     Name of the entity to update. (This is the entity type.)
2612 :    
2613 :     =item id
2614 :    
2615 :     ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2616 :    
2617 :     =item fields
2618 :    
2619 :     Reference to a hash mapping field names to their new values. All of the fields named
2620 :     must be in the entity's primary relation, and they cannot any of them be the ID field.
2621 :    
2622 :     =back
2623 :    
2624 :     =cut
2625 :    
2626 :     sub UpdateEntity {
2627 :     # Get the parameters.
2628 :     my ($self, $entityName, $id, $fields) = @_;
2629 :     # Get a list of the field names being updated.
2630 :     my @fieldList = keys %{$fields};
2631 :     # Verify that the fields exist.
2632 :     my $checker = $self->GetFieldTable($entityName);
2633 :     for my $field (@fieldList) {
2634 :     if ($field eq 'id') {
2635 :     Confess("Cannot update the ID field for entity $entityName.");
2636 :     } elsif ($checker->{$field}->{relation} ne $entityName) {
2637 :     Confess("Cannot find $field in primary relation of $entityName.");
2638 :     }
2639 :     }
2640 :     # Build the SQL statement.
2641 :     my @sets = ();
2642 :     my @valueList = ();
2643 :     for my $field (@fieldList) {
2644 :     push @sets, _FixName($field) . " = ?";
2645 :     push @valueList, $fields->{$field};
2646 :     }
2647 :     my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2648 :     # Add the ID to the list of binding values.
2649 :     push @valueList, $id;
2650 :     # Call SQL to do the work.
2651 :     my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2652 :     # Check for errors.
2653 :     if ($rows == 0) {
2654 :     Confess("Entity $id of type $entityName not found.");
2655 :     }
2656 : parrello 1.1 }
2657 :    
2658 :     =head3 LoadTable
2659 :    
2660 : parrello 1.78 C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2661 : parrello 1.1
2662 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2663 :     first.
2664 : parrello 1.1
2665 :     =over 4
2666 :    
2667 :     =item fileName
2668 :    
2669 :     Name of the file from which the table data should be loaded.
2670 :    
2671 :     =item relationName
2672 :    
2673 :     Name of the relation to be loaded. This is the same as the table name.
2674 :    
2675 :     =item truncateFlag
2676 :    
2677 :     TRUE if the table should be dropped and re-created, else FALSE
2678 :    
2679 :     =item RETURN
2680 :    
2681 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2682 : parrello 1.1
2683 :     =back
2684 :    
2685 :     =cut
2686 :     sub LoadTable {
2687 : parrello 1.10 # Get the parameters.
2688 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2689 :     # Create the statistical return object.
2690 :     my $retVal = _GetLoadStats();
2691 :     # Trace the fact of the load.
2692 :     Trace("Loading table $relationName from $fileName") if T(2);
2693 :     # Get the database handle.
2694 :     my $dbh = $self->{_dbh};
2695 : parrello 1.22 # Get the input file size.
2696 :     my $fileSize = -s $fileName;
2697 : parrello 1.10 # Get the relation data.
2698 :     my $relation = $self->_FindRelation($relationName);
2699 :     # Check the truncation flag.
2700 :     if ($truncateFlag) {
2701 :     Trace("Creating table $relationName") if T(2);
2702 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2703 :     # divide it by the estimated row size, and then multiply by 1.5 to
2704 :     # leave extra room. We postulate a minimum row count of 1000 to
2705 :     # prevent problems with incoming empty load files.
2706 :     my $rowSize = $self->EstimateRowSize($relationName);
2707 :     my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2708 : parrello 1.10 # Re-create the table without its index.
2709 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2710 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2711 :     if ($dbh->{_preIndex}) {
2712 :     eval {
2713 :     $self->CreateIndex($relationName);
2714 :     };
2715 :     if ($@) {
2716 :     $retVal->AddMessage($@);
2717 :     }
2718 :     }
2719 :     }
2720 : parrello 1.3 # Load the table.
2721 : parrello 1.10 my $rv;
2722 :     eval {
2723 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2724 : parrello 1.10 };
2725 :     if (!defined $rv) {
2726 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2727 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2728 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2729 :     } else {
2730 : parrello 1.22 # Here we successfully loaded the table.
2731 :     $retVal->Add("tables");
2732 :     my $size = -s $fileName;
2733 :     Trace("$size bytes loaded into $relationName.") if T(2);
2734 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2735 : parrello 1.70 if ($truncateFlag) {
2736 :     # Indexes are created here for PostGres. For PostGres, indexes are
2737 :     # best built at the end. For MySQL, the reverse is true.
2738 :     if (! $dbh->{_preIndex}) {
2739 :     eval {
2740 :     $self->CreateIndex($relationName);
2741 :     };
2742 :     if ($@) {
2743 :     $retVal->AddMessage($@);
2744 :     }
2745 :     }
2746 :     # The full-text index (if any) is always built last, even for MySQL.
2747 :     # First we need to see if this table has a full-text index. Only
2748 :     # primary relations are allowed that privilege.
2749 : parrello 1.81 Trace("Checking for full-text index on $relationName.") if T(2);
2750 : parrello 1.70 if ($self->_IsPrimary($relationName)) {
2751 : parrello 1.82 $self->CreateSearchIndex($relationName);
2752 : parrello 1.10 }
2753 :     }
2754 :     }
2755 : parrello 1.20 # Analyze the table to improve performance.
2756 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2757 : olson 1.16 $dbh->vacuum_it($relationName);
2758 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2759 : parrello 1.10 # Return the statistics.
2760 :     return $retVal;
2761 : parrello 1.1 }
2762 :    
2763 : parrello 1.82 =head3 CreateSearchIndex
2764 :    
2765 :     C<< $erdb->CreateSearchIndex($objectName); >>
2766 :    
2767 :     Check for a full-text search index on the specified entity or relationship object, and
2768 :     if one is required, rebuild it.
2769 :    
2770 :     =over 4
2771 :    
2772 :     =item objectName
2773 :    
2774 :     Name of the entity or relationship to be indexed.
2775 :    
2776 :     =back
2777 :    
2778 :     =cut
2779 :    
2780 :     sub CreateSearchIndex {
2781 :     # Get the parameters.
2782 :     my ($self, $objectName) = @_;
2783 :     # Get the relation's entity/relationship structure.
2784 :     my $structure = $self->_GetStructure($objectName);
2785 :     # Get the database handle.
2786 :     my $dbh = $self->{_dbh};
2787 :     Trace("Checking for search fields in $objectName.") if T(3);
2788 :     # Check for a searchable fields list.
2789 :     if (exists $structure->{searchFields}) {
2790 :     # Here we know that we need to create a full-text search index.
2791 :     # Get an SQL-formatted field name list.
2792 :     my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2793 :     # Create the index. If it already exists, it will be dropped.
2794 :     $dbh->create_index(tbl => $objectName, idx => "search_idx",
2795 :     flds => $fields, kind => 'fulltext');
2796 :     Trace("Index created for $fields in $objectName.") if T(2);
2797 :     }
2798 :     }
2799 :    
2800 : parrello 1.73 =head3 DropRelation
2801 : parrello 1.1
2802 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2803 : parrello 1.1
2804 : parrello 1.73 Physically drop a relation from the database.
2805 : parrello 1.1
2806 :     =over 4
2807 :    
2808 : parrello 1.73 =item relationName
2809 : parrello 1.1
2810 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2811 :     no effect.
2812 : parrello 1.1
2813 :     =back
2814 :    
2815 :     =cut
2816 :    
2817 : parrello 1.73 sub DropRelation {
2818 : parrello 1.10 # Get the parameters.
2819 : parrello 1.73 my ($self, $relationName) = @_;
2820 :     # Get the database handle.
2821 :     my $dbh = $self->{_dbh};
2822 :     # Drop the relation. The method used here has no effect if the relation
2823 :     # does not exist.
2824 : parrello 1.74 Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2825 :     $dbh->drop_table(tbl => $relationName);
2826 : parrello 1.1 }
2827 :    
2828 : parrello 1.78 =head3 MatchSqlPattern
2829 :    
2830 :     C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2831 :    
2832 :     Determine whether or not a specified value matches an SQL pattern. An SQL
2833 :     pattern has two wild card characters: C<%> that matches multiple characters,
2834 :     and C<_> that matches a single character. These can be escaped using a
2835 :     backslash (C<\>). We pull this off by converting the SQL pattern to a
2836 :     PERL regular expression. As per SQL rules, the match is case-insensitive.
2837 :    
2838 :     =over 4
2839 :    
2840 :     =item value
2841 :    
2842 :     Value to be matched against the pattern. Note that an undefined or empty
2843 :     value will not match anything.
2844 :    
2845 :     =item pattern
2846 :    
2847 :     SQL pattern against which to match the value. An undefined or empty pattern will
2848 :     match everything.
2849 :    
2850 :     =item RETURN
2851 :    
2852 :     Returns TRUE if the value and pattern match, else FALSE.
2853 :    
2854 :     =back
2855 :    
2856 :     =cut
2857 :    
2858 :     sub MatchSqlPattern {
2859 :     # Get the parameters.
2860 :     my ($value, $pattern) = @_;
2861 :     # Declare the return variable.
2862 :     my $retVal;
2863 :     # Insure we have a pattern.
2864 :     if (! defined($pattern) || $pattern eq "") {
2865 :     $retVal = 1;
2866 :     } else {
2867 :     # Break the pattern into pieces around the wildcard characters. Because we
2868 :     # use parentheses in the split function's delimiter expression, we'll get
2869 :     # list elements for the delimiters as well as the rest of the string.
2870 :     my @pieces = split /([_%]|\\[_%])/, $pattern;
2871 :     # Check some fast special cases.
2872 :     if ($pattern eq '%') {
2873 :     # A null pattern matches everything.
2874 :     $retVal = 1;
2875 :     } elsif (@pieces == 1) {
2876 :     # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2877 :     $retVal = (lc($value) eq lc($pattern));
2878 :     } elsif (@pieces == 2 && $pieces[1] eq '%') {
2879 :     # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2880 :     $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2881 :     } else {
2882 :     # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2883 :     my $realPattern = "";
2884 :     for my $piece (@pieces) {
2885 :     # Determine the type of piece.
2886 :     if ($piece eq "") {
2887 :     # Empty pieces are ignored.
2888 :     } elsif ($piece eq "%") {
2889 :     # Here we have a multi-character wildcard. Note that it can match
2890 :     # zero or more characters.
2891 :     $realPattern .= ".*"
2892 :     } elsif ($piece eq "_") {
2893 :     # Here we have a single-character wildcard.
2894 :     $realPattern .= ".";
2895 :     } elsif ($piece eq "\\%" || $piece eq "\\_") {
2896 :     # This is an escape sequence (which is a rare thing, actually).
2897 :     $realPattern .= substr($piece, 1, 1);
2898 :     } else {
2899 :     # Here we have raw text.
2900 :     $realPattern .= quotemeta($piece);
2901 :     }
2902 :     }
2903 :     # Do the match.
2904 :     $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2905 :     }
2906 :     }
2907 :     # Return the result.
2908 :     return $retVal;
2909 :     }
2910 :    
2911 : parrello 1.6 =head3 GetEntity
2912 :    
2913 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2914 : parrello 1.6
2915 :     Return an object describing the entity instance with a specified ID.
2916 :    
2917 :     =over 4
2918 :    
2919 :     =item entityType
2920 :    
2921 :     Entity type name.
2922 :    
2923 :     =item ID
2924 :    
2925 :     ID of the desired entity.
2926 :    
2927 :     =item RETURN
2928 :    
2929 : parrello 1.88 Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2930 : parrello 1.6 instance is found with the specified key.
2931 :    
2932 :     =back
2933 :    
2934 :     =cut
2935 :    
2936 :     sub GetEntity {
2937 : parrello 1.10 # Get the parameters.
2938 :     my ($self, $entityType, $ID) = @_;
2939 :     # Create a query.
2940 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2941 : parrello 1.10 # Get the first (and only) object.
2942 :     my $retVal = $query->Fetch();
2943 :     # Return the result.
2944 :     return $retVal;
2945 : parrello 1.6 }
2946 :    
2947 : parrello 1.69 =head3 GetChoices
2948 :    
2949 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2950 :    
2951 :     Return a list of all the values for the specified field that are represented in the
2952 :     specified entity.
2953 :    
2954 :     Note that if the field is not indexed, then this will be a very slow operation.
2955 :    
2956 :     =over 4
2957 :    
2958 :     =item entityName
2959 :    
2960 :     Name of an entity in the database.
2961 :    
2962 :     =item fieldName
2963 :    
2964 :     Name of a field belonging to the entity. This is a raw field name without
2965 :     the standard parenthesized notation used in most calls.
2966 :    
2967 :     =item RETURN
2968 :    
2969 :     Returns a list of the distinct values for the specified field in the database.
2970 :    
2971 :     =back
2972 :    
2973 :     =cut
2974 :    
2975 :     sub GetChoices {
2976 :     # Get the parameters.
2977 :     my ($self, $entityName, $fieldName) = @_;
2978 :     # Declare the return variable.
2979 :     my @retVal;
2980 :     # Get the entity data structure.
2981 :     my $entityData = $self->_GetStructure($entityName);
2982 :     # Get the field.
2983 :     my $fieldHash = $entityData->{Fields};
2984 :     if (! exists $fieldHash->{$fieldName}) {
2985 :     Confess("$fieldName not found in $entityName.");
2986 :     } else {
2987 :     # Get the name of the relation containing the field.
2988 :     my $relation = $fieldHash->{$fieldName}->{relation};
2989 :     # Fix up the field name.
2990 :     my $realName = _FixName($fieldName);
2991 :     # Get the database handle.
2992 :     my $dbh = $self->{_dbh};
2993 :     # Query the database.
2994 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2995 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
2996 :     @retVal = sort map { $_->[0] } @{$results};
2997 :     }
2998 :     # Return the result.
2999 :     return @retVal;
3000 :     }
3001 :    
3002 : parrello 1.6 =head3 GetEntityValues
3003 :    
3004 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
3005 : parrello 1.6
3006 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
3007 :     does not exist, an empty list is returned.
3008 : parrello 1.6
3009 :     =over 4
3010 :    
3011 :     =item entityType
3012 :    
3013 :     Entity type name.
3014 :    
3015 :     =item ID
3016 :    
3017 :     ID of the desired entity.
3018 :    
3019 :     =item fields
3020 :    
3021 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
3022 :    
3023 :     =item RETURN
3024 :    
3025 :     Returns a flattened list of the values of the specified fields for the specified entity.
3026 :    
3027 :     =back
3028 :    
3029 :     =cut
3030 :    
3031 :     sub GetEntityValues {
3032 : parrello 1.10 # Get the parameters.
3033 :     my ($self, $entityType, $ID, $fields) = @_;
3034 :     # Get the specified entity.
3035 :     my $entity = $self->GetEntity($entityType, $ID);
3036 :     # Declare the return list.
3037 :     my @retVal = ();
3038 :     # If we found the entity, push the values into the return list.
3039 :     if ($entity) {
3040 :     push @retVal, $entity->Values($fields);
3041 :     }
3042 :     # Return the result.
3043 :     return @retVal;
3044 : parrello 1.6 }
3045 : parrello 1.1
3046 : parrello 1.7 =head3 GetAll
3047 :    
3048 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
3049 : parrello 1.7
3050 :     Return a list of values taken from the objects returned by a query. The first three
3051 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
3052 :     a list of the fields desired from each record found by the query. The field name
3053 :     syntax is the standard syntax used for fields in the B<ERDB> system--
3054 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
3055 :     or relationship and I<fieldName> is the name of the field.
3056 :    
3057 :     The list returned will be a list of lists. Each element of the list will contain
3058 :     the values returned for the fields specified in the fourth parameter. If one of the
3059 :     fields specified returns multiple values, they are flattened in with the rest. For
3060 :     example, the following call will return a list of the features in a particular
3061 :     spreadsheet cell, and each feature will be represented by a list containing the
3062 :     feature ID followed by all of its aliases.
3063 :    
3064 : parrello 1.78 C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
3065 : parrello 1.7
3066 :     =over 4
3067 :    
3068 :     =item objectNames
3069 :    
3070 :     List containing the names of the entity and relationship objects to be retrieved.
3071 :    
3072 :     =item filterClause
3073 :    
3074 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
3075 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
3076 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
3077 :     parameter list as additional parameters. The fields in a filter clause can come from primary
3078 :     entity relations, relationship relations, or secondary entity relations; however, all of the
3079 :     entities and relationships involved must be included in the list of object names.
3080 :    
3081 :     =item parameterList
3082 :    
3083 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
3084 :    
3085 :     =item fields
3086 :    
3087 :     List of the fields to be returned in each element of the list returned.
3088 :    
3089 :     =item count
3090 :    
3091 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
3092 :    
3093 :     =item RETURN
3094 :    
3095 :     Returns a list of list references. Each element of the return list contains the values for the
3096 :     fields specified in the B<fields> parameter.
3097 :    
3098 :     =back
3099 :    
3100 :     =cut
3101 :     #: Return Type @@;
3102 :     sub GetAll {
3103 : parrello 1.10 # Get the parameters.
3104 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3105 :     # Translate the parameters from a list reference to a list. If the parameter
3106 :     # list is a scalar we convert it into a singleton list.
3107 :     my @parmList = ();
3108 :     if (ref $parameterList eq "ARRAY") {
3109 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
3110 : parrello 1.10 @parmList = @{$parameterList};
3111 :     } else {
3112 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3113 : parrello 1.10 push @parmList, $parameterList;
3114 :     }
3115 : parrello 1.30 # Insure the counter has a value.
3116 :     if (!defined $count) {
3117 :     $count = 0;
3118 :     }
3119 :     # Add the row limit to the filter clause.
3120 :     if ($count > 0) {
3121 :     $filterClause .= " LIMIT $count";
3122 :     }
3123 : parrello 1.10 # Create the query.
3124 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
3125 : parrello 1.10 # Set up a counter of the number of records read.
3126 :     my $fetched = 0;
3127 :     # Loop through the records returned, extracting the fields. Note that if the
3128 :     # counter is non-zero, we stop when the number of records read hits the count.
3129 :     my @retVal = ();
3130 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3131 :     my @rowData = $row->Values($fields);
3132 :     push @retVal, \@rowData;
3133 :     $fetched++;
3134 :     }
3135 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3136 : parrello 1.10 # Return the resulting list.
3137 :     return @retVal;
3138 : parrello 1.7 }
3139 :    
3140 : parrello 1.55 =head3 Exists
3141 :    
3142 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
3143 :    
3144 :     Return TRUE if an entity exists, else FALSE.
3145 :    
3146 :     =over 4
3147 :    
3148 :     =item entityName
3149 :    
3150 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3151 :    
3152 :     =item entityID
3153 :    
3154 :     ID of the entity instance whose existence is to be checked.
3155 :    
3156 :     =item RETURN
3157 :    
3158 :     Returns TRUE if the entity instance exists, else FALSE.
3159 :    
3160 :     =back
3161 :    
3162 :     =cut
3163 :     #: Return Type $;
3164 :     sub Exists {
3165 :     # Get the parameters.
3166 :     my ($self, $entityName, $entityID) = @_;
3167 :     # Check for the entity instance.
3168 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3169 :     my $testInstance = $self->GetEntity($entityName, $entityID);
3170 :     # Return an existence indicator.
3171 :     my $retVal = ($testInstance ? 1 : 0);
3172 :     return $retVal;
3173 :     }
3174 :    
3175 : parrello 1.18 =head3 EstimateRowSize
3176 :    
3177 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3178 :    
3179 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
3180 :     up the average length for each data type.
3181 :    
3182 :     =over 4
3183 :    
3184 :     =item relName
3185 :    
3186 :     Name of the relation whose estimated row size is desired.
3187 :    
3188 :     =item RETURN
3189 :    
3190 :     Returns an estimate of the row size for the specified relation.
3191 :    
3192 :     =back
3193 :    
3194 :     =cut
3195 :     #: Return Type $;
3196 :     sub EstimateRowSize {
3197 :     # Get the parameters.
3198 :     my ($self, $relName) = @_;
3199 :     # Declare the return variable.
3200 :     my $retVal = 0;
3201 :     # Find the relation descriptor.
3202 :     my $relation = $self->_FindRelation($relName);
3203 :     # Get the list of fields.
3204 :     for my $fieldData (@{$relation->{Fields}}) {
3205 :     # Get the field type and add its length.
3206 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3207 :     $retVal += $fieldLen;
3208 :     }
3209 :     # Return the result.
3210 :     return $retVal;
3211 :     }
3212 :    
3213 : parrello 1.38 =head3 GetFieldTable
3214 :    
3215 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3216 :    
3217 :     Get the field structure for a specified entity or relationship.
3218 :    
3219 :     =over 4
3220 :    
3221 :     =item objectName
3222 :    
3223 :     Name of the desired entity or relationship.
3224 :    
3225 :     =item RETURN
3226 :    
3227 :     The table containing the field descriptors for the specified object.
3228 :    
3229 :     =back
3230 :    
3231 :     =cut
3232 :    
3233 :     sub GetFieldTable {
3234 :     # Get the parameters.
3235 :     my ($self, $objectName) = @_;
3236 :     # Get the descriptor from the metadata.
3237 :     my $objectData = $self->_GetStructure($objectName);
3238 :     # Return the object's field table.
3239 :     return $objectData->{Fields};
3240 :     }
3241 :    
3242 : parrello 1.73 =head3 SplitKeywords
3243 :    
3244 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3245 :    
3246 :     This method returns a list of the positive keywords in the specified
3247 :     keyword string. All of the operators will have been stripped off,
3248 :     and if the keyword is preceded by a minus operator (C<->), it will
3249 :     not be in the list returned. The idea here is to get a list of the
3250 :     keywords the user wants to see. The list will be processed to remove
3251 :     duplicates.
3252 :    
3253 :     It is possible to create a string that confuses this method. For example
3254 :    
3255 :     frog toad -frog
3256 :    
3257 :     would return both C<frog> and C<toad>. If this is a problem we can deal
3258 :     with it later.
3259 :    
3260 :     =over 4
3261 :    
3262 :     =item keywordString
3263 :    
3264 :     The keyword string to be parsed.
3265 :    
3266 :     =item RETURN
3267 :    
3268 :     Returns a list of the words in the keyword string the user wants to
3269 :     see.
3270 :    
3271 :     =back
3272 :    
3273 :     =cut
3274 :    
3275 :     sub SplitKeywords {
3276 :     # Get the parameters.
3277 :     my ($keywordString) = @_;
3278 :     # Make a safety copy of the string. (This helps during debugging.)
3279 :     my $workString = $keywordString;
3280 :     # Convert operators we don't care about to spaces.
3281 :     $workString =~ tr/+"()<>/ /;
3282 :     # Split the rest of the string along space boundaries. Note that we
3283 :     # eliminate any words that are zero length or begin with a minus sign.
3284 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3285 :     # Use a hash to remove duplicates.
3286 :     my %words = map { $_ => 1 } @wordList;
3287 :     # Return the result.
3288 :     return sort keys %words;
3289 :     }
3290 :    
3291 :     =head3 ValidateFieldName
3292 :    
3293 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3294 :    
3295 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3296 :     be hyphenated words subject to certain restrictions.
3297 :    
3298 :     =over 4
3299 :    
3300 :     =item fieldName
3301 :    
3302 :     Field name to be validated.
3303 :    
3304 :     =item RETURN
3305 :    
3306 :     Returns TRUE if the field name is valid, else FALSE.
3307 :    
3308 :     =back
3309 :    
3310 :     =cut
3311 :    
3312 :     sub ValidateFieldName {
3313 :     # Get the parameters.
3314 :     my ($fieldName) = @_;
3315 :     # Declare the return variable. The field name is valid until we hear
3316 :     # differently.
3317 :     my $retVal = 1;
3318 : parrello 1.78 # Compute the maximum name length.
3319 :     my $maxLen = $TypeTable{'name-string'}->{maxLen};
3320 : parrello 1.73 # Look for bad stuff in the name.
3321 :     if ($fieldName =~ /--/) {
3322 :     # Here we have a doubled minus sign.
3323 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3324 :     $retVal = 0;
3325 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
3326 :     # Here the field name is missing the initial letter.
3327 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
3328 :     $retVal = 0;
3329 : parrello 1.78 } elsif (length($fieldName) > $maxLen) {
3330 :     # Here the field name is too long.
3331 :     Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3332 : parrello 1.73 } else {
3333 : parrello 1.75 # Strip out the minus signs. Everything remaining must be a letter,
3334 :     # underscore, or digit.
3335 : parrello 1.73 my $strippedName = $fieldName;
3336 :     $strippedName =~ s/-//g;
3337 : parrello 1.75 if ($strippedName !~ /^(\w|\d)+$/) {
3338 : parrello 1.73 Trace("Field name $fieldName contains illegal characters.") if T(1);
3339 :     $retVal = 0;
3340 :     }
3341 :     }
3342 :     # Return the result.
3343 :     return $retVal;
3344 :     }
3345 :    
3346 :     =head3 ReadMetaXML
3347 :    
3348 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3349 :    
3350 :     This method reads a raw database definition XML file and returns it.
3351 :     Normally, the metadata used by the ERDB system has been processed and
3352 :     modified to make it easier to load and retrieve the data; however,
3353 :     this method can be used to get the data in its raw form.
3354 :    
3355 :     =over 4
3356 :    
3357 :     =item fileName
3358 :    
3359 :     Name of the XML file to read.
3360 :    
3361 :     =item RETURN
3362 :    
3363 :     Returns a hash reference containing the raw XML data from the specified file.
3364 :    
3365 :     =back
3366 :    
3367 :     =cut
3368 :    
3369 :     sub ReadMetaXML {
3370 :     # Get the parameters.
3371 :     my ($fileName) = @_;
3372 :     # Read the XML.
3373 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3374 :     Trace("XML metadata loaded from file $fileName.") if T(1);
3375 :     # Return the result.
3376 :     return $retVal;
3377 :     }
3378 :    
3379 :     =head3 GetEntityFieldHash
3380 :    
3381 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3382 :    
3383 :     Get the field hash of the named entity in the specified raw XML structure.
3384 :     The field hash may not exist, in which case we need to create it.
3385 :    
3386 :     =over 4
3387 :    
3388 :     =item structure
3389 :    
3390 :     Raw XML structure defininng the database. This is not the run-time XML used by
3391 :     an ERDB object, since that has all sorts of optimizations built-in.
3392 :    
3393 :     =item entityName
3394 :    
3395 :     Name of the entity whose field structure is desired.
3396 :    
3397 :     =item RETURN
3398 :    
3399 :     Returns the field hash used to define the entity's fields.
3400 :    
3401 :     =back
3402 :    
3403 :     =cut
3404 :    
3405 :     sub GetEntityFieldHash {
3406 :     # Get the parameters.
3407 :     my ($structure, $entityName) = @_;
3408 :     # Get the entity structure.
3409 :     my $entityData = $structure->{Entities}->{$entityName};
3410 :     # Look for a field structure.
3411 :     my $retVal = $entityData->{Fields};
3412 :     # If it doesn't exist, create it.
3413 :     if (! defined($retVal)) {
3414 :     $entityData->{Fields} = {};
3415 :     $retVal = $entityData->{Fields};
3416 :     }
3417 :     # Return the result.
3418 :     return $retVal;
3419 :     }
3420 :    
3421 :     =head3 WriteMetaXML
3422 :    
3423 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
3424 :    
3425 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3426 :     used to update the database definition. It must be used with care, however, since it
3427 :     will only work on a raw structure, not on the processed structure created by an ERDB
3428 :     constructor.
3429 :    
3430 :     =over 4
3431 :    
3432 :     =item structure
3433 :    
3434 :     XML structure to be written to the file.
3435 :    
3436 :     =item fileName
3437 :    
3438 :     Name of the output file to which the updated XML should be stored.
3439 :    
3440 :     =back
3441 :    
3442 :     =cut
3443 :    
3444 :     sub WriteMetaXML {
3445 :     # Get the parameters.
3446 :     my ($structure, $fileName) = @_;
3447 :     # Compute the output.
3448 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3449 :     # Write it to the file.
3450 :     my $xmlOut = Open(undef, ">$fileName");
3451 :     print $xmlOut $fileString;
3452 :     }
3453 :    
3454 :    
3455 :     =head3 HTMLNote
3456 :    
3457 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3458 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3459 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
3460 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3461 :    
3462 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3463 :    
3464 :     =over 4
3465 :    
3466 :     =item dataString
3467 :    
3468 :     String to convert to HTML.
3469 :    
3470 :     =item RETURN
3471 :    
3472 :     An HTML string derived from the input string.
3473 :    
3474 :     =back
3475 :    
3476 :     =cut
3477 :    
3478 :     sub HTMLNote {
3479 :     # Get the parameter.
3480 :     my ($dataString) = @_;
3481 :     # HTML-escape the text.
3482 :     my $retVal = CGI::escapeHTML($dataString);
3483 :     # Substitute the bulletin board codes.
3484 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3485 :     $retVal =~ s!\[p\]!</p><p>!g;
3486 : parrello 1.83 $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3487 :     $retVal =~ s!\[/link\]!</a>!g;
3488 : parrello 1.73 # Return the result.
3489 :     return $retVal;
3490 :     }
3491 :    
3492 : parrello 1.87 =head3 BeginTran
3493 :    
3494 :     C<< $erdb->BeginTran(); >>
3495 :    
3496 :     Start a database transaction.
3497 :    
3498 :     =cut
3499 :    
3500 :     sub BeginTran {
3501 :     my ($self) = @_;
3502 :     $self->{_dbh}->begin_tran();
3503 :    
3504 :     }
3505 :    
3506 :     =head3 CommitTran
3507 :    
3508 :     C<< $erdb->CommitTran(); >>
3509 :    
3510 :     Commit an active database transaction.
3511 :    
3512 :     =cut
3513 :    
3514 :     sub CommitTran {
3515 :     my ($self) = @_;
3516 :     $self->{_dbh}->commit_tran();
3517 :     }
3518 :    
3519 :     =head3 RollbackTran
3520 :    
3521 :     C<< $erdb->RollbackTran(); >>
3522 :    
3523 :     Roll back an active database transaction.
3524 :    
3525 :     =cut
3526 :    
3527 :     sub RollbackTran {
3528 :     my ($self) = @_;
3529 :     $self->{_dbh}->roll_tran();
3530 :     }
3531 :    
3532 : parrello 1.73
3533 : parrello 1.48 =head2 Data Mining Methods
3534 :    
3535 : parrello 1.38 =head3 GetUsefulCrossValues
3536 :    
3537 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3538 :    
3539 :     Return a list of the useful attributes that would be returned by a B<Cross> call
3540 :     from an entity of the source entity type through the specified relationship. This
3541 :     means it will return the fields of the target entity type and the intersection data
3542 :     fields in the relationship. Only primary table fields are returned. In other words,
3543 :     the field names returned will be for fields where there is always one and only one
3544 :     value.
3545 :    
3546 :     =over 4
3547 :    
3548 :     =item sourceEntity
3549 :    
3550 :     Name of the entity from which the relationship crossing will start.
3551 :    
3552 :     =item relationship
3553 :    
3554 :     Name of the relationship being crossed.
3555 :    
3556 :     =item RETURN
3557 :    
3558 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3559 :    
3560 :     =back
3561 :    
3562 :     =cut
3563 :     #: Return Type @;
3564 :     sub GetUsefulCrossValues {
3565 :     # Get the parameters.
3566 :     my ($self, $sourceEntity, $relationship) = @_;
3567 :     # Declare the return variable.
3568 :     my @retVal = ();
3569 :     # Determine the target entity for the relationship. This is whichever entity is not
3570 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
3571 :     # the TO, and vice versa.
3572 :     my $relStructure = $self->_GetStructure($relationship);
3573 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3574 :     my $targetEntity = $relStructure->{$targetEntityType};
3575 :     # Get the field table for the entity.
3576 :     my $entityFields = $self->GetFieldTable($targetEntity);
3577 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
3578 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
3579 :     # must match the entity name.
3580 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3581 :     keys %{$entityFields};
3582 :     # Push the fields found onto the return variable.
3583 :     push @retVal, sort @fieldList;
3584 :     # Get the field table for the relationship.
3585 :     my $relationshipFields = $self->GetFieldTable($relationship);
3586 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3587 :     # This may end up being an empty set.
3588 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3589 :     keys %{$relationshipFields};
3590 :     # Push these onto the return list.
3591 :     push @retVal, sort @fieldList2;
3592 :     # Return the result.
3593 :     return @retVal;
3594 :     }
3595 :    
3596 : parrello 1.48 =head3 FindColumn
3597 :    
3598 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3599 :    
3600 :     Return the location a desired column in a data mining header line. The data
3601 :     mining header line is a tab-separated list of column names. The column
3602 :     identifier is either the numerical index of a column or the actual column
3603 :     name.
3604 :    
3605 :     =over 4
3606 :    
3607 :     =item headerLine
3608 :    
3609 :     The header line from a data mining command, which consists of a tab-separated
3610 :     list of column names.
3611 :    
3612 :     =item columnIdentifier
3613 :    
3614 :     Either the ordinal number of the desired column (1-based), or the name of the
3615 :     desired column.
3616 :    
3617 :     =item RETURN
3618 :    
3619 :     Returns the array index (0-based) of the desired column.
3620 :    
3621 :     =back
3622 :    
3623 :     =cut
3624 :    
3625 :     sub FindColumn {
3626 :     # Get the parameters.
3627 :     my ($headerLine, $columnIdentifier) = @_;
3628 :     # Declare the return variable.
3629 :     my $retVal;
3630 :     # Split the header line into column names.
3631 :     my @headers = ParseColumns($headerLine);
3632 :     # Determine whether we have a number or a name.
3633 :     if ($columnIdentifier =~ /^\d+$/) {
3634 :     # Here we have a number. Subtract 1 and validate the result.
3635 :     $retVal = $columnIdentifier - 1;
3636 :     if ($retVal < 0 || $retVal > $#headers) {
3637 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3638 :     }
3639 :     } else {
3640 :     # Here we have a name. We need to find it in the list.
3641 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3642 :     if ($headers[$i] eq $columnIdentifier) {
3643 :     $retVal = $i;
3644 :     }
3645 :     }
3646 :     if (! defined($retVal)) {
3647 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3648 :     }
3649 :     }
3650 :     # Return the result.
3651 :     return $retVal;
3652 :     }
3653 :    
3654 :     =head3 ParseColumns
3655 :    
3656 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
3657 : parrello 1.48
3658 :     Convert the specified data line to a list of columns.
3659 :    
3660 :     =over 4
3661 :    
3662 :     =item line
3663 :    
3664 :     A data mining input, consisting of a tab-separated list of columns terminated by a
3665 :     new-line.
3666 :    
3667 :     =item RETURN
3668 :    
3669 :     Returns a list consisting of the column values.
3670 :    
3671 :     =back
3672 :    
3673 :     =cut
3674 :    
3675 :     sub ParseColumns {
3676 :     # Get the parameters.
3677 : parrello 1.50 my ($line) = @_;
3678 : parrello 1.48 # Chop off the line-end.
3679 :     chomp $line;
3680 :     # Split it into a list.
3681 :     my @retVal = split(/\t/, $line);
3682 :     # Return the result.
3683 :     return @retVal;
3684 :     }
3685 :    
3686 : parrello 1.71 =head2 Virtual Methods
3687 :    
3688 : parrello 1.89 =head3 _CreatePPOIndex
3689 :    
3690 :     C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3691 :    
3692 :     Convert the XML for an ERDB index to the XML structure for a PPO
3693 :     index.
3694 :    
3695 :     =over 4
3696 :    
3697 :     ERDB XML structure for an index.
3698 :    
3699 :     =item RETURN
3700 :    
3701 :     PPO XML structure for the same index.
3702 :    
3703 :     =back
3704 :    
3705 :     =cut
3706 :    
3707 :     sub _CreatePPOIndex {
3708 :     # Get the parameters.
3709 :     my ($indexObject) = @_;
3710 :     # The incoming index contains a list of the index fields in the IndexFields
3711 :     # member. We loop through it to create the index tags.
3712 :     my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3713 :     # Wrap the fields in attribute tags.
3714 :     my $retVal = { attribute => \@fields };
3715 :     # Return the result.
3716 :     return $retVal;
3717 :     }
3718 :    
3719 :     =head3 _CreatePPOField
3720 :    
3721 :     C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3722 :    
3723 :     Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3724 :    
3725 :     =over 4
3726 :    
3727 :     =item fieldName
3728 :    
3729 :     Name of the scalar field.
3730 :    
3731 :     =item fieldObject
3732 :    
3733 :     ERDB XML structure describing the field.
3734 :    
3735 :     =item RETURN
3736 :    
3737 :     Returns a PPO XML structure for the same field.
3738 :    
3739 :     =back
3740 :    
3741 :     =cut
3742 :    
3743 :     sub _CreatePPOField {
3744 :     # Get the parameters.
3745 :     my ($fieldName, $fieldObject) = @_;
3746 :     # Get the field type.
3747 :     my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3748 :     # Fix up the field name.
3749 :     $fieldName = _FixName($fieldName);
3750 :     # Build the scalar tag.
3751 :     my $retVal = { label => $fieldName, type => $type };
3752 :     # Return the result.
3753 :     return $retVal;
3754 :     }
3755 :    
3756 : parrello 1.71 =head3 CleanKeywords
3757 :    
3758 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3759 :    
3760 :     Clean up a search expression or keyword list. This is a virtual method that may
3761 :     be overridden by the subclass. The base-class method removes extra spaces
3762 :     and converts everything to lower case.
3763 :    
3764 :     =over 4
3765 :    
3766 :     =item searchExpression
3767 :    
3768 :     Search expression or keyword list to clean. Note that a search expression may
3769 :     contain boolean operators which need to be preserved. This includes leading
3770 :     minus signs.
3771 :    
3772 :     =item RETURN
3773 :    
3774 :     Cleaned expression or keyword list.
3775 :    
3776 :     =back
3777 :    
3778 :     =cut
3779 :    
3780 :     sub CleanKeywords {
3781 :     # Get the parameters.
3782 :     my ($self, $searchExpression) = @_;
3783 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
3784 :     # don't accidentally end up with an undefined value.
3785 :     my $retVal = lc($searchExpression || "");
3786 :     # Remove extra spaces.
3787 :     $retVal =~ s/\s+/ /g;
3788 :     $retVal =~ s/(^\s+)|(\s+$)//g;
3789 :     # Return the result.
3790 :     return $retVal;
3791 :     }
3792 :    
3793 : parrello 1.73 =head3 GetSourceObject
3794 :    
3795 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
3796 :    
3797 :     Return the object to be used in loading special attributes of the specified entity. The
3798 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
3799 :     XML
3800 :    
3801 : parrello 1.1 =head2 Internal Utility Methods
3802 :    
3803 : parrello 1.70 =head3 _RelationMap
3804 :    
3805 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3806 :    
3807 : parrello 1.88 Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3808 : parrello 1.70 to determine how to interpret the results of the query.
3809 :    
3810 :     =over 4
3811 :    
3812 :     =item mappedNameHashRef
3813 :    
3814 :     Reference to a hash that maps modified object names to real object names.
3815 :    
3816 :     =item mappedNameListRef
3817 :    
3818 :     Reference to a list of modified object names in the order they appear in the
3819 :     SELECT list.
3820 :    
3821 :     =item RETURN
3822 :    
3823 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3824 : parrello 1.88 query followed by the actual name of that object. This enables the B<ERDBObject> to
3825 : parrello 1.70 determine the order of the tables in the query and which object name belongs to each
3826 :     mapped object name. Most of the time these two values are the same; however, if a
3827 :     relation occurs twice in the query, the relation name in the field list and WHERE
3828 :     clause will use a mapped name (generally the actual relation name with a numeric
3829 :     suffix) that does not match the actual relation name.
3830 :    
3831 :     =back
3832 :    
3833 :     =cut
3834 :    
3835 :     sub _RelationMap {
3836 :     # Get the parameters.
3837 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3838 :     # Declare the return variable.
3839 :     my @retVal = ();
3840 :     # Build the map.
3841 :     for my $mappedName (@{$mappedNameListRef}) {
3842 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3843 :     }
3844 :     # Return it.
3845 :     return @retVal;
3846 :     }
3847 :    
3848 :    
3849 :     =head3 _SetupSQL
3850 : parrello 1.45
3851 :     Process a list of object names and a filter clause so that they can be used to
3852 :     build an SQL statement. This method takes in a reference to a list of object names
3853 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3854 :     names and the mapped name hash.
3855 :    
3856 :     This is an instance method.
3857 :    
3858 :     =over 4
3859 :    
3860 :     =item objectNames
3861 :    
3862 :     Reference to a list of the object names to be included in the query.
3863 :    
3864 :     =item filterClause
3865 :    
3866 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
3867 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
3868 :    
3869 : parrello 1.70 =item matchClause
3870 :    
3871 :     An optional full-text search clause. If specified, it will be inserted at the
3872 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
3873 :     field names should be in the form I<table>C<.>I<fieldName>.
3874 :    
3875 : parrello 1.45 =item RETURN
3876 :    
3877 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
3878 :     with the FROM clause. The second element is a reference to a list of the names to be
3879 :     used in retrieving the fields. The third element is a hash mapping the names to the
3880 :     objects they represent.
3881 :    
3882 :     =back
3883 :    
3884 :     =cut
3885 :    
3886 :     sub _SetupSQL {
3887 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
3888 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
3889 :     # same object. We start with a hash table keyed on object name that will
3890 :     # return the object suffix. The first time an object is encountered it will
3891 :     # not be found in the hash. The next time the hash will map the object name
3892 :     # to 2, then 3, and so forth.
3893 :     my %objectHash = ();
3894 :     # This list will contain the object names as they are to appear in the
3895 :     # FROM list.
3896 :     my @fromList = ();
3897 :     # This list contains the suffixed object name for each object. It is exactly
3898 :     # parallel to the list in the $objectNames parameter.
3899 :     my @mappedNameList = ();
3900 :     # Finally, this hash translates from a mapped name to its original object name.
3901 :     my %mappedNameHash = ();
3902 :     # Now we create the lists. Note that for every single name we push something into
3903 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
3904 :     # parallel to $objectNames.
3905 :     for my $objectName (@{$objectNames}) {
3906 :     # Get the next suffix for this object.
3907 :     my $suffix = $objectHash{$objectName};
3908 :     if (! $suffix) {
3909 :     # Here we are seeing the object for the first time. The object name
3910 :     # is used as is.
3911 :     push @mappedNameList, $objectName;
3912 :     push @fromList, $objectName;
3913 :     $mappedNameHash{$objectName} = $objectName;
3914 :     # Denote the next suffix will be 2.
3915 :     $objectHash{$objectName} = 2;
3916 :     } else {
3917 :     # Here we've seen the object before. We construct a new name using
3918 :     # the suffix from the hash and update the hash.
3919 :     my $mappedName = "$objectName$suffix";
3920 :     $objectHash{$objectName} = $suffix + 1;
3921 :     # The FROM list has the object name followed by the mapped name. This
3922 :     # tells SQL it's still the same table, but we're using a different name
3923 :     # for it to avoid confusion.
3924 :     push @fromList, "$objectName $mappedName";
3925 :     # The mapped-name list contains the real mapped name.
3926 :     push @mappedNameList, $mappedName;
3927 :     # Finally, enable us to get back from the mapped name to the object name.
3928 :     $mappedNameHash{$mappedName} = $objectName;
3929 :     }
3930 :     }
3931 :     # Begin the SELECT suffix. It starts with
3932 :     #
3933 :     # FROM name1, name2, ... nameN
3934 :     #
3935 :     my $suffix = "FROM " . join(', ', @fromList);
3936 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
3937 :     my $filterString = "";
3938 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
3939 :     # entities and relationships as well as primary relations to secondary ones.
3940 :     my @joinWhere = ();
3941 : parrello 1.45 # Check for a filter clause.
3942 :     if ($filterClause) {
3943 :     # Here we have one, so we convert its field names and add it to the query. First,
3944 :     # We create a copy of the filter string we can work with.
3945 : parrello 1.70 $filterString = $filterClause;
3946 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
3947 :     # object names inside other object names when we're doing our search and replace.
3948 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3949 :     # The final preparatory step is to create a hash table of relation names. The
3950 :     # table begins with the relation names already in the SELECT command. We may
3951 :     # need to add relations later if there is filtering on a field in a secondary
3952 :     # relation. The secondary relations are the ones that contain multiply-
3953 :     # occurring or optional fields.
3954 :     my %fromNames = map { $_ => 1 } @sortedNames;
3955 :     # We are ready to begin. We loop through the object names, replacing each
3956 :     # object name's field references by the corresponding SQL field reference.
3957 :     # Along the way, if we find a secondary relation, we will need to add it
3958 :     # to the FROM clause.
3959 :     for my $mappedName (@sortedNames) {
3960 :     # Get the length of the object name plus 2. This is the value we add to the
3961 :     # size of the field name to determine the size of the field reference as a
3962 :     # whole.
3963 :     my $nameLength = 2 + length $mappedName;
3964 :     # Get the real object name for this mapped name.
3965 :     my $objectName = $mappedNameHash{$mappedName};
3966 :     Trace("Processing $mappedName for object $objectName.") if T(4);
3967 :     # Get the object's field list.
3968 :     my $fieldList = $self->GetFieldTable($objectName);
3969 :     # Find the field references for this object.
3970 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3971 :     # At this point, $1 contains the field name, and the current position
3972 :     # is set immediately after the final parenthesis. We pull out the name of
3973 :     # the field and the position and length of the field reference as a whole.
3974 :     my $fieldName = $1;
3975 :     my $len = $nameLength + length $fieldName;
3976 :     my $pos = pos($filterString) - $len;
3977 :     # Insure the field exists.
3978 :     if (!exists $fieldList->{$fieldName}) {
3979 :     Confess("Field $fieldName not found for object $objectName.");
3980 :     } else {
3981 :     Trace("Processing $fieldName at position $pos.") if T(4);
3982 :     # Get the field's relation.
3983 :     my $relationName = $fieldList->{$fieldName}->{relation};
3984 :     # Now we have a secondary relation. We need to insure it matches the
3985 :     # mapped name of the primary relation. First we peel off the suffix
3986 :     # from the mapped name.
3987 :     my $mappingSuffix = substr $mappedName, length($objectName);
3988 :     # Put the mapping suffix onto the relation name to get the
3989 :     # mapped relation name.
3990 :     my $mappedRelationName = "$relationName$mappingSuffix";
3991 :     # Insure the relation is in the FROM clause.
3992 :     if (!exists $fromNames{$mappedRelationName}) {
3993 :     # Add the relation to the FROM clause.
3994 :     if ($mappedRelationName eq $relationName) {
3995 :     # The name is un-mapped, so we add it without
3996 :     # any frills.
3997 :     $suffix .= ", $relationName";
3998 :     push @joinWhere, "$objectName.id = $relationName.id";
3999 :     } else {
4000 :     # Here we have a mapping situation.
4001 :     $suffix .= ", $relationName $mappedRelationName";
4002 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
4003 :     }
4004 :     # Denote we have this relation available for future fields.
4005 :     $fromNames{$mappedRelationName} = 1;
4006 :     }
4007 :     # Form an SQL field reference from the relation name and the field name.
4008 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
4009 :     # Put it into the filter string in place of the old value.
4010 :     substr($filterString, $pos, $len) = $sqlReference;
4011 :     # Reposition the search.
4012 :     pos $filterString = $pos + length $sqlReference;
4013 :     }
4014 :     }
4015 :     }
4016 : parrello 1.70 }
4017 :     # The next step is to join the objects together. We only need to do this if there
4018 :     # is more than one object in the object list. We start with the first object and
4019 :     # run through the objects after it. Note also that we make a safety copy of the
4020 :     # list before running through it, because we shift off the first object before
4021 :     # processing the rest.
4022 :     my @mappedObjectList = @mappedNameList;
4023 :     my $lastMappedObject = shift @mappedObjectList;
4024 :     # Get the join table.
4025 :     my $joinTable = $self->{_metaData}->{Joins};
4026 :     # Loop through the object list.
4027 :     for my $thisMappedObject (@mappedObjectList) {
4028 :     # Look for a join using the real object names.
4029 :     my $lastObject = $mappedNameHash{$lastMappedObject};
4030 :     my $thisObject = $mappedNameHash{$thisMappedObject};
4031 :     my $joinKey = "$lastObject/$thisObject";
4032 :     if (!exists $joinTable->{$joinKey}) {
4033 :     # Here there's no join, so we throw an error.
4034 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
4035 :     } else {
4036 :     # Get the join clause.
4037 :     my $unMappedJoin = $joinTable->{$joinKey};
4038 :     # Fix the names.
4039 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
4040 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
4041 :     push @joinWhere, $unMappedJoin;
4042 :     # Save this object as the last object for the next iteration.
4043 :     $lastMappedObject = $thisMappedObject;
4044 :     }
4045 :     }
4046 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
4047 :     # here is we want the filter clause to be empty if there's no WHERE filter.
4048 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
4049 :     my $orderClause = "";
4050 :     # This is only necessary if we have a filter string in which the ORDER BY
4051 :     # and LIMIT clauses can live.
4052 :     if ($filterString) {
4053 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
4054 :     # operator so that we find the first occurrence of either verb.
4055 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
4056 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
4057 :     my $pos = pos $filterString;
4058 :     $orderClause = $2 . substr($filterString, $pos);
4059 :     $filterString = $1;
4060 :     }
4061 : parrello 1.70 }
4062 :     # All the things that are supposed to be in the WHERE clause of the
4063 :     # SELECT command need to be put into @joinWhere so we can string them
4064 :     # together. We begin with the match clause. This is important,
4065 :     # because the match clause's parameter mark must precede any parameter
4066 :     # marks in the filter string.
4067 :     if ($matchClause) {
4068 :     push @joinWhere, $matchClause;
4069 :     }
4070 :     # Add the filter string. We put it in parentheses to avoid operator
4071 :     # precedence problems with the match clause or the joins.
4072 :     if ($filterString) {
4073 :     Trace("Filter string is \"$filterString\".") if T(4);
4074 :     push @joinWhere, "($filterString)";
4075 :     }
4076 :     # String it all together into a big filter clause.
4077 :     if (@joinWhere) {
4078 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
4079 :     }
4080 :     # Add the sort or limit clause (if any).
4081 :     if ($orderClause) {
4082 :     $suffix .= " $orderClause";
4083 : parrello 1.45 }
4084 :     # Return the suffix, the mapped name list, and the mapped name hash.
4085 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
4086 :     }
4087 :    
4088 : parrello 1.70 =head3 _GetStatementHandle
4089 : parrello 1.45
4090 :     This method will prepare and execute an SQL query, returning the statement handle.
4091 :     The main reason for doing this here is so that everybody who does SQL queries gets
4092 :     the benefit of tracing.
4093 :    
4094 :     This is an instance method.
4095 :    
4096 :     =over 4
4097 :    
4098 :     =item command
4099 :    
4100 :     Command to prepare and execute.
4101 :    
4102 :     =item params
4103 :    
4104 :     Reference to a list of the values to be substituted in for the parameter marks.
4105 :    
4106 :     =item RETURN
4107 :    
4108 :     Returns a prepared and executed statement handle from which the caller can extract
4109 :     results.
4110 :    
4111 :     =back
4112 :    
4113 :     =cut
4114 :    
4115 :     sub _GetStatementHandle {
4116 :     # Get the parameters.
4117 :     my ($self, $command, $params) = @_;
4118 :     # Trace the query.
4119 :     Trace("SQL query: $command") if T(SQL => 3);
4120 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
4121 :     # Get the database handle.
4122 :     my $dbh = $self->{_dbh};
4123 :     # Prepare the command.
4124 :     my $sth = $dbh->prepare_command($command);
4125 :     # Execute it with the parameters bound in.
4126 : parrello 1.75 $sth->execute(@{$params}) || Confess("SELECT error: " . $sth->errstr());
4127 : parrello 1.45 # Return the statement handle.
4128 :     return $sth;
4129 :     }
4130 :    
4131 : parrello 1.70 =head3 _GetLoadStats
4132 : parrello 1.1
4133 :     Return a blank statistics object for use by the load methods.
4134 :    
4135 :     This is a static method.
4136 :    
4137 :     =cut
4138 :    
4139 : parrello 1.29 sub _GetLoadStats{
4140 : parrello 1.28 return Stats->new();
4141 : parrello 1.1 }
4142 :    
4143 : parrello 1.70 =head3 _DumpRelation
4144 : parrello 1.1
4145 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
4146 : parrello 1.1
4147 :     This is an instance method.
4148 :    
4149 :     =over 4
4150 :    
4151 :     =item outputDirectory
4152 :    
4153 :     Directory to contain the output file.
4154 :    
4155 :     =item relationName
4156 :    
4157 :     Name of the relation to dump.
4158 :    
4159 :     =item relation
4160 :    
4161 :     Structure describing the relation to be dumped.
4162 :    
4163 :     =back
4164 :    
4165 :     =cut
4166 :    
4167 :     sub _DumpRelation {
4168 : parrello 1.10 # Get the parameters.
4169 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
4170 :     # Open the output file.
4171 :     my $fileName = "$outputDirectory/$relationName.dtx";
4172 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
4173 :     # Create a query for the specified relation.
4174 :     my $dbh = $self->{_dbh};
4175 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
4176 :     # Execute the query.
4177 :     $query->execute() || Confess("SELECT error dumping $relationName.");
4178 :     # Loop through the results.
4179 :     while (my @row = $query->fetchrow) {
4180 :     # Escape any tabs or new-lines in the row text.
4181 :     for my $field (@row) {
4182 :     $field =~ s/\n/\\n/g;
4183 :     $field =~ s/\t/\\t/g;
4184 :     }
4185 :     # Tab-join the row and write it to the output file.
4186 :     my $rowText = join("\t", @row);
4187 :     print DTXOUT "$rowText\n";
4188 :     }
4189 :     # Close the output file.
4190 :     close DTXOUT;
4191 : parrello 1.1 }
4192 :    
4193 : parrello 1.70 =head3 _GetStructure
4194 : parrello 1.1
4195 :     Get the data structure for a specified entity or relationship.
4196 :    
4197 :     This is an instance method.
4198 :    
4199 :     =over 4
4200 :    
4201 :     =item objectName
4202 :    
4203 :     Name of the desired entity or relationship.
4204 :    
4205 :     =item RETURN
4206 :    
4207 :     The descriptor for the specified object.
4208 :    
4209 :     =back
4210 :    
4211 :     =cut
4212 :    
4213 :     sub _GetStructure {
4214 : parrello 1.10 # Get the parameters.
4215 :     my ($self, $objectName) = @_;
4216 :     # Get the metadata structure.
4217 :     my $metadata = $self->{_metaData};
4218 :     # Declare the variable to receive the descriptor.
4219 :     my $retVal;
4220 :     # Get the descriptor from the metadata.
4221 :     if (exists $metadata->{Entities}->{$objectName}) {
4222 :     $retVal = $metadata->{Entities}->{$objectName};
4223 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
4224 :     $retVal = $metadata->{Relationships}->{$objectName};
4225 :     } else {
4226 :     Confess("Object $objectName not found in database.");
4227 :     }
4228 :     # Return the descriptor.
4229 :     return $retVal;
4230 : parrello 1.1 }
4231 :    
4232 : parrello 1.70
4233 :    
4234 :     =head3 _GetRelationTable
4235 : parrello 1.1
4236 :     Get the list of relations for a specified entity or relationship.
4237 :    
4238 :     This is an instance method.
4239 :    
4240 :     =over 4
4241 :    
4242 :     =item objectName
4243 :    
4244 :     Name of the desired entity or relationship.
4245 :    
4246 :     =item RETURN
4247 :    
4248 :     A table containing the relations for the specified object.
4249 :    
4250 :     =back
4251 :    
4252 :     =cut
4253 :    
4254 :     sub _GetRelationTable {
4255 : parrello 1.10 # Get the parameters.
4256 :     my ($self, $objectName) = @_;
4257 :     # Get the descriptor from the metadata.
4258 :     my $objectData = $self->_GetStructure($objectName);
4259 :     # Return the object's relation list.
4260 :     return $objectData->{Relations};
4261 : parrello 1.1 }
4262 :    
4263 : parrello 1.70 =head3 _ValidateFieldNames
4264 : parrello 1.1
4265 :     Determine whether or not the field names are valid. A description of the problems with the names
4266 :     will be written to the standard error output. If there is an error, this method will abort. This is
4267 :     a static method.
4268 :    
4269 :     =over 4
4270 :    
4271 :     =item metadata
4272 :    
4273 :     Metadata structure loaded from the XML data definition.
4274 :    
4275 :     =back
4276 :    
4277 :     =cut
4278 :    
4279 :     sub _ValidateFieldNames {
4280 : parrello 1.10 # Get the object.
4281 :     my ($metadata) = @_;
4282 :     # Declare the return value. We assume success.
4283 :     my $retVal = 1;
4284 :     # Loop through the sections of the database definition.
4285 :     for my $section ('Entities', 'Relationships') {
4286 :     # Loop through the objects in this section.
4287 :     for my $object (values %{$metadata->{$section}}) {
4288 :     # Loop through the object's fields.
4289 :     for my $fieldName (keys %{$object->{Fields}}) {
4290 : parrello 1.73 # If this field name is invalid, set the return value to zero
4291 :     # so we know we encountered an error.
4292 :     if (! ValidateFieldName($fieldName)) {
4293 : parrello 1.10 $retVal = 0;
4294 :     }
4295 :     }
4296 :     }
4297 :     }
4298 :     # If an error was found, fail.
4299 :     if ($retVal == 0) {
4300 :     Confess("Errors found in field names.");
4301 :     }
4302 : parrello 1.1 }
4303 :    
4304 : parrello 1.70 =head3 _LoadRelation
4305 : parrello 1.1
4306 :     Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
4307 :     file with the same name as the relation exists in the specified directory.
4308 :    
4309 :     This is an instance method.
4310 :    
4311 :     =over 4
4312 :    
4313 :     =item dbh
4314 :    
4315 :     DBKernel object for accessing the database.
4316 :    
4317 :     =item directoryName
4318 :    
4319 :     Name of the directory containing the tab-delimited data files.
4320 :    
4321 :     =item relationName
4322 :    
4323 :     Name of the relation to load.
4324 :    
4325 :     =item rebuild
4326 :    
4327 :     TRUE if the table should be dropped and re-created before loading.
4328 :    
4329 :     =item RETURN
4330 :    
4331 :     Returns a statistical object describing the number of records read and a list of error messages.
4332 :    
4333 :     =back
4334 :    
4335 :     =cut
4336 :    
4337 :     sub _LoadRelation {
4338 : parrello 1.10 # Get the parameters.
4339 :     my ($self, $directoryName, $relationName, $rebuild) = @_;
4340 :     # Create the file name.
4341 :     my $fileName = "$directoryName/$relationName";
4342 :