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1 : parrello 1.1 package ERDB;
2 :    
3 : parrello 1.10 use strict;
4 :     use Tracer;
5 : olson 1.14 use DBrtns;
6 : parrello 1.10 use Data::Dumper;
7 :     use XML::Simple;
8 :     use DBQuery;
9 :     use DBObject;
10 :     use Stats;
11 :     use Time::HiRes qw(gettimeofday);
12 : parrello 1.42 use Digest::MD5 qw(md5_base64);
13 : parrello 1.19 use FIG;
14 : parrello 1.73 use CGI;
15 : parrello 1.1
16 :     =head1 Entity-Relationship Database Package
17 :    
18 :     =head2 Introduction
19 :    
20 :     The Entity-Relationship Database Package allows the client to create an easily-configurable
21 :     database of Entities connected by Relationships. Each entity is represented by one or more
22 :     relations in an underlying SQL database. Each relationship is represented by a single
23 :     relation that connects two entities.
24 :    
25 :     Although this package is designed for general use, all examples are derived from the
26 :     Sprout database, which is the first database implemented using this package.
27 :    
28 :     Each entity has at least one relation, the I<primary relation>, that has the same name as
29 :     the entity. The primary relation contains a field named C<id> that contains the unique
30 :     identifier of each entity instance. An entity may have additional relations that contain
31 :     fields which are optional or can occur more than once. For example, the B<FEATURE> entity
32 :     has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
33 :     is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
34 :     however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
35 :     relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36 :     The B<FEATURE> entity also contains an optional virulence number. This is implemented
37 :     as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38 : parrello 1.8 (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39 :     the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40 :     number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41 :     C<FeatureVirulence>.
42 : parrello 1.1
43 :     Entities are connected by binary relationships implemented using single relations possessing the
44 :     same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
45 :     or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
46 :     ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
47 :     of the relationship is generally a verb phrase with the source entity as the subject and the
48 :     target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
49 :     and B<SOURCE> entities, and indicates that a particular source organization participated in the
50 :     mapping of the genome. A source organization frequently participates in the mapping
51 :     of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
52 :     this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
53 :     relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
54 :     and C<to-link>, which contains a source ID.
55 :    
56 :     A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
57 :     are implemented as additional fields in the relationship's relation. So, for example, the
58 :     B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
59 :     to determine which sequences make up a contig. The relationship has as an attribute the
60 :     B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61 :     is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62 :    
63 : parrello 1.73 The database itself is described by an XML file. In addition to all the data required to define
64 :     the entities, relationships, and attributes, the schema provides space for notes describing
65 :     the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66 :     for the database.
67 :    
68 :     Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69 :     in which case it will be used to generate a text search index in which the user searches for words
70 :     in the field instead of a particular field value.
71 : parrello 1.1
72 :     Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73 :     is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74 :     was inserted by the L</InsertObject> method.
75 :    
76 : parrello 1.8 =head2 XML Database Description
77 :    
78 :     =head3 Data Types
79 :    
80 :     The ERDB system supports the following data types. Note that there are numerous string
81 :     types depending on the maximum length. Some database packages limit the total number of
82 :     characters you have in an index key; to insure the database works in all environments,
83 :     the type of string should be the shortest one possible that supports all the known values.
84 :    
85 :     =over 4
86 :    
87 :     =item char
88 :    
89 :     single ASCII character
90 :    
91 :     =item int
92 :    
93 :     32-bit signed integer
94 :    
95 : parrello 1.60 =item counter
96 :    
97 :     32-bit unsigned integer
98 :    
99 : parrello 1.8 =item date
100 :    
101 :     64-bit unsigned integer, representing a PERL date/time value
102 :    
103 :     =item text
104 :    
105 :     long string; Text fields cannot be used in indexes or sorting and do not support the
106 :     normal syntax of filter clauses, but can be up to a billion character in length
107 :    
108 :     =item float
109 :    
110 :     double-precision floating-point number
111 :    
112 :     =item boolean
113 :    
114 :     single-bit numeric value; The value is stored as a 16-bit signed integer (for
115 :     compatability with certain database packages), but the only values supported are
116 :     0 and 1.
117 :    
118 : parrello 1.44 =item id-string
119 :    
120 :     variable-length string, maximum 25 characters
121 :    
122 : parrello 1.8 =item key-string
123 :    
124 :     variable-length string, maximum 40 characters
125 :    
126 :     =item name-string
127 :    
128 :     variable-length string, maximum 80 characters
129 :    
130 :     =item medium-string
131 :    
132 :     variable-length string, maximum 160 characters
133 :    
134 :     =item string
135 :    
136 :     variable-length string, maximum 255 characters
137 :    
138 : parrello 1.42 =item hash-string
139 :    
140 :     variable-length string, maximum 22 characters
141 :    
142 : parrello 1.8 =back
143 :    
144 : parrello 1.42 The hash-string data type has a special meaning. The actual key passed into the loader will
145 :     be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146 :     MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147 :     digest. Therefore, it is presumed the keys will be unique. When the database is actually
148 :     in use, the hashed keys will be presented rather than the original values. For this reason,
149 :     they should not be used for entities where the key is meaningful.
150 :    
151 : parrello 1.8 =head3 Global Tags
152 :    
153 :     The entire database definition must be inside a B<Database> tag. The display name of
154 :     the database is given by the text associated with the B<Title> tag. The display name
155 :     is only used in the automated documentation. It has no other effect. The entities and
156 :     relationships are listed inside the B<Entities> and B<Relationships> tags,
157 :     respectively. None of these tags have attributes.
158 :    
159 : parrello 1.10 <Database>
160 :     <Title>... display title here...</Title>
161 :     <Entities>
162 :     ... entity definitions here ...
163 :     </Entities>
164 :     <Relationships>
165 :     ... relationship definitions here...
166 :     </Relationships>
167 :     </Database>
168 : parrello 1.8
169 :     Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170 :     The text inside the B<Notes> tag contains comments that will appear when the database
171 :     documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172 :     italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173 :    
174 :     =head3 Fields
175 :    
176 :     Both entities and relationships have fields described by B<Field> tags. A B<Field>
177 :     tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178 :     object mus be inside B<Fields> tags.
179 :    
180 : parrello 1.10 <Entity ... >
181 :     <Fields>
182 :     ... Field tags ...
183 :     </Fields>
184 :     </Entity>
185 : parrello 1.8
186 :     The attributes for the B<Field> tag are as follows.
187 :    
188 :     =over 4
189 :    
190 :     =item name
191 :    
192 :     Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193 :     and the first character should be a letter. Most underlying databases are case-insensitive
194 : parrello 1.70 with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195 :     the name C<search-relevance> has special meaning for full-text searches and should not be
196 :     used as a field name.
197 : parrello 1.8
198 :     =item type
199 :    
200 :     Data type of the field. The legal data types are given above.
201 :    
202 :     =item relation
203 :    
204 :     Name of the relation containing the field. This should only be specified for entity
205 :     fields. The ERDB system does not support optional fields or multi-occurring fields
206 :     in the primary relation of an entity. Instead, they are put into secondary relations.
207 :     So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208 :     grouping used to select a subset of the genomes. A given genome may not be in any
209 :     groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210 :     value. The relation name specified must be a valid table name. By convention, it is
211 :     usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212 :     entity, the fields without a relation attribute are said to belong to the
213 :     I<primary relation>. This relation has the same name as the entity itself.
214 :    
215 : parrello 1.70 =item searchable
216 :    
217 :     If specified, then the field is a candidate for full-text searching. A single full-text
218 :     index will be created for each relation with at least one searchable field in it.
219 :     For best results, this option should only be used for string or text fields.
220 :    
221 : parrello 1.73 =item special
222 :    
223 :     This attribute allows the subclass to assign special meaning for certain fields.
224 :     The interpretation is up to the subclass itself. Currently, only entity fields
225 :     can have this attribute.
226 :    
227 : parrello 1.8 =back
228 :    
229 :     =head3 Indexes
230 :    
231 :     An entity can have multiple alternate indexes associated with it. The fields must
232 : parrello 1.74 all be from the same relation. The alternate indexes assist in ordering results
233 : parrello 1.8 from a query. A relationship can have up to two indexes-- a I<to-index> and a
234 :     I<from-index>. These order the results when crossing the relationship. For
235 :     example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236 :     from-index would order the contigs of a ganome, and the to-index would order
237 :     the genomes of a contig. A relationship's index must specify only fields in
238 :     the relationship.
239 :    
240 :     The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
241 :     of a relationship is specified using the B<FromIndex> tag; the to-index is specified
242 :     using the B<ToIndex> tag.
243 :    
244 :     Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245 :     tag containing the B<IndexField> tags. These specify, in order, the fields used in
246 :     the index. The attributes of an B<IndexField> tag are as follows.
247 :    
248 :     =over 4
249 :    
250 :     =item name
251 :    
252 :     Name of the field.
253 :    
254 :     =item order
255 :    
256 :     Sort order of the field-- C<ascending> or C<descending>.
257 :    
258 :     =back
259 :    
260 :     The B<Index>, B<FromIndex>, and B<ToIndex> tags themselves have no attributes.
261 :    
262 :     =head3 Object and Field Names
263 :    
264 :     By convention entity and relationship names use capital casing (e.g. C<Genome> or
265 :     C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
266 :     with respect to relation names, converting them internally to all-upper case or
267 :     all-lower case.
268 :    
269 :     If syntax or parsing errors occur when you try to load or use an ERDB database, the
270 :     most likely reason is that one of your objects has an SQL reserved word as its name.
271 :     The list of SQL reserved words keeps increasing; however, most are unlikely to show
272 :     up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
273 :     C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
274 :     C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
275 :    
276 :     Every entity has a field called C<id> that acts as its primary key. Every relationship
277 :     has fields called C<from-link> and C<to-link> that contain copies of the relevant
278 :     entity IDs. These are essentially ERDB's reserved words, and should not be used
279 :     for user-defined field names.
280 :    
281 :     =head3 Entities
282 :    
283 :     An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
284 :     B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
285 :     containing one or more fields. The attributes of the B<Entity> tag are as follows.
286 :    
287 :     =over 4
288 :    
289 :     =item name
290 :    
291 :     Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
292 :     or C<GroupBlock>) and should be a noun or noun phrase.
293 :    
294 :     =item keyType
295 :    
296 :     Data type of the primary key. The primary key is always named C<id>.
297 :    
298 :     =back
299 :    
300 :     =head3 Relationships
301 :    
302 :     A relationship is described by the C<Relationship> tag. Within a relationship,
303 :     there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
304 :     fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
305 :     the to-index.
306 :    
307 :     The C<Relationship> tag has the following attributes.
308 :    
309 :     =over 4
310 :    
311 :     =item name
312 :    
313 :     Name of the relationship. The relationship name, by convention, uses capital casing
314 :     (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
315 :     phrase, designed to fit between the from-entity and the to-entity (e.g.
316 :     Block C<ContainsRegionIn> Genome).
317 :    
318 :     =item from
319 :    
320 :     Name of the entity from which the relationship starts.
321 :    
322 :     =item to
323 :    
324 :     Name of the entity to which the relationship proceeds.
325 :    
326 :     =item arity
327 :    
328 :     Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
329 :    
330 :     =back
331 :    
332 : parrello 1.1 =cut
333 :    
334 :     # GLOBALS
335 :    
336 :     # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
337 :     # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
338 : parrello 1.73 # of the specified type. "avgLen" is the average byte length for estimating
339 : parrello 1.75 # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
340 :     # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
341 :     # index
342 : parrello 1.73 my %TypeTable = ( char => { sqlType => 'CHAR(1)', maxLen => 1, avgLen => 1, sort => "",
343 : parrello 1.75 indexMod => 0, notes => "single ASCII character"},
344 : parrello 1.73 int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n",
345 : parrello 1.75 indexMod => 0, notes => "signed 32-bit integer"},
346 : parrello 1.73 counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n",
347 : parrello 1.75 indexMod => 0, notes => "unsigned 32-bit integer"},
348 : parrello 1.73 string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "",
349 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 255 characters"},
350 : parrello 1.73 text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "",
351 : parrello 1.75 indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
352 : parrello 1.73 date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n",
353 : parrello 1.75 indexMod => 0, notes => "signed, 64-bit integer"},
354 : parrello 1.73 float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g",
355 : parrello 1.75 indexMod => 0, notes => "64-bit double precision floating-point number"},
356 : parrello 1.73 boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n",
357 : parrello 1.75 indexMod => 0, notes => "boolean value: 0 if false, 1 if true"},
358 : parrello 1.42 'hash-string' =>
359 : parrello 1.73 { sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "",
360 : parrello 1.75 indexMod => 0, notes => "string stored in digested form, used for certain types of key fields"},
361 : parrello 1.44 'id-string' =>
362 : parrello 1.73 { sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "",
363 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 25 characters"},
364 : parrello 1.10 'key-string' =>
365 : parrello 1.73 { sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "",
366 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 40 characters"},
367 : parrello 1.10 'name-string' =>
368 : parrello 1.73 { sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "",
369 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 80 characters"},
370 : parrello 1.10 'medium-string' =>
371 : parrello 1.73 { sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "",
372 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 160 characters"},
373 : parrello 1.10 );
374 : parrello 1.1
375 :     # Table translating arities into natural language.
376 :     my %ArityTable = ( '11' => 'one-to-one',
377 : parrello 1.10 '1M' => 'one-to-many',
378 :     'MM' => 'many-to-many'
379 :     );
380 : parrello 1.1
381 : parrello 1.73 # Options for XML input and output.
382 :    
383 :     my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
384 :     Entities => 'Entity',
385 :     Fields => 'Field',
386 :     Indexes => 'Index',
387 :     IndexFields => 'IndexField'
388 :     },
389 :     KeyAttr => { Relationship => 'name',
390 :     Entity => 'name',
391 :     Field => 'name'
392 :     },
393 :     SuppressEmpty => 1,
394 :     );
395 :    
396 :     my %XmlInOpts = (
397 :     ForceArray => ['Field', 'Index', 'IndexField'],
398 :     ForceContent => 1,
399 :     NormalizeSpace => 2,
400 :     );
401 :     my %XmlOutOpts = (
402 :     RootName => 'Database',
403 :     XMLDecl => 1,
404 :     );
405 : parrello 1.1
406 :    
407 :     =head2 Public Methods
408 :    
409 :     =head3 new
410 :    
411 : parrello 1.5 C<< my $database = ERDB->new($dbh, $metaFileName); >>
412 : parrello 1.1
413 :     Create a new ERDB object.
414 :    
415 :     =over 4
416 :    
417 :     =item dbh
418 :    
419 :     DBKernel database object for the target database.
420 :    
421 :     =item metaFileName
422 :    
423 :     Name of the XML file containing the metadata.
424 :    
425 :     =back
426 :    
427 :     =cut
428 :    
429 :     sub new {
430 : parrello 1.10 # Get the parameters.
431 :     my ($class, $dbh, $metaFileName, $options) = @_;
432 :     # Load the meta-data.
433 :     my $metaData = _LoadMetaData($metaFileName);
434 :     # Create the object.
435 :     my $self = { _dbh => $dbh,
436 :     _metaData => $metaData
437 :     };
438 :     # Bless and return it.
439 :     bless $self, $class;
440 :     return $self;
441 : parrello 1.1 }
442 :    
443 :     =head3 ShowMetaData
444 :    
445 : parrello 1.18 C<< $erdb->ShowMetaData($fileName); >>
446 : parrello 1.1
447 :     This method outputs a description of the database. This description can be used to help users create
448 :     the data to be loaded into the relations.
449 :    
450 :     =over 4
451 :    
452 :     =item filename
453 :    
454 :     The name of the output file.
455 :    
456 :     =back
457 :    
458 :     =cut
459 :    
460 :     sub ShowMetaData {
461 : parrello 1.10 # Get the parameters.
462 :     my ($self, $filename) = @_;
463 :     # Get the metadata and the title string.
464 :     my $metadata = $self->{_metaData};
465 :     # Get the title string.
466 :     my $title = $metadata->{Title};
467 :     # Get the entity and relationship lists.
468 :     my $entityList = $metadata->{Entities};
469 :     my $relationshipList = $metadata->{Relationships};
470 :     # Open the output file.
471 :     open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
472 :     Trace("Building MetaData table of contents.") if T(4);
473 :     # Write the HTML heading stuff.
474 :     print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
475 :     print HTMLOUT "</head>\n<body>\n";
476 : parrello 1.45 # Write the documentation.
477 :     print HTMLOUT $self->DisplayMetaData();
478 :     # Close the document.
479 :     print HTMLOUT "</body>\n</html>\n";
480 :     # Close the file.
481 :     close HTMLOUT;
482 :     }
483 :    
484 :     =head3 DisplayMetaData
485 :    
486 :     C<< my $html = $erdb->DisplayMetaData(); >>
487 :    
488 :     Return an HTML description of the database. This description can be used to help users create
489 :     the data to be loaded into the relations and form queries. The output is raw includable HTML
490 :     without any HEAD or BODY tags.
491 :    
492 :     =over 4
493 :    
494 :     =item filename
495 :    
496 :     The name of the output file.
497 :    
498 :     =back
499 :    
500 :     =cut
501 :    
502 :     sub DisplayMetaData {
503 :     # Get the parameters.
504 :     my ($self) = @_;
505 :     # Get the metadata and the title string.
506 :     my $metadata = $self->{_metaData};
507 :     # Get the title string.
508 :     my $title = $metadata->{Title};
509 :     # Get the entity and relationship lists.
510 :     my $entityList = $metadata->{Entities};
511 :     my $relationshipList = $metadata->{Relationships};
512 :     # Declare the return variable.
513 :     my $retVal = "";
514 :     # Open the output file.
515 :     Trace("Building MetaData table of contents.") if T(4);
516 : parrello 1.10 # Here we do the table of contents. It starts as an unordered list of section names. Each
517 :     # section contains an ordered list of entity or relationship subsections.
518 : parrello 1.45 $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
519 : parrello 1.10 # Loop through the Entities, displaying a list item for each.
520 :     foreach my $key (sort keys %{$entityList}) {
521 :     # Display this item.
522 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
523 : parrello 1.10 }
524 :     # Close off the entity section and start the relationship section.
525 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
526 : parrello 1.10 # Loop through the Relationships.
527 :     foreach my $key (sort keys %{$relationshipList}) {
528 :     # Display this item.
529 :     my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
530 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
531 : parrello 1.10 }
532 :     # Close off the relationship section and list the join table section.
533 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
534 : parrello 1.10 # Close off the table of contents itself.
535 : parrello 1.45 $retVal .= "</ul>\n";
536 : parrello 1.10 # Now we start with the actual data. Denote we're starting the entity section.
537 : parrello 1.45 $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
538 : parrello 1.10 # Loop through the entities.
539 :     for my $key (sort keys %{$entityList}) {
540 :     Trace("Building MetaData entry for $key entity.") if T(4);
541 :     # Create the entity header. It contains a bookmark and the entity name.
542 : parrello 1.45 $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
543 : parrello 1.10 # Get the entity data.
544 :     my $entityData = $entityList->{$key};
545 :     # If there's descriptive text, display it.
546 :     if (my $notes = $entityData->{Notes}) {
547 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
548 : parrello 1.10 }
549 :     # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
550 : parrello 1.45 $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
551 : parrello 1.10 # Loop through the relationships.
552 :     for my $relationship (sort keys %{$relationshipList}) {
553 :     # Get the relationship data.
554 :     my $relationshipStructure = $relationshipList->{$relationship};
555 :     # Only use the relationship if if has this entity in its FROM or TO fields.
556 :     if ($relationshipStructure->{from} eq $key || $relationshipStructure->{to} eq $key) {
557 :     # Get the relationship sentence and append the arity.
558 :     my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
559 :     # Display the relationship data.
560 : parrello 1.45 $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
561 : parrello 1.10 }
562 :     }
563 :     # Close off the relationship list.
564 : parrello 1.45 $retVal .= "</ul>\n";
565 : parrello 1.10 # Get the entity's relations.
566 :     my $relationList = $entityData->{Relations};
567 :     # Create a header for the relation subsection.
568 : parrello 1.45 $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
569 : parrello 1.10 # Loop through the relations, displaying them.
570 :     for my $relation (sort keys %{$relationList}) {
571 :     my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
572 : parrello 1.45 $retVal .= $htmlString;
573 : parrello 1.10 }
574 :     }
575 :     # Denote we're starting the relationship section.
576 : parrello 1.45 $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
577 : parrello 1.10 # Loop through the relationships.
578 :     for my $key (sort keys %{$relationshipList}) {
579 :     Trace("Building MetaData entry for $key relationship.") if T(4);
580 :     # Get the relationship's structure.
581 :     my $relationshipStructure = $relationshipList->{$key};
582 :     # Create the relationship header.
583 :     my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
584 : parrello 1.45 $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
585 : parrello 1.10 # Get the entity names.
586 :     my $fromEntity = $relationshipStructure->{from};
587 :     my $toEntity = $relationshipStructure->{to};
588 :     # Describe the relationship arity. Note there's a bit of trickiness involving recursive
589 :     # many-to-many relationships. In a normal many-to-many we use two sentences to describe
590 :     # the arity (one for each direction). This is a bad idea for a recursive relationship,
591 :     # since both sentences will say the same thing.
592 :     my $arity = $relationshipStructure->{arity};
593 :     if ($arity eq "11") {
594 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
595 : parrello 1.10 } else {
596 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
597 : parrello 1.10 if ($arity eq "MM" && $fromEntity ne $toEntity) {
598 : parrello 1.45 $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
599 : parrello 1.10 }
600 :     }
601 : parrello 1.45 $retVal .= "</p>\n";
602 : parrello 1.10 # If there are notes on this relationship, display them.
603 :     if (my $notes = $relationshipStructure->{Notes}) {
604 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
605 : parrello 1.10 }
606 :     # Generate the relationship's relation table.
607 :     my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
608 : parrello 1.45 $retVal .= $htmlString;
609 : parrello 1.10 }
610 :     Trace("Building MetaData join table.") if T(4);
611 :     # Denote we're starting the join table.
612 : parrello 1.45 $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
613 : parrello 1.10 # Create a table header.
614 : parrello 1.45 $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
615 : parrello 1.10 # Loop through the joins.
616 :     my $joinTable = $metadata->{Joins};
617 :     my @joinKeys = keys %{$joinTable};
618 :     for my $joinKey (sort @joinKeys) {
619 :     # Separate out the source, the target, and the join clause.
620 :     $joinKey =~ m!^([^/]+)/(.+)$!;
621 :     my ($sourceRelation, $targetRelation) = ($1, $2);
622 : parrello 1.30 Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
623 : parrello 1.10 my $source = $self->ComputeObjectSentence($sourceRelation);
624 :     my $target = $self->ComputeObjectSentence($targetRelation);
625 :     my $clause = $joinTable->{$joinKey};
626 :     # Display them in a table row.
627 : parrello 1.45 $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
628 : parrello 1.10 }
629 :     # Close the table.
630 : parrello 1.45 $retVal .= _CloseTable();
631 :     Trace("Built MetaData HTML.") if T(3);
632 :     # Return the HTML.
633 :     return $retVal;
634 : parrello 1.1 }
635 :    
636 :     =head3 DumpMetaData
637 :    
638 : parrello 1.18 C<< $erdb->DumpMetaData(); >>
639 : parrello 1.1
640 :     Return a dump of the metadata structure.
641 :    
642 :     =cut
643 :    
644 :     sub DumpMetaData {
645 : parrello 1.10 # Get the parameters.
646 :     my ($self) = @_;
647 :     # Dump the meta-data.
648 :     return Data::Dumper::Dumper($self->{_metaData});
649 : parrello 1.1 }
650 :    
651 : parrello 1.74 =head3 FindIndexForEntity
652 :    
653 :     C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
654 :    
655 :     This method locates the entry in an entity's index list that begins with the
656 :     specified attribute name. If the entity has no index list, one will be
657 :     created. This method works on raw XML, not a live ERDB object.
658 :    
659 :     =over 4
660 :    
661 :     =item xml
662 :    
663 :     The raw XML structure defining the database.
664 :    
665 :     =item entityName
666 :    
667 :     The name of the relevant entity.
668 :    
669 :     =item attributeName
670 :    
671 :     The name of the attribute relevant to the search.
672 :    
673 :     =item RETURN
674 :    
675 :     The numerical index in the index list of the index entry for the specified entity and
676 :     attribute, or C<undef> if no such index exists.
677 :    
678 :     =back
679 :    
680 :     =cut
681 :    
682 :     sub FindIndexForEntity {
683 :     # Get the parameters.
684 :     my ($xml, $entityName, $attributeName) = @_;
685 :     # Declare the return variable.
686 :     my $retVal;
687 :     # Get the named entity.
688 :     my $entityData = $xml->{Entities}->{$entityName};
689 :     if (! $entityData) {
690 :     Confess("Entity $entityName not found in DBD structure.");
691 :     } else {
692 :     # Insure it has an index list.
693 :     if (! exists $entityData->{Indexes}) {
694 :     $entityData->{Indexes} = [];
695 :     } else {
696 :     # Search for the desired index.
697 :     my $indexList = $entityData->{Indexes};
698 :     my $n = scalar @{$indexList};
699 :     Trace("Searching $n indexes in index list for $entityName.") if T(2);
700 :     # We use an indexed FOR here because we're returning an
701 :     # index number instead of an object. We do THAT so we can
702 :     # delete the index from the list if needed.
703 :     for (my $i = 0; $i < $n && !defined($retVal); $i++) {
704 :     my $index = $indexList->[$i];
705 :     my $fields = $index->{IndexFields};
706 :     # Technically this IF should be safe (that is, we are guaranteed
707 :     # the existence of a "$fields->[0]"), because when we load the XML
708 :     # we have SuppressEmpty specified.
709 :     if ($fields->[0]->{name} eq $attributeName) {
710 :     $retVal = $i;
711 :     }
712 :     }
713 :     }
714 :     }
715 :     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
716 :     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
717 :     # Return the result.
718 :     return $retVal;
719 :     }
720 :    
721 : parrello 1.1 =head3 CreateTables
722 :    
723 : parrello 1.18 C<< $erdb->CreateTables(); >>
724 : parrello 1.1
725 :     This method creates the tables for the database from the metadata structure loaded by the
726 :     constructor. It is expected this function will only be used on rare occasions, when the
727 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
728 : parrello 1.1 used by itself with the truncate flag turned on.
729 :    
730 :     =cut
731 :    
732 :     sub CreateTables {
733 : parrello 1.10 # Get the parameters.
734 :     my ($self) = @_;
735 : parrello 1.23 # Get the relation names.
736 :     my @relNames = $self->GetTableNames();
737 :     # Loop through the relations.
738 :     for my $relationName (@relNames) {
739 :     # Create a table for this relation.
740 :     $self->CreateTable($relationName);
741 :     Trace("Relation $relationName created.") if T(2);
742 : parrello 1.10 }
743 : parrello 1.1 }
744 :    
745 :     =head3 CreateTable
746 :    
747 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
748 : parrello 1.1
749 :     Create the table for a relation and optionally create its indexes.
750 :    
751 :     =over 4
752 :    
753 :     =item relationName
754 :    
755 :     Name of the relation (which will also be the table name).
756 :    
757 : parrello 1.18 =item indexFlag
758 : parrello 1.1
759 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
760 :     L</CreateIndexes> must be called later to bring the indexes into existence.
761 :    
762 : parrello 1.18 =item estimatedRows (optional)
763 :    
764 :     If specified, the estimated maximum number of rows for the relation. This
765 :     information allows the creation of tables using storage engines that are
766 :     faster but require size estimates, such as MyISAM.
767 :    
768 : parrello 1.1 =back
769 :    
770 :     =cut
771 :    
772 :     sub CreateTable {
773 : parrello 1.10 # Get the parameters.
774 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
775 : parrello 1.10 # Get the database handle.
776 :     my $dbh = $self->{_dbh};
777 :     # Get the relation data and determine whether or not the relation is primary.
778 :     my $relationData = $self->_FindRelation($relationName);
779 :     my $rootFlag = $self->_IsPrimary($relationName);
780 :     # Create a list of the field data.
781 :     my @fieldList;
782 :     for my $fieldData (@{$relationData->{Fields}}) {
783 :     # Assemble the field name and type.
784 :     my $fieldName = _FixName($fieldData->{name});
785 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
786 :     # Push the result into the field list.
787 :     push @fieldList, $fieldString;
788 :     }
789 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
790 :     if ($rootFlag) {
791 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
792 :     }
793 :     # Convert the field list into a comma-delimited string.
794 :     my $fieldThing = join(', ', @fieldList);
795 :     # Insure the table is not already there.
796 :     $dbh->drop_table(tbl => $relationName);
797 :     Trace("Table $relationName dropped.") if T(2);
798 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
799 :     # faster DB technologies.
800 :     my $estimation = undef;
801 :     if ($estimatedRows) {
802 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
803 :     }
804 : parrello 1.10 # Create the table.
805 :     Trace("Creating table $relationName: $fieldThing") if T(2);
806 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
807 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
808 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
809 :     # index will not be built until the table has been loaded.
810 : parrello 1.10 if ($indexFlag) {
811 :     $self->CreateIndex($relationName);
812 :     }
813 : parrello 1.1 }
814 :    
815 : parrello 1.31 =head3 VerifyFields
816 :    
817 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
818 :    
819 :     Run through the list of proposed field values, insuring that all the character fields are
820 :     below the maximum length. If any fields are too long, they will be truncated in place.
821 :    
822 :     =over 4
823 :    
824 :     =item relName
825 :    
826 :     Name of the relation for which the specified fields are destined.
827 :    
828 :     =item fieldList
829 :    
830 :     Reference to a list, in order, of the fields to be put into the relation.
831 :    
832 :     =item RETURN
833 :    
834 :     Returns the number of fields truncated.
835 :    
836 :     =back
837 :    
838 :     =cut
839 :    
840 :     sub VerifyFields {
841 :     # Get the parameters.
842 :     my ($self, $relName, $fieldList) = @_;
843 :     # Initialize the return value.
844 :     my $retVal = 0;
845 :     # Get the relation definition.
846 :     my $relData = $self->_FindRelation($relName);
847 :     # Get the list of field descriptors.
848 :     my $fieldTypes = $relData->{Fields};
849 :     my $fieldCount = scalar @{$fieldTypes};
850 :     # Loop through the two lists.
851 :     for (my $i = 0; $i < $fieldCount; $i++) {
852 :     # Get the type of the current field.
853 :     my $fieldType = $fieldTypes->[$i]->{type};
854 :     # If it's a character field, verify the length.
855 :     if ($fieldType =~ /string/) {
856 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
857 :     my $oldString = $fieldList->[$i];
858 :     if (length($oldString) > $maxLen) {
859 :     # Here it's too big, so we truncate it.
860 :     Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
861 :     $fieldList->[$i] = substr $oldString, 0, $maxLen;
862 :     $retVal++;
863 :     }
864 :     }
865 :     }
866 :     # Return the truncation count.
867 :     return $retVal;
868 :     }
869 :    
870 : parrello 1.42 =head3 DigestFields
871 :    
872 :     C<< $erdb->DigestFields($relName, $fieldList); >>
873 :    
874 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
875 :     specified relation.
876 :    
877 :     =over 4
878 :    
879 :     =item relName
880 :    
881 :     Name of the relation to which the fields belong.
882 :    
883 :     =item fieldList
884 :    
885 :     List of field contents to be loaded into the relation.
886 :    
887 :     =back
888 :    
889 :     =cut
890 :     #: Return Type ;
891 :     sub DigestFields {
892 :     # Get the parameters.
893 :     my ($self, $relName, $fieldList) = @_;
894 :     # Get the relation definition.
895 :     my $relData = $self->_FindRelation($relName);
896 :     # Get the list of field descriptors.
897 :     my $fieldTypes = $relData->{Fields};
898 :     my $fieldCount = scalar @{$fieldTypes};
899 :     # Loop through the two lists.
900 :     for (my $i = 0; $i < $fieldCount; $i++) {
901 :     # Get the type of the current field.
902 :     my $fieldType = $fieldTypes->[$i]->{type};
903 :     # If it's a hash string, digest it in place.
904 :     if ($fieldType eq 'hash-string') {
905 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
906 : parrello 1.42 }
907 :     }
908 :     }
909 :    
910 : parrello 1.46 =head3 DigestKey
911 :    
912 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
913 :    
914 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
915 :     key-based search into a table with key-type hash-string.
916 :    
917 :     Currently the digesting process is independent of the database structure, but that may not
918 :     always be the case, so this is an instance method instead of a static method.
919 :    
920 :     =over 4
921 :    
922 :     =item keyValue
923 :    
924 :     Key value to digest.
925 :    
926 :     =item RETURN
927 :    
928 : parrello 1.56 Digested value of the key.
929 : parrello 1.46
930 :     =back
931 :    
932 :     =cut
933 :    
934 :     sub DigestKey {
935 :     # Get the parameters.
936 :     my ($self, $keyValue) = @_;
937 :     # Compute the digest.
938 :     my $retVal = md5_base64($keyValue);
939 :     # Return the result.
940 :     return $retVal;
941 :     }
942 :    
943 : parrello 1.1 =head3 CreateIndex
944 :    
945 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
946 : parrello 1.1
947 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
948 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
949 :     If that is the case, then L</CreateTable> should be called with the index flag set to
950 :     FALSE, and this method used after the load to create the indexes for the table.
951 : parrello 1.1
952 :     =cut
953 :    
954 :     sub CreateIndex {
955 : parrello 1.10 # Get the parameters.
956 :     my ($self, $relationName) = @_;
957 :     # Get the relation's descriptor.
958 :     my $relationData = $self->_FindRelation($relationName);
959 :     # Get the database handle.
960 :     my $dbh = $self->{_dbh};
961 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
962 :     my $indexHash = $relationData->{Indexes};
963 :     for my $indexName (keys %{$indexHash}) {
964 :     my $indexData = $indexHash->{$indexName};
965 :     # Get the index's field list.
966 : parrello 1.75 my @rawFields = @{$indexData->{IndexFields}};
967 :     # Get a hash of the relation's field types.
968 :     my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
969 :     # We need to check for text fields. We need a append a length limitation for them. To do
970 :     # that, we need the relation's field list.
971 :     my $relFields = $relationData->{Fields};
972 :     for (my $i = 0; $i <= $#rawFields; $i++) {
973 :     # Get the field type.
974 :     my $field = $rawFields[$i];
975 :     my $type = $types{$field};
976 :     # Ask if it requires using prefix notation for the index.
977 :     my $mod = $TypeTable{$type}->{indexMod};
978 :     Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
979 :     if ($mod) {
980 :     # Append the prefix length to the field name,
981 :     $rawFields[$i] .= "($mod)";
982 :     }
983 :     }
984 :     my @fieldList = _FixNames(@rawFields);
985 : parrello 1.10 my $flds = join(', ', @fieldList);
986 :     # Get the index's uniqueness flag.
987 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
988 : parrello 1.10 # Create the index.
989 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
990 : parrello 1.70 flds => $flds, kind => $unique);
991 : parrello 1.24 if ($rv) {
992 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
993 :     } else {
994 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
995 :     }
996 : parrello 1.10 }
997 : parrello 1.1 }
998 :    
999 : parrello 1.75 =head3 GetSecondaryFields
1000 :    
1001 :     C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1002 :    
1003 :     This method will return a list of the name and type of each of the secondary
1004 :     fields for a specified entity. Secondary fields are stored in two-column tables
1005 :     in addition to the primary entity table. This enables the field to have no value
1006 :     or to have multiple values.
1007 :    
1008 :     =over 4
1009 :    
1010 :     =item entityName
1011 :    
1012 :     Name of the entity whose secondary fields are desired.
1013 :    
1014 :     =item RETURN
1015 :    
1016 :     Returns a hash mapping the field names to their field types.
1017 :    
1018 :     =back
1019 :    
1020 :     =cut
1021 :    
1022 :     sub GetSecondaryFields {
1023 :     # Get the parameters.
1024 :     my ($self, $entityName) = @_;
1025 :     # Declare the return variable.
1026 :     my %retVal = ();
1027 :     # Look for the entity.
1028 :     my $table = $self->GetFieldTable($entityName);
1029 :     # Loop through the fields, pulling out the secondaries.
1030 :     for my $field (sort keys %{$table}) {
1031 :     if ($table->{$field}->{relation} ne $entityName) {
1032 :     # Here we have a secondary field.
1033 :     $retVal{$field} = $table->{$field}->{type};
1034 :     }
1035 :     }
1036 :     # Return the result.
1037 :     return %retVal;
1038 :     }
1039 :    
1040 :     =head3 GetFieldRelationName
1041 :    
1042 :     C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1043 :    
1044 :     Return the name of the relation containing a specified field.
1045 :    
1046 :     =over 4
1047 :    
1048 :     =item objectName
1049 :    
1050 :     Name of the entity or relationship containing the field.
1051 :    
1052 :     =item fieldName
1053 :    
1054 :     Name of the relevant field in that entity or relationship.
1055 :    
1056 :     =item RETURN
1057 :    
1058 :     Returns the name of the database relation containing the field, or C<undef> if
1059 :     the field does not exist.
1060 :    
1061 :     =back
1062 :    
1063 :     =cut
1064 :    
1065 :     sub GetFieldRelationName {
1066 :     # Get the parameters.
1067 :     my ($self, $objectName, $fieldName) = @_;
1068 :     # Declare the return variable.
1069 :     my $retVal;
1070 :     # Get the object field table.
1071 :     my $table = $self->GetFieldTable($objectName);
1072 :     # Only proceed if the field exists.
1073 :     if (exists $table->{$fieldName}) {
1074 :     # Determine the name of the relation that contains this field.
1075 :     $retVal = $table->{$fieldName}->{relation};
1076 :     }
1077 :     # Return the result.
1078 :     return $retVal;
1079 :     }
1080 :    
1081 :     =head3 DeleteValue
1082 :    
1083 :     C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1084 :    
1085 :     Delete secondary field values from the database. This method can be used to delete all
1086 :     values of a specified field for a particular entity instance, or only a single value.
1087 :    
1088 :     Secondary fields are stored in two-column relations separate from an entity's primary
1089 :     table, and as a result a secondary field can legitimately have no value or multiple
1090 :     values. Therefore, it makes sense to talk about deleting secondary fields where it
1091 :     would not make sense for primary fields.
1092 :    
1093 :     =over 4
1094 :    
1095 :     =item entityName
1096 :    
1097 :     Name of the entity from which the fields are to be deleted.
1098 :    
1099 :     =item id
1100 :    
1101 :     ID of the entity instance to be processed. If the instance is not found, this
1102 : parrello 1.76 method will have no effect. If C<undef> is specified, all values for all of
1103 :     the entity instances will be deleted.
1104 : parrello 1.75
1105 :     =item fieldName
1106 :    
1107 :     Name of the field whose values are to be deleted.
1108 :    
1109 :     =item fieldValue (optional)
1110 :    
1111 :     Value to be deleted. If not specified, then all values of the specified field
1112 :     will be deleted for the entity instance. If specified, then only the values which
1113 :     match this parameter will be deleted.
1114 :    
1115 :     =item RETURN
1116 :    
1117 :     Returns the number of rows deleted.
1118 :    
1119 :     =back
1120 :    
1121 :     =cut
1122 :    
1123 :     sub DeleteValue {
1124 :     # Get the parameters.
1125 :     my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1126 :     # Declare the return value.
1127 :     my $retVal = 0;
1128 :     # We need to set up an SQL command to do the deletion. First, we
1129 :     # find the name of the field's relation.
1130 :     my $table = $self->GetFieldTable($entityName);
1131 :     my $field = $table->{$fieldName};
1132 :     my $relation = $field->{relation};
1133 :     # Make sure this is a secondary field.
1134 :     if ($relation eq $entityName) {
1135 :     Confess("Cannot delete values of $fieldName for $entityName.");
1136 :     } else {
1137 :     # Set up the SQL command to delete all values.
1138 : parrello 1.76 my $sql = "DELETE FROM $relation";
1139 :     # Build the filter.
1140 :     my @filters = ();
1141 :     my @parms = ();
1142 :     # Check for a filter by ID.
1143 :     if (defined $id) {
1144 :     push @filters, "id = ?";
1145 :     push @parms, $id;
1146 :     }
1147 :     # Check for a filter by value.
1148 : parrello 1.75 if (defined $fieldValue) {
1149 : parrello 1.76 push @filters, "$fieldName = ?";
1150 : parrello 1.75 push @parms, $fieldValue;
1151 :     }
1152 : parrello 1.76 # Append the filters to the command.
1153 :     if (@filters) {
1154 :     $sql .= " WHERE " . join(" AND ", @filters);
1155 :     }
1156 : parrello 1.75 # Execute the command.
1157 :     my $dbh = $self->{_dbh};
1158 :     $retVal = $dbh->SQL($sql, 0, @parms);
1159 :     }
1160 :     # Return the result.
1161 :     return $retVal;
1162 :     }
1163 :    
1164 : parrello 1.1 =head3 LoadTables
1165 :    
1166 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1167 : parrello 1.1
1168 :     This method will load the database tables from a directory. The tables must already have been created
1169 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1170 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
1171 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1172 :     line of the file will be loaded as a row of the target relation table. The field values should be in
1173 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1174 :     erased before the new data is loaded in.
1175 :    
1176 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1177 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1178 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1179 :    
1180 :     =over 4
1181 :    
1182 :     =item directoryName
1183 :    
1184 :     Name of the directory containing the relation files to be loaded.
1185 :    
1186 :     =item rebuild
1187 :    
1188 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1189 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
1190 :     by all of the DB engines we use.
1191 :    
1192 :     =item RETURN
1193 :    
1194 :     Returns a statistical object describing the number of records read and a list of the error messages.
1195 :    
1196 :     =back
1197 :    
1198 :     =cut
1199 :    
1200 :     sub LoadTables {
1201 : parrello 1.10 # Get the parameters.
1202 :     my ($self, $directoryName, $rebuild) = @_;
1203 :     # Start the timer.
1204 :     my $startTime = gettimeofday;
1205 :     # Clean any trailing slash from the directory name.
1206 :     $directoryName =~ s!/\\$!!;
1207 :     # Declare the return variable.
1208 :     my $retVal = Stats->new();
1209 : parrello 1.23 # Get the relation names.
1210 :     my @relNames = $self->GetTableNames();
1211 :     for my $relationName (@relNames) {
1212 :     # Try to load this relation.
1213 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1214 : parrello 1.10 # Accumulate the statistics.
1215 :     $retVal->Accumulate($result);
1216 :     }
1217 :     # Add the duration of the load to the statistical object.
1218 :     $retVal->Add('duration', gettimeofday - $startTime);
1219 :     # Return the accumulated statistics.
1220 :     return $retVal;
1221 : parrello 1.1 }
1222 :    
1223 : parrello 1.23
1224 : parrello 1.1 =head3 GetTableNames
1225 :    
1226 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
1227 : parrello 1.1
1228 :     Return a list of the relations required to implement this database.
1229 :    
1230 :     =cut
1231 :    
1232 :     sub GetTableNames {
1233 : parrello 1.10 # Get the parameters.
1234 :     my ($self) = @_;
1235 :     # Get the relation list from the metadata.
1236 :     my $relationTable = $self->{_metaData}->{RelationTable};
1237 :     # Return the relation names.
1238 :     return keys %{$relationTable};
1239 : parrello 1.1 }
1240 :    
1241 :     =head3 GetEntityTypes
1242 :    
1243 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
1244 : parrello 1.1
1245 :     Return a list of the entity type names.
1246 :    
1247 :     =cut
1248 :    
1249 :     sub GetEntityTypes {
1250 : parrello 1.10 # Get the database object.
1251 :     my ($self) = @_;
1252 :     # Get the entity list from the metadata object.
1253 :     my $entityList = $self->{_metaData}->{Entities};
1254 :     # Return the list of entity names in alphabetical order.
1255 :     return sort keys %{$entityList};
1256 : parrello 1.1 }
1257 :    
1258 : parrello 1.73 =head3 GetDataTypes
1259 :    
1260 :     C<< my %types = ERDB::GetDataTypes(); >>
1261 :    
1262 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1263 :     The keys of the big hash are the datatypes. Each smaller hash has several
1264 :     values used to manage the data. The most interesting is the SQL type (key
1265 :     C<sqlType>) and the descriptive node (key C<notes>).
1266 :    
1267 :     Note that changing the values in the smaller hashes will seriously break
1268 :     things, so this data should be treated as read-only.
1269 :    
1270 :     =cut
1271 :    
1272 :     sub GetDataTypes {
1273 :     return %TypeTable;
1274 :     }
1275 :    
1276 :    
1277 : parrello 1.20 =head3 IsEntity
1278 :    
1279 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1280 :    
1281 :     Return TRUE if the parameter is an entity name, else FALSE.
1282 :    
1283 :     =over 4
1284 :    
1285 :     =item entityName
1286 :    
1287 :     Object name to be tested.
1288 :    
1289 :     =item RETURN
1290 :    
1291 :     Returns TRUE if the specified string is an entity name, else FALSE.
1292 :    
1293 :     =back
1294 :    
1295 :     =cut
1296 :    
1297 :     sub IsEntity {
1298 :     # Get the parameters.
1299 :     my ($self, $entityName) = @_;
1300 :     # Test to see if it's an entity.
1301 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1302 :     }
1303 :    
1304 : parrello 1.1 =head3 Get
1305 :    
1306 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1307 : parrello 1.1
1308 :     This method returns a query object for entities of a specified type using a specified filter.
1309 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1310 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1311 :     following call requests all B<Genome> objects for the genus specified in the variable
1312 :     $genus.
1313 :    
1314 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1315 : parrello 1.1
1316 :     The WHERE clause contains a single question mark, so there is a single additional
1317 :     parameter representing the parameter value. It would also be possible to code
1318 :    
1319 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1320 : parrello 1.1
1321 :     however, this version of the call would generate a syntax error if there were any quote
1322 :     characters inside the variable C<$genus>.
1323 :    
1324 :     The use of the strange parenthesized notation for field names enables us to distinguish
1325 :     hyphens contained within field names from minus signs that participate in the computation
1326 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1327 :    
1328 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1329 :     one object's data at the same time, which allows highly complex joined queries. For example,
1330 :    
1331 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1332 : parrello 1.1
1333 :     If multiple names are specified, then the query processor will automatically determine a
1334 :     join path between the entities and relationships. The algorithm used is very simplistic.
1335 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1336 :     the entity and the relationship appear. For example, consider a recursive relationship
1337 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1338 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1339 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1340 :    
1341 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1342 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1343 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1344 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1345 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1346 :    
1347 : parrello 1.1 =over 4
1348 :    
1349 :     =item objectNames
1350 :    
1351 :     List containing the names of the entity and relationship objects to be retrieved.
1352 :    
1353 :     =item filterClause
1354 :    
1355 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1356 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1357 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1358 :     in the filter clause should be added to the parameter list as additional parameters. The
1359 :     fields in a filter clause can come from primary entity relations, relationship relations,
1360 :     or secondary entity relations; however, all of the entities and relationships involved must
1361 :     be included in the list of object names.
1362 :    
1363 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1364 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1365 :     particular genus and sorts them by species name.
1366 :    
1367 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1368 :    
1369 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1370 :     be processed. The idea is to make it less likely to find the verb by accident.
1371 :    
1372 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1373 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1374 :     relation.
1375 :    
1376 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1377 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1378 :     a positive number. So, for example
1379 :    
1380 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1381 :    
1382 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1383 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1384 :     use
1385 :    
1386 :     C<< "LIMIT 10" >>
1387 :    
1388 : parrello 1.45 =item params
1389 : parrello 1.1
1390 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1391 : parrello 1.1
1392 :     =item RETURN
1393 :    
1394 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1395 :    
1396 :     =back
1397 :    
1398 :     =cut
1399 :    
1400 :     sub Get {
1401 : parrello 1.10 # Get the parameters.
1402 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1403 :     # Process the SQL stuff.
1404 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1405 :     $self->_SetupSQL($objectNames, $filterClause);
1406 :     # Create the query.
1407 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1408 :     ".* $suffix";
1409 :     my $sth = $self->_GetStatementHandle($command, $params);
1410 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1411 :     # and mapped name for each object in the query.
1412 :     my @relationMap = ();
1413 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1414 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1415 : parrello 1.39 }
1416 : parrello 1.10 # Return the statement object.
1417 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1418 : parrello 1.10 return $retVal;
1419 : parrello 1.1 }
1420 :    
1421 : parrello 1.70 =head3 Search
1422 :    
1423 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1424 :    
1425 :     Perform a full text search with filtering. The search will be against a specified object
1426 :     in the object name list. That object will get an extra field containing the search
1427 :     relevance. Note that except for the search expression, the parameters of this method are
1428 :     the same as those for L</Get> and follow the same rules.
1429 :    
1430 :     =over 4
1431 :    
1432 :     =item searchExpression
1433 :    
1434 : parrello 1.75 Boolean search expression for the text fields of the target object. The default mode for
1435 :     a Boolean search expression is OR, but we want the default to be AND, so we will
1436 :     add a C<+> operator to each word with no other operator before it.
1437 : parrello 1.70
1438 :     =item idx
1439 :    
1440 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1441 :    
1442 :     =item objectNames
1443 :    
1444 :     List containing the names of the entity and relationship objects to be retrieved.
1445 :    
1446 :     =item filterClause
1447 :    
1448 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1449 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1450 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1451 :     in the filter clause should be added to the parameter list as additional parameters. The
1452 :     fields in a filter clause can come from primary entity relations, relationship relations,
1453 :     or secondary entity relations; however, all of the entities and relationships involved must
1454 :     be included in the list of object names.
1455 :    
1456 :     =item params
1457 :    
1458 :     Reference to a list of parameter values to be substituted into the filter clause.
1459 :    
1460 :     =item RETURN
1461 :    
1462 :     Returns a query object for the specified search.
1463 :    
1464 :     =back
1465 :    
1466 :     =cut
1467 :    
1468 :     sub Search {
1469 :     # Get the parameters.
1470 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1471 :     # Declare the return variable.
1472 :     my $retVal;
1473 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1474 :     # a parameter list exists before we copy it.
1475 :     my @myParams = ();
1476 :     if (defined $params) {
1477 :     @myParams = @{$params};
1478 :     }
1479 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1480 :     my $object1Name = $objectNames->[$idx];
1481 :     my $object1Structure = $self->_GetStructure($object1Name);
1482 :     # Get the field list.
1483 :     if (! exists $object1Structure->{searchFields}) {
1484 :     Confess("No searchable index for $object1Name.");
1485 :     } else {
1486 :     # Get the field list.
1487 :     my @fields = @{$object1Structure->{searchFields}};
1488 : parrello 1.71 # Clean the search expression.
1489 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1490 : parrello 1.75 # Prefix a "+" to each uncontrolled word. This converts the default
1491 :     # search mode from OR to AND.
1492 :     $actualKeywords =~ s/(^|\s)(\w)/$1\+$2/g;
1493 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1494 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1495 :     # query itself. Both will use a parameter mark, so we need to push the
1496 :     # search expression onto the front of the parameter list twice.
1497 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1498 : parrello 1.70 # Build the match expression.
1499 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1500 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1501 :     # Process the SQL stuff.
1502 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1503 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1504 :     # Create the query. Note that the match clause is inserted at the front of
1505 :     # the select fields.
1506 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1507 :     ".* $suffix";
1508 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1509 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1510 :     # and mapped name for each object in the query.
1511 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1512 :     # Return the statement object.
1513 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1514 :     }
1515 :     return $retVal;
1516 :     }
1517 :    
1518 : parrello 1.45 =head3 GetFlat
1519 :    
1520 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1521 :    
1522 :     This is a variation of L</GetAll> that asks for only a single field per record and
1523 :     returns a single flattened list.
1524 :    
1525 :     =over 4
1526 :    
1527 :     =item objectNames
1528 :    
1529 :     List containing the names of the entity and relationship objects to be retrieved.
1530 :    
1531 :     =item filterClause
1532 :    
1533 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1534 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1535 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1536 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1537 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1538 :     entities and relationships involved must be included in the list of object names.
1539 :    
1540 :     =item parameterList
1541 :    
1542 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1543 :    
1544 :     =item field
1545 :    
1546 :     Name of the field to be used to get the elements of the list returned.
1547 :    
1548 :     =item RETURN
1549 :    
1550 :     Returns a list of values.
1551 :    
1552 :     =back
1553 :    
1554 :     =cut
1555 :     #: Return Type @;
1556 :     sub GetFlat {
1557 :     # Get the parameters.
1558 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1559 :     # Construct the query.
1560 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1561 :     # Create the result list.
1562 :     my @retVal = ();
1563 :     # Loop through the records, adding the field values found to the result list.
1564 :     while (my $row = $query->Fetch()) {
1565 :     push @retVal, $row->Value($field);
1566 :     }
1567 :     # Return the list created.
1568 :     return @retVal;
1569 :     }
1570 :    
1571 : parrello 1.73 =head3 SpecialFields
1572 :    
1573 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1574 :    
1575 :     Return a hash mapping special fields in the specified entity to the value of their
1576 :     C<special> attribute. This enables the subclass to get access to the special field
1577 :     attributes without needed to plumb the internal ERDB data structures.
1578 :    
1579 :     =over 4
1580 :    
1581 :     =item entityName
1582 :    
1583 :     Name of the entity whose special fields are desired.
1584 :    
1585 :     =item RETURN
1586 :    
1587 :     Returns a hash. The keys of the hash are the special field names, and the values
1588 :     are the values from each special field's C<special> attribute.
1589 :    
1590 :     =back
1591 :    
1592 :     =cut
1593 :    
1594 :     sub SpecialFields {
1595 :     # Get the parameters.
1596 :     my ($self, $entityName) = @_;
1597 :     # Declare the return variable.
1598 :     my %retVal = ();
1599 :     # Find the entity's data structure.
1600 : parrello 1.75 my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1601 : parrello 1.73 # Loop through its fields, adding each special field to the return hash.
1602 :     my $fieldHash = $entityData->{Fields};
1603 :     for my $fieldName (keys %{$fieldHash}) {
1604 :     my $fieldData = $fieldHash->{$fieldName};
1605 :     if (exists $fieldData->{special}) {
1606 :     $retVal{$fieldName} = $fieldData->{special};
1607 :     }
1608 :     }
1609 :     # Return the result.
1610 :     return %retVal;
1611 :     }
1612 :    
1613 : parrello 1.32 =head3 Delete
1614 :    
1615 : parrello 1.77 C<< my $stats = $erdb->Delete($entityName, $objectID, $testFlag); >>
1616 : parrello 1.32
1617 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1618 : parrello 1.77 relationship instances dependent on it. The definition of I<dependence> is recursive.
1619 :    
1620 :     An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1621 :     relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1622 : parrello 1.32 dependent relationship.
1623 :    
1624 :     =over 4
1625 :    
1626 :     =item entityName
1627 :    
1628 :     Name of the entity type for the instance being deleted.
1629 :    
1630 :     =item objectID
1631 :    
1632 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1633 :     then it is presumed to by a LIKE pattern.
1634 :    
1635 :     =item testFlag
1636 :    
1637 :     If TRUE, the delete statements will be traced without being executed.
1638 :    
1639 :     =item RETURN
1640 :    
1641 :     Returns a statistics object indicating how many records of each particular table were
1642 :     deleted.
1643 :    
1644 :     =back
1645 :    
1646 :     =cut
1647 :     #: Return Type $%;
1648 :     sub Delete {
1649 :     # Get the parameters.
1650 :     my ($self, $entityName, $objectID, $testFlag) = @_;
1651 :     # Declare the return variable.
1652 :     my $retVal = Stats->new();
1653 :     # Get the DBKernel object.
1654 :     my $db = $self->{_dbh};
1655 :     # We're going to generate all the paths branching out from the starting entity. One of
1656 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1657 :     # determine if we've hit a loop.
1658 :     my %alreadyFound = ();
1659 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1660 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1661 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1662 :     # sure we don't delete records that might be needed to forge relationships back to the
1663 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1664 :     # FROM-relationships and entities.
1665 :     my @fromPathList = ();
1666 :     my @toPathList = ();
1667 : parrello 1.32 # This final hash is used to remember what work still needs to be done. We push paths
1668 :     # onto the list, then pop them off to extend the paths. We prime it with the starting
1669 :     # point. Note that we will work hard to insure that the last item on a path in the
1670 : parrello 1.75 # to-do list is always an entity.
1671 : parrello 1.32 my @todoList = ([$entityName]);
1672 :     while (@todoList) {
1673 :     # Get the current path.
1674 :     my $current = pop @todoList;
1675 :     # Copy it into a list.
1676 :     my @stackedPath = @{$current};
1677 :     # Pull off the last item on the path. It will always be an entity.
1678 :     my $entityName = pop @stackedPath;
1679 :     # Add it to the alreadyFound list.
1680 :     $alreadyFound{$entityName} = 1;
1681 :     # Get the entity data.
1682 :     my $entityData = $self->_GetStructure($entityName);
1683 :     # The first task is to loop through the entity's relation. A DELETE command will
1684 :     # be needed for each of them.
1685 :     my $relations = $entityData->{Relations};
1686 :     for my $relation (keys %{$relations}) {
1687 :     my @augmentedList = (@stackedPath, $relation);
1688 : parrello 1.33 push @fromPathList, \@augmentedList;
1689 : parrello 1.32 }
1690 :     # Now we need to look for relationships connected to this entity.
1691 :     my $relationshipList = $self->{_metaData}->{Relationships};
1692 :     for my $relationshipName (keys %{$relationshipList}) {
1693 :     my $relationship = $relationshipList->{$relationshipName};
1694 :     # Check the FROM field. We're only interested if it's us.
1695 :     if ($relationship->{from} eq $entityName) {
1696 :     # Add the path to this relationship.
1697 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1698 : parrello 1.33 push @fromPathList, \@augmentedList;
1699 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1700 :     # and the target hasn't been seen yet, we want to
1701 :     # stack the entity for future processing.
1702 :     if ($relationship->{arity} eq '1M') {
1703 :     my $toEntity = $relationship->{to};
1704 :     if (! exists $alreadyFound{$toEntity}) {
1705 :     # Here we have a new entity that's dependent on
1706 :     # the current entity, so we need to stack it.
1707 :     my @stackList = (@augmentedList, $toEntity);
1708 : parrello 1.33 push @fromPathList, \@stackList;
1709 : parrello 1.34 } else {
1710 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1711 : parrello 1.32 }
1712 :     }
1713 :     }
1714 :     # Now check the TO field. In this case only the relationship needs
1715 : parrello 1.33 # deletion.
1716 : parrello 1.32 if ($relationship->{to} eq $entityName) {
1717 :     my @augmentedList = (@stackedPath, $entityName, $relationshipName);
1718 : parrello 1.33 push @toPathList, \@augmentedList;
1719 : parrello 1.32 }
1720 :     }
1721 :     }
1722 :     # Create the first qualifier for the WHERE clause. This selects the
1723 :     # keys of the primary entity records to be deleted. When we're deleting
1724 :     # from a dependent table, we construct a join page from the first qualifier
1725 :     # to the table containing the dependent records to delete.
1726 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1727 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1728 :     # the second through the from-list. The from-list is second because
1729 :     # the to-list may need to pass through some of the entities the
1730 :     # from-list would delete.
1731 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1732 :     # Now it's time to do the deletes. We do it in two passes.
1733 :     for my $keyName ('to_link', 'from_link') {
1734 :     # Get the list for this key.
1735 :     my @pathList = @{$stackList{$keyName}};
1736 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1737 : parrello 1.33 # Loop through this list.
1738 :     while (my $path = pop @pathList) {
1739 :     # Get the table whose rows are to be deleted.
1740 :     my @pathTables = @{$path};
1741 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1742 :     # syntax of a DELETE-USING varies among DBMSs.
1743 : parrello 1.33 my $target = $pathTables[$#pathTables];
1744 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1745 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1746 :     # starting table will either be the entity relation or one of the entity's
1747 :     # sub-relations.
1748 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1749 :     # Now we run through the remaining entities in the path, connecting them up.
1750 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1751 :     # Connect the current relationship to the preceding entity.
1752 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1753 :     # The style of connection depends on the direction of the relationship.
1754 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1755 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1756 :     # Here there's a next entity, so connect that to the relationship's
1757 :     # to-link.
1758 :     my $entity2 = $pathTables[$i+1];
1759 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1760 : parrello 1.32 }
1761 :     }
1762 : parrello 1.33 # Now we have our desired DELETE statement.
1763 :     if ($testFlag) {
1764 :     # Here the user wants to trace without executing.
1765 :     Trace($stmt) if T(0);
1766 :     } else {
1767 : parrello 1.77 # Here we can delete. Note that the SQL method dies with a confession
1768 : parrello 1.33 # if an error occurs, so we just go ahead and do it.
1769 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1770 :     my $rv = $db->SQL($stmt, 0, $objectID);
1771 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1772 :     # are from the target table, so we use its name to record the
1773 :     # statistic.
1774 :     $retVal->Add($target, $rv);
1775 :     }
1776 : parrello 1.32 }
1777 :     }
1778 :     # Return the result.
1779 :     return $retVal;
1780 :     }
1781 :    
1782 : parrello 1.70 =head3 SortNeeded
1783 :    
1784 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
1785 :    
1786 :     Return the pipe command for the sort that should be applied to the specified
1787 :     relation when creating the load file.
1788 :    
1789 :     For example, if the load file should be sorted ascending by the first
1790 :     field, this method would return
1791 :    
1792 :     sort -k1 -t"\t"
1793 :    
1794 :     If the first field is numeric, the method would return
1795 :    
1796 :     sort -k1n -t"\t"
1797 :    
1798 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1799 :     keys using a sort.
1800 :    
1801 :     =over 4
1802 :    
1803 :     =item relationName
1804 :    
1805 :     Name of the relation to be examined.
1806 :    
1807 :     =item
1808 :    
1809 :     Returns the sort command to use for sorting the relation, suitable for piping.
1810 :    
1811 :     =back
1812 :    
1813 :     =cut
1814 :     #: Return Type $;
1815 :     sub SortNeeded {
1816 :     # Get the parameters.
1817 :     my ($self, $relationName) = @_;
1818 :     # Declare a descriptor to hold the names of the key fields.
1819 :     my @keyNames = ();
1820 :     # Get the relation structure.
1821 :     my $relationData = $self->_FindRelation($relationName);
1822 :     # Find out if the relation is a primary entity relation,
1823 :     # a relationship relation, or a secondary entity relation.
1824 :     my $entityTable = $self->{_metaData}->{Entities};
1825 :     my $relationshipTable = $self->{_metaData}->{Relationships};
1826 :     if (exists $entityTable->{$relationName}) {
1827 :     # Here we have a primary entity relation.
1828 :     push @keyNames, "id";
1829 :     } elsif (exists $relationshipTable->{$relationName}) {
1830 :     # Here we have a relationship. We sort using the FROM index.
1831 :     my $relationshipData = $relationshipTable->{$relationName};
1832 : parrello 1.75 my $index = $relationData->{Indexes}->{idxFrom};
1833 : parrello 1.70 push @keyNames, @{$index->{IndexFields}};
1834 :     } else {
1835 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
1836 :     push @keyNames, "id";
1837 :     }
1838 :     # Now we parse the key names into sort parameters. First, we prime the return
1839 :     # string.
1840 :     my $retVal = "sort -t\"\t\" ";
1841 :     # Get the relation's field list.
1842 :     my @fields = @{$relationData->{Fields}};
1843 :     # Loop through the keys.
1844 :     for my $keyData (@keyNames) {
1845 :     # Get the key and the ordering.
1846 :     my ($keyName, $ordering);
1847 :     if ($keyData =~ /^([^ ]+) DESC/) {
1848 :     ($keyName, $ordering) = ($1, "descending");
1849 :     } else {
1850 :     ($keyName, $ordering) = ($keyData, "ascending");
1851 :     }
1852 :     # Find the key's position and type.
1853 :     my $fieldSpec;
1854 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1855 :     my $thisField = $fields[$i];
1856 :     if ($thisField->{name} eq $keyName) {
1857 :     # Get the sort modifier for this field type. The modifier
1858 :     # decides whether we're using a character, numeric, or
1859 :     # floating-point sort.
1860 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
1861 :     # If the index is descending for this field, denote we want
1862 :     # to reverse the sort order on this field.
1863 :     if ($ordering eq 'descending') {
1864 :     $modifier .= "r";
1865 :     }
1866 :     # Store the position and modifier into the field spec, which
1867 :     # will stop the inner loop. Note that the field number is
1868 :     # 1-based in the sort command, so we have to increment the
1869 :     # index.
1870 :     $fieldSpec = ($i + 1) . $modifier;
1871 :     }
1872 :     }
1873 :     # Add this field to the sort command.
1874 :     $retVal .= " -k$fieldSpec";
1875 :     }
1876 :     # Return the result.
1877 :     return $retVal;
1878 :     }
1879 :    
1880 : parrello 1.6 =head3 GetList
1881 :    
1882 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
1883 : parrello 1.6
1884 :     Return a list of object descriptors for the specified objects as determined by the
1885 :     specified filter clause.
1886 :    
1887 :     This method is essentially the same as L</Get> except it returns a list of objects rather
1888 : parrello 1.7 than a query object that can be used to get the results one record at a time.
1889 : parrello 1.6
1890 :     =over 4
1891 :    
1892 :     =item objectNames
1893 :    
1894 :     List containing the names of the entity and relationship objects to be retrieved.
1895 :    
1896 :     =item filterClause
1897 :    
1898 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1899 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1900 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1901 :     in the filter clause should be added to the parameter list as additional parameters. The
1902 :     fields in a filter clause can come from primary entity relations, relationship relations,
1903 :     or secondary entity relations; however, all of the entities and relationships involved must
1904 :     be included in the list of object names.
1905 :    
1906 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1907 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1908 :     particular genus and sorts them by species name.
1909 :    
1910 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1911 :    
1912 :     The rules for field references in a sort order are the same as those for field references in the
1913 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1914 :     relation.
1915 :    
1916 : parrello 1.45 =item params
1917 : parrello 1.6
1918 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1919 : parrello 1.6
1920 :     =item RETURN
1921 :    
1922 :     Returns a list of B<DBObject>s that satisfy the query conditions.
1923 :    
1924 :     =back
1925 :    
1926 :     =cut
1927 :     #: Return Type @%
1928 :     sub GetList {
1929 :     # Get the parameters.
1930 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1931 : parrello 1.10 # Declare the return variable.
1932 :     my @retVal = ();
1933 :     # Perform the query.
1934 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
1935 : parrello 1.10 # Loop through the results.
1936 :     while (my $object = $query->Fetch) {
1937 :     push @retVal, $object;
1938 :     }
1939 : parrello 1.6 # Return the result.
1940 :     return @retVal;
1941 :     }
1942 :    
1943 : parrello 1.45 =head3 GetCount
1944 :    
1945 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
1946 :    
1947 :     Return the number of rows found by a specified query. This method would
1948 :     normally be used to count the records in a single table. For example, in a
1949 :     genetics database
1950 :    
1951 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
1952 :    
1953 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
1954 :     to use it to return records based on a join. For example,
1955 :    
1956 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
1957 : parrello 1.45 ['homo %']);
1958 :    
1959 :     would return the number of features for genomes in the genus I<homo>. Note that
1960 :     only the rows from the first table are counted. If the above command were
1961 :    
1962 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
1963 :     ['homo %']);
1964 :    
1965 :     it would return the number of genomes, not the number of genome/feature pairs.
1966 :    
1967 :     =over 4
1968 :    
1969 :     =item objectNames
1970 :    
1971 :     Reference to a list of the objects (entities and relationships) included in the
1972 :     query.
1973 :    
1974 :     =item filter
1975 :    
1976 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
1977 :     method.
1978 :    
1979 :     =item params
1980 :    
1981 :     Reference to a list of the parameter values to be substituted for the parameter marks
1982 :     in the filter.
1983 :    
1984 :     =item RETURN
1985 :    
1986 :     Returns a count of the number of records in the first table that would satisfy
1987 :     the query.
1988 :    
1989 :     =back
1990 :    
1991 :     =cut
1992 :    
1993 :     sub GetCount {
1994 :     # Get the parameters.
1995 :     my ($self, $objectNames, $filter, $params) = @_;
1996 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
1997 :     if (! defined($params)) {
1998 :     $params = [];
1999 :     }
2000 : parrello 1.45 # Declare the return variable.
2001 :     my $retVal;
2002 : parrello 1.47 # Find out if we're counting an entity or a relationship.
2003 :     my $countedField;
2004 :     if ($self->IsEntity($objectNames->[0])) {
2005 :     $countedField = "id";
2006 :     } else {
2007 :     # For a relationship we count the to-link because it's usually more
2008 :     # numerous. Note we're automatically converting to the SQL form
2009 :     # of the field name (to_link vs. to-link).
2010 :     $countedField = "to_link";
2011 :     }
2012 : parrello 1.45 # Create the SQL command suffix to get the desired records.
2013 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2014 :     $filter);
2015 :     # Prefix it with text telling it we want a record count.
2016 :     my $firstObject = $mappedNameListRef->[0];
2017 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2018 : parrello 1.45 # Prepare and execute the command.
2019 :     my $sth = $self->_GetStatementHandle($command, $params);
2020 :     # Get the count value.
2021 :     ($retVal) = $sth->fetchrow_array();
2022 :     # Check for a problem.
2023 :     if (! defined($retVal)) {
2024 :     if ($sth->err) {
2025 :     # Here we had an SQL error.
2026 :     Confess("Error retrieving row count: " . $sth->errstr());
2027 :     } else {
2028 :     # Here we have no result.
2029 :     Confess("No result attempting to retrieve row count.");
2030 :     }
2031 :     }
2032 :     # Return the result.
2033 :     return $retVal;
2034 :     }
2035 :    
2036 : parrello 1.1 =head3 ComputeObjectSentence
2037 :    
2038 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2039 : parrello 1.1
2040 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
2041 :    
2042 :     =over 4
2043 :    
2044 :     =item objectName
2045 :    
2046 :     Name of the entity or relationship.
2047 :    
2048 :     =item RETURN
2049 :    
2050 :     Returns a string containing the entity name or a relationship sentence.
2051 :    
2052 :     =back
2053 :    
2054 :     =cut
2055 :    
2056 :     sub ComputeObjectSentence {
2057 : parrello 1.10 # Get the parameters.
2058 :     my ($self, $objectName) = @_;
2059 :     # Set the default return value.
2060 :     my $retVal = $objectName;
2061 :     # Look for the object as a relationship.
2062 :     my $relTable = $self->{_metaData}->{Relationships};
2063 :     if (exists $relTable->{$objectName}) {
2064 :     # Get the relationship sentence.
2065 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2066 :     }
2067 :     # Return the result.
2068 :     return $retVal;
2069 : parrello 1.1 }
2070 :    
2071 :     =head3 DumpRelations
2072 :    
2073 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
2074 : parrello 1.1
2075 :     Write the contents of all the relations to tab-delimited files in the specified directory.
2076 :     Each file will have the same name as the relation dumped, with an extension of DTX.
2077 :    
2078 :     =over 4
2079 :    
2080 :     =item outputDirectory
2081 :    
2082 :     Name of the directory into which the relation files should be dumped.
2083 :    
2084 :     =back
2085 :    
2086 :     =cut
2087 :    
2088 :     sub DumpRelations {
2089 : parrello 1.10 # Get the parameters.
2090 :     my ($self, $outputDirectory) = @_;
2091 :     # Now we need to run through all the relations. First, we loop through the entities.
2092 :     my $metaData = $self->{_metaData};
2093 :     my $entities = $metaData->{Entities};
2094 :     for my $entityName (keys %{$entities}) {
2095 :     my $entityStructure = $entities->{$entityName};
2096 :     # Get the entity's relations.
2097 :     my $relationList = $entityStructure->{Relations};
2098 :     # Loop through the relations, dumping them.
2099 :     for my $relationName (keys %{$relationList}) {
2100 :     my $relation = $relationList->{$relationName};
2101 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
2102 :     }
2103 :     }
2104 :     # Next, we loop through the relationships.
2105 :     my $relationships = $metaData->{Relationships};
2106 :     for my $relationshipName (keys %{$relationships}) {
2107 :     my $relationshipStructure = $relationships->{$relationshipName};
2108 :     # Dump this relationship's relation.
2109 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2110 :     }
2111 : parrello 1.1 }
2112 :    
2113 : parrello 1.51 =head3 InsertValue
2114 :    
2115 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2116 :    
2117 :     This method will insert a new value into the database. The value must be one
2118 :     associated with a secondary relation, since primary values cannot be inserted:
2119 :     they occur exactly once. Secondary values, on the other hand, can be missing
2120 :     or multiply-occurring.
2121 :    
2122 :     =over 4
2123 :    
2124 :     =item entityID
2125 :    
2126 :     ID of the object that is to receive the new value.
2127 :    
2128 :     =item fieldName
2129 :    
2130 :     Field name for the new value-- this includes the entity name, since
2131 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2132 :    
2133 :     =item value
2134 :    
2135 :     New value to be put in the field.
2136 :    
2137 :     =back
2138 :    
2139 :     =cut
2140 :    
2141 :     sub InsertValue {
2142 :     # Get the parameters.
2143 :     my ($self, $entityID, $fieldName, $value) = @_;
2144 :     # Parse the entity name and the real field name.
2145 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2146 :     my $entityName = $1;
2147 :     my $fieldTitle = $2;
2148 :     # Get its descriptor.
2149 :     if (!$self->IsEntity($entityName)) {
2150 :     Confess("$entityName is not a valid entity.");
2151 :     } else {
2152 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2153 :     # Find the relation containing this field.
2154 :     my $fieldHash = $entityData->{Fields};
2155 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
2156 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
2157 :     } else {
2158 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
2159 :     if ($relation eq $entityName) {
2160 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2161 :     } else {
2162 :     # Now we can create an INSERT statement.
2163 :     my $dbh = $self->{_dbh};
2164 :     my $fixedName = _FixName($fieldTitle);
2165 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2166 : parrello 1.51 # Execute the command.
2167 :     $dbh->SQL($statement, 0, $entityID, $value);
2168 :     }
2169 :     }
2170 :     }
2171 :     } else {
2172 :     Confess("$fieldName is not a valid field name.");
2173 :     }
2174 :     }
2175 :    
2176 : parrello 1.1 =head3 InsertObject
2177 :    
2178 : parrello 1.18 C<< my $ok = $erdb->InsertObject($objectType, \%fieldHash); >>
2179 : parrello 1.1
2180 :     Insert an object into the database. The object is defined by a type name and then a hash
2181 :     of field names to values. Field values in the primary relation are represented by scalars.
2182 :     (Note that for relationships, the primary relation is the B<only> relation.)
2183 :     Field values for the other relations comprising the entity are always list references. For
2184 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2185 :     C<ZP_00210270.1> and C<gi|46206278>.
2186 :    
2187 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2188 : parrello 1.1
2189 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2190 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2191 :    
2192 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2193 : parrello 1.1
2194 :     =over 4
2195 :    
2196 :     =item newObjectType
2197 :    
2198 :     Type name of the object to insert.
2199 :    
2200 :     =item fieldHash
2201 :    
2202 :     Hash of field names to values.
2203 :    
2204 :     =item RETURN
2205 :    
2206 :     Returns 1 if successful, 0 if an error occurred.
2207 :    
2208 :     =back
2209 :    
2210 :     =cut
2211 :    
2212 :     sub InsertObject {
2213 : parrello 1.10 # Get the parameters.
2214 :     my ($self, $newObjectType, $fieldHash) = @_;
2215 :     # Denote that so far we appear successful.
2216 :     my $retVal = 1;
2217 :     # Get the database handle.
2218 :     my $dbh = $self->{_dbh};
2219 :     # Get the relation list.
2220 :     my $relationTable = $self->_GetRelationTable($newObjectType);
2221 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
2222 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
2223 :     # stop the loop.
2224 :     my @relationList = keys %{$relationTable};
2225 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2226 :     my $relationName = $relationList[$i];
2227 :     my $relationDefinition = $relationTable->{$relationName};
2228 :     # Get the relation's fields. For each field we will collect a value in the corresponding
2229 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
2230 :     # @missing list.
2231 :     my @fieldList = @{$relationDefinition->{Fields}};
2232 :     my @fieldNameList = ();
2233 :     my @valueList = ();
2234 :     my @missing = ();
2235 :     my $recordCount = 1;
2236 :     for my $fieldDescriptor (@fieldList) {
2237 :     # Get the field name and save it. Note we need to fix it up so the hyphens
2238 :     # are converted to underscores.
2239 :     my $fieldName = $fieldDescriptor->{name};
2240 :     push @fieldNameList, _FixName($fieldName);
2241 :     # Look for the named field in the incoming structure. Note that we are looking
2242 :     # for the real field name, not the fixed-up one!
2243 :     if (exists $fieldHash->{$fieldName}) {
2244 :     # Here we found the field. Stash it in the value list.
2245 :     my $value = $fieldHash->{$fieldName};
2246 :     push @valueList, $value;
2247 :     # If the value is a list, we may need to increment the record count.
2248 :     if (ref $value eq "ARRAY") {
2249 :     my $thisCount = @{$value};
2250 :     if ($recordCount == 1) {
2251 :     # Here we have our first list, so we save its count.
2252 :     $recordCount = $thisCount;
2253 :     } elsif ($recordCount != $thisCount) {
2254 :     # Here we have a second list, so its length has to match the
2255 :     # previous lists.
2256 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2257 :     $retVal = 0;
2258 :     }
2259 :     }
2260 :     } else {
2261 :     # Here the field is not present. Flag it as missing.
2262 :     push @missing, $fieldName;
2263 :     }
2264 :     }
2265 :     # If we are the primary relation, add the new-record flag.
2266 :     if ($relationName eq $newObjectType) {
2267 :     push @valueList, 1;
2268 :     push @fieldNameList, "new_record";
2269 :     }
2270 :     # Only proceed if there are no missing fields.
2271 :     if (@missing > 0) {
2272 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2273 :     join(' ', @missing)) if T(1);
2274 :     } else {
2275 :     # Build the INSERT statement.
2276 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2277 :     ") VALUES (";
2278 :     # Create a marker list of the proper size and put it in the statement.
2279 :     my @markers = ();
2280 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2281 :     $statement .= join(', ', @markers) . ")";
2282 :     # We have the insert statement, so prepare it.
2283 :     my $sth = $dbh->prepare_command($statement);
2284 :     Trace("Insert statement prepared: $statement") if T(3);
2285 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2286 :     # a list, we use the current element. The values are stored in the @parameterList array.
2287 :     my $done = 0;
2288 :     for (my $i = 0; $i < $recordCount; $i++) {
2289 :     # Clear the parameter list array.
2290 :     my @parameterList = ();
2291 :     # Loop through the values.
2292 :     for my $value (@valueList) {
2293 :     # Check to see if this is a scalar value.
2294 :     if (ref $value eq "ARRAY") {
2295 :     # Here we have a list value. Pull the current entry.
2296 :     push @parameterList, $value->[$i];
2297 :     } else {
2298 :     # Here we have a scalar value. Use it unmodified.
2299 :     push @parameterList, $value;
2300 :     }
2301 :     }
2302 :     # Execute the INSERT statement with the specified parameter list.
2303 :     $retVal = $sth->execute(@parameterList);
2304 :     if (!$retVal) {
2305 :     my $errorString = $sth->errstr();
2306 :     Trace("Insert error: $errorString.") if T(0);
2307 :     }
2308 :     }
2309 :     }
2310 :     }
2311 :     # Return the success indicator.
2312 :     return $retVal;
2313 : parrello 1.1 }
2314 :    
2315 :     =head3 LoadTable
2316 :    
2317 : parrello 1.18 C<< my %results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2318 : parrello 1.1
2319 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2320 :     first.
2321 : parrello 1.1
2322 :     =over 4
2323 :    
2324 :     =item fileName
2325 :    
2326 :     Name of the file from which the table data should be loaded.
2327 :    
2328 :     =item relationName
2329 :    
2330 :     Name of the relation to be loaded. This is the same as the table name.
2331 :    
2332 :     =item truncateFlag
2333 :    
2334 :     TRUE if the table should be dropped and re-created, else FALSE
2335 :    
2336 :     =item RETURN
2337 :    
2338 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2339 : parrello 1.1
2340 :     =back
2341 :    
2342 :     =cut
2343 :     sub LoadTable {
2344 : parrello 1.10 # Get the parameters.
2345 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2346 :     # Create the statistical return object.
2347 :     my $retVal = _GetLoadStats();
2348 :     # Trace the fact of the load.
2349 :     Trace("Loading table $relationName from $fileName") if T(2);
2350 :     # Get the database handle.
2351 :     my $dbh = $self->{_dbh};
2352 : parrello 1.22 # Get the input file size.
2353 :     my $fileSize = -s $fileName;
2354 : parrello 1.10 # Get the relation data.
2355 :     my $relation = $self->_FindRelation($relationName);
2356 :     # Check the truncation flag.
2357 :     if ($truncateFlag) {
2358 :     Trace("Creating table $relationName") if T(2);
2359 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2360 :     # divide it by the estimated row size, and then multiply by 1.5 to
2361 :     # leave extra room. We postulate a minimum row count of 1000 to
2362 :     # prevent problems with incoming empty load files.
2363 :     my $rowSize = $self->EstimateRowSize($relationName);
2364 :     my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2365 : parrello 1.10 # Re-create the table without its index.
2366 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2367 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2368 :     if ($dbh->{_preIndex}) {
2369 :     eval {
2370 :     $self->CreateIndex($relationName);
2371 :     };
2372 :     if ($@) {
2373 :     $retVal->AddMessage($@);
2374 :     }
2375 :     }
2376 :     }
2377 : parrello 1.3 # Load the table.
2378 : parrello 1.10 my $rv;
2379 :     eval {
2380 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2381 : parrello 1.10 };
2382 :     if (!defined $rv) {
2383 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2384 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2385 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2386 :     } else {
2387 : parrello 1.22 # Here we successfully loaded the table.
2388 :     $retVal->Add("tables");
2389 :     my $size = -s $fileName;
2390 :     Trace("$size bytes loaded into $relationName.") if T(2);
2391 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2392 : parrello 1.70 if ($truncateFlag) {
2393 :     # Indexes are created here for PostGres. For PostGres, indexes are
2394 :     # best built at the end. For MySQL, the reverse is true.
2395 :     if (! $dbh->{_preIndex}) {
2396 :     eval {
2397 :     $self->CreateIndex($relationName);
2398 :     };
2399 :     if ($@) {
2400 :     $retVal->AddMessage($@);
2401 :     }
2402 :     }
2403 :     # The full-text index (if any) is always built last, even for MySQL.
2404 :     # First we need to see if this table has a full-text index. Only
2405 :     # primary relations are allowed that privilege.
2406 :     if ($self->_IsPrimary($relationName)) {
2407 :     # Get the relation's entity/relationship structure.
2408 :     my $structure = $self->_GetStructure($relationName);
2409 :     # Check for a searchable fields list.
2410 :     if (exists $structure->{searchFields}) {
2411 :     # Here we know that we need to create a full-text search index.
2412 :     # Get an SQL-formatted field name list.
2413 :     my $fields = join(", ", $self->_FixNames(@{$structure->{searchFields}}));
2414 :     # Create the index.
2415 : parrello 1.75 $dbh->create_index(tbl => $relationName, idx => "search_idx",
2416 : parrello 1.70 flds => $fields, kind => 'fulltext');
2417 :     }
2418 : parrello 1.10 }
2419 :     }
2420 :     }
2421 : parrello 1.20 # Analyze the table to improve performance.
2422 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2423 : olson 1.16 $dbh->vacuum_it($relationName);
2424 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2425 : parrello 1.10 # Return the statistics.
2426 :     return $retVal;
2427 : parrello 1.1 }
2428 :    
2429 : parrello 1.73 =head3 DropRelation
2430 : parrello 1.1
2431 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2432 : parrello 1.1
2433 : parrello 1.73 Physically drop a relation from the database.
2434 : parrello 1.1
2435 :     =over 4
2436 :    
2437 : parrello 1.73 =item relationName
2438 : parrello 1.1
2439 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2440 :     no effect.
2441 : parrello 1.1
2442 :     =back
2443 :    
2444 :     =cut
2445 :    
2446 : parrello 1.73 sub DropRelation {
2447 : parrello 1.10 # Get the parameters.
2448 : parrello 1.73 my ($self, $relationName) = @_;
2449 :     # Get the database handle.
2450 :     my $dbh = $self->{_dbh};
2451 :     # Drop the relation. The method used here has no effect if the relation
2452 :     # does not exist.
2453 : parrello 1.74 Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2454 :     $dbh->drop_table(tbl => $relationName);
2455 : parrello 1.1 }
2456 :    
2457 : parrello 1.6 =head3 GetEntity
2458 :    
2459 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2460 : parrello 1.6
2461 :     Return an object describing the entity instance with a specified ID.
2462 :    
2463 :     =over 4
2464 :    
2465 :     =item entityType
2466 :    
2467 :     Entity type name.
2468 :    
2469 :     =item ID
2470 :    
2471 :     ID of the desired entity.
2472 :    
2473 :     =item RETURN
2474 :    
2475 :     Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2476 :     instance is found with the specified key.
2477 :    
2478 :     =back
2479 :    
2480 :     =cut
2481 :    
2482 :     sub GetEntity {
2483 : parrello 1.10 # Get the parameters.
2484 :     my ($self, $entityType, $ID) = @_;
2485 :     # Create a query.
2486 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2487 : parrello 1.10 # Get the first (and only) object.
2488 :     my $retVal = $query->Fetch();
2489 :     # Return the result.
2490 :     return $retVal;
2491 : parrello 1.6 }
2492 :    
2493 : parrello 1.69 =head3 GetChoices
2494 :    
2495 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2496 :    
2497 :     Return a list of all the values for the specified field that are represented in the
2498 :     specified entity.
2499 :    
2500 :     Note that if the field is not indexed, then this will be a very slow operation.
2501 :    
2502 :     =over 4
2503 :    
2504 :     =item entityName
2505 :    
2506 :     Name of an entity in the database.
2507 :    
2508 :     =item fieldName
2509 :    
2510 :     Name of a field belonging to the entity. This is a raw field name without
2511 :     the standard parenthesized notation used in most calls.
2512 :    
2513 :     =item RETURN
2514 :    
2515 :     Returns a list of the distinct values for the specified field in the database.
2516 :    
2517 :     =back
2518 :    
2519 :     =cut
2520 :    
2521 :     sub GetChoices {
2522 :     # Get the parameters.
2523 :     my ($self, $entityName, $fieldName) = @_;
2524 :     # Declare the return variable.
2525 :     my @retVal;
2526 :     # Get the entity data structure.
2527 :     my $entityData = $self->_GetStructure($entityName);
2528 :     # Get the field.
2529 :     my $fieldHash = $entityData->{Fields};
2530 :     if (! exists $fieldHash->{$fieldName}) {
2531 :     Confess("$fieldName not found in $entityName.");
2532 :     } else {
2533 :     # Get the name of the relation containing the field.
2534 :     my $relation = $fieldHash->{$fieldName}->{relation};
2535 :     # Fix up the field name.
2536 :     my $realName = _FixName($fieldName);
2537 :     # Get the database handle.
2538 :     my $dbh = $self->{_dbh};
2539 :     # Query the database.
2540 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2541 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
2542 :     @retVal = sort map { $_->[0] } @{$results};
2543 :     }
2544 :     # Return the result.
2545 :     return @retVal;
2546 :     }
2547 :    
2548 : parrello 1.6 =head3 GetEntityValues
2549 :    
2550 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2551 : parrello 1.6
2552 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
2553 :     does not exist, an empty list is returned.
2554 : parrello 1.6
2555 :     =over 4
2556 :    
2557 :     =item entityType
2558 :    
2559 :     Entity type name.
2560 :    
2561 :     =item ID
2562 :    
2563 :     ID of the desired entity.
2564 :    
2565 :     =item fields
2566 :    
2567 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2568 :    
2569 :     =item RETURN
2570 :    
2571 :     Returns a flattened list of the values of the specified fields for the specified entity.
2572 :    
2573 :     =back
2574 :    
2575 :     =cut
2576 :    
2577 :     sub GetEntityValues {
2578 : parrello 1.10 # Get the parameters.
2579 :     my ($self, $entityType, $ID, $fields) = @_;
2580 :     # Get the specified entity.
2581 :     my $entity = $self->GetEntity($entityType, $ID);
2582 :     # Declare the return list.
2583 :     my @retVal = ();
2584 :     # If we found the entity, push the values into the return list.
2585 :     if ($entity) {
2586 :     push @retVal, $entity->Values($fields);
2587 :     }
2588 :     # Return the result.
2589 :     return @retVal;
2590 : parrello 1.6 }
2591 : parrello 1.1
2592 : parrello 1.7 =head3 GetAll
2593 :    
2594 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2595 : parrello 1.7
2596 :     Return a list of values taken from the objects returned by a query. The first three
2597 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
2598 :     a list of the fields desired from each record found by the query. The field name
2599 :     syntax is the standard syntax used for fields in the B<ERDB> system--
2600 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2601 :     or relationship and I<fieldName> is the name of the field.
2602 :    
2603 :     The list returned will be a list of lists. Each element of the list will contain
2604 :     the values returned for the fields specified in the fourth parameter. If one of the
2605 :     fields specified returns multiple values, they are flattened in with the rest. For
2606 :     example, the following call will return a list of the features in a particular
2607 :     spreadsheet cell, and each feature will be represented by a list containing the
2608 :     feature ID followed by all of its aliases.
2609 :    
2610 : parrello 1.18 C<< $query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2611 : parrello 1.7
2612 :     =over 4
2613 :    
2614 :     =item objectNames
2615 :    
2616 :     List containing the names of the entity and relationship objects to be retrieved.
2617 :    
2618 :     =item filterClause
2619 :    
2620 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2621 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2622 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2623 :     parameter list as additional parameters. The fields in a filter clause can come from primary
2624 :     entity relations, relationship relations, or secondary entity relations; however, all of the
2625 :     entities and relationships involved must be included in the list of object names.
2626 :    
2627 :     =item parameterList
2628 :    
2629 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
2630 :    
2631 :     =item fields
2632 :    
2633 :     List of the fields to be returned in each element of the list returned.
2634 :    
2635 :     =item count
2636 :    
2637 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
2638 :    
2639 :     =item RETURN
2640 :    
2641 :     Returns a list of list references. Each element of the return list contains the values for the
2642 :     fields specified in the B<fields> parameter.
2643 :    
2644 :     =back
2645 :    
2646 :     =cut
2647 :     #: Return Type @@;
2648 :     sub GetAll {
2649 : parrello 1.10 # Get the parameters.
2650 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2651 :     # Translate the parameters from a list reference to a list. If the parameter
2652 :     # list is a scalar we convert it into a singleton list.
2653 :     my @parmList = ();
2654 :     if (ref $parameterList eq "ARRAY") {
2655 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
2656 : parrello 1.10 @parmList = @{$parameterList};
2657 :     } else {
2658 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2659 : parrello 1.10 push @parmList, $parameterList;
2660 :     }
2661 : parrello 1.30 # Insure the counter has a value.
2662 :     if (!defined $count) {
2663 :     $count = 0;
2664 :     }
2665 :     # Add the row limit to the filter clause.
2666 :     if ($count > 0) {
2667 :     $filterClause .= " LIMIT $count";
2668 :     }
2669 : parrello 1.10 # Create the query.
2670 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
2671 : parrello 1.10 # Set up a counter of the number of records read.
2672 :     my $fetched = 0;
2673 :     # Loop through the records returned, extracting the fields. Note that if the
2674 :     # counter is non-zero, we stop when the number of records read hits the count.
2675 :     my @retVal = ();
2676 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2677 :     my @rowData = $row->Values($fields);
2678 :     push @retVal, \@rowData;
2679 :     $fetched++;
2680 :     }
2681 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2682 : parrello 1.10 # Return the resulting list.
2683 :     return @retVal;
2684 : parrello 1.7 }
2685 :    
2686 : parrello 1.55 =head3 Exists
2687 :    
2688 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
2689 :    
2690 :     Return TRUE if an entity exists, else FALSE.
2691 :    
2692 :     =over 4
2693 :    
2694 :     =item entityName
2695 :    
2696 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2697 :    
2698 :     =item entityID
2699 :    
2700 :     ID of the entity instance whose existence is to be checked.
2701 :    
2702 :     =item RETURN
2703 :    
2704 :     Returns TRUE if the entity instance exists, else FALSE.
2705 :    
2706 :     =back
2707 :    
2708 :     =cut
2709 :     #: Return Type $;
2710 :     sub Exists {
2711 :     # Get the parameters.
2712 :     my ($self, $entityName, $entityID) = @_;
2713 :     # Check for the entity instance.
2714 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2715 :     my $testInstance = $self->GetEntity($entityName, $entityID);
2716 :     # Return an existence indicator.
2717 :     my $retVal = ($testInstance ? 1 : 0);
2718 :     return $retVal;
2719 :     }
2720 :    
2721 : parrello 1.18 =head3 EstimateRowSize
2722 :    
2723 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2724 :    
2725 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
2726 :     up the average length for each data type.
2727 :    
2728 :     =over 4
2729 :    
2730 :     =item relName
2731 :    
2732 :     Name of the relation whose estimated row size is desired.
2733 :    
2734 :     =item RETURN
2735 :    
2736 :     Returns an estimate of the row size for the specified relation.
2737 :    
2738 :     =back
2739 :    
2740 :     =cut
2741 :     #: Return Type $;
2742 :     sub EstimateRowSize {
2743 :     # Get the parameters.
2744 :     my ($self, $relName) = @_;
2745 :     # Declare the return variable.
2746 :     my $retVal = 0;
2747 :     # Find the relation descriptor.
2748 :     my $relation = $self->_FindRelation($relName);
2749 :     # Get the list of fields.
2750 :     for my $fieldData (@{$relation->{Fields}}) {
2751 :     # Get the field type and add its length.
2752 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
2753 :     $retVal += $fieldLen;
2754 :     }
2755 :     # Return the result.
2756 :     return $retVal;
2757 :     }
2758 :    
2759 : parrello 1.38 =head3 GetFieldTable
2760 :    
2761 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
2762 :    
2763 :     Get the field structure for a specified entity or relationship.
2764 :    
2765 :     =over 4
2766 :    
2767 :     =item objectName
2768 :    
2769 :     Name of the desired entity or relationship.
2770 :    
2771 :     =item RETURN
2772 :    
2773 :     The table containing the field descriptors for the specified object.
2774 :    
2775 :     =back
2776 :    
2777 :     =cut
2778 :    
2779 :     sub GetFieldTable {
2780 :     # Get the parameters.
2781 :     my ($self, $objectName) = @_;
2782 :     # Get the descriptor from the metadata.
2783 :     my $objectData = $self->_GetStructure($objectName);
2784 :     # Return the object's field table.
2785 :     return $objectData->{Fields};
2786 :     }
2787 :    
2788 : parrello 1.73 =head3 SplitKeywords
2789 :    
2790 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
2791 :    
2792 :     This method returns a list of the positive keywords in the specified
2793 :     keyword string. All of the operators will have been stripped off,
2794 :     and if the keyword is preceded by a minus operator (C<->), it will
2795 :     not be in the list returned. The idea here is to get a list of the
2796 :     keywords the user wants to see. The list will be processed to remove
2797 :     duplicates.
2798 :    
2799 :     It is possible to create a string that confuses this method. For example
2800 :    
2801 :     frog toad -frog
2802 :    
2803 :     would return both C<frog> and C<toad>. If this is a problem we can deal
2804 :     with it later.
2805 :    
2806 :     =over 4
2807 :    
2808 :     =item keywordString
2809 :    
2810 :     The keyword string to be parsed.
2811 :    
2812 :     =item RETURN
2813 :    
2814 :     Returns a list of the words in the keyword string the user wants to
2815 :     see.
2816 :    
2817 :     =back
2818 :    
2819 :     =cut
2820 :    
2821 :     sub SplitKeywords {
2822 :     # Get the parameters.
2823 :     my ($keywordString) = @_;
2824 :     # Make a safety copy of the string. (This helps during debugging.)
2825 :     my $workString = $keywordString;
2826 :     # Convert operators we don't care about to spaces.
2827 :     $workString =~ tr/+"()<>/ /;
2828 :     # Split the rest of the string along space boundaries. Note that we
2829 :     # eliminate any words that are zero length or begin with a minus sign.
2830 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
2831 :     # Use a hash to remove duplicates.
2832 :     my %words = map { $_ => 1 } @wordList;
2833 :     # Return the result.
2834 :     return sort keys %words;
2835 :     }
2836 :    
2837 :     =head3 ValidateFieldName
2838 :    
2839 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
2840 :    
2841 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
2842 :     be hyphenated words subject to certain restrictions.
2843 :    
2844 :     =over 4
2845 :    
2846 :     =item fieldName
2847 :    
2848 :     Field name to be validated.
2849 :    
2850 :     =item RETURN
2851 :    
2852 :     Returns TRUE if the field name is valid, else FALSE.
2853 :    
2854 :     =back
2855 :    
2856 :     =cut
2857 :    
2858 :     sub ValidateFieldName {
2859 :     # Get the parameters.
2860 :     my ($fieldName) = @_;
2861 :     # Declare the return variable. The field name is valid until we hear
2862 :     # differently.
2863 :     my $retVal = 1;
2864 :     # Look for bad stuff in the name.
2865 :     if ($fieldName =~ /--/) {
2866 :     # Here we have a doubled minus sign.
2867 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
2868 :     $retVal = 0;
2869 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
2870 :     # Here the field name is missing the initial letter.
2871 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
2872 :     $retVal = 0;
2873 :     } else {
2874 : parrello 1.75 # Strip out the minus signs. Everything remaining must be a letter,
2875 :     # underscore, or digit.
2876 : parrello 1.73 my $strippedName = $fieldName;
2877 :     $strippedName =~ s/-//g;
2878 : parrello 1.75 if ($strippedName !~ /^(\w|\d)+$/) {
2879 : parrello 1.73 Trace("Field name $fieldName contains illegal characters.") if T(1);
2880 :     $retVal = 0;
2881 :     }
2882 :     }
2883 :     # Return the result.
2884 :     return $retVal;
2885 :     }
2886 :    
2887 :     =head3 ReadMetaXML
2888 :    
2889 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
2890 :    
2891 :     This method reads a raw database definition XML file and returns it.
2892 :     Normally, the metadata used by the ERDB system has been processed and
2893 :     modified to make it easier to load and retrieve the data; however,
2894 :     this method can be used to get the data in its raw form.
2895 :    
2896 :     =over 4
2897 :    
2898 :     =item fileName
2899 :    
2900 :     Name of the XML file to read.
2901 :    
2902 :     =item RETURN
2903 :    
2904 :     Returns a hash reference containing the raw XML data from the specified file.
2905 :    
2906 :     =back
2907 :    
2908 :     =cut
2909 :    
2910 :     sub ReadMetaXML {
2911 :     # Get the parameters.
2912 :     my ($fileName) = @_;
2913 :     # Read the XML.
2914 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
2915 :     Trace("XML metadata loaded from file $fileName.") if T(1);
2916 :     # Return the result.
2917 :     return $retVal;
2918 :     }
2919 :    
2920 :     =head3 GetEntityFieldHash
2921 :    
2922 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
2923 :    
2924 :     Get the field hash of the named entity in the specified raw XML structure.
2925 :     The field hash may not exist, in which case we need to create it.
2926 :    
2927 :     =over 4
2928 :    
2929 :     =item structure
2930 :    
2931 :     Raw XML structure defininng the database. This is not the run-time XML used by
2932 :     an ERDB object, since that has all sorts of optimizations built-in.
2933 :    
2934 :     =item entityName
2935 :    
2936 :     Name of the entity whose field structure is desired.
2937 :    
2938 :     =item RETURN
2939 :    
2940 :     Returns the field hash used to define the entity's fields.
2941 :    
2942 :     =back
2943 :    
2944 :     =cut
2945 :    
2946 :     sub GetEntityFieldHash {
2947 :     # Get the parameters.
2948 :     my ($structure, $entityName) = @_;
2949 :     # Get the entity structure.
2950 :     my $entityData = $structure->{Entities}->{$entityName};
2951 :     # Look for a field structure.
2952 :     my $retVal = $entityData->{Fields};
2953 :     # If it doesn't exist, create it.
2954 :     if (! defined($retVal)) {
2955 :     $entityData->{Fields} = {};
2956 :     $retVal = $entityData->{Fields};
2957 :     }
2958 :     # Return the result.
2959 :     return $retVal;
2960 :     }
2961 :    
2962 :     =head3 WriteMetaXML
2963 :    
2964 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
2965 :    
2966 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
2967 :     used to update the database definition. It must be used with care, however, since it
2968 :     will only work on a raw structure, not on the processed structure created by an ERDB
2969 :     constructor.
2970 :    
2971 :     =over 4
2972 :    
2973 :     =item structure
2974 :    
2975 :     XML structure to be written to the file.
2976 :    
2977 :     =item fileName
2978 :    
2979 :     Name of the output file to which the updated XML should be stored.
2980 :    
2981 :     =back
2982 :    
2983 :     =cut
2984 :    
2985 :     sub WriteMetaXML {
2986 :     # Get the parameters.
2987 :     my ($structure, $fileName) = @_;
2988 :     # Compute the output.
2989 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
2990 :     # Write it to the file.
2991 :     my $xmlOut = Open(undef, ">$fileName");
2992 :     print $xmlOut $fileString;
2993 :     }
2994 :    
2995 :    
2996 :     =head3 HTMLNote
2997 :    
2998 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
2999 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3000 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
3001 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3002 :    
3003 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3004 :    
3005 :     =over 4
3006 :    
3007 :     =item dataString
3008 :    
3009 :     String to convert to HTML.
3010 :    
3011 :     =item RETURN
3012 :    
3013 :     An HTML string derived from the input string.
3014 :    
3015 :     =back
3016 :    
3017 :     =cut
3018 :    
3019 :     sub HTMLNote {
3020 :     # Get the parameter.
3021 :     my ($dataString) = @_;
3022 :     # HTML-escape the text.
3023 :     my $retVal = CGI::escapeHTML($dataString);
3024 :     # Substitute the bulletin board codes.
3025 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3026 :     $retVal =~ s!\[p\]!</p><p>!g;
3027 :     # Return the result.
3028 :     return $retVal;
3029 :     }
3030 :    
3031 :    
3032 : parrello 1.48 =head2 Data Mining Methods
3033 :    
3034 : parrello 1.38 =head3 GetUsefulCrossValues
3035 :    
3036 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3037 :    
3038 :     Return a list of the useful attributes that would be returned by a B<Cross> call
3039 :     from an entity of the source entity type through the specified relationship. This
3040 :     means it will return the fields of the target entity type and the intersection data
3041 :     fields in the relationship. Only primary table fields are returned. In other words,
3042 :     the field names returned will be for fields where there is always one and only one
3043 :     value.
3044 :    
3045 :     =over 4
3046 :    
3047 :     =item sourceEntity
3048 :    
3049 :     Name of the entity from which the relationship crossing will start.
3050 :    
3051 :     =item relationship
3052 :    
3053 :     Name of the relationship being crossed.
3054 :    
3055 :     =item RETURN
3056 :    
3057 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3058 :    
3059 :     =back
3060 :    
3061 :     =cut
3062 :     #: Return Type @;
3063 :     sub GetUsefulCrossValues {
3064 :     # Get the parameters.
3065 :     my ($self, $sourceEntity, $relationship) = @_;
3066 :     # Declare the return variable.
3067 :     my @retVal = ();
3068 :     # Determine the target entity for the relationship. This is whichever entity is not
3069 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
3070 :     # the TO, and vice versa.
3071 :     my $relStructure = $self->_GetStructure($relationship);
3072 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3073 :     my $targetEntity = $relStructure->{$targetEntityType};
3074 :     # Get the field table for the entity.
3075 :     my $entityFields = $self->GetFieldTable($targetEntity);
3076 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
3077 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
3078 :     # must match the entity name.
3079 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3080 :     keys %{$entityFields};
3081 :     # Push the fields found onto the return variable.
3082 :     push @retVal, sort @fieldList;
3083 :     # Get the field table for the relationship.
3084 :     my $relationshipFields = $self->GetFieldTable($relationship);
3085 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3086 :     # This may end up being an empty set.
3087 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3088 :     keys %{$relationshipFields};
3089 :     # Push these onto the return list.
3090 :     push @retVal, sort @fieldList2;
3091 :     # Return the result.
3092 :     return @retVal;
3093 :     }
3094 :    
3095 : parrello 1.48 =head3 FindColumn
3096 :    
3097 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3098 :    
3099 :     Return the location a desired column in a data mining header line. The data
3100 :     mining header line is a tab-separated list of column names. The column
3101 :     identifier is either the numerical index of a column or the actual column
3102 :     name.
3103 :    
3104 :     =over 4
3105 :    
3106 :     =item headerLine
3107 :    
3108 :     The header line from a data mining command, which consists of a tab-separated
3109 :     list of column names.
3110 :    
3111 :     =item columnIdentifier
3112 :    
3113 :     Either the ordinal number of the desired column (1-based), or the name of the
3114 :     desired column.
3115 :    
3116 :     =item RETURN
3117 :    
3118 :     Returns the array index (0-based) of the desired column.
3119 :    
3120 :     =back
3121 :    
3122 :     =cut
3123 :    
3124 :     sub FindColumn {
3125 :     # Get the parameters.
3126 :     my ($headerLine, $columnIdentifier) = @_;
3127 :     # Declare the return variable.
3128 :     my $retVal;
3129 :     # Split the header line into column names.
3130 :     my @headers = ParseColumns($headerLine);
3131 :     # Determine whether we have a number or a name.
3132 :     if ($columnIdentifier =~ /^\d+$/) {
3133 :     # Here we have a number. Subtract 1 and validate the result.
3134 :     $retVal = $columnIdentifier - 1;
3135 :     if ($retVal < 0 || $retVal > $#headers) {
3136 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3137 :     }
3138 :     } else {
3139 :     # Here we have a name. We need to find it in the list.
3140 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3141 :     if ($headers[$i] eq $columnIdentifier) {
3142 :     $retVal = $i;
3143 :     }
3144 :     }
3145 :     if (! defined($retVal)) {
3146 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3147 :     }
3148 :     }
3149 :     # Return the result.
3150 :     return $retVal;
3151 :     }
3152 :    
3153 :     =head3 ParseColumns
3154 :    
3155 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
3156 : parrello 1.48
3157 :     Convert the specified data line to a list of columns.
3158 :    
3159 :     =over 4
3160 :    
3161 :     =item line
3162 :    
3163 :     A data mining input, consisting of a tab-separated list of columns terminated by a
3164 :     new-line.
3165 :    
3166 :     =item RETURN
3167 :    
3168 :     Returns a list consisting of the column values.
3169 :    
3170 :     =back
3171 :    
3172 :     =cut
3173 :    
3174 :     sub ParseColumns {
3175 :     # Get the parameters.
3176 : parrello 1.50 my ($line) = @_;
3177 : parrello 1.48 # Chop off the line-end.
3178 :     chomp $line;
3179 :     # Split it into a list.
3180 :     my @retVal = split(/\t/, $line);
3181 :     # Return the result.
3182 :     return @retVal;
3183 :     }
3184 :    
3185 : parrello 1.71 =head2 Virtual Methods
3186 :    
3187 :     =head3 CleanKeywords
3188 :    
3189 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3190 :    
3191 :     Clean up a search expression or keyword list. This is a virtual method that may
3192 :     be overridden by the subclass. The base-class method removes extra spaces
3193 :     and converts everything to lower case.
3194 :    
3195 :     =over 4
3196 :    
3197 :     =item searchExpression
3198 :    
3199 :     Search expression or keyword list to clean. Note that a search expression may
3200 :     contain boolean operators which need to be preserved. This includes leading
3201 :     minus signs.
3202 :    
3203 :     =item RETURN
3204 :    
3205 :     Cleaned expression or keyword list.
3206 :    
3207 :     =back
3208 :    
3209 :     =cut
3210 :    
3211 :     sub CleanKeywords {
3212 :     # Get the parameters.
3213 :     my ($self, $searchExpression) = @_;
3214 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
3215 :     # don't accidentally end up with an undefined value.
3216 :     my $retVal = lc($searchExpression || "");
3217 :     # Remove extra spaces.
3218 :     $retVal =~ s/\s+/ /g;
3219 :     $retVal =~ s/(^\s+)|(\s+$)//g;
3220 :     # Return the result.
3221 :     return $retVal;
3222 :     }
3223 :    
3224 : parrello 1.73 =head3 GetSourceObject
3225 :    
3226 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
3227 :    
3228 :     Return the object to be used in loading special attributes of the specified entity. The
3229 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
3230 :     XML
3231 :    
3232 : parrello 1.1 =head2 Internal Utility Methods
3233 :    
3234 : parrello 1.70 =head3 _RelationMap
3235 :    
3236 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3237 :    
3238 :     Create the relation map for an SQL query. The relation map is used by B<DBObject>
3239 :     to determine how to interpret the results of the query.
3240 :    
3241 :     =over 4
3242 :    
3243 :     =item mappedNameHashRef
3244 :    
3245 :     Reference to a hash that maps modified object names to real object names.
3246 :    
3247 :     =item mappedNameListRef
3248 :    
3249 :     Reference to a list of modified object names in the order they appear in the
3250 :     SELECT list.
3251 :    
3252 :     =item RETURN
3253 :    
3254 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3255 :     query followed by the actual name of that object. This enables the B<DBObject> to
3256 :     determine the order of the tables in the query and which object name belongs to each
3257 :     mapped object name. Most of the time these two values are the same; however, if a
3258 :     relation occurs twice in the query, the relation name in the field list and WHERE
3259 :     clause will use a mapped name (generally the actual relation name with a numeric
3260 :     suffix) that does not match the actual relation name.
3261 :    
3262 :     =back
3263 :    
3264 :     =cut
3265 :    
3266 :     sub _RelationMap {
3267 :     # Get the parameters.
3268 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3269 :     # Declare the return variable.
3270 :     my @retVal = ();
3271 :     # Build the map.
3272 :     for my $mappedName (@{$mappedNameListRef}) {
3273 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3274 :     }
3275 :     # Return it.
3276 :     return @retVal;
3277 :     }
3278 :    
3279 :    
3280 :     =head3 _SetupSQL
3281 : parrello 1.45
3282 :     Process a list of object names and a filter clause so that they can be used to
3283 :     build an SQL statement. This method takes in a reference to a list of object names
3284 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3285 :     names and the mapped name hash.
3286 :    
3287 :     This is an instance method.
3288 :    
3289 :     =over 4
3290 :    
3291 :     =item objectNames
3292 :    
3293 :     Reference to a list of the object names to be included in the query.
3294 :    
3295 :     =item filterClause
3296 :    
3297 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
3298 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
3299 :    
3300 : parrello 1.70 =item matchClause
3301 :    
3302 :     An optional full-text search clause. If specified, it will be inserted at the
3303 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
3304 :     field names should be in the form I<table>C<.>I<fieldName>.
3305 :    
3306 : parrello 1.45 =item RETURN
3307 :    
3308 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
3309 :     with the FROM clause. The second element is a reference to a list of the names to be
3310 :     used in retrieving the fields. The third element is a hash mapping the names to the
3311 :     objects they represent.
3312 :    
3313 :     =back
3314 :    
3315 :     =cut
3316 :    
3317 :     sub _SetupSQL {
3318 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
3319 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
3320 :     # same object. We start with a hash table keyed on object name that will
3321 :     # return the object suffix. The first time an object is encountered it will
3322 :     # not be found in the hash. The next time the hash will map the object name
3323 :     # to 2, then 3, and so forth.
3324 :     my %objectHash = ();
3325 :     # This list will contain the object names as they are to appear in the
3326 :     # FROM list.
3327 :     my @fromList = ();
3328 :     # This list contains the suffixed object name for each object. It is exactly
3329 :     # parallel to the list in the $objectNames parameter.
3330 :     my @mappedNameList = ();
3331 :     # Finally, this hash translates from a mapped name to its original object name.
3332 :     my %mappedNameHash = ();
3333 :     # Now we create the lists. Note that for every single name we push something into
3334 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
3335 :     # parallel to $objectNames.
3336 :     for my $objectName (@{$objectNames}) {
3337 :     # Get the next suffix for this object.
3338 :     my $suffix = $objectHash{$objectName};
3339 :     if (! $suffix) {
3340 :     # Here we are seeing the object for the first time. The object name
3341 :     # is used as is.
3342 :     push @mappedNameList, $objectName;
3343 :     push @fromList, $objectName;
3344 :     $mappedNameHash{$objectName} = $objectName;
3345 :     # Denote the next suffix will be 2.
3346 :     $objectHash{$objectName} = 2;
3347 :     } else {
3348 :     # Here we've seen the object before. We construct a new name using
3349 :     # the suffix from the hash and update the hash.
3350 :     my $mappedName = "$objectName$suffix";
3351 :     $objectHash{$objectName} = $suffix + 1;
3352 :     # The FROM list has the object name followed by the mapped name. This
3353 :     # tells SQL it's still the same table, but we're using a different name
3354 :     # for it to avoid confusion.
3355 :     push @fromList, "$objectName $mappedName";
3356 :     # The mapped-name list contains the real mapped name.
3357 :     push @mappedNameList, $mappedName;
3358 :     # Finally, enable us to get back from the mapped name to the object name.
3359 :     $mappedNameHash{$mappedName} = $objectName;
3360 :     }
3361 :     }
3362 :     # Begin the SELECT suffix. It starts with
3363 :     #
3364 :     # FROM name1, name2, ... nameN
3365 :     #
3366 :     my $suffix = "FROM " . join(', ', @fromList);
3367 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
3368 :     my $filterString = "";
3369 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
3370 :     # entities and relationships as well as primary relations to secondary ones.
3371 :     my @joinWhere = ();
3372 : parrello 1.45 # Check for a filter clause.
3373 :     if ($filterClause) {
3374 :     # Here we have one, so we convert its field names and add it to the query. First,
3375 :     # We create a copy of the filter string we can work with.
3376 : parrello 1.70 $filterString = $filterClause;
3377 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
3378 :     # object names inside other object names when we're doing our search and replace.
3379 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3380 :     # The final preparatory step is to create a hash table of relation names. The
3381 :     # table begins with the relation names already in the SELECT command. We may
3382 :     # need to add relations later if there is filtering on a field in a secondary
3383 :     # relation. The secondary relations are the ones that contain multiply-
3384 :     # occurring or optional fields.
3385 :     my %fromNames = map { $_ => 1 } @sortedNames;
3386 :     # We are ready to begin. We loop through the object names, replacing each
3387 :     # object name's field references by the corresponding SQL field reference.
3388 :     # Along the way, if we find a secondary relation, we will need to add it
3389 :     # to the FROM clause.
3390 :     for my $mappedName (@sortedNames) {
3391 :     # Get the length of the object name plus 2. This is the value we add to the
3392 :     # size of the field name to determine the size of the field reference as a
3393 :     # whole.
3394 :     my $nameLength = 2 + length $mappedName;
3395 :     # Get the real object name for this mapped name.
3396 :     my $objectName = $mappedNameHash{$mappedName};
3397 :     Trace("Processing $mappedName for object $objectName.") if T(4);
3398 :     # Get the object's field list.
3399 :     my $fieldList = $self->GetFieldTable($objectName);
3400 :     # Find the field references for this object.
3401 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3402 :     # At this point, $1 contains the field name, and the current position
3403 :     # is set immediately after the final parenthesis. We pull out the name of
3404 :     # the field and the position and length of the field reference as a whole.
3405 :     my $fieldName = $1;
3406 :     my $len = $nameLength + length $fieldName;
3407 :     my $pos = pos($filterString) - $len;
3408 :     # Insure the field exists.
3409 :     if (!exists $fieldList->{$fieldName}) {
3410 :     Confess("Field $fieldName not found for object $objectName.");
3411 :     } else {
3412 :     Trace("Processing $fieldName at position $pos.") if T(4);
3413 :     # Get the field's relation.
3414 :     my $relationName = $fieldList->{$fieldName}->{relation};
3415 :     # Now we have a secondary relation. We need to insure it matches the
3416 :     # mapped name of the primary relation. First we peel off the suffix
3417 :     # from the mapped name.
3418 :     my $mappingSuffix = substr $mappedName, length($objectName);
3419 :     # Put the mapping suffix onto the relation name to get the
3420 :     # mapped relation name.
3421 :     my $mappedRelationName = "$relationName$mappingSuffix";
3422 :     # Insure the relation is in the FROM clause.
3423 :     if (!exists $fromNames{$mappedRelationName}) {
3424 :     # Add the relation to the FROM clause.
3425 :     if ($mappedRelationName eq $relationName) {
3426 :     # The name is un-mapped, so we add it without
3427 :     # any frills.
3428 :     $suffix .= ", $relationName";
3429 :     push @joinWhere, "$objectName.id = $relationName.id";
3430 :     } else {
3431 :     # Here we have a mapping situation.
3432 :     $suffix .= ", $relationName $mappedRelationName";
3433 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3434 :     }
3435 :     # Denote we have this relation available for future fields.
3436 :     $fromNames{$mappedRelationName} = 1;
3437 :     }
3438 :     # Form an SQL field reference from the relation name and the field name.
3439 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3440 :     # Put it into the filter string in place of the old value.
3441 :     substr($filterString, $pos, $len) = $sqlReference;
3442 :     # Reposition the search.
3443 :     pos $filterString = $pos + length $sqlReference;
3444 :     }
3445 :     }
3446 :     }
3447 : parrello 1.70 }
3448 :     # The next step is to join the objects together. We only need to do this if there
3449 :     # is more than one object in the object list. We start with the first object and
3450 :     # run through the objects after it. Note also that we make a safety copy of the
3451 :     # list before running through it, because we shift off the first object before
3452 :     # processing the rest.
3453 :     my @mappedObjectList = @mappedNameList;
3454 :     my $lastMappedObject = shift @mappedObjectList;
3455 :     # Get the join table.
3456 :     my $joinTable = $self->{_metaData}->{Joins};
3457 :     # Loop through the object list.
3458 :     for my $thisMappedObject (@mappedObjectList) {
3459 :     # Look for a join using the real object names.
3460 :     my $lastObject = $mappedNameHash{$lastMappedObject};
3461 :     my $thisObject = $mappedNameHash{$thisMappedObject};
3462 :     my $joinKey = "$lastObject/$thisObject";
3463 :     if (!exists $joinTable->{$joinKey}) {
3464 :     # Here there's no join, so we throw an error.
3465 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3466 :     } else {
3467 :     # Get the join clause.
3468 :     my $unMappedJoin = $joinTable->{$joinKey};
3469 :     # Fix the names.
3470 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3471 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3472 :     push @joinWhere, $unMappedJoin;
3473 :     # Save this object as the last object for the next iteration.
3474 :     $lastMappedObject = $thisMappedObject;
3475 :     }
3476 :     }
3477 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3478 :     # here is we want the filter clause to be empty if there's no WHERE filter.
3479 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
3480 :     my $orderClause = "";
3481 :     # This is only necessary if we have a filter string in which the ORDER BY
3482 :     # and LIMIT clauses can live.
3483 :     if ($filterString) {
3484 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3485 :     # operator so that we find the first occurrence of either verb.
3486 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3487 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3488 :     my $pos = pos $filterString;
3489 :     $orderClause = $2 . substr($filterString, $pos);
3490 :     $filterString = $1;
3491 :     }
3492 : parrello 1.70 }
3493 :     # All the things that are supposed to be in the WHERE clause of the
3494 :     # SELECT command need to be put into @joinWhere so we can string them
3495 :     # together. We begin with the match clause. This is important,
3496 :     # because the match clause's parameter mark must precede any parameter
3497 :     # marks in the filter string.
3498 :     if ($matchClause) {
3499 :     push @joinWhere, $matchClause;
3500 :     }
3501 :     # Add the filter string. We put it in parentheses to avoid operator
3502 :     # precedence problems with the match clause or the joins.
3503 :     if ($filterString) {
3504 :     Trace("Filter string is \"$filterString\".") if T(4);
3505 :     push @joinWhere, "($filterString)";
3506 :     }
3507 :     # String it all together into a big filter clause.
3508 :     if (@joinWhere) {
3509 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
3510 :     }
3511 :     # Add the sort or limit clause (if any).
3512 :     if ($orderClause) {
3513 :     $suffix .= " $orderClause";
3514 : parrello 1.45 }
3515 :     # Return the suffix, the mapped name list, and the mapped name hash.
3516 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
3517 :     }
3518 :    
3519 : parrello 1.70 =head3 _GetStatementHandle
3520 : parrello 1.45
3521 :     This method will prepare and execute an SQL query, returning the statement handle.
3522 :     The main reason for doing this here is so that everybody who does SQL queries gets
3523 :     the benefit of tracing.
3524 :    
3525 :     This is an instance method.
3526 :    
3527 :     =over 4
3528 :    
3529 :     =item command
3530 :    
3531 :     Command to prepare and execute.
3532 :    
3533 :     =item params
3534 :    
3535 :     Reference to a list of the values to be substituted in for the parameter marks.
3536 :    
3537 :     =item RETURN
3538 :    
3539 :     Returns a prepared and executed statement handle from which the caller can extract
3540 :     results.
3541 :    
3542 :     =back
3543 :    
3544 :     =cut
3545 :    
3546 :     sub _GetStatementHandle {
3547 :     # Get the parameters.
3548 :     my ($self, $command, $params) = @_;
3549 :     # Trace the query.
3550 :     Trace("SQL query: $command") if T(SQL => 3);
3551 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3552 :     # Get the database handle.
3553 :     my $dbh = $self->{_dbh};
3554 :     # Prepare the command.
3555 :     my $sth = $dbh->prepare_command($command);
3556 :     # Execute it with the parameters bound in.
3557 : parrello 1.75 $sth->execute(@{$params}) || Confess("SELECT error: " . $sth->errstr());
3558 : parrello 1.45 # Return the statement handle.
3559 :     return $sth;
3560 :     }
3561 :    
3562 : parrello 1.70 =head3 _GetLoadStats
3563 : parrello 1.1
3564 :     Return a blank statistics object for use by the load methods.
3565 :    
3566 :     This is a static method.
3567 :    
3568 :     =cut
3569 :    
3570 : parrello 1.29 sub _GetLoadStats{
3571 : parrello 1.28 return Stats->new();
3572 : parrello 1.1 }
3573 :    
3574 : parrello 1.70 =head3 _DumpRelation
3575 : parrello 1.1
3576 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
3577 : parrello 1.1
3578 :     This is an instance method.
3579 :    
3580 :     =over 4
3581 :    
3582 :     =item outputDirectory
3583 :    
3584 :     Directory to contain the output file.
3585 :    
3586 :     =item relationName
3587 :    
3588 :     Name of the relation to dump.
3589 :    
3590 :     =item relation
3591 :    
3592 :     Structure describing the relation to be dumped.
3593 :    
3594 :     =back
3595 :    
3596 :     =cut
3597 :    
3598 :     sub _DumpRelation {
3599 : parrello 1.10 # Get the parameters.
3600 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
3601 :     # Open the output file.
3602 :     my $fileName = "$outputDirectory/$relationName.dtx";
3603 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
3604 :     # Create a query for the specified relation.
3605 :     my $dbh = $self->{_dbh};
3606 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
3607 :     # Execute the query.
3608 :     $query->execute() || Confess("SELECT error dumping $relationName.");
3609 :     # Loop through the results.
3610 :     while (my @row = $query->fetchrow) {
3611 :     # Escape any tabs or new-lines in the row text.
3612 :     for my $field (@row) {
3613 :     $field =~ s/\n/\\n/g;
3614 :     $field =~ s/\t/\\t/g;
3615 :     }
3616 :     # Tab-join the row and write it to the output file.
3617 :     my $rowText = join("\t", @row);
3618 :     print DTXOUT "$rowText\n";
3619 :     }
3620 :     # Close the output file.
3621 :     close DTXOUT;
3622 : parrello 1.1 }
3623 :    
3624 : parrello 1.70 =head3 _GetStructure
3625 : parrello 1.1
3626 :     Get the data structure for a specified entity or relationship.
3627 :    
3628 :     This is an instance method.
3629 :    
3630 :     =over 4
3631 :    
3632 :     =item objectName
3633 :    
3634 :     Name of the desired entity or relationship.
3635 :    
3636 :     =item RETURN
3637 :    
3638 :     The descriptor for the specified object.
3639 :    
3640 :     =back
3641 :    
3642 :     =cut
3643 :    
3644 :     sub _GetStructure {
3645 : parrello 1.10 # Get the parameters.
3646 :     my ($self, $objectName) = @_;
3647 :     # Get the metadata structure.
3648 :     my $metadata = $self->{_metaData};
3649 :     # Declare the variable to receive the descriptor.
3650 :     my $retVal;
3651 :     # Get the descriptor from the metadata.
3652 :     if (exists $metadata->{Entities}->{$objectName}) {
3653 :     $retVal = $metadata->{Entities}->{$objectName};
3654 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
3655 :     $retVal = $metadata->{Relationships}->{$objectName};
3656 :     } else {
3657 :     Confess("Object $objectName not found in database.");
3658 :     }
3659 :     # Return the descriptor.
3660 :     return $retVal;
3661 : parrello 1.1 }
3662 :    
3663 : parrello 1.70
3664 :    
3665 :     =head3 _GetRelationTable
3666 : parrello 1.1
3667 :     Get the list of relations for a specified entity or relationship.
3668 :    
3669 :     This is an instance method.
3670 :    
3671 :     =over 4
3672 :    
3673 :     =item objectName
3674 :    
3675 :     Name of the desired entity or relationship.
3676 :    
3677 :     =item RETURN
3678 :    
3679 :     A table containing the relations for the specified object.
3680 :    
3681 :     =back
3682 :    
3683 :     =cut
3684 :    
3685 :     sub _GetRelationTable {
3686 : parrello 1.10 # Get the parameters.
3687 :     my ($self, $objectName) = @_;
3688 :     # Get the descriptor from the metadata.
3689 :     my $objectData = $self->_GetStructure($objectName);
3690 :     # Return the object's relation list.
3691 :     return $objectData->{Relations};
3692 : parrello 1.1 }
3693 :    
3694 : parrello 1.70 =head3 _ValidateFieldNames
3695 : parrello 1.1
3696 :     Determine whether or not the field names are valid. A description of the problems with the names
3697 :     will be written to the standard error output. If there is an error, this method will abort. This is
3698 :     a static method.
3699 :    
3700 :     =over 4
3701 :    
3702 :     =item metadata
3703 :    
3704 :     Metadata structure loaded from the XML data definition.
3705 :    
3706 :     =back
3707 :    
3708 :     =cut
3709 :    
3710 :     sub _ValidateFieldNames {
3711 : parrello 1.10 # Get the object.
3712 :     my ($metadata) = @_;
3713 :     # Declare the return value. We assume success.
3714 :     my $retVal = 1;
3715 :     # Loop through the sections of the database definition.
3716 :     for my $section ('Entities', 'Relationships') {
3717 :     # Loop through the objects in this section.
3718 :     for my $object (values %{$metadata->{$section}}) {
3719 :     # Loop through the object's fields.
3720 :     for my $fieldName (keys %{$object->{Fields}}) {
3721 : parrello 1.73 # If this field name is invalid, set the return value to zero
3722 :     # so we know we encountered an error.
3723 :     if (! ValidateFieldName($fieldName)) {
3724 : parrello 1.10 $retVal = 0;
3725 :     }
3726 :     }
3727 :     }
3728 :     }
3729 :     # If an error was found, fail.
3730 :     if ($retVal == 0) {
3731 :     Confess("Errors found in field names.");
3732 :     }
3733 : parrello 1.1 }
3734 :    
3735 : parrello 1.70 =head3 _LoadRelation
3736 : parrello 1.1
3737 :     Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
3738 :     file with the same name as the relation exists in the specified directory.
3739 :    
3740 :     This is an instance method.
3741 :    
3742 :     =over 4
3743 :    
3744 :     =item dbh
3745 :    
3746 :     DBKernel object for accessing the database.
3747 :    
3748 :     =item directoryName
3749 :    
3750 :     Name of the directory containing the tab-delimited data files.
3751 :    
3752 :     =item relationName
3753 :    
3754 :     Name of the relation to load.
3755 :    
3756 :     =item rebuild
3757 :    
3758 :     TRUE if the table should be dropped and re-created before loading.
3759 :    
3760 :     =item RETURN
3761 :    
3762 :     Returns a statistical object describing the number of records read and a list of error messages.
3763 :    
3764 :     =back
3765 :    
3766 :     =cut
3767 :    
3768 :     sub _LoadRelation {
3769 : parrello 1.10 # Get the parameters.
3770 :     my ($self, $directoryName, $relationName, $rebuild) = @_;
3771 :     # Create the file name.
3772 :     my $fileName = "$directoryName/$relationName";
3773 :     # If the file doesn't exist, try adding the .dtx suffix.
3774 :     if (! -e $fileName) {
3775 :     $fileName .= ".dtx";
3776 :     if (! -e $fileName) {
3777 :     $fileName = "";
3778 :     }
3779 :     }
3780 :     # Create the return object.
3781 :     my $retVal = _GetLoadStats();
3782 :     # If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
3783 :     # be a null string.
3784 :     if ($fileName ne "") {
3785 :     # Load the relation from the file.
3786 :     $retVal = $self->LoadTable($fileName, $relationName, $rebuild);
3787 :     } elsif ($rebuild) {
3788 :     # Here we are rebuilding, but no file exists, so we just re-create the table.
3789 :     $self->CreateTable($relationName, 1);
3790 :     }
3791 :     # Return the statistics from the load.
3792 :     return $retVal;
3793 : parrello 1.1 }
3794 :    
3795 : parrello 1.73
3796 : parrello 1.70 =head3 _LoadMetaData
3797 : parrello 1.1
3798 :     This method loads the data describing this database from an XML file into a metadata structure.
3799 :     The resulting structure is a set of nested hash tables containing all the information needed to
3800 :     load or use the database. The schema for the XML file is F<ERDatabase.xml>.
3801 :    
3802 :     This is a static method.
3803 :    
3804 :     =over 4
3805 :    
3806 :     =item filename
3807 :    
3808 :     Name of the file containing the database definition.
3809 :    
3810 :     =item RETURN
3811 :    
3812 :     Returns a structure describing the database.
3813 :    
3814 :     =back
3815 :    
3816 :     =cut
3817 :    
3818 :     sub _LoadMetaData {
3819 : parrello 1.10 # Get the parameters.
3820 :     my ($filename) = @_;
3821 : parrello 1.75 Trace("Reading DBD from $filename.") if T(2);
3822 : parrello 1.10 # Slurp the XML file into a variable. Extensive use of options is used to insure we
3823 :     # get the exact structure we want.
3824 : parrello 1.73 my $metadata = ReadMetaXML($filename);
3825 : parrello 1.10 # Before we go any farther, we need to validate the field and object names. If an error is found,
3826 :     # the method below will fail.
3827 :     _ValidateFieldNames($metadata);
3828 :     # Next we need to create a hash table for finding relations. The entities and relationships are
3829 :     # implemented as one or more database relations.
3830 :     my %masterRelationTable = ();
3831 :     # Loop through the entities.
3832 :     my $entityList = $metadata->{Entities};
3833 :     for my $entityName (keys %{$entityList}) {
3834 :     my $entityStructure = $entityList->{$entityName};
3835 :     #
3836 : parrello 1.12 # The first step is to create all the entity's default values. For C<Field> elements,
3837 : parrello 1.10 # the relation name must be added where it is not specified. For relationships,
3838 :     # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
3839 :     # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
3840 :     # added that can be used to pull the implicit fields to the top when displaying the field
3841 :     # documentation. The PrettySort values are 1-based and indicate in which pass through a
3842 :     # relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
3843 :     # and so on.
3844 :     #
3845 :     # Fix up this entity.
3846 :     _FixupFields($entityStructure, $entityName, 2, 3);
3847 :     # Add the ID field.
3848 :     _AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
3849 :     relation => $entityName,
3850 :     Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
3851 :     PrettySort => 1});
3852 :     #
3853 :     # The current field list enables us to quickly find the relation containing a particular field.
3854 :     # We also need a list that tells us the fields in each relation. We do this by creating a
3855 :     # Relations structure in the entity structure and collating the fields into it based on their
3856 :     # C<relation> property. There is one tricky bit, which is that every relation has to have the
3857 :     # C<id> field in it. Note also that the field list is put into a C<Fields> member of the
3858 :     # relation's structure so that it looks more like the entity and relationship structures.
3859 :     #
3860 :     # First we need to create the relations list.
3861 :     my $relationTable = { };
3862 :     # Loop through the fields. We use a list of field names to prevent a problem with
3863 :     # the hash table cursor losing its place during the loop.
3864 :     my $fieldList = $entityStructure->{Fields};
3865 :     my @fieldNames = keys %{$fieldList};
3866 :     for my $fieldName (@fieldNames) {
3867 :     my $fieldData = $fieldList->{$fieldName};
3868 :     # Get the current field's relation name.
3869 :     my $relationName = $fieldData->{relation};
3870 :     # Insure the relation exists.
3871 :     if (!exists $relationTable->{$relationName}) {
3872 :     $relationTable->{$relationName} = { Fields => { } };
3873 :     }
3874 :     # Add the field to the relation's field structure.
3875 :     $relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
3876 :     }
3877 :     # Now that we've organized all our fields by relation name we need to do some serious
3878 :     # housekeeping. We must add the C<id> field to every relation and convert each relation
3879 :     # to a list of fields. First, we need the ID field itself.
3880 :     my $idField = $fieldList->{id};
3881 :     # Loop through the relations.
3882 :     for my $relationName (keys %{$relationTable}) {
3883 :     my $relation = $relationTable->{$relationName};
3884 :     # Get the relation's field list.
3885 :     my $relationFieldList = $relation->{Fields};
3886 :     # Add the ID field to it. If the field's already there, it will not make any
3887 :     # difference.
3888 :     $relationFieldList->{id} = $idField;
3889 :     # Convert the field set from a hash into a list using the pretty-sort number.
3890 :     $relation->{Fields} = _ReOrderRelationTable($relationFieldList);
3891 :     # Add the relation to the master table.
3892 :     $masterRelationTable{$relationName} = $relation;
3893 :     }
3894 :     # The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
3895 :     # The other relations must have at least one index that begins with the ID field. In addition, the
3896 :     # metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
3897 :     # get the entity's field list and index list.
3898 :     my $indexList = $entityStructure->{Indexes};
3899 :     # Loop through the indexes.
3900 :     for my $indexData (@{$indexList}) {
3901 :     # We need to find this index's fields. All of them should belong to the same relation.
3902 :     # The ID field is an exception, since it's in all relations.
3903 :     my $relationName = '0';
3904 :     for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
3905 :     # Get this field's name.
3906 :     my $fieldName = $fieldDescriptor->{name};
3907 :     # Only proceed if it is NOT the ID field.
3908 :     if ($fieldName ne 'id') {
3909 :     # Find the relation containing the current index field.
3910 :     my $thisName = $fieldList->{$fieldName}->{relation};
3911 :     if ($relationName eq '0') {
3912 :     # Here we're looking at the first field, so we save its relation name.
3913 :     $relationName = $thisName;
3914 :     } elsif ($relationName ne $thisName) {
3915 :     # Here we have a field mismatch.
3916 :     Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
3917 :     }
3918 :     }
3919 :     }
3920 :     # Now $relationName is the name of the relation that contains this index. Add the index structure
3921 :     # to the relation.
3922 :     push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
3923 :     }
3924 :     # Now each index has been put in a relation. We need to add the primary index for the primary
3925 :     # relation.
3926 :     push @{$relationTable->{$entityName}->{Indexes}},
3927 :     { IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
3928 :     Notes => { content => "Primary index for $entityName." }
3929 :     };
3930 :     # The next step is to insure that each relation has at least one index that begins with the ID field.
3931 :     # After that, we convert each relation's index list to an index table. We first need to loop through
3932 :     # the relations.
3933 :     for my $relationName (keys %{$relationTable}) {
3934 :     my $relation = $relationTable->{$relationName};
3935 :     # Get the relation's index list.
3936 :     my $indexList = $relation->{Indexes};
3937 :     # Insure this relation has an ID index.
3938 :     my $found = 0;
3939 :     for my $index (@{$indexList}) {
3940 :     if ($index->{IndexFields}->[0]->{name} eq "id") {
3941 :     $found = 1;
3942 :     }
3943 :     }
3944 :     if ($found == 0) {
3945 :     push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
3946 :     }
3947 :     # Now we need to convert the relation's index list to an index table. We begin by creating
3948 :     # an empty table in the relation structure.
3949 :     $relation->{Indexes} = { };
3950 :     # Loop through the indexes.
3951 :     my $count = 0;
3952 :     for my $index (@{$indexList}) {
3953 :     # Add this index to the index table.
3954 : parrello 1.75 _AddIndex("idx$count", $relation, $index);
3955 : parrello 1.10 # Increment the counter so that the next index has a different name.
3956 :     $count++;
3957 :     }
3958 :     }
3959 :     # Finally, we add the relation structure to the entity.
3960 :     $entityStructure->{Relations} = $relationTable;
3961 :     }
3962 :     # Loop through the relationships. Relationships actually turn out to be much simpler than entities.
3963 :     # For one thing, there is only a single constituent relation.
3964 :     my $relationshipList = $metadata->{Relationships};
3965 :     for my $relationshipName (keys %{$relationshipList}) {
3966 :     my $relationshipStructure = $relationshipList->{$relationshipName};
3967 :     # Fix up this relationship.
3968 :     _FixupFields($relationshipStructure, $relationshipName, 2, 3);
3969 :     # Format a description for the FROM field.
3970 :     my $fromEntity = $relationshipStructure->{from};
3971 :     my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
3972 :     # Get the FROM entity's key type.
3973 :     my $fromType = $entityList->{$fromEntity}->{keyType};
3974 :     # Add the FROM field.
3975 :     _AddField($relationshipStructure, 'from-link', { type => $fromType,
3976 :     relation => $relationshipName,
3977 :     Notes => { content => $fromComment },
3978 :     PrettySort => 1});
3979 :     # Format a description for the TO field.
3980 :     my $toEntity = $relationshipStructure->{to};
3981 :     my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
3982 :     # Get the TO entity's key type.
3983 :     my $toType = $entityList->{$toEntity}->{keyType};
3984 :     # Add the TO field.
3985 :     _AddField($relationshipStructure, 'to-link', { type=> $toType,
3986 :     relation => $relationshipName,
3987 :     Notes => { content => $toComment },
3988 :     PrettySort => 1});
3989 :     # Create an index-free relation from the fields.
3990 :     my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
3991 :     Indexes => { } };
3992 :     $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
3993 :     # Create the FROM and TO indexes.
3994 :     _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
3995 :     _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
3996 :     # Add the relation to the master table.
3997 :     $masterRelationTable{$relationshipName} = $thisRelation;
3998 :     }
3999 :     # Now store the master relation table in the metadata structure.
4000 :     $metadata->{RelationTable} = \%masterRelationTable;
4001 :     # Our final task is to create the join table. The join table is a hash that describes all
4002 :     # the join clauses for traveling through the relationships. The join clause is an equality
4003 :     # condition that can be put into a WHERE clause in order to join two objects. Two relationships
4004 :     # can be joined if they share an entity in common; and an entity can be joined to a relationship
4005 :     # if the entity is at either end of the relationship.
4006 :     my %joinTable = ();
4007 :     # Loop through the entities.
4008 :     for my $entityName (keys %{$entityList}) {
4009 :     # Build three lists of the relationships connected to this entity. One will be
4010 :     # for relationships from the entity, one for relationships to the entity, and
4011 :     # one for recursive relationships.
4012 :     my @fromList = ();
4013 :     my @toList = ();
4014 :     my @bothList = ();
4015 : parrello 1.21 Trace("Join table build for $entityName.") if T(metadata => 4);
4016 : parrello 1.10 for my $relationshipName (keys %{$relationshipList}) {
4017 :     my $relationship = $relationshipList->{$relationshipName};
4018 :     # Determine if this relationship has our entity in one of its link fields.
4019 :     my $fromEntity = $relationship->{from};
4020 :     my $toEntity = $relationship->{to};
4021 : parrello 1.41 Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4022 : parrello 1.10 if ($fromEntity eq $entityName) {
4023 :     if ($toEntity eq $entityName) {
4024 :     # Here the relationship is recursive.
4025 :     push @bothList, $relationshipName;
4026 : parrello 1.21 Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
4027 : parrello 1.10 } else {
4028 :     # Here the relationship comes from the entity.
4029 :     push @fromList, $relationshipName;
4030 : parrello 1.21 Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
4031 : parrello 1.10 }
4032 :     } elsif ($toEntity eq $entityName) {
4033 :     # Here the relationship goes to the entity.
4034 :     push @toList, $relationshipName;
4035 : parrello 1.21 Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
4036 : parrello 1.10 }
4037 :     }
4038 :     # Create the nonrecursive joins. Note that we build two hashes for running
4039 :     # through the nonrecursive relationships since we'll have an outer loop
4040 :     # and an inner loop, and we can't do two "each" iterations on the same
4041 :     # hash table at the same time.
4042 :     my %directRelationships = ( from => \@fromList, to => \@toList );
4043 :     my %otherRelationships = ( from => \@fromList, to => \@toList );
4044 :     for my $linkType (keys %directRelationships) {
4045 :     my $relationships = $directRelationships{$linkType};
4046 :     # Loop through all the relationships.
4047 :     for my $relationshipName (@{$relationships}) {
4048 :     # Create joins between the entity and this relationship.
4049 :     my $linkField = "$relationshipName.${linkType}_link";
4050 :     my $joinClause = "$entityName.id = $linkField";
4051 : parrello 1.21 Trace("Entity join clause is $joinClause for $entityName and $relationshipName.") if T(metadata => 4);
4052 : parrello 1.10 $joinTable{"$entityName/$relationshipName"} = $joinClause;
4053 :     $joinTable{"$relationshipName/$entityName"} = $joinClause;
4054 :     # Create joins between this relationship and the other relationships.
4055 :     for my $otherType (keys %otherRelationships) {
4056 :     my $otherships = $otherRelationships{$otherType};
4057 :     for my $otherName (@{$otherships}) {
4058 :     # Get the key for this join.
4059 :     my $joinKey = "$otherName/$relationshipName";
4060 :     # Check for a duplicate or a self-join.
4061 :     if (exists $joinTable{$joinKey}) {
4062 :     # Here we have a duplicate, which means that the join
4063 :     # path is ambiguous. We delete the join from the join
4064 :     # table to prevent it from being used.
4065 :     delete $joinTable{$joinKey};
4066 :     Trace("Deleting ambiguous join $joinKey.") if T(4);
4067 :     } elsif ($otherName ne $relationshipName) {
4068 :     # Here we have a valid join. Note that joins between a
4069 :     # relationship and itself are prohibited.
4070 :     my $relJoinClause = "$otherName.${otherType}_link = $linkField";
4071 :     $joinTable{$joinKey} = $relJoinClause;
4072 : parrello 1.21 Trace("Relationship join clause is $relJoinClause for $joinKey.") if T(metadata => 4);
4073 : parrello 1.10 }
4074 :     }
4075 :     }
4076 :     # Create joins between this relationship and the recursive relationships.
4077 :     # We don't need to check for ambiguous joins here, because a recursive
4078 :     # relationship can only be ambiguous with another recursive relationship,
4079 :     # and the incoming relationship from the outer loop is never recursive.
4080 :     for my $otherName (@bothList) {
4081 : parrello 1.21 Trace("Setting up relationship joins to recursive relationship $otherName with $relationshipName.") if T(metadata => 4);
4082 : parrello 1.10 # Join from the left.
4083 :     $joinTable{"$relationshipName/$otherName"} =
4084 :     "$linkField = $otherName.from_link";
4085 :     # Join from the right.
4086 :     $joinTable{"$otherName/$relationshipName"} =
4087 :     "$otherName.to_link = $linkField";
4088 :     }
4089 :     }
4090 :     }
4091 :     # Create entity joins for the recursive relationships. Unlike the non-recursive
4092 :     # joins, the direction makes a difference with the recursive joins. This can give
4093 :     # rise to situations where we can't create the path we want; however, it is always
4094 :     # possible to get the same effect using multiple queries.
4095 :     for my $relationshipName (@bothList) {
4096 : parrello 1.21 Trace("Setting up entity joins to recursive relationship $relationshipName with $entityName.") if T(metadata => 4);
4097 : parrello 1.10 # Join to the entity from each direction.
4098 :     $joinTable{"$entityName/$relationshipName"} =
4099 :     "$entityName.id = $relationshipName.from_link";
4100 :     $joinTable{"$relationshipName/$entityName"} =
4101 :     "$relationshipName.to_link = $entityName.id";
4102 :     }
4103 :     }
4104 :     # Add the join table to the structure.
4105 :     $metadata->{Joins} = \%joinTable;
4106 :     # Return the slurped and fixed-up structure.
4107 :     return $metadata;
4108 : parrello 1.1 }
4109 :    
4110 : parrello 1.70 =head3 _CreateRelationshipIndex
4111 : parrello 1.1
4112 :     Create an index for a relationship's relation.
4113 :    
4114 :     This is a static method.
4115 :    
4116 :     =over 4
4117 :    
4118 :     =item indexKey
4119 :    
4120 :     Type of index: either C<"From"> or C<"To">.
4121 :    
4122 :     =item relationshipName
4123 :    
4124 :     Name of the relationship.
4125 :    
4126 :     =item relationshipStructure
4127 :    
4128 :     Structure describing the relationship that the index will sort.
4129 :    
4130 :     =back
4131 :    
4132 :     =cut
4133 :    
4134 :     sub _CreateRelationshipIndex {
4135 : parrello 1.10 # Get the parameters.
4136 :     my ($indexKey, $relationshipName, $relationshipStructure) = @_;
4137 :     # Get the target relation.
4138 :     my $relationStructure = $relationshipStructure->{Relations}->{$relationshipName};
4139 :     # Create a descriptor for the link field that goes at the beginning of this index.
4140 :     my $firstField = { name => lcfirst $indexKey . '-link', order => 'ascending' };
4141 :     # Get the target index descriptor.
4142 :     my $newIndex = $relationshipStructure->{$indexKey . "Index"};
4143 :     # Add the first field to the index's field list. Due to the craziness of PERL, if the
4144 :     # index descriptor does not exist, it will be created automatically so we can add
4145 :     # the field to it.
4146 :     unshift @{$newIndex->{IndexFields}}, $firstField;
4147 : parrello 1.12 # If this is a one-to-many relationship, the "To" index is unique.
4148 :     if ($relationshipStructure->{arity} eq "1M" && $indexKey eq "To") {
4149 :     $newIndex->{Unique} = 'true';
4150 :     }
4151 : parrello 1.10 # Add the index to the relation.
4152 : parrello 1.75 _AddIndex("idx$indexKey", $relationStructure, $newIndex);
4153 : parrello 1.1 }
4154 :    
4155 : parrello 1.70 =head3 _AddIndex
4156 : parrello 1.1
4157 :     Add an index to a relation structure.
4158 :    
4159 :     This is a static method.
4160 :    
4161 :     =over 4
4162 :    
4163 :     =item indexName
4164 :    
4165 :     Name to give to the new index.
4166 :    
4167 :     =item relationStructure
4168 :    
4169 :     Relation structure to which the new index should be added.
4170 :    
4171 :     =item newIndex
4172 :    
4173 :     New index to add.
4174 :    
4175 :     =back
4176 :    
4177 :     =cut
4178 :    
4179 :     sub _AddIndex {
4180 : parrello 1.10 # Get the parameters.
4181 :     my ($indexName, $relationStructure, $newIndex) = @_;
4182 :     # We want to re-do the index's field list. Instead of an object for each field,
4183 :     # we want a string consisting of the field name optionally followed by the token DESC.
4184 :     my @fieldList = ( );
4185 :     for my $field (@{$newIndex->{IndexFields}}) {
4186 :     # Create a string containing the field name.
4187 :     my $fieldString = $field->{name};
4188 :     # Add the ordering token if needed.
4189 :     if ($field->{order} eq "descending") {
4190 :     $fieldString .= " DESC";
4191 :     }
4192 :     # Push the result onto the field list.
4193 :     push @fieldList, $fieldString;
4194 :     }
4195 :     # Store the field list just created as the new index field list.
4196 :     $newIndex->{IndexFields} = \@fieldList;
4197 :     # Add the index to the relation's index list.
4198 :     $relationStructure->{Indexes}->{$indexName} = $newIndex;
4199 : parrello 1.1 }
4200 :    
4201 : parrello 1.70 =head3 _FixupFields
4202 : parrello 1.1
4203 :     This method fixes the field list for an entity or relationship. It will add the caller-specified
4204 :     relation name to fields that do not have a name and set the C<PrettySort> value as specified.
4205 :    
4206 :     This is a static method.
4207 :    
4208 :     =over 4
4209 :    
4210 :     =item structure
4211 :    
4212 :     Entity or relationship structure to be fixed up.
4213 :    
4214 :     =item defaultRelationName
4215 :    
4216 :     Default relation name to be added to the fields.
4217 :    
4218 :     =item prettySortValue
4219 :    
4220 :     C<PrettySort> value for the relation's normal fields.
4221 :    
4222 :     =item textPrettySortValue
4223 :    
4224 :     C<PrettySort> value for the relation's text fields. This value can be set to one greater than the
4225 :     normal pretty sort value so that text fields go at the end of each relation.
4226 :    
4227 :     =back
4228 :    
4229 :     =cut
4230 :    
4231 :     sub _FixupFields {
4232 : parrello 1.10 # Get the parameters.
4233 :     my ($structure, $defaultRelationName, $prettySortValue, $textPrettySortValue) = @_;
4234 :     # Insure the structure has a field list.
4235 :     if (!exists $structure->{Fields}) {
4236 :     # Here it doesn't, so we create a new one.
4237 :     $structure->{Fields} = { };
4238 :     } else {
4239 : parrello 1.70 # Here we have a field list. We need to track the searchable fields, so we
4240 :     # create a list for stashing them.
4241 :     my @textFields = ();
4242 :     # Loop through the fields.
4243 : parrello 1.10 my $fieldStructures = $structure->{Fields};
4244 :     for my $fieldName (keys %{$fieldStructures}) {
4245 : parrello 1.8 Trace("Processing field $fieldName of $defaultRelationName.") if T(4);
4246 : parrello 1.10 my $fieldData = $fieldStructures->{$fieldName};
4247 :     # Get the field type.
4248 :     my $type = $fieldData->{type};
4249 :     # Plug in a relation name if it is needed.
4250 :     Tracer::MergeOptions($fieldData, { relation => $defaultRelationName });
4251 : parrello 1.70 # Check for searchability.
4252 :     if ($fieldData->{searchable}) {
4253 :     # Only allow this for a primary relation.
4254 :     if ($fieldData->{relation} ne $defaultRelationName) {
4255 :     Confess("Field $fieldName of $defaultRelationName is in secondary relations and cannot be searchable.");
4256 :     } else {
4257 :     push @textFields, $fieldName;
4258 :     }
4259 :     }
4260 : parrello 1.10 # Add the PrettySortValue.
4261 :     $fieldData->{PrettySort} = (($type eq "text") ? $textPrettySortValue : $prettySortValue);
4262 :     }
4263 : parrello 1.70 # If there are searchable fields, remember the fact.
4264 :     if (@textFields) {
4265 :     $structure->{searchFields} = \@textFields;
4266 :     }
4267 : parrello 1.10 }
4268 : parrello 1.1 }
4269 :    
4270 : parrello 1.70 =head3 _FixName
4271 : parrello 1.1
4272 :     Fix the incoming field name so that it is a legal SQL column name.
4273 :    
4274 :     This is a static method.
4275 :    
4276 :     =over 4
4277 :    
4278 :     =item fieldName
4279 :    
4280 :     Field name to fix.
4281 :    
4282 :     =item RETURN
4283 :    
4284 :     Returns the fixed-up field name.
4285 :    
4286 :     =back
4287 :    
4288 :     =cut
4289 :    
4290 :     sub _FixName {
4291 : parrello 1.10 # Get the parameter.
4292 :     my ($fieldName) = @_;
4293 :     # Replace its minus signs with underscores.
4294 :     $fieldName =~ s/-/_/g;
4295 :     # Return the result.
4296 :     return $fieldName;
4297 : parrello 1.1 }
4298 :    
4299 : parrello 1.70 =head3 _FixNames
4300 : parrello 1.1
4301 :     Fix all the field names in a list.
4302 :    
4303 :     This is a static method.
4304 :    
4305 :     =over 4
4306 :    
4307 :     =item field1, field2, field3, ... fieldn
4308 :    
4309 :     List of field names to fix.
4310 :    
4311 :     =item RETURN
4312 :    
4313 :     Returns a list of fixed-up versions of the incoming field names.
4314 :    
4315 :     =back
4316 :    
4317 :     =cut
4318 :    
4319 :