[Bio] / Sprout / ERDB.pm Repository:
ViewVC logotype

Annotation of /Sprout/ERDB.pm

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.92 - (view) (download) (as text)

1 : parrello 1.1 package ERDB;
2 :    
3 : parrello 1.10 use strict;
4 :     use Tracer;
5 : olson 1.14 use DBrtns;
6 : parrello 1.10 use Data::Dumper;
7 :     use XML::Simple;
8 :     use DBQuery;
9 : parrello 1.88 use ERDBObject;
10 : parrello 1.10 use Stats;
11 :     use Time::HiRes qw(gettimeofday);
12 : parrello 1.42 use Digest::MD5 qw(md5_base64);
13 : parrello 1.73 use CGI;
14 : parrello 1.1
15 :     =head1 Entity-Relationship Database Package
16 :    
17 :     =head2 Introduction
18 :    
19 :     The Entity-Relationship Database Package allows the client to create an easily-configurable
20 :     database of Entities connected by Relationships. Each entity is represented by one or more
21 :     relations in an underlying SQL database. Each relationship is represented by a single
22 :     relation that connects two entities.
23 :    
24 :     Although this package is designed for general use, all examples are derived from the
25 :     Sprout database, which is the first database implemented using this package.
26 :    
27 :     Each entity has at least one relation, the I<primary relation>, that has the same name as
28 :     the entity. The primary relation contains a field named C<id> that contains the unique
29 :     identifier of each entity instance. An entity may have additional relations that contain
30 :     fields which are optional or can occur more than once. For example, the B<FEATURE> entity
31 :     has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
32 :     is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
33 :     however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
34 :     relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
35 :     The B<FEATURE> entity also contains an optional virulence number. This is implemented
36 :     as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
37 : parrello 1.8 (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
38 :     the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
39 :     number. If the virulence of I<ABC> is not known, there will not be any rows for it in
40 :     C<FeatureVirulence>.
41 : parrello 1.1
42 :     Entities are connected by binary relationships implemented using single relations possessing the
43 :     same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
44 :     or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
45 :     ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
46 :     of the relationship is generally a verb phrase with the source entity as the subject and the
47 :     target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
48 :     and B<SOURCE> entities, and indicates that a particular source organization participated in the
49 :     mapping of the genome. A source organization frequently participates in the mapping
50 :     of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
51 :     this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
52 :     relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
53 :     and C<to-link>, which contains a source ID.
54 :    
55 :     A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
56 :     are implemented as additional fields in the relationship's relation. So, for example, the
57 :     B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
58 :     to determine which sequences make up a contig. The relationship has as an attribute the
59 :     B<start-position>, which indicates where in the contig that the sequence begins. This attribute
60 :     is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
61 :    
62 : parrello 1.73 The database itself is described by an XML file. In addition to all the data required to define
63 :     the entities, relationships, and attributes, the schema provides space for notes describing
64 :     the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
65 :     for the database.
66 :    
67 :     Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
68 :     in which case it will be used to generate a text search index in which the user searches for words
69 :     in the field instead of a particular field value.
70 : parrello 1.1
71 :     Finally, every entity and relationship object has a flag indicating if it is new or old. The object
72 :     is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
73 :     was inserted by the L</InsertObject> method.
74 :    
75 : parrello 1.8 =head2 XML Database Description
76 :    
77 :     =head3 Data Types
78 :    
79 :     The ERDB system supports the following data types. Note that there are numerous string
80 :     types depending on the maximum length. Some database packages limit the total number of
81 :     characters you have in an index key; to insure the database works in all environments,
82 :     the type of string should be the shortest one possible that supports all the known values.
83 :    
84 :     =over 4
85 :    
86 :     =item char
87 :    
88 :     single ASCII character
89 :    
90 :     =item int
91 :    
92 :     32-bit signed integer
93 :    
94 : parrello 1.60 =item counter
95 :    
96 :     32-bit unsigned integer
97 :    
98 : parrello 1.8 =item date
99 :    
100 :     64-bit unsigned integer, representing a PERL date/time value
101 :    
102 :     =item text
103 :    
104 :     long string; Text fields cannot be used in indexes or sorting and do not support the
105 :     normal syntax of filter clauses, but can be up to a billion character in length
106 :    
107 :     =item float
108 :    
109 :     double-precision floating-point number
110 :    
111 :     =item boolean
112 :    
113 :     single-bit numeric value; The value is stored as a 16-bit signed integer (for
114 :     compatability with certain database packages), but the only values supported are
115 :     0 and 1.
116 :    
117 : parrello 1.44 =item id-string
118 :    
119 :     variable-length string, maximum 25 characters
120 :    
121 : parrello 1.8 =item key-string
122 :    
123 :     variable-length string, maximum 40 characters
124 :    
125 :     =item name-string
126 :    
127 :     variable-length string, maximum 80 characters
128 :    
129 :     =item medium-string
130 :    
131 :     variable-length string, maximum 160 characters
132 :    
133 :     =item string
134 :    
135 :     variable-length string, maximum 255 characters
136 :    
137 : parrello 1.42 =item hash-string
138 :    
139 :     variable-length string, maximum 22 characters
140 :    
141 : parrello 1.8 =back
142 :    
143 : parrello 1.42 The hash-string data type has a special meaning. The actual key passed into the loader will
144 :     be a string, but it will be digested into a 22-character MD5 code to save space. Although the
145 :     MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
146 :     digest. Therefore, it is presumed the keys will be unique. When the database is actually
147 :     in use, the hashed keys will be presented rather than the original values. For this reason,
148 :     they should not be used for entities where the key is meaningful.
149 :    
150 : parrello 1.8 =head3 Global Tags
151 :    
152 :     The entire database definition must be inside a B<Database> tag. The display name of
153 :     the database is given by the text associated with the B<Title> tag. The display name
154 :     is only used in the automated documentation. It has no other effect. The entities and
155 :     relationships are listed inside the B<Entities> and B<Relationships> tags,
156 :     respectively. None of these tags have attributes.
157 :    
158 : parrello 1.10 <Database>
159 :     <Title>... display title here...</Title>
160 :     <Entities>
161 :     ... entity definitions here ...
162 :     </Entities>
163 :     <Relationships>
164 :     ... relationship definitions here...
165 :     </Relationships>
166 :     </Database>
167 : parrello 1.8
168 :     Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
169 :     The text inside the B<Notes> tag contains comments that will appear when the database
170 :     documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
171 :     italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
172 :    
173 :     =head3 Fields
174 :    
175 :     Both entities and relationships have fields described by B<Field> tags. A B<Field>
176 :     tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
177 :     object mus be inside B<Fields> tags.
178 :    
179 : parrello 1.10 <Entity ... >
180 :     <Fields>
181 :     ... Field tags ...
182 :     </Fields>
183 :     </Entity>
184 : parrello 1.8
185 :     The attributes for the B<Field> tag are as follows.
186 :    
187 :     =over 4
188 :    
189 :     =item name
190 :    
191 :     Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
192 :     and the first character should be a letter. Most underlying databases are case-insensitive
193 : parrello 1.70 with the respect to field names, so a best practice is to use lower-case letters only. Finally,
194 :     the name C<search-relevance> has special meaning for full-text searches and should not be
195 :     used as a field name.
196 : parrello 1.8
197 :     =item type
198 :    
199 :     Data type of the field. The legal data types are given above.
200 :    
201 :     =item relation
202 :    
203 :     Name of the relation containing the field. This should only be specified for entity
204 :     fields. The ERDB system does not support optional fields or multi-occurring fields
205 :     in the primary relation of an entity. Instead, they are put into secondary relations.
206 :     So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
207 :     grouping used to select a subset of the genomes. A given genome may not be in any
208 :     groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
209 :     value. The relation name specified must be a valid table name. By convention, it is
210 :     usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
211 :     entity, the fields without a relation attribute are said to belong to the
212 :     I<primary relation>. This relation has the same name as the entity itself.
213 :    
214 : parrello 1.70 =item searchable
215 :    
216 :     If specified, then the field is a candidate for full-text searching. A single full-text
217 :     index will be created for each relation with at least one searchable field in it.
218 :     For best results, this option should only be used for string or text fields.
219 :    
220 : parrello 1.73 =item special
221 :    
222 :     This attribute allows the subclass to assign special meaning for certain fields.
223 :     The interpretation is up to the subclass itself. Currently, only entity fields
224 :     can have this attribute.
225 :    
226 : parrello 1.8 =back
227 :    
228 :     =head3 Indexes
229 :    
230 : parrello 1.86 An entity can have multiple alternate indexes associated with it. The fields in an
231 :     index must all be from the same relation. The alternate indexes assist in searching
232 :     on fields other than the entity ID. A relationship has at least two indexes-- a I<to-index> and a
233 :     I<from-index> that order the results when crossing the relationship. For
234 : parrello 1.8 example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
235 :     from-index would order the contigs of a ganome, and the to-index would order
236 : parrello 1.86 the genomes of a contig. In addition, it can have zero or more alternate
237 :     indexes. A relationship's index must specify only fields in
238 : parrello 1.8 the relationship.
239 :    
240 : parrello 1.86 The alternate indexes for an entity or relationship must be listed inside the B<Indexes> tag.
241 :     The from-index of a relationship is specified using the B<FromIndex> tag; the to-index is
242 :     specified using the B<ToIndex> tag.
243 : parrello 1.8
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 : parrello 1.78 The B<FromIndex>, and B<ToIndex> tags have no attributes. The B<Index> tag can
261 :     have a B<Unique> attribute. If specified, the index will be generated as a unique
262 :     index.
263 : parrello 1.8
264 :     =head3 Object and Field Names
265 :    
266 :     By convention entity and relationship names use capital casing (e.g. C<Genome> or
267 :     C<HasRegionsIn>. Most underlying databases, however, are aggressively case-insensitive
268 :     with respect to relation names, converting them internally to all-upper case or
269 :     all-lower case.
270 :    
271 :     If syntax or parsing errors occur when you try to load or use an ERDB database, the
272 :     most likely reason is that one of your objects has an SQL reserved word as its name.
273 :     The list of SQL reserved words keeps increasing; however, most are unlikely to show
274 :     up as a noun or declarative verb phrase. The exceptions are C<Group>, C<User>,
275 :     C<Table>, C<Index>, C<Object>, C<Date>, C<Number>, C<Update>, C<Time>, C<Percent>,
276 :     C<Memo>, C<Order>, and C<Sum>. This problem can crop up in field names as well.
277 :    
278 :     Every entity has a field called C<id> that acts as its primary key. Every relationship
279 :     has fields called C<from-link> and C<to-link> that contain copies of the relevant
280 :     entity IDs. These are essentially ERDB's reserved words, and should not be used
281 :     for user-defined field names.
282 :    
283 :     =head3 Entities
284 :    
285 :     An entity is described by the B<Entity> tag. The entity can contain B<Notes>, an
286 :     B<Indexes> tag containing one or more secondary indexes, and a B<Fields> tag
287 :     containing one or more fields. The attributes of the B<Entity> tag are as follows.
288 :    
289 :     =over 4
290 :    
291 :     =item name
292 :    
293 :     Name of the entity. The entity name, by convention, uses capital casing (e.g. C<Genome>
294 :     or C<GroupBlock>) and should be a noun or noun phrase.
295 :    
296 :     =item keyType
297 :    
298 :     Data type of the primary key. The primary key is always named C<id>.
299 :    
300 :     =back
301 :    
302 :     =head3 Relationships
303 :    
304 :     A relationship is described by the C<Relationship> tag. Within a relationship,
305 :     there can be a C<Notes> tag, a C<Fields> tag containing the intersection data
306 : parrello 1.86 fields, a C<FromIndex> tag containing the from-index, a C<ToIndex> tag containing
307 :     the to-index, and an C<Indexes> tag containing the alternate indexes.
308 : parrello 1.8
309 :     The C<Relationship> tag has the following attributes.
310 :    
311 :     =over 4
312 :    
313 :     =item name
314 :    
315 :     Name of the relationship. The relationship name, by convention, uses capital casing
316 :     (e.g. C<ContainsRegionIn> or C<HasContig>), and should be a declarative verb
317 :     phrase, designed to fit between the from-entity and the to-entity (e.g.
318 :     Block C<ContainsRegionIn> Genome).
319 :    
320 :     =item from
321 :    
322 :     Name of the entity from which the relationship starts.
323 :    
324 :     =item to
325 :    
326 :     Name of the entity to which the relationship proceeds.
327 :    
328 :     =item arity
329 :    
330 :     Relationship type: C<1M> for one-to-many and C<MM> for many-to-many.
331 :    
332 :     =back
333 :    
334 : parrello 1.1 =cut
335 :    
336 :     # GLOBALS
337 :    
338 :     # Table of information about our datatypes. "sqlType" is the corresponding SQL datatype string.
339 :     # "maxLen" is the maximum permissible length of the incoming string data used to populate a field
340 : parrello 1.73 # of the specified type. "avgLen" is the average byte length for estimating
341 : parrello 1.75 # record sizes. "sort" is the key modifier for the sort command, "notes" is a type description,
342 :     # and "indexMod", if non-zero, is the number of characters to use when the field is specified in an
343 :     # index
344 : parrello 1.73 my %TypeTable = ( char => { sqlType => 'CHAR(1)', maxLen => 1, avgLen => 1, sort => "",
345 : parrello 1.75 indexMod => 0, notes => "single ASCII character"},
346 : parrello 1.73 int => { sqlType => 'INTEGER', maxLen => 20, avgLen => 4, sort => "n",
347 : parrello 1.75 indexMod => 0, notes => "signed 32-bit integer"},
348 : parrello 1.73 counter => { sqlType => 'INTEGER UNSIGNED', maxLen => 20, avgLen => 4, sort => "n",
349 : parrello 1.75 indexMod => 0, notes => "unsigned 32-bit integer"},
350 : parrello 1.73 string => { sqlType => 'VARCHAR(255)', maxLen => 255, avgLen => 100, sort => "",
351 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 255 characters"},
352 : parrello 1.73 text => { sqlType => 'TEXT', maxLen => 1000000000, avgLen => 500, sort => "",
353 : parrello 1.75 indexMod => 255, notes => "character string, nearly unlimited length, only first 255 characters are indexed"},
354 : parrello 1.73 date => { sqlType => 'BIGINT', maxLen => 80, avgLen => 8, sort => "n",
355 : parrello 1.75 indexMod => 0, notes => "signed, 64-bit integer"},
356 : parrello 1.73 float => { sqlType => 'DOUBLE PRECISION', maxLen => 40, avgLen => 8, sort => "g",
357 : parrello 1.75 indexMod => 0, notes => "64-bit double precision floating-point number"},
358 : parrello 1.73 boolean => { sqlType => 'SMALLINT', maxLen => 1, avgLen => 1, sort => "n",
359 : parrello 1.75 indexMod => 0, notes => "boolean value: 0 if false, 1 if true"},
360 : parrello 1.42 'hash-string' =>
361 : parrello 1.73 { sqlType => 'VARCHAR(22)', maxLen => 22, avgLen => 22, sort => "",
362 : parrello 1.75 indexMod => 0, notes => "string stored in digested form, used for certain types of key fields"},
363 : parrello 1.44 'id-string' =>
364 : parrello 1.73 { sqlType => 'VARCHAR(25)', maxLen => 25, avgLen => 25, sort => "",
365 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 25 characters"},
366 : parrello 1.10 'key-string' =>
367 : parrello 1.73 { sqlType => 'VARCHAR(40)', maxLen => 40, avgLen => 10, sort => "",
368 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 40 characters"},
369 : parrello 1.10 'name-string' =>
370 : parrello 1.73 { sqlType => 'VARCHAR(80)', maxLen => 80, avgLen => 40, sort => "",
371 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 80 characters"},
372 : parrello 1.10 'medium-string' =>
373 : parrello 1.73 { sqlType => 'VARCHAR(160)', maxLen => 160, avgLen => 40, sort => "",
374 : parrello 1.75 indexMod => 0, notes => "character string, 0 to 160 characters"},
375 : parrello 1.91 'long-string' =>
376 :     { sqlType => 'VARCHAR(500)', maxLen => 500, avglen => 255, sort => "",
377 :     indexMod => 0, notes => "character string, 0 to 500 characters"},
378 : parrello 1.10 );
379 : parrello 1.1
380 :     # Table translating arities into natural language.
381 :     my %ArityTable = ( '11' => 'one-to-one',
382 : parrello 1.10 '1M' => 'one-to-many',
383 :     'MM' => 'many-to-many'
384 :     );
385 : parrello 1.1
386 : parrello 1.73 # Options for XML input and output.
387 :    
388 :     my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
389 :     Entities => 'Entity',
390 :     Fields => 'Field',
391 :     Indexes => 'Index',
392 :     IndexFields => 'IndexField'
393 :     },
394 :     KeyAttr => { Relationship => 'name',
395 :     Entity => 'name',
396 :     Field => 'name'
397 :     },
398 :     SuppressEmpty => 1,
399 :     );
400 :    
401 :     my %XmlInOpts = (
402 : parrello 1.78 ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
403 : parrello 1.73 ForceContent => 1,
404 :     NormalizeSpace => 2,
405 :     );
406 :     my %XmlOutOpts = (
407 :     RootName => 'Database',
408 :     XMLDecl => 1,
409 :     );
410 : parrello 1.1
411 :    
412 :     =head2 Public Methods
413 :    
414 :     =head3 new
415 :    
416 : parrello 1.5 C<< my $database = ERDB->new($dbh, $metaFileName); >>
417 : parrello 1.1
418 :     Create a new ERDB object.
419 :    
420 :     =over 4
421 :    
422 :     =item dbh
423 :    
424 :     DBKernel database object for the target database.
425 :    
426 :     =item metaFileName
427 :    
428 :     Name of the XML file containing the metadata.
429 :    
430 :     =back
431 :    
432 :     =cut
433 :    
434 :     sub new {
435 : parrello 1.10 # Get the parameters.
436 :     my ($class, $dbh, $metaFileName, $options) = @_;
437 :     # Load the meta-data.
438 :     my $metaData = _LoadMetaData($metaFileName);
439 :     # Create the object.
440 :     my $self = { _dbh => $dbh,
441 :     _metaData => $metaData
442 :     };
443 :     # Bless and return it.
444 :     bless $self, $class;
445 :     return $self;
446 : parrello 1.1 }
447 :    
448 :     =head3 ShowMetaData
449 :    
450 : parrello 1.18 C<< $erdb->ShowMetaData($fileName); >>
451 : parrello 1.1
452 :     This method outputs a description of the database. This description can be used to help users create
453 :     the data to be loaded into the relations.
454 :    
455 :     =over 4
456 :    
457 :     =item filename
458 :    
459 :     The name of the output file.
460 :    
461 :     =back
462 :    
463 :     =cut
464 :    
465 :     sub ShowMetaData {
466 : parrello 1.10 # Get the parameters.
467 :     my ($self, $filename) = @_;
468 :     # Get the metadata and the title string.
469 :     my $metadata = $self->{_metaData};
470 :     # Get the title string.
471 :     my $title = $metadata->{Title};
472 :     # Get the entity and relationship lists.
473 :     my $entityList = $metadata->{Entities};
474 :     my $relationshipList = $metadata->{Relationships};
475 :     # Open the output file.
476 :     open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
477 :     Trace("Building MetaData table of contents.") if T(4);
478 :     # Write the HTML heading stuff.
479 :     print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
480 :     print HTMLOUT "</head>\n<body>\n";
481 : parrello 1.45 # Write the documentation.
482 :     print HTMLOUT $self->DisplayMetaData();
483 :     # Close the document.
484 :     print HTMLOUT "</body>\n</html>\n";
485 :     # Close the file.
486 :     close HTMLOUT;
487 :     }
488 :    
489 :     =head3 DisplayMetaData
490 :    
491 :     C<< my $html = $erdb->DisplayMetaData(); >>
492 :    
493 :     Return an HTML description of the database. This description can be used to help users create
494 :     the data to be loaded into the relations and form queries. The output is raw includable HTML
495 :     without any HEAD or BODY tags.
496 :    
497 :     =over 4
498 :    
499 :     =item filename
500 :    
501 :     The name of the output file.
502 :    
503 :     =back
504 :    
505 :     =cut
506 :    
507 :     sub DisplayMetaData {
508 :     # Get the parameters.
509 :     my ($self) = @_;
510 :     # Get the metadata and the title string.
511 :     my $metadata = $self->{_metaData};
512 :     # Get the title string.
513 :     my $title = $metadata->{Title};
514 :     # Get the entity and relationship lists.
515 :     my $entityList = $metadata->{Entities};
516 :     my $relationshipList = $metadata->{Relationships};
517 :     # Declare the return variable.
518 :     my $retVal = "";
519 :     # Open the output file.
520 :     Trace("Building MetaData table of contents.") if T(4);
521 : parrello 1.10 # Here we do the table of contents. It starts as an unordered list of section names. Each
522 :     # section contains an ordered list of entity or relationship subsections.
523 : parrello 1.45 $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
524 : parrello 1.10 # Loop through the Entities, displaying a list item for each.
525 :     foreach my $key (sort keys %{$entityList}) {
526 :     # Display this item.
527 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
528 : parrello 1.10 }
529 :     # Close off the entity section and start the relationship section.
530 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
531 : parrello 1.10 # Loop through the Relationships.
532 :     foreach my $key (sort keys %{$relationshipList}) {
533 :     # Display this item.
534 :     my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
535 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
536 : parrello 1.10 }
537 :     # Close off the relationship section and list the join table section.
538 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
539 : parrello 1.10 # Close off the table of contents itself.
540 : parrello 1.45 $retVal .= "</ul>\n";
541 : parrello 1.10 # Now we start with the actual data. Denote we're starting the entity section.
542 : parrello 1.45 $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
543 : parrello 1.10 # Loop through the entities.
544 :     for my $key (sort keys %{$entityList}) {
545 :     Trace("Building MetaData entry for $key entity.") if T(4);
546 :     # Create the entity header. It contains a bookmark and the entity name.
547 : parrello 1.45 $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
548 : parrello 1.10 # Get the entity data.
549 :     my $entityData = $entityList->{$key};
550 :     # If there's descriptive text, display it.
551 :     if (my $notes = $entityData->{Notes}) {
552 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
553 : parrello 1.10 }
554 : parrello 1.83 # See if we need a list of the entity's relationships.
555 :     my $relCount = keys %{$relationshipList};
556 :     if ($relCount > 0) {
557 :     # First, we set up the relationship subsection.
558 :     $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
559 :     # Loop through the relationships.
560 :     for my $relationship (sort keys %{$relationshipList}) {
561 :     # Get the relationship data.
562 :     my $relationshipStructure = $relationshipList->{$relationship};
563 :     # Only use the relationship if if has this entity in its FROM or TO fields.
564 :     if ($relationshipStructure->{from} eq $key || $relationshipStructure->{to} eq $key) {
565 :     # Get the relationship sentence and append the arity.
566 :     my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
567 :     # Display the relationship data.
568 :     $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
569 :     }
570 : parrello 1.10 }
571 : parrello 1.83 # Close off the relationship list.
572 :     $retVal .= "</ul>\n";
573 : parrello 1.10 }
574 :     # Get the entity's relations.
575 :     my $relationList = $entityData->{Relations};
576 :     # Create a header for the relation subsection.
577 : parrello 1.45 $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
578 : parrello 1.10 # Loop through the relations, displaying them.
579 :     for my $relation (sort keys %{$relationList}) {
580 :     my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
581 : parrello 1.45 $retVal .= $htmlString;
582 : parrello 1.10 }
583 :     }
584 :     # Denote we're starting the relationship section.
585 : parrello 1.45 $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
586 : parrello 1.10 # Loop through the relationships.
587 :     for my $key (sort keys %{$relationshipList}) {
588 :     Trace("Building MetaData entry for $key relationship.") if T(4);
589 :     # Get the relationship's structure.
590 :     my $relationshipStructure = $relationshipList->{$key};
591 :     # Create the relationship header.
592 :     my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
593 : parrello 1.45 $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
594 : parrello 1.10 # Get the entity names.
595 :     my $fromEntity = $relationshipStructure->{from};
596 :     my $toEntity = $relationshipStructure->{to};
597 :     # Describe the relationship arity. Note there's a bit of trickiness involving recursive
598 :     # many-to-many relationships. In a normal many-to-many we use two sentences to describe
599 :     # the arity (one for each direction). This is a bad idea for a recursive relationship,
600 :     # since both sentences will say the same thing.
601 :     my $arity = $relationshipStructure->{arity};
602 :     if ($arity eq "11") {
603 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
604 : parrello 1.10 } else {
605 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
606 : parrello 1.10 if ($arity eq "MM" && $fromEntity ne $toEntity) {
607 : parrello 1.45 $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
608 : parrello 1.10 }
609 :     }
610 : parrello 1.45 $retVal .= "</p>\n";
611 : parrello 1.10 # If there are notes on this relationship, display them.
612 :     if (my $notes = $relationshipStructure->{Notes}) {
613 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
614 : parrello 1.10 }
615 :     # Generate the relationship's relation table.
616 :     my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
617 : parrello 1.45 $retVal .= $htmlString;
618 : parrello 1.10 }
619 :     Trace("Building MetaData join table.") if T(4);
620 :     # Denote we're starting the join table.
621 : parrello 1.45 $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
622 : parrello 1.10 # Create a table header.
623 : parrello 1.45 $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
624 : parrello 1.10 # Loop through the joins.
625 :     my $joinTable = $metadata->{Joins};
626 :     my @joinKeys = keys %{$joinTable};
627 :     for my $joinKey (sort @joinKeys) {
628 :     # Separate out the source, the target, and the join clause.
629 :     $joinKey =~ m!^([^/]+)/(.+)$!;
630 :     my ($sourceRelation, $targetRelation) = ($1, $2);
631 : parrello 1.30 Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
632 : parrello 1.10 my $source = $self->ComputeObjectSentence($sourceRelation);
633 :     my $target = $self->ComputeObjectSentence($targetRelation);
634 :     my $clause = $joinTable->{$joinKey};
635 :     # Display them in a table row.
636 : parrello 1.45 $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
637 : parrello 1.10 }
638 :     # Close the table.
639 : parrello 1.45 $retVal .= _CloseTable();
640 :     Trace("Built MetaData HTML.") if T(3);
641 :     # Return the HTML.
642 :     return $retVal;
643 : parrello 1.1 }
644 :    
645 :     =head3 DumpMetaData
646 :    
647 : parrello 1.18 C<< $erdb->DumpMetaData(); >>
648 : parrello 1.1
649 :     Return a dump of the metadata structure.
650 :    
651 :     =cut
652 :    
653 :     sub DumpMetaData {
654 : parrello 1.10 # Get the parameters.
655 :     my ($self) = @_;
656 :     # Dump the meta-data.
657 :     return Data::Dumper::Dumper($self->{_metaData});
658 : parrello 1.1 }
659 :    
660 : parrello 1.89 =head3 CreatePPO
661 :    
662 :     C<< ERDB::CreatePPO($erdbXMLFile, $ppoXMLFile); >>
663 :    
664 :     Create a PPO XML file from an ERDB data definition XML file. At the
665 :     current time, the PPO XML file can be used to create a database with
666 :     similar functionality. Eventually, the PPO will be able to use the
667 :     created XML to access the live ERDB database.
668 :    
669 :     =over 4
670 :    
671 :     =item erdbXMLFile
672 :    
673 :     Name of the XML data definition file for the ERDB database. This
674 :     file must exist.
675 :    
676 :     =item ppoXMLFile
677 :    
678 :     Output file for the PPO XML definition. If this file exists, it
679 :     will be overwritten.
680 :    
681 :     =back
682 :    
683 :     =cut
684 :    
685 :     sub CreatePPO {
686 :     # Get the parameters.
687 :     my ($erdbXMLFile, $ppoXMLFile) = @_;
688 :     # First, we want to slurp in the ERDB XML file in its raw form.
689 :     my $xml = ReadMetaXML($erdbXMLFile);
690 :     # Create a variable to hold all of the objects in the PPO project.
691 :     my @objects = ();
692 :     # Get the relationship hash.
693 :     my $relationships = $xml->{Relationships};
694 :     # Loop through the entities.
695 :     my $entities = $xml->{Entities};
696 :     for my $entityName (keys %{$entities}) {
697 :     # Get the entity's data structures.
698 :     my $entityObject = $entities->{$entityName};
699 :     # We put the object's fields in here, according to their type.
700 :     my (@object_refs, @scalars, @indexes, @arrays);
701 :     # Create the ID field for the entity. We get the key type from the
702 :     # entity object and compute the corresponding SQL type.
703 :     my $type = $TypeTable{$entityObject->{keyType}}->{sqlType};
704 :     push @scalars, { label => 'id', type => $type };
705 :     # Loop through the entity fields.
706 :     for my $fieldName ( keys %{$entityObject->{Fields}} ) {
707 :     # Get the field object.
708 :     my $fieldObject = $entityObject->{Fields}->{$fieldName};
709 :     # Convert it to a scalar tag.
710 :     my $scalar = _CreatePPOField($fieldName, $fieldObject);
711 :     # If we have a relation, this field is stored in an array.
712 :     # otherwise, it is a scalar. The array tag has scalars
713 :     # stored as an XML array. In ERDB, there is only ever one,
714 :     # but PPO can have more.
715 :     my $relation = $fieldObject->{relation};
716 :     if ($relation) {
717 :     push @arrays, { scalar => [$scalar] };
718 :     } else {
719 :     push @scalars, $scalar;
720 :     }
721 :     }
722 :     # Loop through the relationships. If this entity is the to-entity
723 :     # on a relationship of 1M arity, then it is implemented as a PPO
724 :     # object reference.
725 :     for my $relationshipName (keys %{$relationships}) {
726 :     # Get the relationship data.
727 :     my $relationshipData = $relationships->{$relationshipName};
728 :     # If we have a from for this entity and an arity of 1M, we
729 :     # have an object reference.
730 :     if ($relationshipData->{to} eq $entityName &&
731 :     $relationshipData->{arity} eq '1M') {
732 :     # Build the object reference tag.
733 :     push @object_refs, { label => $relationshipName,
734 :     type => $relationshipData->{from} };
735 :     }
736 :     }
737 :     # Create the indexes.
738 :     my $indexList = $entityObject->{Indexes};
739 :     push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
740 :     # Build the object XML tree.
741 :     my $object = { label => $entityName,
742 :     object_ref => \@object_refs,
743 :     scalar => \@scalars,
744 :     index => \@indexes,
745 :     array => \@arrays
746 :     };
747 :     # Push the object onto the objects list.
748 :     push @objects, $object;
749 :     }
750 :     # Loop through the relationships, searching for MMs. The 1Ms were
751 :     # already handled by the entity search above.
752 :     for my $relationshipName (keys %{$relationships}) {
753 :     # Get this relationship's object.
754 :     my $relationshipObject = $relationships->{$relationshipName};
755 :     # Only proceed if it's many-to-many.
756 :     if ($relationshipObject->{arity} eq 'MM') {
757 :     # Create the tag lists for the relationship object.
758 :     my (@object_refs, @scalars, @indexes);
759 :     # The relationship will be created as an object with object
760 :     # references for its links to the participating entities.
761 : parrello 1.90 my %links = ( from_link => $relationshipObject->{from},
762 :     to_link => $relationshipObject->{to} );
763 : parrello 1.89 for my $link (keys %links) {
764 :     # Create an object_ref tag for this piece of the
765 :     # relationship (from or to).
766 :     my $object_ref = { label => $link,
767 :     type => $links{$link} };
768 :     push @object_refs, $object_ref;
769 :     }
770 :     # Loop through the intersection data fields, creating scalar tags.
771 :     # There are no fancy array tags in a relationship.
772 :     for my $fieldName (keys %{$relationshipObject->{Fields}}) {
773 :     my $fieldObject = $relationshipObject->{Fields}->{$fieldName};
774 :     push @scalars, _CreatePPOField($fieldName, $fieldObject);
775 :     }
776 :     # Finally, the indexes: currently we cannot support the to-index and
777 :     # from-index in PPO, so we just process the alternate indexes.
778 :     my $indexList = $relationshipObject->{Indexes};
779 :     push @indexes, map { _CreatePPOIndex($_) } @{$indexList};
780 :     # Wrap up all the stuff about this relationship.
781 :     my $object = { label => $relationshipName,
782 :     scalar => \@scalars,
783 :     object_ref => \@object_refs,
784 :     index => \@indexes
785 :     };
786 :     # Push it into the object list.
787 :     push @objects, $object;
788 :     }
789 :     }
790 :     # Compute a title.
791 :     my $title;
792 : parrello 1.90 if ($erdbXMLFile =~ /(\/|^)([^\/]+)DBD\.xml/) {
793 : parrello 1.89 # Here we have a standard file name we can use for a title.
794 : parrello 1.90 $title = $2;
795 : parrello 1.89 } else {
796 :     # Here the file name is non-standard, so we carve up the
797 :     # database title.
798 :     $title = $xml->{Title}->{content};
799 :     $title =~ s/\s\.,//g;
800 :     }
801 :     # Wrap up the XML as a project.
802 :     my $ppoXML = { project => { label => $title,
803 :     object => \@objects }};
804 :     # Write out the results.
805 :     my $ppoString = XML::Simple::XMLout($ppoXML,
806 :     AttrIndent => 1,
807 :     KeepRoot => 1);
808 :     Tracer::PutFile($ppoXMLFile, [ $ppoString ]);
809 :     }
810 :    
811 : parrello 1.74 =head3 FindIndexForEntity
812 :    
813 :     C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
814 :    
815 :     This method locates the entry in an entity's index list that begins with the
816 :     specified attribute name. If the entity has no index list, one will be
817 :     created. This method works on raw XML, not a live ERDB object.
818 :    
819 :     =over 4
820 :    
821 :     =item xml
822 :    
823 :     The raw XML structure defining the database.
824 :    
825 :     =item entityName
826 :    
827 :     The name of the relevant entity.
828 :    
829 :     =item attributeName
830 :    
831 :     The name of the attribute relevant to the search.
832 :    
833 :     =item RETURN
834 :    
835 :     The numerical index in the index list of the index entry for the specified entity and
836 :     attribute, or C<undef> if no such index exists.
837 :    
838 :     =back
839 :    
840 :     =cut
841 :    
842 :     sub FindIndexForEntity {
843 :     # Get the parameters.
844 :     my ($xml, $entityName, $attributeName) = @_;
845 :     # Declare the return variable.
846 :     my $retVal;
847 :     # Get the named entity.
848 :     my $entityData = $xml->{Entities}->{$entityName};
849 :     if (! $entityData) {
850 :     Confess("Entity $entityName not found in DBD structure.");
851 :     } else {
852 :     # Insure it has an index list.
853 :     if (! exists $entityData->{Indexes}) {
854 :     $entityData->{Indexes} = [];
855 :     } else {
856 :     # Search for the desired index.
857 :     my $indexList = $entityData->{Indexes};
858 :     my $n = scalar @{$indexList};
859 :     Trace("Searching $n indexes in index list for $entityName.") if T(2);
860 :     # We use an indexed FOR here because we're returning an
861 :     # index number instead of an object. We do THAT so we can
862 :     # delete the index from the list if needed.
863 :     for (my $i = 0; $i < $n && !defined($retVal); $i++) {
864 :     my $index = $indexList->[$i];
865 :     my $fields = $index->{IndexFields};
866 :     # Technically this IF should be safe (that is, we are guaranteed
867 :     # the existence of a "$fields->[0]"), because when we load the XML
868 :     # we have SuppressEmpty specified.
869 :     if ($fields->[0]->{name} eq $attributeName) {
870 :     $retVal = $i;
871 :     }
872 :     }
873 :     }
874 :     }
875 :     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
876 :     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
877 :     # Return the result.
878 :     return $retVal;
879 :     }
880 :    
881 : parrello 1.1 =head3 CreateTables
882 :    
883 : parrello 1.18 C<< $erdb->CreateTables(); >>
884 : parrello 1.1
885 :     This method creates the tables for the database from the metadata structure loaded by the
886 :     constructor. It is expected this function will only be used on rare occasions, when the
887 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
888 : parrello 1.1 used by itself with the truncate flag turned on.
889 :    
890 :     =cut
891 :    
892 :     sub CreateTables {
893 : parrello 1.10 # Get the parameters.
894 :     my ($self) = @_;
895 : parrello 1.23 # Get the relation names.
896 :     my @relNames = $self->GetTableNames();
897 :     # Loop through the relations.
898 :     for my $relationName (@relNames) {
899 :     # Create a table for this relation.
900 : parrello 1.87 $self->CreateTable($relationName, 1);
901 : parrello 1.23 Trace("Relation $relationName created.") if T(2);
902 : parrello 1.10 }
903 : parrello 1.1 }
904 :    
905 :     =head3 CreateTable
906 :    
907 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
908 : parrello 1.1
909 :     Create the table for a relation and optionally create its indexes.
910 :    
911 :     =over 4
912 :    
913 :     =item relationName
914 :    
915 :     Name of the relation (which will also be the table name).
916 :    
917 : parrello 1.18 =item indexFlag
918 : parrello 1.1
919 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
920 :     L</CreateIndexes> must be called later to bring the indexes into existence.
921 :    
922 : parrello 1.18 =item estimatedRows (optional)
923 :    
924 :     If specified, the estimated maximum number of rows for the relation. This
925 :     information allows the creation of tables using storage engines that are
926 :     faster but require size estimates, such as MyISAM.
927 :    
928 : parrello 1.1 =back
929 :    
930 :     =cut
931 :    
932 :     sub CreateTable {
933 : parrello 1.10 # Get the parameters.
934 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
935 : parrello 1.10 # Get the database handle.
936 :     my $dbh = $self->{_dbh};
937 :     # Get the relation data and determine whether or not the relation is primary.
938 :     my $relationData = $self->_FindRelation($relationName);
939 :     my $rootFlag = $self->_IsPrimary($relationName);
940 :     # Create a list of the field data.
941 :     my @fieldList;
942 :     for my $fieldData (@{$relationData->{Fields}}) {
943 :     # Assemble the field name and type.
944 :     my $fieldName = _FixName($fieldData->{name});
945 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
946 :     # Push the result into the field list.
947 :     push @fieldList, $fieldString;
948 :     }
949 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
950 :     if ($rootFlag) {
951 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
952 :     }
953 :     # Convert the field list into a comma-delimited string.
954 :     my $fieldThing = join(', ', @fieldList);
955 :     # Insure the table is not already there.
956 :     $dbh->drop_table(tbl => $relationName);
957 :     Trace("Table $relationName dropped.") if T(2);
958 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
959 :     # faster DB technologies.
960 :     my $estimation = undef;
961 :     if ($estimatedRows) {
962 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
963 :     }
964 : parrello 1.10 # Create the table.
965 :     Trace("Creating table $relationName: $fieldThing") if T(2);
966 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
967 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
968 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
969 :     # index will not be built until the table has been loaded.
970 : parrello 1.10 if ($indexFlag) {
971 :     $self->CreateIndex($relationName);
972 :     }
973 : parrello 1.1 }
974 :    
975 : parrello 1.31 =head3 VerifyFields
976 :    
977 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
978 :    
979 :     Run through the list of proposed field values, insuring that all the character fields are
980 :     below the maximum length. If any fields are too long, they will be truncated in place.
981 :    
982 :     =over 4
983 :    
984 :     =item relName
985 :    
986 :     Name of the relation for which the specified fields are destined.
987 :    
988 :     =item fieldList
989 :    
990 :     Reference to a list, in order, of the fields to be put into the relation.
991 :    
992 :     =item RETURN
993 :    
994 :     Returns the number of fields truncated.
995 :    
996 :     =back
997 :    
998 :     =cut
999 :    
1000 :     sub VerifyFields {
1001 :     # Get the parameters.
1002 :     my ($self, $relName, $fieldList) = @_;
1003 :     # Initialize the return value.
1004 :     my $retVal = 0;
1005 :     # Get the relation definition.
1006 :     my $relData = $self->_FindRelation($relName);
1007 :     # Get the list of field descriptors.
1008 :     my $fieldTypes = $relData->{Fields};
1009 :     my $fieldCount = scalar @{$fieldTypes};
1010 :     # Loop through the two lists.
1011 :     for (my $i = 0; $i < $fieldCount; $i++) {
1012 :     # Get the type of the current field.
1013 :     my $fieldType = $fieldTypes->[$i]->{type};
1014 :     # If it's a character field, verify the length.
1015 :     if ($fieldType =~ /string/) {
1016 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
1017 :     my $oldString = $fieldList->[$i];
1018 :     if (length($oldString) > $maxLen) {
1019 :     # Here it's too big, so we truncate it.
1020 : parrello 1.92 Trace("Truncating field $i ($fieldTypes->[$i]->{name}) in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
1021 : parrello 1.31 $fieldList->[$i] = substr $oldString, 0, $maxLen;
1022 :     $retVal++;
1023 :     }
1024 :     }
1025 :     }
1026 :     # Return the truncation count.
1027 :     return $retVal;
1028 :     }
1029 :    
1030 : parrello 1.42 =head3 DigestFields
1031 :    
1032 :     C<< $erdb->DigestFields($relName, $fieldList); >>
1033 :    
1034 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
1035 :     specified relation.
1036 :    
1037 :     =over 4
1038 :    
1039 :     =item relName
1040 :    
1041 :     Name of the relation to which the fields belong.
1042 :    
1043 :     =item fieldList
1044 :    
1045 :     List of field contents to be loaded into the relation.
1046 :    
1047 :     =back
1048 :    
1049 :     =cut
1050 :     #: Return Type ;
1051 :     sub DigestFields {
1052 :     # Get the parameters.
1053 :     my ($self, $relName, $fieldList) = @_;
1054 :     # Get the relation definition.
1055 :     my $relData = $self->_FindRelation($relName);
1056 :     # Get the list of field descriptors.
1057 :     my $fieldTypes = $relData->{Fields};
1058 :     my $fieldCount = scalar @{$fieldTypes};
1059 :     # Loop through the two lists.
1060 :     for (my $i = 0; $i < $fieldCount; $i++) {
1061 :     # Get the type of the current field.
1062 :     my $fieldType = $fieldTypes->[$i]->{type};
1063 :     # If it's a hash string, digest it in place.
1064 :     if ($fieldType eq 'hash-string') {
1065 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
1066 : parrello 1.42 }
1067 :     }
1068 :     }
1069 :    
1070 : parrello 1.46 =head3 DigestKey
1071 :    
1072 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
1073 :    
1074 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
1075 :     key-based search into a table with key-type hash-string.
1076 :    
1077 :     Currently the digesting process is independent of the database structure, but that may not
1078 :     always be the case, so this is an instance method instead of a static method.
1079 :    
1080 :     =over 4
1081 :    
1082 :     =item keyValue
1083 :    
1084 :     Key value to digest.
1085 :    
1086 :     =item RETURN
1087 :    
1088 : parrello 1.56 Digested value of the key.
1089 : parrello 1.46
1090 :     =back
1091 :    
1092 :     =cut
1093 :    
1094 :     sub DigestKey {
1095 :     # Get the parameters.
1096 :     my ($self, $keyValue) = @_;
1097 :     # Compute the digest.
1098 :     my $retVal = md5_base64($keyValue);
1099 :     # Return the result.
1100 :     return $retVal;
1101 :     }
1102 :    
1103 : parrello 1.1 =head3 CreateIndex
1104 :    
1105 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
1106 : parrello 1.1
1107 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
1108 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
1109 :     If that is the case, then L</CreateTable> should be called with the index flag set to
1110 :     FALSE, and this method used after the load to create the indexes for the table.
1111 : parrello 1.1
1112 :     =cut
1113 :    
1114 :     sub CreateIndex {
1115 : parrello 1.10 # Get the parameters.
1116 :     my ($self, $relationName) = @_;
1117 :     # Get the relation's descriptor.
1118 :     my $relationData = $self->_FindRelation($relationName);
1119 :     # Get the database handle.
1120 :     my $dbh = $self->{_dbh};
1121 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
1122 :     my $indexHash = $relationData->{Indexes};
1123 :     for my $indexName (keys %{$indexHash}) {
1124 :     my $indexData = $indexHash->{$indexName};
1125 :     # Get the index's field list.
1126 : parrello 1.75 my @rawFields = @{$indexData->{IndexFields}};
1127 :     # Get a hash of the relation's field types.
1128 :     my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
1129 : parrello 1.78 # We need to check for text fields so we can append a length limitation for them. To do
1130 : parrello 1.75 # that, we need the relation's field list.
1131 :     my $relFields = $relationData->{Fields};
1132 :     for (my $i = 0; $i <= $#rawFields; $i++) {
1133 :     # Get the field type.
1134 :     my $field = $rawFields[$i];
1135 :     my $type = $types{$field};
1136 :     # Ask if it requires using prefix notation for the index.
1137 :     my $mod = $TypeTable{$type}->{indexMod};
1138 :     Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
1139 :     if ($mod) {
1140 :     # Append the prefix length to the field name,
1141 :     $rawFields[$i] .= "($mod)";
1142 :     }
1143 :     }
1144 :     my @fieldList = _FixNames(@rawFields);
1145 : parrello 1.10 my $flds = join(', ', @fieldList);
1146 :     # Get the index's uniqueness flag.
1147 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
1148 : parrello 1.10 # Create the index.
1149 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
1150 : parrello 1.70 flds => $flds, kind => $unique);
1151 : parrello 1.24 if ($rv) {
1152 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
1153 :     } else {
1154 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
1155 :     }
1156 : parrello 1.10 }
1157 : parrello 1.1 }
1158 :    
1159 : parrello 1.75 =head3 GetSecondaryFields
1160 :    
1161 :     C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1162 :    
1163 :     This method will return a list of the name and type of each of the secondary
1164 :     fields for a specified entity. Secondary fields are stored in two-column tables
1165 :     in addition to the primary entity table. This enables the field to have no value
1166 :     or to have multiple values.
1167 :    
1168 :     =over 4
1169 :    
1170 :     =item entityName
1171 :    
1172 :     Name of the entity whose secondary fields are desired.
1173 :    
1174 :     =item RETURN
1175 :    
1176 :     Returns a hash mapping the field names to their field types.
1177 :    
1178 :     =back
1179 :    
1180 :     =cut
1181 :    
1182 :     sub GetSecondaryFields {
1183 :     # Get the parameters.
1184 :     my ($self, $entityName) = @_;
1185 :     # Declare the return variable.
1186 :     my %retVal = ();
1187 :     # Look for the entity.
1188 :     my $table = $self->GetFieldTable($entityName);
1189 :     # Loop through the fields, pulling out the secondaries.
1190 :     for my $field (sort keys %{$table}) {
1191 :     if ($table->{$field}->{relation} ne $entityName) {
1192 :     # Here we have a secondary field.
1193 :     $retVal{$field} = $table->{$field}->{type};
1194 :     }
1195 :     }
1196 :     # Return the result.
1197 :     return %retVal;
1198 :     }
1199 :    
1200 :     =head3 GetFieldRelationName
1201 :    
1202 :     C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1203 :    
1204 :     Return the name of the relation containing a specified field.
1205 :    
1206 :     =over 4
1207 :    
1208 :     =item objectName
1209 :    
1210 :     Name of the entity or relationship containing the field.
1211 :    
1212 :     =item fieldName
1213 :    
1214 :     Name of the relevant field in that entity or relationship.
1215 :    
1216 :     =item RETURN
1217 :    
1218 :     Returns the name of the database relation containing the field, or C<undef> if
1219 :     the field does not exist.
1220 :    
1221 :     =back
1222 :    
1223 :     =cut
1224 :    
1225 :     sub GetFieldRelationName {
1226 :     # Get the parameters.
1227 :     my ($self, $objectName, $fieldName) = @_;
1228 :     # Declare the return variable.
1229 :     my $retVal;
1230 :     # Get the object field table.
1231 :     my $table = $self->GetFieldTable($objectName);
1232 :     # Only proceed if the field exists.
1233 :     if (exists $table->{$fieldName}) {
1234 :     # Determine the name of the relation that contains this field.
1235 :     $retVal = $table->{$fieldName}->{relation};
1236 :     }
1237 :     # Return the result.
1238 :     return $retVal;
1239 :     }
1240 :    
1241 :     =head3 DeleteValue
1242 :    
1243 :     C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1244 :    
1245 :     Delete secondary field values from the database. This method can be used to delete all
1246 :     values of a specified field for a particular entity instance, or only a single value.
1247 :    
1248 :     Secondary fields are stored in two-column relations separate from an entity's primary
1249 :     table, and as a result a secondary field can legitimately have no value or multiple
1250 :     values. Therefore, it makes sense to talk about deleting secondary fields where it
1251 :     would not make sense for primary fields.
1252 :    
1253 :     =over 4
1254 :    
1255 :     =item entityName
1256 :    
1257 :     Name of the entity from which the fields are to be deleted.
1258 :    
1259 :     =item id
1260 :    
1261 :     ID of the entity instance to be processed. If the instance is not found, this
1262 : parrello 1.76 method will have no effect. If C<undef> is specified, all values for all of
1263 :     the entity instances will be deleted.
1264 : parrello 1.75
1265 :     =item fieldName
1266 :    
1267 :     Name of the field whose values are to be deleted.
1268 :    
1269 :     =item fieldValue (optional)
1270 :    
1271 :     Value to be deleted. If not specified, then all values of the specified field
1272 :     will be deleted for the entity instance. If specified, then only the values which
1273 :     match this parameter will be deleted.
1274 :    
1275 :     =item RETURN
1276 :    
1277 :     Returns the number of rows deleted.
1278 :    
1279 :     =back
1280 :    
1281 :     =cut
1282 :    
1283 :     sub DeleteValue {
1284 :     # Get the parameters.
1285 :     my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1286 :     # Declare the return value.
1287 :     my $retVal = 0;
1288 :     # We need to set up an SQL command to do the deletion. First, we
1289 :     # find the name of the field's relation.
1290 :     my $table = $self->GetFieldTable($entityName);
1291 :     my $field = $table->{$fieldName};
1292 :     my $relation = $field->{relation};
1293 :     # Make sure this is a secondary field.
1294 :     if ($relation eq $entityName) {
1295 :     Confess("Cannot delete values of $fieldName for $entityName.");
1296 :     } else {
1297 :     # Set up the SQL command to delete all values.
1298 : parrello 1.76 my $sql = "DELETE FROM $relation";
1299 :     # Build the filter.
1300 :     my @filters = ();
1301 :     my @parms = ();
1302 :     # Check for a filter by ID.
1303 :     if (defined $id) {
1304 :     push @filters, "id = ?";
1305 :     push @parms, $id;
1306 :     }
1307 :     # Check for a filter by value.
1308 : parrello 1.75 if (defined $fieldValue) {
1309 : parrello 1.76 push @filters, "$fieldName = ?";
1310 : parrello 1.75 push @parms, $fieldValue;
1311 :     }
1312 : parrello 1.76 # Append the filters to the command.
1313 :     if (@filters) {
1314 :     $sql .= " WHERE " . join(" AND ", @filters);
1315 :     }
1316 : parrello 1.75 # Execute the command.
1317 :     my $dbh = $self->{_dbh};
1318 :     $retVal = $dbh->SQL($sql, 0, @parms);
1319 :     }
1320 :     # Return the result.
1321 :     return $retVal;
1322 :     }
1323 :    
1324 : parrello 1.1 =head3 LoadTables
1325 :    
1326 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1327 : parrello 1.1
1328 :     This method will load the database tables from a directory. The tables must already have been created
1329 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1330 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
1331 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1332 :     line of the file will be loaded as a row of the target relation table. The field values should be in
1333 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1334 :     erased before the new data is loaded in.
1335 :    
1336 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1337 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1338 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1339 :    
1340 :     =over 4
1341 :    
1342 :     =item directoryName
1343 :    
1344 :     Name of the directory containing the relation files to be loaded.
1345 :    
1346 :     =item rebuild
1347 :    
1348 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1349 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
1350 :     by all of the DB engines we use.
1351 :    
1352 :     =item RETURN
1353 :    
1354 :     Returns a statistical object describing the number of records read and a list of the error messages.
1355 :    
1356 :     =back
1357 :    
1358 :     =cut
1359 :    
1360 :     sub LoadTables {
1361 : parrello 1.10 # Get the parameters.
1362 :     my ($self, $directoryName, $rebuild) = @_;
1363 :     # Start the timer.
1364 :     my $startTime = gettimeofday;
1365 :     # Clean any trailing slash from the directory name.
1366 :     $directoryName =~ s!/\\$!!;
1367 :     # Declare the return variable.
1368 :     my $retVal = Stats->new();
1369 : parrello 1.23 # Get the relation names.
1370 :     my @relNames = $self->GetTableNames();
1371 :     for my $relationName (@relNames) {
1372 :     # Try to load this relation.
1373 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1374 : parrello 1.10 # Accumulate the statistics.
1375 :     $retVal->Accumulate($result);
1376 :     }
1377 :     # Add the duration of the load to the statistical object.
1378 :     $retVal->Add('duration', gettimeofday - $startTime);
1379 :     # Return the accumulated statistics.
1380 :     return $retVal;
1381 : parrello 1.1 }
1382 :    
1383 : parrello 1.23
1384 : parrello 1.1 =head3 GetTableNames
1385 :    
1386 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
1387 : parrello 1.1
1388 :     Return a list of the relations required to implement this database.
1389 :    
1390 :     =cut
1391 :    
1392 :     sub GetTableNames {
1393 : parrello 1.10 # Get the parameters.
1394 :     my ($self) = @_;
1395 :     # Get the relation list from the metadata.
1396 :     my $relationTable = $self->{_metaData}->{RelationTable};
1397 :     # Return the relation names.
1398 :     return keys %{$relationTable};
1399 : parrello 1.1 }
1400 :    
1401 :     =head3 GetEntityTypes
1402 :    
1403 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
1404 : parrello 1.1
1405 :     Return a list of the entity type names.
1406 :    
1407 :     =cut
1408 :    
1409 :     sub GetEntityTypes {
1410 : parrello 1.10 # Get the database object.
1411 :     my ($self) = @_;
1412 :     # Get the entity list from the metadata object.
1413 :     my $entityList = $self->{_metaData}->{Entities};
1414 :     # Return the list of entity names in alphabetical order.
1415 :     return sort keys %{$entityList};
1416 : parrello 1.1 }
1417 :    
1418 : parrello 1.73 =head3 GetDataTypes
1419 :    
1420 :     C<< my %types = ERDB::GetDataTypes(); >>
1421 :    
1422 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1423 :     The keys of the big hash are the datatypes. Each smaller hash has several
1424 :     values used to manage the data. The most interesting is the SQL type (key
1425 :     C<sqlType>) and the descriptive node (key C<notes>).
1426 :    
1427 :     Note that changing the values in the smaller hashes will seriously break
1428 :     things, so this data should be treated as read-only.
1429 :    
1430 :     =cut
1431 :    
1432 :     sub GetDataTypes {
1433 :     return %TypeTable;
1434 :     }
1435 :    
1436 :    
1437 : parrello 1.20 =head3 IsEntity
1438 :    
1439 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1440 :    
1441 :     Return TRUE if the parameter is an entity name, else FALSE.
1442 :    
1443 :     =over 4
1444 :    
1445 :     =item entityName
1446 :    
1447 :     Object name to be tested.
1448 :    
1449 :     =item RETURN
1450 :    
1451 :     Returns TRUE if the specified string is an entity name, else FALSE.
1452 :    
1453 :     =back
1454 :    
1455 :     =cut
1456 :    
1457 :     sub IsEntity {
1458 :     # Get the parameters.
1459 :     my ($self, $entityName) = @_;
1460 :     # Test to see if it's an entity.
1461 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1462 :     }
1463 :    
1464 : parrello 1.1 =head3 Get
1465 :    
1466 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1467 : parrello 1.1
1468 :     This method returns a query object for entities of a specified type using a specified filter.
1469 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1470 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1471 :     following call requests all B<Genome> objects for the genus specified in the variable
1472 :     $genus.
1473 :    
1474 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1475 : parrello 1.1
1476 :     The WHERE clause contains a single question mark, so there is a single additional
1477 :     parameter representing the parameter value. It would also be possible to code
1478 :    
1479 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1480 : parrello 1.1
1481 :     however, this version of the call would generate a syntax error if there were any quote
1482 :     characters inside the variable C<$genus>.
1483 :    
1484 :     The use of the strange parenthesized notation for field names enables us to distinguish
1485 :     hyphens contained within field names from minus signs that participate in the computation
1486 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1487 :    
1488 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1489 :     one object's data at the same time, which allows highly complex joined queries. For example,
1490 :    
1491 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1492 : parrello 1.1
1493 :     If multiple names are specified, then the query processor will automatically determine a
1494 :     join path between the entities and relationships. The algorithm used is very simplistic.
1495 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1496 :     the entity and the relationship appear. For example, consider a recursive relationship
1497 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1498 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1499 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1500 :    
1501 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1502 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1503 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1504 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1505 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1506 :    
1507 : parrello 1.1 =over 4
1508 :    
1509 :     =item objectNames
1510 :    
1511 :     List containing the names of the entity and relationship objects to be retrieved.
1512 :    
1513 :     =item filterClause
1514 :    
1515 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1516 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1517 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1518 :     in the filter clause should be added to the parameter list as additional parameters. The
1519 :     fields in a filter clause can come from primary entity relations, relationship relations,
1520 :     or secondary entity relations; however, all of the entities and relationships involved must
1521 :     be included in the list of object names.
1522 :    
1523 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1524 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1525 :     particular genus and sorts them by species name.
1526 :    
1527 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1528 :    
1529 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1530 :     be processed. The idea is to make it less likely to find the verb by accident.
1531 :    
1532 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1533 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1534 :     relation.
1535 :    
1536 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1537 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1538 :     a positive number. So, for example
1539 :    
1540 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1541 :    
1542 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1543 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1544 :     use
1545 :    
1546 :     C<< "LIMIT 10" >>
1547 :    
1548 : parrello 1.45 =item params
1549 : parrello 1.1
1550 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1551 : parrello 1.1
1552 :     =item RETURN
1553 :    
1554 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1555 :    
1556 :     =back
1557 :    
1558 :     =cut
1559 :    
1560 :     sub Get {
1561 : parrello 1.10 # Get the parameters.
1562 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1563 :     # Process the SQL stuff.
1564 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1565 :     $self->_SetupSQL($objectNames, $filterClause);
1566 :     # Create the query.
1567 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1568 :     ".* $suffix";
1569 :     my $sth = $self->_GetStatementHandle($command, $params);
1570 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1571 :     # and mapped name for each object in the query.
1572 :     my @relationMap = ();
1573 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1574 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1575 : parrello 1.39 }
1576 : parrello 1.10 # Return the statement object.
1577 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1578 : parrello 1.10 return $retVal;
1579 : parrello 1.1 }
1580 :    
1581 : parrello 1.78
1582 :    
1583 : parrello 1.70 =head3 Search
1584 :    
1585 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1586 :    
1587 :     Perform a full text search with filtering. The search will be against a specified object
1588 :     in the object name list. That object will get an extra field containing the search
1589 :     relevance. Note that except for the search expression, the parameters of this method are
1590 :     the same as those for L</Get> and follow the same rules.
1591 :    
1592 :     =over 4
1593 :    
1594 :     =item searchExpression
1595 :    
1596 : parrello 1.75 Boolean search expression for the text fields of the target object. The default mode for
1597 :     a Boolean search expression is OR, but we want the default to be AND, so we will
1598 :     add a C<+> operator to each word with no other operator before it.
1599 : parrello 1.70
1600 :     =item idx
1601 :    
1602 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1603 :    
1604 :     =item objectNames
1605 :    
1606 :     List containing the names of the entity and relationship objects to be retrieved.
1607 :    
1608 :     =item filterClause
1609 :    
1610 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1611 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1612 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1613 :     in the filter clause should be added to the parameter list as additional parameters. The
1614 :     fields in a filter clause can come from primary entity relations, relationship relations,
1615 :     or secondary entity relations; however, all of the entities and relationships involved must
1616 :     be included in the list of object names.
1617 :    
1618 :     =item params
1619 :    
1620 :     Reference to a list of parameter values to be substituted into the filter clause.
1621 :    
1622 :     =item RETURN
1623 :    
1624 :     Returns a query object for the specified search.
1625 :    
1626 :     =back
1627 :    
1628 :     =cut
1629 :    
1630 :     sub Search {
1631 :     # Get the parameters.
1632 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1633 :     # Declare the return variable.
1634 :     my $retVal;
1635 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1636 :     # a parameter list exists before we copy it.
1637 :     my @myParams = ();
1638 :     if (defined $params) {
1639 :     @myParams = @{$params};
1640 :     }
1641 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1642 :     my $object1Name = $objectNames->[$idx];
1643 :     my $object1Structure = $self->_GetStructure($object1Name);
1644 :     # Get the field list.
1645 :     if (! exists $object1Structure->{searchFields}) {
1646 :     Confess("No searchable index for $object1Name.");
1647 :     } else {
1648 :     # Get the field list.
1649 :     my @fields = @{$object1Structure->{searchFields}};
1650 : parrello 1.71 # Clean the search expression.
1651 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1652 : parrello 1.75 # Prefix a "+" to each uncontrolled word. This converts the default
1653 :     # search mode from OR to AND.
1654 : parrello 1.80 $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1655 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1656 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1657 :     # query itself. Both will use a parameter mark, so we need to push the
1658 :     # search expression onto the front of the parameter list twice.
1659 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1660 : parrello 1.70 # Build the match expression.
1661 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1662 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1663 :     # Process the SQL stuff.
1664 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1665 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1666 :     # Create the query. Note that the match clause is inserted at the front of
1667 :     # the select fields.
1668 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1669 :     ".* $suffix";
1670 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1671 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1672 :     # and mapped name for each object in the query.
1673 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1674 :     # Return the statement object.
1675 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1676 :     }
1677 :     return $retVal;
1678 :     }
1679 :    
1680 : parrello 1.45 =head3 GetFlat
1681 :    
1682 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1683 :    
1684 :     This is a variation of L</GetAll> that asks for only a single field per record and
1685 :     returns a single flattened list.
1686 :    
1687 :     =over 4
1688 :    
1689 :     =item objectNames
1690 :    
1691 :     List containing the names of the entity and relationship objects to be retrieved.
1692 :    
1693 :     =item filterClause
1694 :    
1695 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1696 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1697 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1698 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1699 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1700 :     entities and relationships involved must be included in the list of object names.
1701 :    
1702 :     =item parameterList
1703 :    
1704 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1705 :    
1706 :     =item field
1707 :    
1708 :     Name of the field to be used to get the elements of the list returned.
1709 :    
1710 :     =item RETURN
1711 :    
1712 :     Returns a list of values.
1713 :    
1714 :     =back
1715 :    
1716 :     =cut
1717 :     #: Return Type @;
1718 :     sub GetFlat {
1719 :     # Get the parameters.
1720 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1721 :     # Construct the query.
1722 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1723 :     # Create the result list.
1724 :     my @retVal = ();
1725 :     # Loop through the records, adding the field values found to the result list.
1726 :     while (my $row = $query->Fetch()) {
1727 :     push @retVal, $row->Value($field);
1728 :     }
1729 :     # Return the list created.
1730 :     return @retVal;
1731 :     }
1732 :    
1733 : parrello 1.73 =head3 SpecialFields
1734 :    
1735 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1736 :    
1737 :     Return a hash mapping special fields in the specified entity to the value of their
1738 :     C<special> attribute. This enables the subclass to get access to the special field
1739 :     attributes without needed to plumb the internal ERDB data structures.
1740 :    
1741 :     =over 4
1742 :    
1743 :     =item entityName
1744 :    
1745 :     Name of the entity whose special fields are desired.
1746 :    
1747 :     =item RETURN
1748 :    
1749 :     Returns a hash. The keys of the hash are the special field names, and the values
1750 :     are the values from each special field's C<special> attribute.
1751 :    
1752 :     =back
1753 :    
1754 :     =cut
1755 :    
1756 :     sub SpecialFields {
1757 :     # Get the parameters.
1758 :     my ($self, $entityName) = @_;
1759 :     # Declare the return variable.
1760 :     my %retVal = ();
1761 :     # Find the entity's data structure.
1762 : parrello 1.75 my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1763 : parrello 1.73 # Loop through its fields, adding each special field to the return hash.
1764 :     my $fieldHash = $entityData->{Fields};
1765 :     for my $fieldName (keys %{$fieldHash}) {
1766 :     my $fieldData = $fieldHash->{$fieldName};
1767 :     if (exists $fieldData->{special}) {
1768 :     $retVal{$fieldName} = $fieldData->{special};
1769 :     }
1770 :     }
1771 :     # Return the result.
1772 :     return %retVal;
1773 :     }
1774 :    
1775 : parrello 1.32 =head3 Delete
1776 :    
1777 : parrello 1.78 C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1778 : parrello 1.32
1779 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1780 : parrello 1.77 relationship instances dependent on it. The definition of I<dependence> is recursive.
1781 :    
1782 :     An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1783 :     relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1784 : parrello 1.32 dependent relationship.
1785 :    
1786 :     =over 4
1787 :    
1788 :     =item entityName
1789 :    
1790 :     Name of the entity type for the instance being deleted.
1791 :    
1792 :     =item objectID
1793 :    
1794 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1795 :     then it is presumed to by a LIKE pattern.
1796 :    
1797 : parrello 1.78 =item options
1798 : parrello 1.32
1799 : parrello 1.78 A hash detailing the options for this delete operation.
1800 : parrello 1.32
1801 :     =item RETURN
1802 :    
1803 :     Returns a statistics object indicating how many records of each particular table were
1804 :     deleted.
1805 :    
1806 :     =back
1807 :    
1808 : parrello 1.78 The permissible options for this method are as follows.
1809 :    
1810 :     =over 4
1811 :    
1812 :     =item testMode
1813 :    
1814 :     If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1815 :    
1816 :     =item keepRoot
1817 :    
1818 :     If TRUE, then the entity instances will not be deleted, only the dependent records.
1819 :    
1820 :     =back
1821 :    
1822 : parrello 1.32 =cut
1823 :     #: Return Type $%;
1824 :     sub Delete {
1825 :     # Get the parameters.
1826 : parrello 1.78 my ($self, $entityName, $objectID, %options) = @_;
1827 : parrello 1.32 # Declare the return variable.
1828 :     my $retVal = Stats->new();
1829 :     # Get the DBKernel object.
1830 :     my $db = $self->{_dbh};
1831 :     # We're going to generate all the paths branching out from the starting entity. One of
1832 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1833 :     # determine if we've hit a loop.
1834 :     my %alreadyFound = ();
1835 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1836 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1837 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1838 :     # sure we don't delete records that might be needed to forge relationships back to the
1839 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1840 :     # FROM-relationships and entities.
1841 :     my @fromPathList = ();
1842 :     my @toPathList = ();
1843 : parrello 1.78 # This final list is used to remember what work still needs to be done. We push paths
1844 : parrello 1.32 # onto the list, then pop them off to extend the paths. We prime it with the starting
1845 :     # point. Note that we will work hard to insure that the last item on a path in the
1846 : parrello 1.75 # to-do list is always an entity.
1847 : parrello 1.32 my @todoList = ([$entityName]);
1848 :     while (@todoList) {
1849 :     # Get the current path.
1850 :     my $current = pop @todoList;
1851 :     # Copy it into a list.
1852 :     my @stackedPath = @{$current};
1853 :     # Pull off the last item on the path. It will always be an entity.
1854 : parrello 1.78 my $myEntityName = pop @stackedPath;
1855 : parrello 1.32 # Add it to the alreadyFound list.
1856 : parrello 1.78 $alreadyFound{$myEntityName} = 1;
1857 :     # Figure out if we need to delete this entity.
1858 :     if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1859 :     # Get the entity data.
1860 :     my $entityData = $self->_GetStructure($myEntityName);
1861 :     # Loop through the entity's relations. A DELETE command will be needed for each of them.
1862 :     my $relations = $entityData->{Relations};
1863 :     for my $relation (keys %{$relations}) {
1864 :     my @augmentedList = (@stackedPath, $relation);
1865 :     push @fromPathList, \@augmentedList;
1866 :     }
1867 : parrello 1.32 }
1868 :     # Now we need to look for relationships connected to this entity.
1869 :     my $relationshipList = $self->{_metaData}->{Relationships};
1870 :     for my $relationshipName (keys %{$relationshipList}) {
1871 :     my $relationship = $relationshipList->{$relationshipName};
1872 :     # Check the FROM field. We're only interested if it's us.
1873 : parrello 1.78 if ($relationship->{from} eq $myEntityName) {
1874 : parrello 1.32 # Add the path to this relationship.
1875 : parrello 1.78 my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1876 : parrello 1.33 push @fromPathList, \@augmentedList;
1877 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1878 :     # and the target hasn't been seen yet, we want to
1879 :     # stack the entity for future processing.
1880 :     if ($relationship->{arity} eq '1M') {
1881 :     my $toEntity = $relationship->{to};
1882 :     if (! exists $alreadyFound{$toEntity}) {
1883 :     # Here we have a new entity that's dependent on
1884 :     # the current entity, so we need to stack it.
1885 :     my @stackList = (@augmentedList, $toEntity);
1886 : parrello 1.33 push @fromPathList, \@stackList;
1887 : parrello 1.34 } else {
1888 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1889 : parrello 1.32 }
1890 :     }
1891 :     }
1892 :     # Now check the TO field. In this case only the relationship needs
1893 : parrello 1.33 # deletion.
1894 : parrello 1.78 if ($relationship->{to} eq $myEntityName) {
1895 :     my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1896 : parrello 1.33 push @toPathList, \@augmentedList;
1897 : parrello 1.32 }
1898 :     }
1899 :     }
1900 :     # Create the first qualifier for the WHERE clause. This selects the
1901 :     # keys of the primary entity records to be deleted. When we're deleting
1902 : parrello 1.78 # from a dependent table, we construct a join path from the first qualifier
1903 : parrello 1.32 # to the table containing the dependent records to delete.
1904 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1905 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1906 :     # the second through the from-list. The from-list is second because
1907 :     # the to-list may need to pass through some of the entities the
1908 :     # from-list would delete.
1909 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1910 :     # Now it's time to do the deletes. We do it in two passes.
1911 :     for my $keyName ('to_link', 'from_link') {
1912 :     # Get the list for this key.
1913 :     my @pathList = @{$stackList{$keyName}};
1914 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1915 : parrello 1.33 # Loop through this list.
1916 :     while (my $path = pop @pathList) {
1917 :     # Get the table whose rows are to be deleted.
1918 :     my @pathTables = @{$path};
1919 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1920 :     # syntax of a DELETE-USING varies among DBMSs.
1921 : parrello 1.33 my $target = $pathTables[$#pathTables];
1922 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1923 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1924 :     # starting table will either be the entity relation or one of the entity's
1925 :     # sub-relations.
1926 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1927 :     # Now we run through the remaining entities in the path, connecting them up.
1928 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1929 :     # Connect the current relationship to the preceding entity.
1930 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1931 :     # The style of connection depends on the direction of the relationship.
1932 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1933 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1934 :     # Here there's a next entity, so connect that to the relationship's
1935 :     # to-link.
1936 :     my $entity2 = $pathTables[$i+1];
1937 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1938 : parrello 1.32 }
1939 :     }
1940 : parrello 1.33 # Now we have our desired DELETE statement.
1941 : parrello 1.78 if ($options{testMode}) {
1942 : parrello 1.33 # Here the user wants to trace without executing.
1943 :     Trace($stmt) if T(0);
1944 :     } else {
1945 : parrello 1.77 # Here we can delete. Note that the SQL method dies with a confession
1946 : parrello 1.33 # if an error occurs, so we just go ahead and do it.
1947 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1948 :     my $rv = $db->SQL($stmt, 0, $objectID);
1949 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1950 :     # are from the target table, so we use its name to record the
1951 :     # statistic.
1952 :     $retVal->Add($target, $rv);
1953 :     }
1954 : parrello 1.32 }
1955 :     }
1956 :     # Return the result.
1957 :     return $retVal;
1958 :     }
1959 :    
1960 : parrello 1.78 =head3 Disconnect
1961 :    
1962 :     C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1963 :    
1964 :     Disconnect an entity instance from all the objects to which it is related. This
1965 :     will delete each relationship instance that connects to the specified entity.
1966 :    
1967 :     =over 4
1968 :    
1969 :     =item relationshipName
1970 :    
1971 :     Name of the relationship whose instances are to be deleted.
1972 :    
1973 :     =item originEntityName
1974 :    
1975 :     Name of the entity that is to be disconnected.
1976 :    
1977 :     =item originEntityID
1978 :    
1979 :     ID of the entity that is to be disconnected.
1980 :    
1981 :     =back
1982 :    
1983 :     =cut
1984 :    
1985 :     sub Disconnect {
1986 :     # Get the parameters.
1987 :     my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1988 :     # Get the relationship descriptor.
1989 :     my $structure = $self->_GetStructure($relationshipName);
1990 :     # Insure we have a relationship.
1991 :     if (! exists $structure->{from}) {
1992 :     Confess("$relationshipName is not a relationship in the database.");
1993 :     } else {
1994 :     # Get the database handle.
1995 :     my $dbh = $self->{_dbh};
1996 :     # We'll set this value to 1 if we find our entity.
1997 :     my $found = 0;
1998 :     # Loop through the ends of the relationship.
1999 :     for my $dir ('from', 'to') {
2000 :     if ($structure->{$dir} eq $originEntityName) {
2001 :     # Delete all relationship instances on this side of the entity instance.
2002 : parrello 1.84 Trace("Disconnecting in $dir direction with ID \"$originEntityID\".");
2003 : parrello 1.78 $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
2004 :     $found = 1;
2005 :     }
2006 :     }
2007 :     # Insure we found the entity on at least one end.
2008 :     if (! $found) {
2009 :     Confess("Entity \"$originEntityName\" does not use $relationshipName.");
2010 :     }
2011 :     }
2012 :     }
2013 :    
2014 : parrello 1.79 =head3 DeleteRow
2015 :    
2016 :     C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
2017 :    
2018 :     Delete a row from a relationship. In most cases, only the from-link and to-link are
2019 :     needed; however, for relationships with intersection data values can be specified
2020 :     for the other fields using a hash.
2021 :    
2022 :     =over 4
2023 :    
2024 :     =item relationshipName
2025 :    
2026 :     Name of the relationship from which the row is to be deleted.
2027 :    
2028 :     =item fromLink
2029 :    
2030 :     ID of the entity instance in the From direction.
2031 :    
2032 :     =item toLink
2033 :    
2034 :     ID of the entity instance in the To direction.
2035 :    
2036 :     =item values
2037 :    
2038 :     Reference to a hash of other values to be used for filtering the delete.
2039 :    
2040 :     =back
2041 :    
2042 :     =cut
2043 :    
2044 :     sub DeleteRow {
2045 :     # Get the parameters.
2046 :     my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
2047 :     # Create a hash of all the filter information.
2048 :     my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
2049 :     if (defined $values) {
2050 :     for my $key (keys %{$values}) {
2051 :     $filter{$key} = $values->{$key};
2052 :     }
2053 :     }
2054 :     # Build an SQL statement out of the hash.
2055 :     my @filters = ();
2056 :     my @parms = ();
2057 :     for my $key (keys %filter) {
2058 :     push @filters, _FixName($key) . " = ?";
2059 :     push @parms, $filter{$key};
2060 :     }
2061 :     Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
2062 :     my $command = "DELETE FROM $relationshipName WHERE " .
2063 :     join(" AND ", @filters);
2064 :     # Execute it.
2065 :     my $dbh = $self->{_dbh};
2066 :     $dbh->SQL($command, undef, @parms);
2067 :     }
2068 :    
2069 : parrello 1.91 =head3 DeleteLike
2070 :    
2071 :     C<< my $deleteCount = $erdb->DeleteLike($relName, $filter, \@parms); >>
2072 :    
2073 :     Delete all the relationship rows that satisfy a particular filter condition. Unlike a normal
2074 :     filter, only fields from the relationship itself can be used.
2075 :    
2076 :     =over 4
2077 :    
2078 :     =item relName
2079 :    
2080 :     Name of the relationship whose records are to be deleted.
2081 :    
2082 :     =item filter
2083 :    
2084 :     A filter clause (L</Get>-style) for the delete query.
2085 :    
2086 :     =item parms
2087 :    
2088 :     Reference to a list of parameters for the filter clause.
2089 :    
2090 :     =item RETURN
2091 :    
2092 :     Returns a count of the number of rows deleted.
2093 :    
2094 :     =back
2095 :    
2096 :     =cut
2097 :    
2098 :     sub DeleteLike {
2099 :     # Get the parameters.
2100 :     my ($self, $objectName, $filter, $parms) = @_;
2101 :     # Declare the return variable.
2102 :     my $retVal;
2103 :     # Insure the parms argument is an array reference if the caller left it off.
2104 :     if (! defined($parms)) {
2105 :     $parms = [];
2106 :     }
2107 :     # Insure we have a relationship. The main reason for this is if we delete an entity
2108 :     # instance we have to yank out a bunch of other stuff with it.
2109 :     if ($self->IsEntity($objectName)) {
2110 :     Confess("Cannot use DeleteLike on $objectName, because it is not a relationship.");
2111 :     } else {
2112 :     # Create the SQL command suffix to get the desierd records.
2113 :     my ($suffix) = $self->_SetupSQL([$objectName], $filter);
2114 :     # Convert it to a DELETE command.
2115 :     my $command = "DELETE $suffix";
2116 :     # Execute the command.
2117 :     my $dbh = $self->{_dbh};
2118 :     my $result = $dbh->SQL($command, 0, @{$parms});
2119 :     # Check the results. Note we convert the "0D0" result to a real zero.
2120 :     # A failure causes an abnormal termination, so the caller isn't going to
2121 :     # worry about it.
2122 :     if (! defined $result) {
2123 :     Confess("Error deleting from $objectName: " . $dbh->errstr());
2124 :     } elsif ($result == 0) {
2125 :     $retVal = 0;
2126 :     } else {
2127 :     $retVal = $result;
2128 :     }
2129 :     }
2130 :     # Return the result count.
2131 :     return $retVal;
2132 :     }
2133 :    
2134 : parrello 1.70 =head3 SortNeeded
2135 :    
2136 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
2137 :    
2138 :     Return the pipe command for the sort that should be applied to the specified
2139 :     relation when creating the load file.
2140 :    
2141 :     For example, if the load file should be sorted ascending by the first
2142 :     field, this method would return
2143 :    
2144 :     sort -k1 -t"\t"
2145 :    
2146 :     If the first field is numeric, the method would return
2147 :    
2148 :     sort -k1n -t"\t"
2149 :    
2150 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
2151 :     keys using a sort.
2152 :    
2153 :     =over 4
2154 :    
2155 :     =item relationName
2156 :    
2157 :     Name of the relation to be examined.
2158 :    
2159 :     =item
2160 :    
2161 :     Returns the sort command to use for sorting the relation, suitable for piping.
2162 :    
2163 :     =back
2164 :    
2165 :     =cut
2166 :     #: Return Type $;
2167 :     sub SortNeeded {
2168 :     # Get the parameters.
2169 :     my ($self, $relationName) = @_;
2170 :     # Declare a descriptor to hold the names of the key fields.
2171 :     my @keyNames = ();
2172 :     # Get the relation structure.
2173 :     my $relationData = $self->_FindRelation($relationName);
2174 :     # Find out if the relation is a primary entity relation,
2175 :     # a relationship relation, or a secondary entity relation.
2176 :     my $entityTable = $self->{_metaData}->{Entities};
2177 :     my $relationshipTable = $self->{_metaData}->{Relationships};
2178 :     if (exists $entityTable->{$relationName}) {
2179 :     # Here we have a primary entity relation.
2180 :     push @keyNames, "id";
2181 :     } elsif (exists $relationshipTable->{$relationName}) {
2182 :     # Here we have a relationship. We sort using the FROM index.
2183 :     my $relationshipData = $relationshipTable->{$relationName};
2184 : parrello 1.75 my $index = $relationData->{Indexes}->{idxFrom};
2185 : parrello 1.70 push @keyNames, @{$index->{IndexFields}};
2186 :     } else {
2187 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
2188 :     push @keyNames, "id";
2189 :     }
2190 :     # Now we parse the key names into sort parameters. First, we prime the return
2191 :     # string.
2192 :     my $retVal = "sort -t\"\t\" ";
2193 :     # Get the relation's field list.
2194 :     my @fields = @{$relationData->{Fields}};
2195 :     # Loop through the keys.
2196 :     for my $keyData (@keyNames) {
2197 :     # Get the key and the ordering.
2198 :     my ($keyName, $ordering);
2199 :     if ($keyData =~ /^([^ ]+) DESC/) {
2200 :     ($keyName, $ordering) = ($1, "descending");
2201 :     } else {
2202 :     ($keyName, $ordering) = ($keyData, "ascending");
2203 :     }
2204 :     # Find the key's position and type.
2205 :     my $fieldSpec;
2206 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
2207 :     my $thisField = $fields[$i];
2208 :     if ($thisField->{name} eq $keyName) {
2209 :     # Get the sort modifier for this field type. The modifier
2210 :     # decides whether we're using a character, numeric, or
2211 :     # floating-point sort.
2212 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
2213 :     # If the index is descending for this field, denote we want
2214 :     # to reverse the sort order on this field.
2215 :     if ($ordering eq 'descending') {
2216 :     $modifier .= "r";
2217 :     }
2218 :     # Store the position and modifier into the field spec, which
2219 :     # will stop the inner loop. Note that the field number is
2220 :     # 1-based in the sort command, so we have to increment the
2221 :     # index.
2222 :     $fieldSpec = ($i + 1) . $modifier;
2223 :     }
2224 :     }
2225 :     # Add this field to the sort command.
2226 :     $retVal .= " -k$fieldSpec";
2227 :     }
2228 :     # Return the result.
2229 :     return $retVal;
2230 :     }
2231 :    
2232 : parrello 1.6 =head3 GetList
2233 :    
2234 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2235 : parrello 1.6
2236 :     Return a list of object descriptors for the specified objects as determined by the
2237 :     specified filter clause.
2238 :    
2239 :     This method is essentially the same as L</Get> except it returns a list of objects rather
2240 : parrello 1.7 than a query object that can be used to get the results one record at a time.
2241 : parrello 1.6
2242 :     =over 4
2243 :    
2244 :     =item objectNames
2245 :    
2246 :     List containing the names of the entity and relationship objects to be retrieved.
2247 :    
2248 :     =item filterClause
2249 :    
2250 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2251 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2252 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2253 :     in the filter clause should be added to the parameter list as additional parameters. The
2254 :     fields in a filter clause can come from primary entity relations, relationship relations,
2255 :     or secondary entity relations; however, all of the entities and relationships involved must
2256 :     be included in the list of object names.
2257 :    
2258 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
2259 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
2260 :     particular genus and sorts them by species name.
2261 :    
2262 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2263 :    
2264 :     The rules for field references in a sort order are the same as those for field references in the
2265 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
2266 :     relation.
2267 :    
2268 : parrello 1.45 =item params
2269 : parrello 1.6
2270 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
2271 : parrello 1.6
2272 :     =item RETURN
2273 :    
2274 : parrello 1.88 Returns a list of B<ERDBObject>s that satisfy the query conditions.
2275 : parrello 1.6
2276 :     =back
2277 :    
2278 :     =cut
2279 :     #: Return Type @%
2280 :     sub GetList {
2281 :     # Get the parameters.
2282 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
2283 : parrello 1.10 # Declare the return variable.
2284 :     my @retVal = ();
2285 :     # Perform the query.
2286 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
2287 : parrello 1.10 # Loop through the results.
2288 :     while (my $object = $query->Fetch) {
2289 :     push @retVal, $object;
2290 :     }
2291 : parrello 1.6 # Return the result.
2292 :     return @retVal;
2293 :     }
2294 :    
2295 : parrello 1.45 =head3 GetCount
2296 :    
2297 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2298 :    
2299 :     Return the number of rows found by a specified query. This method would
2300 :     normally be used to count the records in a single table. For example, in a
2301 :     genetics database
2302 :    
2303 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2304 :    
2305 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
2306 :     to use it to return records based on a join. For example,
2307 :    
2308 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2309 : parrello 1.45 ['homo %']);
2310 :    
2311 :     would return the number of features for genomes in the genus I<homo>. Note that
2312 :     only the rows from the first table are counted. If the above command were
2313 :    
2314 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2315 :     ['homo %']);
2316 :    
2317 :     it would return the number of genomes, not the number of genome/feature pairs.
2318 :    
2319 :     =over 4
2320 :    
2321 :     =item objectNames
2322 :    
2323 :     Reference to a list of the objects (entities and relationships) included in the
2324 :     query.
2325 :    
2326 :     =item filter
2327 :    
2328 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
2329 :     method.
2330 :    
2331 :     =item params
2332 :    
2333 :     Reference to a list of the parameter values to be substituted for the parameter marks
2334 :     in the filter.
2335 :    
2336 :     =item RETURN
2337 :    
2338 :     Returns a count of the number of records in the first table that would satisfy
2339 :     the query.
2340 :    
2341 :     =back
2342 :    
2343 :     =cut
2344 :    
2345 :     sub GetCount {
2346 :     # Get the parameters.
2347 :     my ($self, $objectNames, $filter, $params) = @_;
2348 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
2349 :     if (! defined($params)) {
2350 :     $params = [];
2351 :     }
2352 : parrello 1.45 # Declare the return variable.
2353 :     my $retVal;
2354 : parrello 1.47 # Find out if we're counting an entity or a relationship.
2355 :     my $countedField;
2356 :     if ($self->IsEntity($objectNames->[0])) {
2357 :     $countedField = "id";
2358 :     } else {
2359 :     # For a relationship we count the to-link because it's usually more
2360 :     # numerous. Note we're automatically converting to the SQL form
2361 :     # of the field name (to_link vs. to-link).
2362 :     $countedField = "to_link";
2363 :     }
2364 : parrello 1.45 # Create the SQL command suffix to get the desired records.
2365 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2366 :     $filter);
2367 :     # Prefix it with text telling it we want a record count.
2368 :     my $firstObject = $mappedNameListRef->[0];
2369 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2370 : parrello 1.45 # Prepare and execute the command.
2371 :     my $sth = $self->_GetStatementHandle($command, $params);
2372 :     # Get the count value.
2373 :     ($retVal) = $sth->fetchrow_array();
2374 :     # Check for a problem.
2375 :     if (! defined($retVal)) {
2376 :     if ($sth->err) {
2377 :     # Here we had an SQL error.
2378 :     Confess("Error retrieving row count: " . $sth->errstr());
2379 :     } else {
2380 :     # Here we have no result.
2381 :     Confess("No result attempting to retrieve row count.");
2382 :     }
2383 :     }
2384 :     # Return the result.
2385 :     return $retVal;
2386 :     }
2387 :    
2388 : parrello 1.1 =head3 ComputeObjectSentence
2389 :    
2390 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2391 : parrello 1.1
2392 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
2393 :    
2394 :     =over 4
2395 :    
2396 :     =item objectName
2397 :    
2398 :     Name of the entity or relationship.
2399 :    
2400 :     =item RETURN
2401 :    
2402 :     Returns a string containing the entity name or a relationship sentence.
2403 :    
2404 :     =back
2405 :    
2406 :     =cut
2407 :    
2408 :     sub ComputeObjectSentence {
2409 : parrello 1.10 # Get the parameters.
2410 :     my ($self, $objectName) = @_;
2411 :     # Set the default return value.
2412 :     my $retVal = $objectName;
2413 :     # Look for the object as a relationship.
2414 :     my $relTable = $self->{_metaData}->{Relationships};
2415 :     if (exists $relTable->{$objectName}) {
2416 :     # Get the relationship sentence.
2417 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2418 :     }
2419 :     # Return the result.
2420 :     return $retVal;
2421 : parrello 1.1 }
2422 :    
2423 :     =head3 DumpRelations
2424 :    
2425 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
2426 : parrello 1.1
2427 :     Write the contents of all the relations to tab-delimited files in the specified directory.
2428 :     Each file will have the same name as the relation dumped, with an extension of DTX.
2429 :    
2430 :     =over 4
2431 :    
2432 :     =item outputDirectory
2433 :    
2434 :     Name of the directory into which the relation files should be dumped.
2435 :    
2436 :     =back
2437 :    
2438 :     =cut
2439 :    
2440 :     sub DumpRelations {
2441 : parrello 1.10 # Get the parameters.
2442 :     my ($self, $outputDirectory) = @_;
2443 :     # Now we need to run through all the relations. First, we loop through the entities.
2444 :     my $metaData = $self->{_metaData};
2445 :     my $entities = $metaData->{Entities};
2446 :     for my $entityName (keys %{$entities}) {
2447 :     my $entityStructure = $entities->{$entityName};
2448 :     # Get the entity's relations.
2449 :     my $relationList = $entityStructure->{Relations};
2450 :     # Loop through the relations, dumping them.
2451 :     for my $relationName (keys %{$relationList}) {
2452 :     my $relation = $relationList->{$relationName};
2453 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
2454 :     }
2455 :     }
2456 :     # Next, we loop through the relationships.
2457 :     my $relationships = $metaData->{Relationships};
2458 :     for my $relationshipName (keys %{$relationships}) {
2459 :     my $relationshipStructure = $relationships->{$relationshipName};
2460 :     # Dump this relationship's relation.
2461 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2462 :     }
2463 : parrello 1.1 }
2464 :    
2465 : parrello 1.51 =head3 InsertValue
2466 :    
2467 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2468 :    
2469 :     This method will insert a new value into the database. The value must be one
2470 :     associated with a secondary relation, since primary values cannot be inserted:
2471 :     they occur exactly once. Secondary values, on the other hand, can be missing
2472 :     or multiply-occurring.
2473 :    
2474 :     =over 4
2475 :    
2476 :     =item entityID
2477 :    
2478 :     ID of the object that is to receive the new value.
2479 :    
2480 :     =item fieldName
2481 :    
2482 :     Field name for the new value-- this includes the entity name, since
2483 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2484 :    
2485 :     =item value
2486 :    
2487 :     New value to be put in the field.
2488 :    
2489 :     =back
2490 :    
2491 :     =cut
2492 :    
2493 :     sub InsertValue {
2494 :     # Get the parameters.
2495 :     my ($self, $entityID, $fieldName, $value) = @_;
2496 :     # Parse the entity name and the real field name.
2497 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2498 :     my $entityName = $1;
2499 :     my $fieldTitle = $2;
2500 :     # Get its descriptor.
2501 :     if (!$self->IsEntity($entityName)) {
2502 :     Confess("$entityName is not a valid entity.");
2503 :     } else {
2504 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2505 :     # Find the relation containing this field.
2506 :     my $fieldHash = $entityData->{Fields};
2507 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
2508 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
2509 :     } else {
2510 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
2511 :     if ($relation eq $entityName) {
2512 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2513 :     } else {
2514 :     # Now we can create an INSERT statement.
2515 :     my $dbh = $self->{_dbh};
2516 :     my $fixedName = _FixName($fieldTitle);
2517 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2518 : parrello 1.51 # Execute the command.
2519 :     $dbh->SQL($statement, 0, $entityID, $value);
2520 :     }
2521 :     }
2522 :     }
2523 :     } else {
2524 :     Confess("$fieldName is not a valid field name.");
2525 :     }
2526 :     }
2527 :    
2528 : parrello 1.1 =head3 InsertObject
2529 :    
2530 : parrello 1.78 C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2531 : parrello 1.1
2532 :     Insert an object into the database. The object is defined by a type name and then a hash
2533 :     of field names to values. Field values in the primary relation are represented by scalars.
2534 :     (Note that for relationships, the primary relation is the B<only> relation.)
2535 :     Field values for the other relations comprising the entity are always list references. For
2536 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2537 :     C<ZP_00210270.1> and C<gi|46206278>.
2538 :    
2539 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2540 : parrello 1.1
2541 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2542 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2543 :    
2544 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2545 : parrello 1.1
2546 :     =over 4
2547 :    
2548 :     =item newObjectType
2549 :    
2550 :     Type name of the object to insert.
2551 :    
2552 :     =item fieldHash
2553 :    
2554 :     Hash of field names to values.
2555 :    
2556 :     =back
2557 :    
2558 :     =cut
2559 :    
2560 :     sub InsertObject {
2561 : parrello 1.10 # Get the parameters.
2562 :     my ($self, $newObjectType, $fieldHash) = @_;
2563 :     # Denote that so far we appear successful.
2564 :     my $retVal = 1;
2565 :     # Get the database handle.
2566 :     my $dbh = $self->{_dbh};
2567 :     # Get the relation list.
2568 :     my $relationTable = $self->_GetRelationTable($newObjectType);
2569 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
2570 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
2571 :     # stop the loop.
2572 :     my @relationList = keys %{$relationTable};
2573 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2574 :     my $relationName = $relationList[$i];
2575 :     my $relationDefinition = $relationTable->{$relationName};
2576 :     # Get the relation's fields. For each field we will collect a value in the corresponding
2577 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
2578 :     # @missing list.
2579 :     my @fieldList = @{$relationDefinition->{Fields}};
2580 :     my @fieldNameList = ();
2581 :     my @valueList = ();
2582 :     my @missing = ();
2583 :     my $recordCount = 1;
2584 :     for my $fieldDescriptor (@fieldList) {
2585 :     # Get the field name and save it. Note we need to fix it up so the hyphens
2586 :     # are converted to underscores.
2587 :     my $fieldName = $fieldDescriptor->{name};
2588 :     push @fieldNameList, _FixName($fieldName);
2589 :     # Look for the named field in the incoming structure. Note that we are looking
2590 :     # for the real field name, not the fixed-up one!
2591 :     if (exists $fieldHash->{$fieldName}) {
2592 :     # Here we found the field. Stash it in the value list.
2593 :     my $value = $fieldHash->{$fieldName};
2594 :     push @valueList, $value;
2595 :     # If the value is a list, we may need to increment the record count.
2596 :     if (ref $value eq "ARRAY") {
2597 :     my $thisCount = @{$value};
2598 :     if ($recordCount == 1) {
2599 :     # Here we have our first list, so we save its count.
2600 :     $recordCount = $thisCount;
2601 :     } elsif ($recordCount != $thisCount) {
2602 :     # Here we have a second list, so its length has to match the
2603 :     # previous lists.
2604 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2605 :     $retVal = 0;
2606 :     }
2607 :     }
2608 :     } else {
2609 :     # Here the field is not present. Flag it as missing.
2610 :     push @missing, $fieldName;
2611 :     }
2612 :     }
2613 :     # If we are the primary relation, add the new-record flag.
2614 :     if ($relationName eq $newObjectType) {
2615 :     push @valueList, 1;
2616 :     push @fieldNameList, "new_record";
2617 :     }
2618 :     # Only proceed if there are no missing fields.
2619 :     if (@missing > 0) {
2620 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2621 :     join(' ', @missing)) if T(1);
2622 :     } else {
2623 :     # Build the INSERT statement.
2624 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2625 :     ") VALUES (";
2626 :     # Create a marker list of the proper size and put it in the statement.
2627 :     my @markers = ();
2628 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2629 :     $statement .= join(', ', @markers) . ")";
2630 :     # We have the insert statement, so prepare it.
2631 :     my $sth = $dbh->prepare_command($statement);
2632 :     Trace("Insert statement prepared: $statement") if T(3);
2633 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2634 :     # a list, we use the current element. The values are stored in the @parameterList array.
2635 :     my $done = 0;
2636 :     for (my $i = 0; $i < $recordCount; $i++) {
2637 :     # Clear the parameter list array.
2638 :     my @parameterList = ();
2639 :     # Loop through the values.
2640 :     for my $value (@valueList) {
2641 :     # Check to see if this is a scalar value.
2642 :     if (ref $value eq "ARRAY") {
2643 :     # Here we have a list value. Pull the current entry.
2644 :     push @parameterList, $value->[$i];
2645 :     } else {
2646 :     # Here we have a scalar value. Use it unmodified.
2647 :     push @parameterList, $value;
2648 :     }
2649 :     }
2650 :     # Execute the INSERT statement with the specified parameter list.
2651 :     $retVal = $sth->execute(@parameterList);
2652 :     if (!$retVal) {
2653 :     my $errorString = $sth->errstr();
2654 : parrello 1.78 Confess("Error inserting into $relationName: $errorString");
2655 : parrello 1.85 } else {
2656 :     Trace("Insert successful using $parameterList[0].") if T(3);
2657 : parrello 1.10 }
2658 :     }
2659 :     }
2660 :     }
2661 : parrello 1.78 # Return a 1 for backward compatability.
2662 :     return 1;
2663 :     }
2664 :    
2665 :     =head3 UpdateEntity
2666 :    
2667 :     C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2668 :    
2669 :     Update the values of an entity. This is an unprotected update, so it should only be
2670 :     done if the database resides on a database server.
2671 :    
2672 :     =over 4
2673 :    
2674 :     =item entityName
2675 :    
2676 :     Name of the entity to update. (This is the entity type.)
2677 :    
2678 :     =item id
2679 :    
2680 :     ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2681 :    
2682 :     =item fields
2683 :    
2684 :     Reference to a hash mapping field names to their new values. All of the fields named
2685 :     must be in the entity's primary relation, and they cannot any of them be the ID field.
2686 :    
2687 :     =back
2688 :    
2689 :     =cut
2690 :    
2691 :     sub UpdateEntity {
2692 :     # Get the parameters.
2693 :     my ($self, $entityName, $id, $fields) = @_;
2694 :     # Get a list of the field names being updated.
2695 :     my @fieldList = keys %{$fields};
2696 :     # Verify that the fields exist.
2697 :     my $checker = $self->GetFieldTable($entityName);
2698 :     for my $field (@fieldList) {
2699 :     if ($field eq 'id') {
2700 :     Confess("Cannot update the ID field for entity $entityName.");
2701 :     } elsif ($checker->{$field}->{relation} ne $entityName) {
2702 :     Confess("Cannot find $field in primary relation of $entityName.");
2703 :     }
2704 :     }
2705 :     # Build the SQL statement.
2706 :     my @sets = ();
2707 :     my @valueList = ();
2708 :     for my $field (@fieldList) {
2709 :     push @sets, _FixName($field) . " = ?";
2710 :     push @valueList, $fields->{$field};
2711 :     }
2712 :     my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2713 :     # Add the ID to the list of binding values.
2714 :     push @valueList, $id;
2715 :     # Call SQL to do the work.
2716 :     my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2717 :     # Check for errors.
2718 :     if ($rows == 0) {
2719 :     Confess("Entity $id of type $entityName not found.");
2720 :     }
2721 : parrello 1.1 }
2722 :    
2723 :     =head3 LoadTable
2724 :    
2725 : parrello 1.78 C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2726 : parrello 1.1
2727 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2728 :     first.
2729 : parrello 1.1
2730 :     =over 4
2731 :    
2732 :     =item fileName
2733 :    
2734 :     Name of the file from which the table data should be loaded.
2735 :    
2736 :     =item relationName
2737 :    
2738 :     Name of the relation to be loaded. This is the same as the table name.
2739 :    
2740 :     =item truncateFlag
2741 :    
2742 :     TRUE if the table should be dropped and re-created, else FALSE
2743 :    
2744 :     =item RETURN
2745 :    
2746 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2747 : parrello 1.1
2748 :     =back
2749 :    
2750 :     =cut
2751 :     sub LoadTable {
2752 : parrello 1.10 # Get the parameters.
2753 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2754 :     # Create the statistical return object.
2755 :     my $retVal = _GetLoadStats();
2756 :     # Trace the fact of the load.
2757 :     Trace("Loading table $relationName from $fileName") if T(2);
2758 :     # Get the database handle.
2759 :     my $dbh = $self->{_dbh};
2760 : parrello 1.22 # Get the input file size.
2761 :     my $fileSize = -s $fileName;
2762 : parrello 1.10 # Get the relation data.
2763 :     my $relation = $self->_FindRelation($relationName);
2764 :     # Check the truncation flag.
2765 :     if ($truncateFlag) {
2766 :     Trace("Creating table $relationName") if T(2);
2767 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2768 :     # divide it by the estimated row size, and then multiply by 1.5 to
2769 :     # leave extra room. We postulate a minimum row count of 1000 to
2770 :     # prevent problems with incoming empty load files.
2771 :     my $rowSize = $self->EstimateRowSize($relationName);
2772 : parrello 1.90 my $estimate = $fileSize * 1.5 / $rowSize;
2773 :     if ($estimate < 1000) {
2774 :     $estimate = 1000;
2775 :     }
2776 : parrello 1.10 # Re-create the table without its index.
2777 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2778 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2779 :     if ($dbh->{_preIndex}) {
2780 :     eval {
2781 :     $self->CreateIndex($relationName);
2782 :     };
2783 :     if ($@) {
2784 :     $retVal->AddMessage($@);
2785 :     }
2786 :     }
2787 :     }
2788 : parrello 1.3 # Load the table.
2789 : parrello 1.10 my $rv;
2790 :     eval {
2791 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2792 : parrello 1.10 };
2793 :     if (!defined $rv) {
2794 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2795 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2796 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2797 :     } else {
2798 : parrello 1.22 # Here we successfully loaded the table.
2799 :     $retVal->Add("tables");
2800 :     my $size = -s $fileName;
2801 :     Trace("$size bytes loaded into $relationName.") if T(2);
2802 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2803 : parrello 1.70 if ($truncateFlag) {
2804 :     # Indexes are created here for PostGres. For PostGres, indexes are
2805 :     # best built at the end. For MySQL, the reverse is true.
2806 :     if (! $dbh->{_preIndex}) {
2807 :     eval {
2808 :     $self->CreateIndex($relationName);
2809 :     };
2810 :     if ($@) {
2811 :     $retVal->AddMessage($@);
2812 :     }
2813 :     }
2814 :     # The full-text index (if any) is always built last, even for MySQL.
2815 :     # First we need to see if this table has a full-text index. Only
2816 :     # primary relations are allowed that privilege.
2817 : parrello 1.81 Trace("Checking for full-text index on $relationName.") if T(2);
2818 : parrello 1.70 if ($self->_IsPrimary($relationName)) {
2819 : parrello 1.82 $self->CreateSearchIndex($relationName);
2820 : parrello 1.10 }
2821 :     }
2822 :     }
2823 : parrello 1.20 # Analyze the table to improve performance.
2824 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2825 : olson 1.16 $dbh->vacuum_it($relationName);
2826 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2827 : parrello 1.10 # Return the statistics.
2828 :     return $retVal;
2829 : parrello 1.1 }
2830 :    
2831 : parrello 1.82 =head3 CreateSearchIndex
2832 :    
2833 :     C<< $erdb->CreateSearchIndex($objectName); >>
2834 :    
2835 :     Check for a full-text search index on the specified entity or relationship object, and
2836 :     if one is required, rebuild it.
2837 :    
2838 :     =over 4
2839 :    
2840 :     =item objectName
2841 :    
2842 :     Name of the entity or relationship to be indexed.
2843 :    
2844 :     =back
2845 :    
2846 :     =cut
2847 :    
2848 :     sub CreateSearchIndex {
2849 :     # Get the parameters.
2850 :     my ($self, $objectName) = @_;
2851 :     # Get the relation's entity/relationship structure.
2852 :     my $structure = $self->_GetStructure($objectName);
2853 :     # Get the database handle.
2854 :     my $dbh = $self->{_dbh};
2855 :     Trace("Checking for search fields in $objectName.") if T(3);
2856 :     # Check for a searchable fields list.
2857 :     if (exists $structure->{searchFields}) {
2858 :     # Here we know that we need to create a full-text search index.
2859 :     # Get an SQL-formatted field name list.
2860 :     my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2861 :     # Create the index. If it already exists, it will be dropped.
2862 :     $dbh->create_index(tbl => $objectName, idx => "search_idx",
2863 :     flds => $fields, kind => 'fulltext');
2864 :     Trace("Index created for $fields in $objectName.") if T(2);
2865 :     }
2866 :     }
2867 :    
2868 : parrello 1.73 =head3 DropRelation
2869 : parrello 1.1
2870 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2871 : parrello 1.1
2872 : parrello 1.73 Physically drop a relation from the database.
2873 : parrello 1.1
2874 :     =over 4
2875 :    
2876 : parrello 1.73 =item relationName
2877 : parrello 1.1
2878 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2879 :     no effect.
2880 : parrello 1.1
2881 :     =back
2882 :    
2883 :     =cut
2884 :    
2885 : parrello 1.73 sub DropRelation {
2886 : parrello 1.10 # Get the parameters.
2887 : parrello 1.73 my ($self, $relationName) = @_;
2888 :     # Get the database handle.
2889 :     my $dbh = $self->{_dbh};
2890 :     # Drop the relation. The method used here has no effect if the relation
2891 :     # does not exist.
2892 : parrello 1.74 Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2893 :     $dbh->drop_table(tbl => $relationName);
2894 : parrello 1.1 }
2895 :    
2896 : parrello 1.78 =head3 MatchSqlPattern
2897 :    
2898 :     C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2899 :    
2900 :     Determine whether or not a specified value matches an SQL pattern. An SQL
2901 :     pattern has two wild card characters: C<%> that matches multiple characters,
2902 :     and C<_> that matches a single character. These can be escaped using a
2903 :     backslash (C<\>). We pull this off by converting the SQL pattern to a
2904 :     PERL regular expression. As per SQL rules, the match is case-insensitive.
2905 :    
2906 :     =over 4
2907 :    
2908 :     =item value
2909 :    
2910 :     Value to be matched against the pattern. Note that an undefined or empty
2911 :     value will not match anything.
2912 :    
2913 :     =item pattern
2914 :    
2915 :     SQL pattern against which to match the value. An undefined or empty pattern will
2916 :     match everything.
2917 :    
2918 :     =item RETURN
2919 :    
2920 :     Returns TRUE if the value and pattern match, else FALSE.
2921 :    
2922 :     =back
2923 :    
2924 :     =cut
2925 :    
2926 :     sub MatchSqlPattern {
2927 :     # Get the parameters.
2928 :     my ($value, $pattern) = @_;
2929 :     # Declare the return variable.
2930 :     my $retVal;
2931 :     # Insure we have a pattern.
2932 :     if (! defined($pattern) || $pattern eq "") {
2933 :     $retVal = 1;
2934 :     } else {
2935 :     # Break the pattern into pieces around the wildcard characters. Because we
2936 :     # use parentheses in the split function's delimiter expression, we'll get
2937 :     # list elements for the delimiters as well as the rest of the string.
2938 :     my @pieces = split /([_%]|\\[_%])/, $pattern;
2939 :     # Check some fast special cases.
2940 :     if ($pattern eq '%') {
2941 :     # A null pattern matches everything.
2942 :     $retVal = 1;
2943 :     } elsif (@pieces == 1) {
2944 :     # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2945 :     $retVal = (lc($value) eq lc($pattern));
2946 :     } elsif (@pieces == 2 && $pieces[1] eq '%') {
2947 :     # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2948 :     $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2949 :     } else {
2950 :     # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2951 :     my $realPattern = "";
2952 :     for my $piece (@pieces) {
2953 :     # Determine the type of piece.
2954 :     if ($piece eq "") {
2955 :     # Empty pieces are ignored.
2956 :     } elsif ($piece eq "%") {
2957 :     # Here we have a multi-character wildcard. Note that it can match
2958 :     # zero or more characters.
2959 :     $realPattern .= ".*"
2960 :     } elsif ($piece eq "_") {
2961 :     # Here we have a single-character wildcard.
2962 :     $realPattern .= ".";
2963 :     } elsif ($piece eq "\\%" || $piece eq "\\_") {
2964 :     # This is an escape sequence (which is a rare thing, actually).
2965 :     $realPattern .= substr($piece, 1, 1);
2966 :     } else {
2967 :     # Here we have raw text.
2968 :     $realPattern .= quotemeta($piece);
2969 :     }
2970 :     }
2971 :     # Do the match.
2972 :     $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2973 :     }
2974 :     }
2975 :     # Return the result.
2976 :     return $retVal;
2977 :     }
2978 :    
2979 : parrello 1.6 =head3 GetEntity
2980 :    
2981 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2982 : parrello 1.6
2983 :     Return an object describing the entity instance with a specified ID.
2984 :    
2985 :     =over 4
2986 :    
2987 :     =item entityType
2988 :    
2989 :     Entity type name.
2990 :    
2991 :     =item ID
2992 :    
2993 :     ID of the desired entity.
2994 :    
2995 :     =item RETURN
2996 :    
2997 : parrello 1.88 Returns a B<ERDBObject> representing the desired entity instance, or an undefined value if no
2998 : parrello 1.6 instance is found with the specified key.
2999 :    
3000 :     =back
3001 :    
3002 :     =cut
3003 :    
3004 :     sub GetEntity {
3005 : parrello 1.10 # Get the parameters.
3006 :     my ($self, $entityType, $ID) = @_;
3007 :     # Create a query.
3008 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
3009 : parrello 1.10 # Get the first (and only) object.
3010 :     my $retVal = $query->Fetch();
3011 :     # Return the result.
3012 :     return $retVal;
3013 : parrello 1.6 }
3014 :    
3015 : parrello 1.69 =head3 GetChoices
3016 :    
3017 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
3018 :    
3019 :     Return a list of all the values for the specified field that are represented in the
3020 :     specified entity.
3021 :    
3022 :     Note that if the field is not indexed, then this will be a very slow operation.
3023 :    
3024 :     =over 4
3025 :    
3026 :     =item entityName
3027 :    
3028 :     Name of an entity in the database.
3029 :    
3030 :     =item fieldName
3031 :    
3032 :     Name of a field belonging to the entity. This is a raw field name without
3033 :     the standard parenthesized notation used in most calls.
3034 :    
3035 :     =item RETURN
3036 :    
3037 :     Returns a list of the distinct values for the specified field in the database.
3038 :    
3039 :     =back
3040 :    
3041 :     =cut
3042 :    
3043 :     sub GetChoices {
3044 :     # Get the parameters.
3045 :     my ($self, $entityName, $fieldName) = @_;
3046 :     # Declare the return variable.
3047 :     my @retVal;
3048 :     # Get the entity data structure.
3049 :     my $entityData = $self->_GetStructure($entityName);
3050 :     # Get the field.
3051 :     my $fieldHash = $entityData->{Fields};
3052 :     if (! exists $fieldHash->{$fieldName}) {
3053 :     Confess("$fieldName not found in $entityName.");
3054 :     } else {
3055 :     # Get the name of the relation containing the field.
3056 :     my $relation = $fieldHash->{$fieldName}->{relation};
3057 :     # Fix up the field name.
3058 :     my $realName = _FixName($fieldName);
3059 :     # Get the database handle.
3060 :     my $dbh = $self->{_dbh};
3061 :     # Query the database.
3062 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
3063 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
3064 :     @retVal = sort map { $_->[0] } @{$results};
3065 :     }
3066 :     # Return the result.
3067 :     return @retVal;
3068 :     }
3069 :    
3070 : parrello 1.6 =head3 GetEntityValues
3071 :    
3072 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
3073 : parrello 1.6
3074 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
3075 :     does not exist, an empty list is returned.
3076 : parrello 1.6
3077 :     =over 4
3078 :    
3079 :     =item entityType
3080 :    
3081 :     Entity type name.
3082 :    
3083 :     =item ID
3084 :    
3085 :     ID of the desired entity.
3086 :    
3087 :     =item fields
3088 :    
3089 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
3090 :    
3091 :     =item RETURN
3092 :    
3093 :     Returns a flattened list of the values of the specified fields for the specified entity.
3094 :    
3095 :     =back
3096 :    
3097 :     =cut
3098 :    
3099 :     sub GetEntityValues {
3100 : parrello 1.10 # Get the parameters.
3101 :     my ($self, $entityType, $ID, $fields) = @_;
3102 :     # Get the specified entity.
3103 :     my $entity = $self->GetEntity($entityType, $ID);
3104 :     # Declare the return list.
3105 :     my @retVal = ();
3106 :     # If we found the entity, push the values into the return list.
3107 :     if ($entity) {
3108 :     push @retVal, $entity->Values($fields);
3109 :     }
3110 :     # Return the result.
3111 :     return @retVal;
3112 : parrello 1.6 }
3113 : parrello 1.1
3114 : parrello 1.7 =head3 GetAll
3115 :    
3116 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
3117 : parrello 1.7
3118 :     Return a list of values taken from the objects returned by a query. The first three
3119 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
3120 :     a list of the fields desired from each record found by the query. The field name
3121 :     syntax is the standard syntax used for fields in the B<ERDB> system--
3122 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
3123 :     or relationship and I<fieldName> is the name of the field.
3124 :    
3125 :     The list returned will be a list of lists. Each element of the list will contain
3126 :     the values returned for the fields specified in the fourth parameter. If one of the
3127 :     fields specified returns multiple values, they are flattened in with the rest. For
3128 :     example, the following call will return a list of the features in a particular
3129 :     spreadsheet cell, and each feature will be represented by a list containing the
3130 : parrello 1.92 feature ID followed by all of its essentiality determinations.
3131 : parrello 1.7
3132 : parrello 1.92 C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(essential)']); >>
3133 : parrello 1.7
3134 :     =over 4
3135 :    
3136 :     =item objectNames
3137 :    
3138 :     List containing the names of the entity and relationship objects to be retrieved.
3139 :    
3140 :     =item filterClause
3141 :    
3142 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
3143 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
3144 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
3145 :     parameter list as additional parameters. The fields in a filter clause can come from primary
3146 :     entity relations, relationship relations, or secondary entity relations; however, all of the
3147 :     entities and relationships involved must be included in the list of object names.
3148 :    
3149 :     =item parameterList
3150 :    
3151 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
3152 :    
3153 :     =item fields
3154 :    
3155 :     List of the fields to be returned in each element of the list returned.
3156 :    
3157 :     =item count
3158 :    
3159 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
3160 :    
3161 :     =item RETURN
3162 :    
3163 :     Returns a list of list references. Each element of the return list contains the values for the
3164 :     fields specified in the B<fields> parameter.
3165 :    
3166 :     =back
3167 :    
3168 :     =cut
3169 :     #: Return Type @@;
3170 :     sub GetAll {
3171 : parrello 1.10 # Get the parameters.
3172 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
3173 :     # Translate the parameters from a list reference to a list. If the parameter
3174 :     # list is a scalar we convert it into a singleton list.
3175 :     my @parmList = ();
3176 :     if (ref $parameterList eq "ARRAY") {
3177 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
3178 : parrello 1.10 @parmList = @{$parameterList};
3179 :     } else {
3180 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
3181 : parrello 1.10 push @parmList, $parameterList;
3182 :     }
3183 : parrello 1.30 # Insure the counter has a value.
3184 :     if (!defined $count) {
3185 :     $count = 0;
3186 :     }
3187 :     # Add the row limit to the filter clause.
3188 :     if ($count > 0) {
3189 :     $filterClause .= " LIMIT $count";
3190 :     }
3191 : parrello 1.10 # Create the query.
3192 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
3193 : parrello 1.10 # Set up a counter of the number of records read.
3194 :     my $fetched = 0;
3195 :     # Loop through the records returned, extracting the fields. Note that if the
3196 :     # counter is non-zero, we stop when the number of records read hits the count.
3197 :     my @retVal = ();
3198 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
3199 :     my @rowData = $row->Values($fields);
3200 :     push @retVal, \@rowData;
3201 :     $fetched++;
3202 :     }
3203 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
3204 : parrello 1.10 # Return the resulting list.
3205 :     return @retVal;
3206 : parrello 1.7 }
3207 :    
3208 : parrello 1.55 =head3 Exists
3209 :    
3210 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
3211 :    
3212 :     Return TRUE if an entity exists, else FALSE.
3213 :    
3214 :     =over 4
3215 :    
3216 :     =item entityName
3217 :    
3218 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
3219 :    
3220 :     =item entityID
3221 :    
3222 :     ID of the entity instance whose existence is to be checked.
3223 :    
3224 :     =item RETURN
3225 :    
3226 :     Returns TRUE if the entity instance exists, else FALSE.
3227 :    
3228 :     =back
3229 :    
3230 :     =cut
3231 :     #: Return Type $;
3232 :     sub Exists {
3233 :     # Get the parameters.
3234 :     my ($self, $entityName, $entityID) = @_;
3235 :     # Check for the entity instance.
3236 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
3237 :     my $testInstance = $self->GetEntity($entityName, $entityID);
3238 :     # Return an existence indicator.
3239 :     my $retVal = ($testInstance ? 1 : 0);
3240 :     return $retVal;
3241 :     }
3242 :    
3243 : parrello 1.18 =head3 EstimateRowSize
3244 :    
3245 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
3246 :    
3247 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
3248 :     up the average length for each data type.
3249 :    
3250 :     =over 4
3251 :    
3252 :     =item relName
3253 :    
3254 :     Name of the relation whose estimated row size is desired.
3255 :    
3256 :     =item RETURN
3257 :    
3258 :     Returns an estimate of the row size for the specified relation.
3259 :    
3260 :     =back
3261 :    
3262 :     =cut
3263 :     #: Return Type $;
3264 :     sub EstimateRowSize {
3265 :     # Get the parameters.
3266 :     my ($self, $relName) = @_;
3267 :     # Declare the return variable.
3268 :     my $retVal = 0;
3269 :     # Find the relation descriptor.
3270 :     my $relation = $self->_FindRelation($relName);
3271 :     # Get the list of fields.
3272 :     for my $fieldData (@{$relation->{Fields}}) {
3273 :     # Get the field type and add its length.
3274 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3275 :     $retVal += $fieldLen;
3276 :     }
3277 :     # Return the result.
3278 :     return $retVal;
3279 :     }
3280 :    
3281 : parrello 1.38 =head3 GetFieldTable
3282 :    
3283 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3284 :    
3285 :     Get the field structure for a specified entity or relationship.
3286 :    
3287 :     =over 4
3288 :    
3289 :     =item objectName
3290 :    
3291 :     Name of the desired entity or relationship.
3292 :    
3293 :     =item RETURN
3294 :    
3295 :     The table containing the field descriptors for the specified object.
3296 :    
3297 :     =back
3298 :    
3299 :     =cut
3300 :    
3301 :     sub GetFieldTable {
3302 :     # Get the parameters.
3303 :     my ($self, $objectName) = @_;
3304 :     # Get the descriptor from the metadata.
3305 :     my $objectData = $self->_GetStructure($objectName);
3306 :     # Return the object's field table.
3307 :     return $objectData->{Fields};
3308 :     }
3309 :    
3310 : parrello 1.73 =head3 SplitKeywords
3311 :    
3312 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3313 :    
3314 :     This method returns a list of the positive keywords in the specified
3315 :     keyword string. All of the operators will have been stripped off,
3316 :     and if the keyword is preceded by a minus operator (C<->), it will
3317 :     not be in the list returned. The idea here is to get a list of the
3318 :     keywords the user wants to see. The list will be processed to remove
3319 :     duplicates.
3320 :    
3321 :     It is possible to create a string that confuses this method. For example
3322 :    
3323 :     frog toad -frog
3324 :    
3325 :     would return both C<frog> and C<toad>. If this is a problem we can deal
3326 :     with it later.
3327 :    
3328 :     =over 4
3329 :    
3330 :     =item keywordString
3331 :    
3332 :     The keyword string to be parsed.
3333 :    
3334 :     =item RETURN
3335 :    
3336 :     Returns a list of the words in the keyword string the user wants to
3337 :     see.
3338 :    
3339 :     =back
3340 :    
3341 :     =cut
3342 :    
3343 :     sub SplitKeywords {
3344 :     # Get the parameters.
3345 :     my ($keywordString) = @_;
3346 :     # Make a safety copy of the string. (This helps during debugging.)
3347 :     my $workString = $keywordString;
3348 :     # Convert operators we don't care about to spaces.
3349 :     $workString =~ tr/+"()<>/ /;
3350 :     # Split the rest of the string along space boundaries. Note that we
3351 :     # eliminate any words that are zero length or begin with a minus sign.
3352 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3353 :     # Use a hash to remove duplicates.
3354 :     my %words = map { $_ => 1 } @wordList;
3355 :     # Return the result.
3356 :     return sort keys %words;
3357 :     }
3358 :    
3359 :     =head3 ValidateFieldName
3360 :    
3361 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3362 :    
3363 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3364 :     be hyphenated words subject to certain restrictions.
3365 :    
3366 :     =over 4
3367 :    
3368 :     =item fieldName
3369 :    
3370 :     Field name to be validated.
3371 :    
3372 :     =item RETURN
3373 :    
3374 :     Returns TRUE if the field name is valid, else FALSE.
3375 :    
3376 :     =back
3377 :    
3378 :     =cut
3379 :    
3380 :     sub ValidateFieldName {
3381 :     # Get the parameters.
3382 :     my ($fieldName) = @_;
3383 :     # Declare the return variable. The field name is valid until we hear
3384 :     # differently.
3385 :     my $retVal = 1;
3386 : parrello 1.78 # Compute the maximum name length.
3387 :     my $maxLen = $TypeTable{'name-string'}->{maxLen};
3388 : parrello 1.73 # Look for bad stuff in the name.
3389 :     if ($fieldName =~ /--/) {
3390 :     # Here we have a doubled minus sign.
3391 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3392 :     $retVal = 0;
3393 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
3394 :     # Here the field name is missing the initial letter.
3395 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
3396 :     $retVal = 0;
3397 : parrello 1.78 } elsif (length($fieldName) > $maxLen) {
3398 :     # Here the field name is too long.
3399 :     Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3400 : parrello 1.73 } else {
3401 : parrello 1.75 # Strip out the minus signs. Everything remaining must be a letter,
3402 :     # underscore, or digit.
3403 : parrello 1.73 my $strippedName = $fieldName;
3404 :     $strippedName =~ s/-//g;
3405 : parrello 1.75 if ($strippedName !~ /^(\w|\d)+$/) {
3406 : parrello 1.73 Trace("Field name $fieldName contains illegal characters.") if T(1);
3407 :     $retVal = 0;
3408 :     }
3409 :     }
3410 :     # Return the result.
3411 :     return $retVal;
3412 :     }
3413 :    
3414 :     =head3 ReadMetaXML
3415 :    
3416 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3417 :    
3418 :     This method reads a raw database definition XML file and returns it.
3419 :     Normally, the metadata used by the ERDB system has been processed and
3420 :     modified to make it easier to load and retrieve the data; however,
3421 :     this method can be used to get the data in its raw form.
3422 :    
3423 :     =over 4
3424 :    
3425 :     =item fileName
3426 :    
3427 :     Name of the XML file to read.
3428 :    
3429 :     =item RETURN
3430 :    
3431 :     Returns a hash reference containing the raw XML data from the specified file.
3432 :    
3433 :     =back
3434 :    
3435 :     =cut
3436 :    
3437 :     sub ReadMetaXML {
3438 :     # Get the parameters.
3439 :     my ($fileName) = @_;
3440 :     # Read the XML.
3441 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3442 :     Trace("XML metadata loaded from file $fileName.") if T(1);
3443 :     # Return the result.
3444 :     return $retVal;
3445 :     }
3446 :    
3447 :     =head3 GetEntityFieldHash
3448 :    
3449 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3450 :    
3451 :     Get the field hash of the named entity in the specified raw XML structure.
3452 :     The field hash may not exist, in which case we need to create it.
3453 :    
3454 :     =over 4
3455 :    
3456 :     =item structure
3457 :    
3458 :     Raw XML structure defininng the database. This is not the run-time XML used by
3459 :     an ERDB object, since that has all sorts of optimizations built-in.
3460 :    
3461 :     =item entityName
3462 :    
3463 :     Name of the entity whose field structure is desired.
3464 :    
3465 :     =item RETURN
3466 :    
3467 :     Returns the field hash used to define the entity's fields.
3468 :    
3469 :     =back
3470 :    
3471 :     =cut
3472 :    
3473 :     sub GetEntityFieldHash {
3474 :     # Get the parameters.
3475 :     my ($structure, $entityName) = @_;
3476 :     # Get the entity structure.
3477 :     my $entityData = $structure->{Entities}->{$entityName};
3478 :     # Look for a field structure.
3479 :     my $retVal = $entityData->{Fields};
3480 :     # If it doesn't exist, create it.
3481 :     if (! defined($retVal)) {
3482 :     $entityData->{Fields} = {};
3483 :     $retVal = $entityData->{Fields};
3484 :     }
3485 :     # Return the result.
3486 :     return $retVal;
3487 :     }
3488 :    
3489 :     =head3 WriteMetaXML
3490 :    
3491 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
3492 :    
3493 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3494 :     used to update the database definition. It must be used with care, however, since it
3495 :     will only work on a raw structure, not on the processed structure created by an ERDB
3496 :     constructor.
3497 :    
3498 :     =over 4
3499 :    
3500 :     =item structure
3501 :    
3502 :     XML structure to be written to the file.
3503 :    
3504 :     =item fileName
3505 :    
3506 :     Name of the output file to which the updated XML should be stored.
3507 :    
3508 :     =back
3509 :    
3510 :     =cut
3511 :    
3512 :     sub WriteMetaXML {
3513 :     # Get the parameters.
3514 :     my ($structure, $fileName) = @_;
3515 :     # Compute the output.
3516 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3517 :     # Write it to the file.
3518 :     my $xmlOut = Open(undef, ">$fileName");
3519 :     print $xmlOut $fileString;
3520 :     }
3521 :    
3522 :    
3523 :     =head3 HTMLNote
3524 :    
3525 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3526 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3527 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
3528 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3529 :    
3530 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3531 :    
3532 :     =over 4
3533 :    
3534 :     =item dataString
3535 :    
3536 :     String to convert to HTML.
3537 :    
3538 :     =item RETURN
3539 :    
3540 :     An HTML string derived from the input string.
3541 :    
3542 :     =back
3543 :    
3544 :     =cut
3545 :    
3546 :     sub HTMLNote {
3547 :     # Get the parameter.
3548 :     my ($dataString) = @_;
3549 :     # HTML-escape the text.
3550 :     my $retVal = CGI::escapeHTML($dataString);
3551 :     # Substitute the bulletin board codes.
3552 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3553 :     $retVal =~ s!\[p\]!</p><p>!g;
3554 : parrello 1.83 $retVal =~ s!\[link\s+([^\]]+)\]!<a href="$1">!g;
3555 :     $retVal =~ s!\[/link\]!</a>!g;
3556 : parrello 1.73 # Return the result.
3557 :     return $retVal;
3558 :     }
3559 :    
3560 : parrello 1.87 =head3 BeginTran
3561 :    
3562 :     C<< $erdb->BeginTran(); >>
3563 :    
3564 :     Start a database transaction.
3565 :    
3566 :     =cut
3567 :    
3568 :     sub BeginTran {
3569 :     my ($self) = @_;
3570 :     $self->{_dbh}->begin_tran();
3571 :    
3572 :     }
3573 :    
3574 :     =head3 CommitTran
3575 :    
3576 :     C<< $erdb->CommitTran(); >>
3577 :    
3578 :     Commit an active database transaction.
3579 :    
3580 :     =cut
3581 :    
3582 :     sub CommitTran {
3583 :     my ($self) = @_;
3584 :     $self->{_dbh}->commit_tran();
3585 :     }
3586 :    
3587 :     =head3 RollbackTran
3588 :    
3589 :     C<< $erdb->RollbackTran(); >>
3590 :    
3591 :     Roll back an active database transaction.
3592 :    
3593 :     =cut
3594 :    
3595 :     sub RollbackTran {
3596 :     my ($self) = @_;
3597 :     $self->{_dbh}->roll_tran();
3598 :     }
3599 :    
3600 : parrello 1.90 =head3 UpdateField
3601 :    
3602 :     C<< my $count = $erdb->UpdateField($objectNames, $fieldName, $oldValue, $newValue, $filter, $parms); >>
3603 :    
3604 :     Update all occurrences of a specific field value to a new value. The number of rows changed will be
3605 :     returned.
3606 :    
3607 :     =over 4
3608 :    
3609 :     =item fieldName
3610 :    
3611 :     Name of the field in standard I<objectName>C<(>I<fieldName>C<)> format.
3612 :    
3613 :     =item oldValue
3614 :    
3615 :     Value to be modified. All occurrences of this value in the named field will be replaced by the
3616 :     new value.
3617 :    
3618 :     =item newValue
3619 :    
3620 :     New value to be substituted for the old value when it's found.
3621 :    
3622 :     =item filter
3623 :    
3624 :     A standard ERDB filter clause (see L</Get>). The filter will be applied before any substitutions take place.
3625 :    
3626 :     =item parms
3627 :    
3628 :     Reference to a list of parameter values in the filter.
3629 :    
3630 :     =item RETURN
3631 :    
3632 :     Returns the number of rows modified.
3633 :    
3634 :     =back
3635 :    
3636 :     =cut
3637 :    
3638 :     sub UpdateField {
3639 :     # Get the parameters.
3640 :     my ($self, $fieldName, $oldValue, $newValue, $filter, $parms) = @_;
3641 :     # Get the object and field names from the field name parameter.
3642 :     $fieldName =~ /^([^(]+)\(([^)]+)\)/;
3643 :     my $objectName = $1;
3644 :     my $realFieldName = _FixName($2);
3645 :     # Add the old value to the filter. Note we allow the possibility that no
3646 :     # filter was specified.
3647 :     my $realFilter = "$fieldName = ?";
3648 :     if ($filter) {
3649 :     $realFilter .= " AND $filter";
3650 :     }
3651 :     # Format the query filter.
3652 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
3653 :     $self->_SetupSQL([$objectName], $realFilter);
3654 :     # Create the query. Since there is only one object name, the mapped-name data is not
3655 :     # necessary. Neither is the FROM clause.
3656 :     $suffix =~ s/^FROM.+WHERE\s+//;
3657 :     # Create the update statement.
3658 :     my $command = "UPDATE $objectName SET $realFieldName = ? WHERE $suffix";
3659 :     # Get the database handle.
3660 :     my $dbh = $self->{_dbh};
3661 :     # Add the old and new values to the parameter list. Note we allow the possibility that
3662 :     # there are no user-supplied parameters.
3663 :     my @params = ($newValue, $oldValue);
3664 :     if (defined $parms) {
3665 :     push @params, @{$parms};
3666 :     }
3667 :     # Execute the update.
3668 :     my $retVal = $dbh->SQL($command, 0, @params);
3669 :     # Make the funky zero a real zero.
3670 :     if ($retVal == 0) {
3671 :     $retVal = 0;
3672 :     }
3673 :     # Return the result.
3674 :     return $retVal;
3675 :     }
3676 :    
3677 : parrello 1.73
3678 : parrello 1.48 =head2 Data Mining Methods
3679 :    
3680 : parrello 1.38 =head3 GetUsefulCrossValues
3681 :    
3682 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3683 :    
3684 :     Return a list of the useful attributes that would be returned by a B<Cross> call
3685 :     from an entity of the source entity type through the specified relationship. This
3686 :     means it will return the fields of the target entity type and the intersection data
3687 :     fields in the relationship. Only primary table fields are returned. In other words,
3688 :     the field names returned will be for fields where there is always one and only one
3689 :     value.
3690 :    
3691 :     =over 4
3692 :    
3693 :     =item sourceEntity
3694 :    
3695 :     Name of the entity from which the relationship crossing will start.
3696 :    
3697 :     =item relationship
3698 :    
3699 :     Name of the relationship being crossed.
3700 :    
3701 :     =item RETURN
3702 :    
3703 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3704 :    
3705 :     =back
3706 :    
3707 :     =cut
3708 :     #: Return Type @;
3709 :     sub GetUsefulCrossValues {
3710 :     # Get the parameters.
3711 :     my ($self, $sourceEntity, $relationship) = @_;
3712 :     # Declare the return variable.
3713 :     my @retVal = ();
3714 :     # Determine the target entity for the relationship. This is whichever entity is not
3715 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
3716 :     # the TO, and vice versa.
3717 :     my $relStructure = $self->_GetStructure($relationship);
3718 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3719 :     my $targetEntity = $relStructure->{$targetEntityType};
3720 :     # Get the field table for the entity.
3721 :     my $entityFields = $self->GetFieldTable($targetEntity);
3722 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
3723 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
3724 :     # must match the entity name.
3725 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3726 :     keys %{$entityFields};
3727 :     # Push the fields found onto the return variable.
3728 :     push @retVal, sort @fieldList;
3729 :     # Get the field table for the relationship.
3730 :     my $relationshipFields = $self->GetFieldTable($relationship);
3731 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3732 :     # This may end up being an empty set.
3733 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3734 :     keys %{$relationshipFields};
3735 :     # Push these onto the return list.
3736 :     push @retVal, sort @fieldList2;
3737 :     # Return the result.
3738 :     return @retVal;
3739 :     }
3740 :    
3741 : parrello 1.48 =head3 FindColumn
3742 :    
3743 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3744 :    
3745 :     Return the location a desired column in a data mining header line. The data
3746 :     mining header line is a tab-separated list of column names. The column
3747 :     identifier is either the numerical index of a column or the actual column
3748 :     name.
3749 :    
3750 :     =over 4
3751 :    
3752 :     =item headerLine
3753 :    
3754 :     The header line from a data mining command, which consists of a tab-separated
3755 :     list of column names.
3756 :    
3757 :     =item columnIdentifier
3758 :    
3759 :     Either the ordinal number of the desired column (1-based), or the name of the
3760 :     desired column.
3761 :    
3762 :     =item RETURN
3763 :    
3764 :     Returns the array index (0-based) of the desired column.
3765 :    
3766 :     =back
3767 :    
3768 :     =cut
3769 :    
3770 :     sub FindColumn {
3771 :     # Get the parameters.
3772 :     my ($headerLine, $columnIdentifier) = @_;
3773 :     # Declare the return variable.
3774 :     my $retVal;
3775 :     # Split the header line into column names.
3776 :     my @headers = ParseColumns($headerLine);
3777 :     # Determine whether we have a number or a name.
3778 :     if ($columnIdentifier =~ /^\d+$/) {
3779 :     # Here we have a number. Subtract 1 and validate the result.
3780 :     $retVal = $columnIdentifier - 1;
3781 :     if ($retVal < 0 || $retVal > $#headers) {
3782 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3783 :     }
3784 :     } else {
3785 :     # Here we have a name. We need to find it in the list.
3786 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3787 :     if ($headers[$i] eq $columnIdentifier) {
3788 :     $retVal = $i;
3789 :     }
3790 :     }
3791 :     if (! defined($retVal)) {
3792 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3793 :     }
3794 :     }
3795 :     # Return the result.
3796 :     return $retVal;
3797 :     }
3798 :    
3799 :     =head3 ParseColumns
3800 :    
3801 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
3802 : parrello 1.48
3803 :     Convert the specified data line to a list of columns.
3804 :    
3805 :     =over 4
3806 :    
3807 :     =item line
3808 :    
3809 :     A data mining input, consisting of a tab-separated list of columns terminated by a
3810 :     new-line.
3811 :    
3812 :     =item RETURN
3813 :    
3814 :     Returns a list consisting of the column values.
3815 :    
3816 :     =back
3817 :    
3818 :     =cut
3819 :    
3820 :     sub ParseColumns {
3821 :     # Get the parameters.
3822 : parrello 1.50 my ($line) = @_;
3823 : parrello 1.48 # Chop off the line-end.
3824 :     chomp $line;
3825 :     # Split it into a list.
3826 :     my @retVal = split(/\t/, $line);
3827 :     # Return the result.
3828 :     return @retVal;
3829 :     }
3830 :    
3831 : parrello 1.71 =head2 Virtual Methods
3832 :    
3833 : parrello 1.89 =head3 _CreatePPOIndex
3834 :    
3835 :     C<< my $index = ERDB::_CreatePPOIndex($indexObject); >>
3836 :    
3837 :     Convert the XML for an ERDB index to the XML structure for a PPO
3838 :     index.
3839 :    
3840 :     =over 4
3841 :    
3842 :     ERDB XML structure for an index.
3843 :    
3844 :     =item RETURN
3845 :    
3846 :     PPO XML structure for the same index.
3847 :    
3848 :     =back
3849 :    
3850 :     =cut
3851 :    
3852 :     sub _CreatePPOIndex {
3853 :     # Get the parameters.
3854 :     my ($indexObject) = @_;
3855 :     # The incoming index contains a list of the index fields in the IndexFields
3856 :     # member. We loop through it to create the index tags.
3857 :     my @fields = map { { label => _FixName($_->{name}) } } @{$indexObject->{IndexFields}};
3858 :     # Wrap the fields in attribute tags.
3859 :     my $retVal = { attribute => \@fields };
3860 :     # Return the result.
3861 :     return $retVal;
3862 :     }
3863 :    
3864 :     =head3 _CreatePPOField
3865 :    
3866 :     C<< my $fieldXML = ERDB::_CreatePPOField($fieldName, $fieldObject); >>
3867 :    
3868 :     Convert the ERDB XML structure for a field to a PPO scalar XML structure.
3869 :    
3870 :     =over 4
3871 :    
3872 :     =item fieldName
3873 :    
3874 :     Name of the scalar field.
3875 :    
3876 :     =item fieldObject
3877 :    
3878 :     ERDB XML structure describing the field.
3879 :    
3880 :     =item RETURN
3881 :    
3882 :     Returns a PPO XML structure for the same field.
3883 :    
3884 :     =back
3885 :    
3886 :     =cut
3887 :    
3888 :     sub _CreatePPOField {
3889 :     # Get the parameters.
3890 :     my ($fieldName, $fieldObject) = @_;
3891 :     # Get the field type.
3892 :     my $type = $TypeTable{$fieldObject->{type}}->{sqlType};
3893 :     # Fix up the field name.
3894 :     $fieldName = _FixName($fieldName);
3895 :     # Build the scalar tag.
3896 :     my $retVal = { label => $fieldName, type => $type };
3897 :     # Return the result.
3898 :     return $retVal;
3899 :     }
3900 :    
3901 : parrello 1.71 =head3 CleanKeywords
3902 :    
3903 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3904 :    
3905 :     Clean up a search expression or keyword list. This is a virtual method that may
3906 :     be overridden by the subclass. The base-class method removes extra spaces
3907 :     and converts everything to lower case.
3908 :    
3909 :     =over 4
3910 :    
3911 :     =item searchExpression
3912 :    
3913 :     Search expression or keyword list to clean. Note that a search expression may
3914 :     contain boolean operators which need to be preserved. This includes leading
3915 :     minus signs.
3916 :    
3917 :     =item RETURN
3918 :    
3919 :     Cleaned expression or keyword list.
3920 :    
3921 :     =back
3922 :    
3923 :     =cut
3924 :    
3925 :     sub CleanKeywords {
3926 :     # Get the parameters.
3927 :     my ($self, $searchExpression) = @_;
3928 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
3929 :     # don't accidentally end up with an undefined value.
3930 :     my $retVal = lc($searchExpression || "");
3931 :     # Remove extra spaces.
3932 :     $retVal =~ s/\s+/ /g;
3933 :     $retVal =~ s/(^\s+)|(\s+$)//g;
3934 :     # Return the result.
3935 :     return $retVal;
3936 :     }
3937 :    
3938 : parrello 1.73 =head3 GetSourceObject
3939 :    
3940 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
3941 :    
3942 :     Return the object to be used in loading special attributes of the specified entity. The
3943 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
3944 :     XML
3945 :    
3946 : parrello 1.1 =head2 Internal Utility Methods
3947 :    
3948 : parrello 1.70 =head3 _RelationMap
3949 :    
3950 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3951 :    
3952 : parrello 1.88 Create the relation map for an SQL query. The relation map is used by B<ERDBObject>
3953 : parrello 1.70 to determine how to interpret the results of the query.
3954 :    
3955 :     =over 4
3956 :    
3957 :     =item mappedNameHashRef
3958 :    
3959 :     Reference to a hash that maps modified object names to real object names.
3960 :    
3961 :     =item mappedNameListRef
3962 :    
3963 :     Reference to a list of modified object names in the order they appear in the
3964 :     SELECT list.
3965 :    
3966 :     =item RETURN
3967 :    
3968 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3969 : parrello 1.88 query followed by the actual name of that object. This enables the B<ERDBObject> to
3970 : parrello 1.70 determine the order of the tables in the query and which object name belongs to each
3971 :     mapped object name. Most of the time these two values are the same; however, if a
3972 :     relation occurs twice in the query, the relation name in the field list and WHERE
3973 :     clause will use a mapped name (generally the actual relation name with a numeric
3974 :     suffix) that does not match the actual relation name.
3975 :    
3976 :     =back
3977 :    
3978 :     =cut
3979 :    
3980 :     sub _RelationMap {
3981 :     # Get the parameters.
3982 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3983 :     # Declare the return variable.
3984 :     my @retVal = ();
3985 :     # Build the map.
3986 :     for my $mappedName (@{$mappedNameListRef}) {
3987 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3988 :     }
3989 :     # Return it.
3990 :     return @retVal;
3991 :     }
3992 :    
3993 :    
3994 :     =head3 _SetupSQL
3995 : parrello 1.45
3996 :     Process a list of object names and a filter clause so that they can be used to
3997 :     build an SQL statement. This method takes in a reference to a list of object names
3998 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3999 :     names and the mapped name hash.
4000 :    
4001 :     This is an instance method.
4002 :    
4003 :     =over 4
4004 :    
4005 :     =item objectNames
4006 :    
4007 :     Reference to a list of the object names to be included in the query.
4008 :    
4009 :     =item filterClause
4010 :    
4011 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
4012 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
4013 :    
4014 : parrello 1.70 =item matchClause
4015 :    
4016 :     An optional full-text search clause. If specified, it will be inserted at the
4017 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
4018 :     field names should be in the form I<table>C<.>I<fieldName>.
4019 :    
4020 : parrello 1.45 =item RETURN
4021 :    
4022 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
4023 :     with the FROM clause. The second element is a reference to a list of the names to be
4024 :     used in retrieving the fields. The third element is a hash mapping the names to the
4025 :     objects they represent.
4026 :    
4027 :     =back
4028 :    
4029 :     =cut
4030 :    
4031 :     sub _SetupSQL {
4032 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
4033 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
4034 :     # same object. We start with a hash table keyed on object name that will
4035 :     # return the object suffix. The first time an object is encountered it will
4036 :     # not be found in the hash. The next time the hash will map the object name
4037 :     # to 2, then 3, and so forth.
4038 :     my %objectHash = ();
4039 :     # This list will contain the object names as they are to appear in the
4040 :     # FROM list.
4041 :     my @fromList = ();
4042 :     # This list contains the suffixed object name for each object. It is exactly
4043 :     # parallel to the list in the $objectNames parameter.
4044 :     my @mappedNameList = ();
4045 :     # Finally, this hash translates from a mapped name to its original object name.
4046 :     my %mappedNameHash = ();
4047 :     # Now we create the lists. Note that for every single name we push something into
4048 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
4049 :     # parallel to $objectNames.
4050 :     for my $objectName (@{$objectNames}) {
4051 :     # Get the next suffix for this object.
4052 :     my $suffix = $objectHash{$objectName};
4053 :     if (! $suffix) {
4054 :     # Here we are seeing the object for the first time. The object name
4055 :     # is used as is.
4056 :     push @mappedNameList, $objectName;
4057 :     push @fromList, $objectName;
4058 :     $mappedNameHash{$objectName} = $objectName;
4059 :     # Denote the next suffix will be 2.
4060 :     $objectHash{$objectName} = 2;
4061 :     } else {
4062 :     # Here we've seen the object before. We construct a new name using
4063 :     # the suffix from the hash and update the hash.
4064 :     my $mappedName = "$objectName$suffix";
4065 :     $objectHash{$objectName} = $suffix + 1;
4066 :     # The FROM list has the object name followed by the mapped name. This
4067 :     # tells SQL it's still the same table, but we're using a different name
4068 :     # for it to avoid confusion.
4069 :     push @fromList, "$objectName $mappedName";
4070 :     # The mapped-name list contains the real mapped name.
4071 :     push @mappedNameList, $mappedName;
4072 :     # Finally, enable us to get back from the mapped name to the object name.
4073 :     $mappedNameHash{$mappedName} = $objectName;
4074 :     }
4075 :     }
4076 :     # Begin the SELECT suffix. It starts with
4077 :     #
4078 :     # FROM name1, name2, ... nameN
4079 :     #
4080 :     my $suffix = "FROM " . join(', ', @fromList);
4081 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
4082 :     my $filterString = "";
4083 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
4084 :     # entities and relationships as well as primary relations to secondary ones.
4085 :     my @joinWhere = ();
4086 : parrello 1.45 # Check for a filter clause.
4087 :     if ($filterClause) {
4088 :     # Here we have one, so we convert its field names and add it to the query. First,
4089 :     # We create a copy of the filter string we can work with.
4090 : parrello 1.70 $filterString = $filterClause;
4091 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
4092 :     # object names inside other object names when we're doing our search and replace.
4093 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
4094 :     # The final preparatory step is to create a hash table of relation names. The
4095 :     # table begins with the relation names already in the SELECT command. We may
4096 :     # need to add relations later if there is filtering on a field in a secondary
4097 :     # relation. The secondary relations are the ones that contain multiply-
4098 :     # occurring or optional fields.
4099 :     my %fromNames = map { $_ => 1 } @sortedNames;
4100 :     # We are ready to begin. We loop through the object names, replacing each
4101 :     # object name's field references by the corresponding SQL field reference.
4102 :     # Along the way, if we find a secondary relation, we will need to add it
4103 :     # to the FROM clause.
4104 :     for my $mappedName (@sortedNames) {
4105 :     # Get the length of the object name plus 2. This is the value we add to the
4106 :     # size of the field name to determine the size of the field reference as a
4107 :     # whole.
4108 :     my $nameLength = 2 + length $mappedName;
4109 :     # Get the real object name for this mapped name.
4110 :     my $objectName = $mappedNameHash{$mappedName};
4111 :     Trace("Processing $mappedName for object $objectName.") if T(4);
4112 :     # Get the object's field list.
4113 :     my $fieldList = $self->GetFieldTable($objectName);
4114 :     # Find the field references for this object.
4115 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
4116 :     # At this point, $1 contains the field name, and the current position
4117 :     # is set immediately after the final parenthesis. We pull out the name of
4118 :     # the field and the position and length of the field reference as a whole.
4119 :     my $fieldName = $1;
4120 :     my $len = $nameLength + length $fieldName;
4121 :     my $pos = pos($filterString) - $len;
4122 :     # Insure the field exists.
4123 :     if (!exists $fieldList->{$fieldName}) {
4124 :     Confess("Field $fieldName not found for object $objectName.");
4125 :     } else {
4126 :     Trace("Processing $fieldName at position $pos.") if T(4);
4127 :     # Get the field's relation.
4128 :     my $relationName = $fieldList->{$fieldName}->{relation};
4129 :     # Now we have a secondary relation. We need to insure it matches the
4130 :     # mapped name of the primary relation. First we peel off the suffix
4131 :     # from the mapped name.
4132 :     my $mappingSuffix = substr $mappedName, length($objectName);
4133 :     # Put the mapping suffix onto the relation name to get the
4134 :     # mapped relation name.
4135 :     my $mappedRelationName = "$relationName$mappingSuffix";
4136 :     # Insure the relation is in the FROM clause.
4137 :     if (!exists $fromNames{$mappedRelationName}) {
4138 :     # Add the relation to the FROM clause.
4139 :     if ($mappedRelationName eq $relationName) {
4140 :     # The name is un-mapped, so we add it without
4141 :     # any frills.
4142 :     $suffix .= ", $relationName";
4143 :     push @joinWhere, "$objectName.id = $relationName.id";
4144 :     } else {
4145 :     # Here we have a mapping situation.
4146 :     $suffix .= ", $relationName $mappedRelationName";
4147 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
4148 :     }
4149 :     # Denote we have this relation available for future fields.
4150 :     $fromNames{$mappedRelationName} = 1;
4151 :     }
4152 :     # Form an SQL field reference from the relation name and the field name.
4153 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
4154 :     # Put it into the filter string in place of the old value.
4155 :     substr($filterString, $pos, $len) = $sqlReference;
4156 :     # Reposition the search.
4157 :     pos $filterString = $pos + length $sqlReference;
4158 :     }
4159 :     }
4160 :     }
4161 : parrello 1.70 }
4162 :     # The next step is to join the objects together. We only need to do this if there
4163 :     # is more than one object in the object list. We start with the first object and
4164 :     # run through the objects after it. Note also that we make a safety copy of the
4165 :     # list before running through it, because we shift off the first object before
4166 :     # processing the rest.
4167 :     my @mappedObjectList = @mappedNameList;
4168 :     my $lastMappedObject = shift @mappedObjectList;
4169 :     # Get the join table.
4170 :     my $joinTable = $self->{_metaData}->{Joins};
4171 :     # Loop through the object list.
4172 :     for my $thisMappedObject (@mappedObjectList) {
4173 :     # Look for a join using the real object names.
4174 :     my $lastObject = $mappedNameHash{$lastMappedObject};
4175 :     my $thisObject = $mappedNameHash{$thisMappedObject};
4176 :     my $joinKey = "$lastObject/$thisObject";
4177 :     if (!exists $joinTable->{$joinKey}) {
4178 :     # Here there's no join, so we throw an error.
4179 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
4180 :     } else {
4181 :     # Get the join clause.
4182 :     my $unMappedJoin = $joinTable->{$joinKey};
4183 :     # Fix the names.
4184 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
4185 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
4186 :     push @joinWhere, $unMappedJoin;
4187 :     # Save this object as the last object for the next iteration.
4188 :     $lastMappedObject = $thisMappedObject;
4189 :     }
4190 :     }
4191 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
4192 :     # here is we want the filter clause to be empty if there's no WHERE filter.
4193 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
4194 :     my $orderClause = "";
4195 :     # This is only necessary if we have a filter string in which the ORDER BY
4196 :     # and LIMIT clauses can live.
4197 :     if ($filterString) {
4198 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
4199 :     # operator so that we find the first occurrence of either verb.
4200 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
4201 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
4202 :     my $pos = pos $filterString;
4203 :     $orderClause = $2 . substr($filterString, $pos);
4204 :     $filterString = $1;
4205 :     }
4206 : parrello 1.70 }
4207 :     # All the things that are supposed to be in the WHERE clause of the
4208 :     # SELECT command need to be put into @joinWhere so we can string them
4209 :     # together. We begin with the match clause. This is important,
4210 :     # because the match clause's parameter mark must precede any parameter
4211 :     # marks in the filter string.
4212 :     if ($matchClause) {
4213 :     push @joinWhere, $matchClause;
4214 :     }
4215 :     # Add the filter string. We put it in parentheses to avoid operator
4216 :     # precedence problems with the match clause or the joins.
4217 :     if ($filterString) {
4218 :     Trace("Filter string is \"$filterString\".") if T(4);
4219 :     push @joinWhere, "($filterString)";
4220 :     }
4221 :     # String it all together into a big filter clause.
4222 :     if (@joinWhere) {
4223 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
4224 :     }
4225 :     # Add the sort or limit clause (if any).
4226 :     if ($orderClause) {
4227 :     $suffix .= " $orderClause";
4228 : parrello 1.45 }
4229 :     # Return the suffix, the mapped name list, and the mapped name hash.
4230 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
4231 :     }
4232 :    
4233 : parrello 1.70 =head3 _GetStatementHandle
4234 : parrello 1.45
4235 :     This method will prepare and execute an SQL query, returning the statement handle.
4236 :     The main reason for doing this here is so that everybody who does SQL queries gets
4237 :     the benefit of tracing.
4238 :    
4239 :     This is an instance method.
4240 :    
4241 :     =over 4
4242 :    
4243 :     =item command
4244 :    
4245 :     Command to prepare and execute.
4246 :    
4247 :     =item params
4248 :    
4249 :     Reference to a list of the values to be substituted in for the parameter marks.
4250 :    
4251 :     =item RETURN
4252 :    
4253 :     Returns a prepared and executed statement handle from which the caller can extract
4254 :     results.
4255 :    
4256 :     =back
4257 :    
4258 :     =cut
4259 :    
4260 :     sub _GetStatementHandle {
4261 :     # Get the parameters.
4262 :     my ($self, $command, $params) = @_;
4263 :     # Trace the query.
4264 :     Trace("SQL query: $command") if T(SQL => 3);
4265 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
4266 :     # Get the database handle.
4267 :     my $dbh = $self->{_dbh};
4268 :     # Prepare the command.
4269 :     my $sth = $dbh->prepare_command($command);
4270 :     # Execute it with the parameters bound in.
4271 : parrello 1.75 $sth->execute(@{$params}) || Confess("SELECT error: " . $sth->errstr());
4272 : parrello 1.45 # Return the statement handle.
4273 :     return $sth;
4274 :     }
4275 :    
4276 : parrello 1.70 =head3 _GetLoadStats
4277 : parrello 1.1
4278 :     Return a blank statistics object for use by the load methods.
4279 :    
4280 :     This is a static method.
4281 :    
4282 :     =cut
4283 :    
4284 : parrello 1.29 sub _GetLoadStats{
4285 : parrello 1.28 return Stats->new();
4286 : parrello 1.1 }
4287 :    
4288 : parrello 1.70 =head3 _DumpRelation
4289 : parrello 1.1
4290 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
4291 : parrello 1.1
4292 :     This is an instance method.
4293 :    
4294 :     =over 4
4295 :    
4296 :     =item outputDirectory
4297 :    
4298 :     Directory to contain the output file.
4299 :    
4300 :     =item relationName
4301 :    
4302 :     Name of the relation to dump.
4303 :    
4304 :     =item relation
4305 :    
4306 :     Structure describing the relation to be dumped.
4307 :    
4308 :     =back
4309 :    
4310 :     =cut
4311 :    
4312 :     sub _DumpRelation {
4313 : parrello 1.10 # Get the parameters.
4314 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
4315 :     # Open the output file.
4316 :     my $fileName = "$outputDirectory/$relationName.dtx";
4317 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
4318 :     # Create a query for the specified relation.
4319 :     my $dbh = $self->{_dbh};
4320 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
4321 :     # Execute the query.
4322 :     $query->execute() || Confess("SELECT error dumping $relationName.");
4323 :     # Loop through the results.
4324 :     while (my @row = $query->fetchrow) {
4325 :     # Escape any tabs or new-lines in the row text.
4326 :     for my $field (@row) {
4327 :     $field =~ s/\n/\\n/g;
4328 :     $field =~ s/\t/\\t/g;
4329 :     }
4330 :     # Tab-join the row and write it to the output file.
4331 :     my $rowText = join("\t", @row);
4332 :     print DTXOUT "$rowText\n";
4333 :     }
4334 :     # Close the output file.
4335 :     close DTXOUT;
4336 : parrello 1.1 }
4337 :    
4338 : parrello 1.70 =head3 _GetStructure
4339 : parrello 1.1
4340 :     Get the data structure for a specified entity or relationship.
4341 :    
4342 :     This is an instance method.
4343 :    
4344 :     =over 4
4345 :    
4346 :     =item objectName
4347 :    
4348 :     Name of the desired entity or relationship.
4349 :    
4350 :     =item RETURN
4351 :    
4352 :     The descriptor for the specified object.
4353 :    
4354 :     =back
4355 :    
4356 :     =cut
4357 :    
4358 :     sub _GetStructure {
4359 : parrello 1.10 # Get the parameters.
4360 :     my ($self, $objectName) = @_;
4361 :     # Get the metadata structure.
4362 :     my $metadata = $self->{_metaData};
4363 :     # Declare the variable to receive the descriptor.
4364 :     my $retVal;
4365 :     # Get the descriptor from the metadata.
4366 :     if (exists $metadata->{Entities}->{$objectName}) {
4367 :     $retVal = $metadata->{Entities}->{$objectName};
4368 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
4369 :     $retVal = $metadata->{Relationships}->{$objectName};
4370 :     } else {
4371 :     Confess("Ob