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1 : parrello 1.1 package ERDB;
2 :    
3 : parrello 1.10 use strict;
4 :     use Tracer;
5 : olson 1.14 use DBrtns;
6 : parrello 1.10 use Data::Dumper;
7 :     use XML::Simple;
8 :     use DBQuery;
9 :     use DBObject;
10 :     use Stats;
11 :     use Time::HiRes qw(gettimeofday);
12 : parrello 1.42 use Digest::MD5 qw(md5_base64);
13 : parrello 1.19 use FIG;
14 : parrello 1.73 use CGI;
15 : parrello 1.1
16 :     =head1 Entity-Relationship Database Package
17 :    
18 :     =head2 Introduction
19 :    
20 :     The Entity-Relationship Database Package allows the client to create an easily-configurable
21 :     database of Entities connected by Relationships. Each entity is represented by one or more
22 :     relations in an underlying SQL database. Each relationship is represented by a single
23 :     relation that connects two entities.
24 :    
25 :     Although this package is designed for general use, all examples are derived from the
26 :     Sprout database, which is the first database implemented using this package.
27 :    
28 :     Each entity has at least one relation, the I<primary relation>, that has the same name as
29 :     the entity. The primary relation contains a field named C<id> that contains the unique
30 :     identifier of each entity instance. An entity may have additional relations that contain
31 :     fields which are optional or can occur more than once. For example, the B<FEATURE> entity
32 :     has a B<feature-type> attribute that occurs exactly once for each feature. This attribute
33 :     is implemented by a C<feature_type> column in the primary relation C<Feature>. In addition,
34 :     however, a feature may have zero or more aliases. These are implemented using a C<FeatureAlias>
35 :     relation that contains two fields-- the feature ID (C<id>) and the alias name (C<alias>).
36 :     The B<FEATURE> entity also contains an optional virulence number. This is implemented
37 :     as a separate relation C<FeatureVirulence> which contains an ID (C<id>) and a virulence number
38 : parrello 1.8 (C<virulence>). If the virulence of a feature I<ABC> is known to be 6, there will be one row in
39 :     the C<FeatureVirulence> relation possessing the value I<ABC> as its ID and 6 as its virulence
40 :     number. If the virulence of I<ABC> is not known, there will not be any rows for it in
41 :     C<FeatureVirulence>.
42 : parrello 1.1
43 :     Entities are connected by binary relationships implemented using single relations possessing the
44 :     same name as the relationship itself and that has an I<arity> of 1-to-1 (C<11>), 1-to-many (C<1M>),
45 :     or many-to-many (C<MM>). Each relationship's relation contains a C<from-link> field that contains the
46 :     ID of the source entity and a C<to-link> field that contains the ID of the target entity. The name
47 :     of the relationship is generally a verb phrase with the source entity as the subject and the
48 :     target entity as the object. So, for example, the B<ComesFrom> relationship connects the B<GENOME>
49 :     and B<SOURCE> entities, and indicates that a particular source organization participated in the
50 :     mapping of the genome. A source organization frequently participates in the mapping
51 :     of many genomes, and many source organizations can cooperate in the mapping of a single genome, so
52 :     this relationship has an arity of many-to-many (C<MM>). The relation that implements the B<ComesFrom>
53 :     relationship is called C<ComesFrom> and contains two fields-- C<from-link>, which contains a genome ID,
54 :     and C<to-link>, which contains a source ID.
55 :    
56 :     A relationship may itself have attributes. These attributes, known as I<intersection data attributes>,
57 :     are implemented as additional fields in the relationship's relation. So, for example, the
58 :     B<IsMadeUpOf> relationship connects the B<Contig> entity to the B<Sequence> entity, and is used
59 :     to determine which sequences make up a contig. The relationship has as an attribute the
60 :     B<start-position>, which indicates where in the contig that the sequence begins. This attribute
61 :     is implemented as the C<start_position> field in the C<IsMadeUpOf> relation.
62 :    
63 : parrello 1.73 The database itself is described by an XML file. In addition to all the data required to define
64 :     the entities, relationships, and attributes, the schema provides space for notes describing
65 :     the data and what it means. These notes are used by L</ShowMetaData> to generate documentation
66 :     for the database.
67 :    
68 :     Special support is provided for text searching. An entity field can be marked as <em>searchable</em>,
69 :     in which case it will be used to generate a text search index in which the user searches for words
70 :     in the field instead of a particular field value.
71 : parrello 1.1
72 :     Finally, every entity and relationship object has a flag indicating if it is new or old. The object
73 :     is considered I<old> if it was loaded by the L</LoadTables> method. It is considered I<new> if it
74 :     was inserted by the L</InsertObject> method.
75 :    
76 : parrello 1.8 =head2 XML Database Description
77 :    
78 :     =head3 Data Types
79 :    
80 :     The ERDB system supports the following data types. Note that there are numerous string
81 :     types depending on the maximum length. Some database packages limit the total number of
82 :     characters you have in an index key; to insure the database works in all environments,
83 :     the type of string should be the shortest one possible that supports all the known values.
84 :    
85 :     =over 4
86 :    
87 :     =item char
88 :    
89 :     single ASCII character
90 :    
91 :     =item int
92 :    
93 :     32-bit signed integer
94 :    
95 : parrello 1.60 =item counter
96 :    
97 :     32-bit unsigned integer
98 :    
99 : parrello 1.8 =item date
100 :    
101 :     64-bit unsigned integer, representing a PERL date/time value
102 :    
103 :     =item text
104 :    
105 :     long string; Text fields cannot be used in indexes or sorting and do not support the
106 :     normal syntax of filter clauses, but can be up to a billion character in length
107 :    
108 :     =item float
109 :    
110 :     double-precision floating-point number
111 :    
112 :     =item boolean
113 :    
114 :     single-bit numeric value; The value is stored as a 16-bit signed integer (for
115 :     compatability with certain database packages), but the only values supported are
116 :     0 and 1.
117 :    
118 : parrello 1.44 =item id-string
119 :    
120 :     variable-length string, maximum 25 characters
121 :    
122 : parrello 1.8 =item key-string
123 :    
124 :     variable-length string, maximum 40 characters
125 :    
126 :     =item name-string
127 :    
128 :     variable-length string, maximum 80 characters
129 :    
130 :     =item medium-string
131 :    
132 :     variable-length string, maximum 160 characters
133 :    
134 :     =item string
135 :    
136 :     variable-length string, maximum 255 characters
137 :    
138 : parrello 1.42 =item hash-string
139 :    
140 :     variable-length string, maximum 22 characters
141 :    
142 : parrello 1.8 =back
143 :    
144 : parrello 1.42 The hash-string data type has a special meaning. The actual key passed into the loader will
145 :     be a string, but it will be digested into a 22-character MD5 code to save space. Although the
146 :     MD5 algorithm is not perfect, it is extremely unlikely two strings will have the same
147 :     digest. Therefore, it is presumed the keys will be unique. When the database is actually
148 :     in use, the hashed keys will be presented rather than the original values. For this reason,
149 :     they should not be used for entities where the key is meaningful.
150 :    
151 : parrello 1.8 =head3 Global Tags
152 :    
153 :     The entire database definition must be inside a B<Database> tag. The display name of
154 :     the database is given by the text associated with the B<Title> tag. The display name
155 :     is only used in the automated documentation. It has no other effect. The entities and
156 :     relationships are listed inside the B<Entities> and B<Relationships> tags,
157 :     respectively. None of these tags have attributes.
158 :    
159 : parrello 1.10 <Database>
160 :     <Title>... display title here...</Title>
161 :     <Entities>
162 :     ... entity definitions here ...
163 :     </Entities>
164 :     <Relationships>
165 :     ... relationship definitions here...
166 :     </Relationships>
167 :     </Database>
168 : parrello 1.8
169 :     Entities, relationships, indexes, and fields all allow a text tag called B<Notes>.
170 :     The text inside the B<Notes> tag contains comments that will appear when the database
171 :     documentation is generated. Within a B<Notes> tag, you may use C<[i]> and C<[/i]> for
172 :     italics, C<[b]> and C<[/b]> for bold, and C<[p]> for a new paragraph.
173 :    
174 :     =head3 Fields
175 :    
176 :     Both entities and relationships have fields described by B<Field> tags. A B<Field>
177 :     tag can have B<Notes> associated with it. The complete set of B<Field> tags for an
178 :     object mus be inside B<Fields> tags.
179 :    
180 : parrello 1.10 <Entity ... >
181 :     <Fields>
182 :     ... Field tags ...
183 :     </Fields>
184 :     </Entity>
185 : parrello 1.8
186 :     The attributes for the B<Field> tag are as follows.
187 :    
188 :     =over 4
189 :    
190 :     =item name
191 :    
192 :     Name of the field. The field name should contain only letters, digits, and hyphens (C<->),
193 :     and the first character should be a letter. Most underlying databases are case-insensitive
194 : parrello 1.70 with the respect to field names, so a best practice is to use lower-case letters only. Finally,
195 :     the name C<search-relevance> has special meaning for full-text searches and should not be
196 :     used as a field name.
197 : parrello 1.8
198 :     =item type
199 :    
200 :     Data type of the field. The legal data types are given above.
201 :    
202 :     =item relation
203 :    
204 :     Name of the relation containing the field. This should only be specified for entity
205 :     fields. The ERDB system does not support optional fields or multi-occurring fields
206 :     in the primary relation of an entity. Instead, they are put into secondary relations.
207 :     So, for example, in the C<Genome> entity, the C<group-name> field indicates a special
208 :     grouping used to select a subset of the genomes. A given genome may not be in any
209 :     groups or may be in multiple groups. Therefore, C<group-name> specifies a relation
210 :     value. The relation name specified must be a valid table name. By convention, it is
211 :     usually the entity name followed by a qualifying word (e.g. C<GenomeGroup>). In an
212 :     entity, the fields without a relation attribute are said to belong to the
213 :     I<primary relation>. This relation has the same name as the entity itself.
214 :    
215 : parrello 1.70 =item searchable
216 :    
217 :     If specified, then the field is a candidate for full-text searching. A single full-text
218 :     index will be created for each relation with at least one searchable field in it.
219 :     For best results, this option should only be used for string or text fields.
220 :    
221 : parrello 1.73 =item special
222 :    
223 :     This attribute allows the subclass to assign special meaning for certain fields.
224 :     The interpretation is up to the subclass itself. Currently, only entity fields
225 :     can have this attribute.
226 :    
227 : parrello 1.8 =back
228 :    
229 :     =head3 Indexes
230 :    
231 :     An entity can have multiple alternate indexes associated with it. The fields must
232 : parrello 1.74 all be from the same relation. The alternate indexes assist in ordering results
233 : parrello 1.8 from a query. A relationship can have up to two indexes-- a I<to-index> and a
234 :     I<from-index>. These order the results when crossing the relationship. For
235 :     example, in the relationship C<HasContig> from C<Genome> to C<Contig>, the
236 :     from-index would order the contigs of a ganome, and the to-index would order
237 :     the genomes of a contig. A relationship's index must specify only fields in
238 :     the relationship.
239 :    
240 :     The indexes for an entity must be listed inside the B<Indexes> tag. The from-index
241 :     of a relationship is specified using the B<FromIndex> tag; the to-index is specified
242 :     using the B<ToIndex> tag.
243 :    
244 :     Each index can contain a B<Notes> tag. In addition, it will have an B<IndexFields>
245 :     tag containing the B<IndexField> tags. These specify, in order, the fields used in
246 :     the index. The attributes of an B<IndexField> tag are as follows.
247 :    
248 :     =over 4
249 :    
250 :     =item name
251 :    
252 :     Name of the field.
253 :    
254 :     =item order
255 :    
256 :     Sort order of the field-- C<ascending> or C<descending>.
257 :    
258 :     =back
259 :    
260 : 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 :     fields, a C<FromIndex> tag containing the from-index, and a C<ToIndex> tag containing
307 :     the to-index.
308 :    
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 1.10 );
376 : parrello 1.1
377 :     # Table translating arities into natural language.
378 :     my %ArityTable = ( '11' => 'one-to-one',
379 : parrello 1.10 '1M' => 'one-to-many',
380 :     'MM' => 'many-to-many'
381 :     );
382 : parrello 1.1
383 : parrello 1.73 # Options for XML input and output.
384 :    
385 :     my %XmlOptions = (GroupTags => { Relationships => 'Relationship',
386 :     Entities => 'Entity',
387 :     Fields => 'Field',
388 :     Indexes => 'Index',
389 :     IndexFields => 'IndexField'
390 :     },
391 :     KeyAttr => { Relationship => 'name',
392 :     Entity => 'name',
393 :     Field => 'name'
394 :     },
395 :     SuppressEmpty => 1,
396 :     );
397 :    
398 :     my %XmlInOpts = (
399 : parrello 1.78 ForceArray => ['Field', 'Index', 'IndexField', 'Relationship', 'Entity'],
400 : parrello 1.73 ForceContent => 1,
401 :     NormalizeSpace => 2,
402 :     );
403 :     my %XmlOutOpts = (
404 :     RootName => 'Database',
405 :     XMLDecl => 1,
406 :     );
407 : parrello 1.1
408 :    
409 :     =head2 Public Methods
410 :    
411 :     =head3 new
412 :    
413 : parrello 1.5 C<< my $database = ERDB->new($dbh, $metaFileName); >>
414 : parrello 1.1
415 :     Create a new ERDB object.
416 :    
417 :     =over 4
418 :    
419 :     =item dbh
420 :    
421 :     DBKernel database object for the target database.
422 :    
423 :     =item metaFileName
424 :    
425 :     Name of the XML file containing the metadata.
426 :    
427 :     =back
428 :    
429 :     =cut
430 :    
431 :     sub new {
432 : parrello 1.10 # Get the parameters.
433 :     my ($class, $dbh, $metaFileName, $options) = @_;
434 :     # Load the meta-data.
435 :     my $metaData = _LoadMetaData($metaFileName);
436 :     # Create the object.
437 :     my $self = { _dbh => $dbh,
438 :     _metaData => $metaData
439 :     };
440 :     # Bless and return it.
441 :     bless $self, $class;
442 :     return $self;
443 : parrello 1.1 }
444 :    
445 :     =head3 ShowMetaData
446 :    
447 : parrello 1.18 C<< $erdb->ShowMetaData($fileName); >>
448 : parrello 1.1
449 :     This method outputs a description of the database. This description can be used to help users create
450 :     the data to be loaded into the relations.
451 :    
452 :     =over 4
453 :    
454 :     =item filename
455 :    
456 :     The name of the output file.
457 :    
458 :     =back
459 :    
460 :     =cut
461 :    
462 :     sub ShowMetaData {
463 : parrello 1.10 # Get the parameters.
464 :     my ($self, $filename) = @_;
465 :     # Get the metadata and the title string.
466 :     my $metadata = $self->{_metaData};
467 :     # Get the title string.
468 :     my $title = $metadata->{Title};
469 :     # Get the entity and relationship lists.
470 :     my $entityList = $metadata->{Entities};
471 :     my $relationshipList = $metadata->{Relationships};
472 :     # Open the output file.
473 :     open(HTMLOUT, ">$filename") || Confess("Could not open MetaData display file $filename: $!");
474 :     Trace("Building MetaData table of contents.") if T(4);
475 :     # Write the HTML heading stuff.
476 :     print HTMLOUT "<html>\n<head>\n<title>$title</title>\n";
477 :     print HTMLOUT "</head>\n<body>\n";
478 : parrello 1.45 # Write the documentation.
479 :     print HTMLOUT $self->DisplayMetaData();
480 :     # Close the document.
481 :     print HTMLOUT "</body>\n</html>\n";
482 :     # Close the file.
483 :     close HTMLOUT;
484 :     }
485 :    
486 :     =head3 DisplayMetaData
487 :    
488 :     C<< my $html = $erdb->DisplayMetaData(); >>
489 :    
490 :     Return an HTML description of the database. This description can be used to help users create
491 :     the data to be loaded into the relations and form queries. The output is raw includable HTML
492 :     without any HEAD or BODY tags.
493 :    
494 :     =over 4
495 :    
496 :     =item filename
497 :    
498 :     The name of the output file.
499 :    
500 :     =back
501 :    
502 :     =cut
503 :    
504 :     sub DisplayMetaData {
505 :     # Get the parameters.
506 :     my ($self) = @_;
507 :     # Get the metadata and the title string.
508 :     my $metadata = $self->{_metaData};
509 :     # Get the title string.
510 :     my $title = $metadata->{Title};
511 :     # Get the entity and relationship lists.
512 :     my $entityList = $metadata->{Entities};
513 :     my $relationshipList = $metadata->{Relationships};
514 :     # Declare the return variable.
515 :     my $retVal = "";
516 :     # Open the output file.
517 :     Trace("Building MetaData table of contents.") if T(4);
518 : parrello 1.10 # Here we do the table of contents. It starts as an unordered list of section names. Each
519 :     # section contains an ordered list of entity or relationship subsections.
520 : parrello 1.45 $retVal .= "<ul>\n<li><a href=\"#EntitiesSection\">Entities</a>\n<ol>\n";
521 : parrello 1.10 # Loop through the Entities, displaying a list item for each.
522 :     foreach my $key (sort keys %{$entityList}) {
523 :     # Display this item.
524 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$key</a></li>\n";
525 : parrello 1.10 }
526 :     # Close off the entity section and start the relationship section.
527 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#RelationshipsSection\">Relationships</a>\n<ol>\n";
528 : parrello 1.10 # Loop through the Relationships.
529 :     foreach my $key (sort keys %{$relationshipList}) {
530 :     # Display this item.
531 :     my $relationshipTitle = _ComputeRelationshipSentence($key, $relationshipList->{$key});
532 : parrello 1.45 $retVal .= "<li><a href=\"#$key\">$relationshipTitle</a></li>\n";
533 : parrello 1.10 }
534 :     # Close off the relationship section and list the join table section.
535 : parrello 1.45 $retVal .= "</ol></li>\n<li><a href=\"#JoinTable\">Join Table</a></li>\n";
536 : parrello 1.10 # Close off the table of contents itself.
537 : parrello 1.45 $retVal .= "</ul>\n";
538 : parrello 1.10 # Now we start with the actual data. Denote we're starting the entity section.
539 : parrello 1.45 $retVal .= "<a name=\"EntitiesSection\"></a><h2>Entities</h2>\n";
540 : parrello 1.10 # Loop through the entities.
541 :     for my $key (sort keys %{$entityList}) {
542 :     Trace("Building MetaData entry for $key entity.") if T(4);
543 :     # Create the entity header. It contains a bookmark and the entity name.
544 : parrello 1.45 $retVal .= "<a name=\"$key\"></a><h3>$key</h3>\n";
545 : parrello 1.10 # Get the entity data.
546 :     my $entityData = $entityList->{$key};
547 :     # If there's descriptive text, display it.
548 :     if (my $notes = $entityData->{Notes}) {
549 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
550 : parrello 1.10 }
551 :     # Now we want a list of the entity's relationships. First, we set up the relationship subsection.
552 : parrello 1.45 $retVal .= "<h4>Relationships for <b>$key</b></h4>\n<ul>\n";
553 : parrello 1.10 # Loop through the relationships.
554 :     for my $relationship (sort keys %{$relationshipList}) {
555 :     # Get the relationship data.
556 :     my $relationshipStructure = $relationshipList->{$relationship};
557 :     # Only use the relationship if if has this entity in its FROM or TO fields.
558 :     if ($relationshipStructure->{from} eq $key || $relationshipStructure->{to} eq $key) {
559 :     # Get the relationship sentence and append the arity.
560 :     my $relationshipDescription = _ComputeRelationshipSentence($relationship, $relationshipStructure);
561 :     # Display the relationship data.
562 : parrello 1.45 $retVal .= "<li><a href=\"#$relationship\">$relationshipDescription</a></li>\n";
563 : parrello 1.10 }
564 :     }
565 :     # Close off the relationship list.
566 : parrello 1.45 $retVal .= "</ul>\n";
567 : parrello 1.10 # Get the entity's relations.
568 :     my $relationList = $entityData->{Relations};
569 :     # Create a header for the relation subsection.
570 : parrello 1.45 $retVal .= "<h4>Relations for <b>$key</b></h4>\n";
571 : parrello 1.10 # Loop through the relations, displaying them.
572 :     for my $relation (sort keys %{$relationList}) {
573 :     my $htmlString = _ShowRelationTable($relation, $relationList->{$relation});
574 : parrello 1.45 $retVal .= $htmlString;
575 : parrello 1.10 }
576 :     }
577 :     # Denote we're starting the relationship section.
578 : parrello 1.45 $retVal .= "<a name=\"RelationshipsSection\"></a><h2>Relationships</h2>\n";
579 : parrello 1.10 # Loop through the relationships.
580 :     for my $key (sort keys %{$relationshipList}) {
581 :     Trace("Building MetaData entry for $key relationship.") if T(4);
582 :     # Get the relationship's structure.
583 :     my $relationshipStructure = $relationshipList->{$key};
584 :     # Create the relationship header.
585 :     my $headerText = _ComputeRelationshipHeading($key, $relationshipStructure);
586 : parrello 1.45 $retVal .= "<h3><a name=\"$key\"></a>$headerText</h3>\n";
587 : parrello 1.10 # Get the entity names.
588 :     my $fromEntity = $relationshipStructure->{from};
589 :     my $toEntity = $relationshipStructure->{to};
590 :     # Describe the relationship arity. Note there's a bit of trickiness involving recursive
591 :     # many-to-many relationships. In a normal many-to-many we use two sentences to describe
592 :     # the arity (one for each direction). This is a bad idea for a recursive relationship,
593 :     # since both sentences will say the same thing.
594 :     my $arity = $relationshipStructure->{arity};
595 :     if ($arity eq "11") {
596 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to at most one <b>$toEntity</b>.\n";
597 : parrello 1.10 } else {
598 : parrello 1.45 $retVal .= "<p>Each <b>$fromEntity</b> relates to multiple <b>$toEntity</b>s.\n";
599 : parrello 1.10 if ($arity eq "MM" && $fromEntity ne $toEntity) {
600 : parrello 1.45 $retVal .= "Each <b>$toEntity</b> relates to multiple <b>$fromEntity</b>s.\n";
601 : parrello 1.10 }
602 :     }
603 : parrello 1.45 $retVal .= "</p>\n";
604 : parrello 1.10 # If there are notes on this relationship, display them.
605 :     if (my $notes = $relationshipStructure->{Notes}) {
606 : parrello 1.73 $retVal .= "<p>" . HTMLNote($notes->{content}) . "</p>\n";
607 : parrello 1.10 }
608 :     # Generate the relationship's relation table.
609 :     my $htmlString = _ShowRelationTable($key, $relationshipStructure->{Relations}->{$key});
610 : parrello 1.45 $retVal .= $htmlString;
611 : parrello 1.10 }
612 :     Trace("Building MetaData join table.") if T(4);
613 :     # Denote we're starting the join table.
614 : parrello 1.45 $retVal .= "<a name=\"JoinTable\"></a><h3>Join Table</h3>\n";
615 : parrello 1.10 # Create a table header.
616 : parrello 1.45 $retVal .= _OpenTable("Join Table", "Source", "Target", "Join Condition");
617 : parrello 1.10 # Loop through the joins.
618 :     my $joinTable = $metadata->{Joins};
619 :     my @joinKeys = keys %{$joinTable};
620 :     for my $joinKey (sort @joinKeys) {
621 :     # Separate out the source, the target, and the join clause.
622 :     $joinKey =~ m!^([^/]+)/(.+)$!;
623 :     my ($sourceRelation, $targetRelation) = ($1, $2);
624 : parrello 1.30 Trace("Join with key $joinKey is from $sourceRelation to $targetRelation.") if T(Joins => 4);
625 : parrello 1.10 my $source = $self->ComputeObjectSentence($sourceRelation);
626 :     my $target = $self->ComputeObjectSentence($targetRelation);
627 :     my $clause = $joinTable->{$joinKey};
628 :     # Display them in a table row.
629 : parrello 1.45 $retVal .= "<tr><td>$source</td><td>$target</td><td>$clause</td></tr>\n";
630 : parrello 1.10 }
631 :     # Close the table.
632 : parrello 1.45 $retVal .= _CloseTable();
633 :     Trace("Built MetaData HTML.") if T(3);
634 :     # Return the HTML.
635 :     return $retVal;
636 : parrello 1.1 }
637 :    
638 :     =head3 DumpMetaData
639 :    
640 : parrello 1.18 C<< $erdb->DumpMetaData(); >>
641 : parrello 1.1
642 :     Return a dump of the metadata structure.
643 :    
644 :     =cut
645 :    
646 :     sub DumpMetaData {
647 : parrello 1.10 # Get the parameters.
648 :     my ($self) = @_;
649 :     # Dump the meta-data.
650 :     return Data::Dumper::Dumper($self->{_metaData});
651 : parrello 1.1 }
652 :    
653 : parrello 1.74 =head3 FindIndexForEntity
654 :    
655 :     C<< my $indexFound = ERDB::FindIndexForEntity($xml, $entityName, $attributeName); >>
656 :    
657 :     This method locates the entry in an entity's index list that begins with the
658 :     specified attribute name. If the entity has no index list, one will be
659 :     created. This method works on raw XML, not a live ERDB object.
660 :    
661 :     =over 4
662 :    
663 :     =item xml
664 :    
665 :     The raw XML structure defining the database.
666 :    
667 :     =item entityName
668 :    
669 :     The name of the relevant entity.
670 :    
671 :     =item attributeName
672 :    
673 :     The name of the attribute relevant to the search.
674 :    
675 :     =item RETURN
676 :    
677 :     The numerical index in the index list of the index entry for the specified entity and
678 :     attribute, or C<undef> if no such index exists.
679 :    
680 :     =back
681 :    
682 :     =cut
683 :    
684 :     sub FindIndexForEntity {
685 :     # Get the parameters.
686 :     my ($xml, $entityName, $attributeName) = @_;
687 :     # Declare the return variable.
688 :     my $retVal;
689 :     # Get the named entity.
690 :     my $entityData = $xml->{Entities}->{$entityName};
691 :     if (! $entityData) {
692 :     Confess("Entity $entityName not found in DBD structure.");
693 :     } else {
694 :     # Insure it has an index list.
695 :     if (! exists $entityData->{Indexes}) {
696 :     $entityData->{Indexes} = [];
697 :     } else {
698 :     # Search for the desired index.
699 :     my $indexList = $entityData->{Indexes};
700 :     my $n = scalar @{$indexList};
701 :     Trace("Searching $n indexes in index list for $entityName.") if T(2);
702 :     # We use an indexed FOR here because we're returning an
703 :     # index number instead of an object. We do THAT so we can
704 :     # delete the index from the list if needed.
705 :     for (my $i = 0; $i < $n && !defined($retVal); $i++) {
706 :     my $index = $indexList->[$i];
707 :     my $fields = $index->{IndexFields};
708 :     # Technically this IF should be safe (that is, we are guaranteed
709 :     # the existence of a "$fields->[0]"), because when we load the XML
710 :     # we have SuppressEmpty specified.
711 :     if ($fields->[0]->{name} eq $attributeName) {
712 :     $retVal = $i;
713 :     }
714 :     }
715 :     }
716 :     }
717 :     Trace("Index for $attributeName of $entityName found at position $retVal.") if defined($retVal) && T(3);
718 :     Trace("Index for $attributeName not found in $entityName.") if !defined($retVal) && T(3);
719 :     # Return the result.
720 :     return $retVal;
721 :     }
722 :    
723 : parrello 1.1 =head3 CreateTables
724 :    
725 : parrello 1.18 C<< $erdb->CreateTables(); >>
726 : parrello 1.1
727 :     This method creates the tables for the database from the metadata structure loaded by the
728 :     constructor. It is expected this function will only be used on rare occasions, when the
729 : parrello 1.2 user needs to start with an empty database. Otherwise, the L</LoadTables> method can be
730 : parrello 1.1 used by itself with the truncate flag turned on.
731 :    
732 :     =cut
733 :    
734 :     sub CreateTables {
735 : parrello 1.10 # Get the parameters.
736 :     my ($self) = @_;
737 : parrello 1.23 # Get the relation names.
738 :     my @relNames = $self->GetTableNames();
739 :     # Loop through the relations.
740 :     for my $relationName (@relNames) {
741 :     # Create a table for this relation.
742 :     $self->CreateTable($relationName);
743 :     Trace("Relation $relationName created.") if T(2);
744 : parrello 1.10 }
745 : parrello 1.1 }
746 :    
747 :     =head3 CreateTable
748 :    
749 : parrello 1.18 C<< $erdb->CreateTable($tableName, $indexFlag, $estimatedRows); >>
750 : parrello 1.1
751 :     Create the table for a relation and optionally create its indexes.
752 :    
753 :     =over 4
754 :    
755 :     =item relationName
756 :    
757 :     Name of the relation (which will also be the table name).
758 :    
759 : parrello 1.18 =item indexFlag
760 : parrello 1.1
761 :     TRUE if the indexes for the relation should be created, else FALSE. If FALSE,
762 :     L</CreateIndexes> must be called later to bring the indexes into existence.
763 :    
764 : parrello 1.18 =item estimatedRows (optional)
765 :    
766 :     If specified, the estimated maximum number of rows for the relation. This
767 :     information allows the creation of tables using storage engines that are
768 :     faster but require size estimates, such as MyISAM.
769 :    
770 : parrello 1.1 =back
771 :    
772 :     =cut
773 :    
774 :     sub CreateTable {
775 : parrello 1.10 # Get the parameters.
776 : parrello 1.18 my ($self, $relationName, $indexFlag, $estimatedRows) = @_;
777 : parrello 1.10 # Get the database handle.
778 :     my $dbh = $self->{_dbh};
779 :     # Get the relation data and determine whether or not the relation is primary.
780 :     my $relationData = $self->_FindRelation($relationName);
781 :     my $rootFlag = $self->_IsPrimary($relationName);
782 :     # Create a list of the field data.
783 :     my @fieldList;
784 :     for my $fieldData (@{$relationData->{Fields}}) {
785 :     # Assemble the field name and type.
786 :     my $fieldName = _FixName($fieldData->{name});
787 :     my $fieldString = "$fieldName $TypeTable{$fieldData->{type}}->{sqlType} NOT NULL ";
788 :     # Push the result into the field list.
789 :     push @fieldList, $fieldString;
790 :     }
791 :     # If this is a root table, add the "new_record" flag. It defaults to 0, so
792 :     if ($rootFlag) {
793 :     push @fieldList, "new_record $TypeTable{boolean}->{sqlType} NOT NULL DEFAULT 0";
794 :     }
795 :     # Convert the field list into a comma-delimited string.
796 :     my $fieldThing = join(', ', @fieldList);
797 :     # Insure the table is not already there.
798 :     $dbh->drop_table(tbl => $relationName);
799 :     Trace("Table $relationName dropped.") if T(2);
800 : parrello 1.18 # If there are estimated rows, create an estimate so we can take advantage of
801 :     # faster DB technologies.
802 :     my $estimation = undef;
803 :     if ($estimatedRows) {
804 :     $estimation = [$self->EstimateRowSize($relationName), $estimatedRows];
805 :     }
806 : parrello 1.10 # Create the table.
807 :     Trace("Creating table $relationName: $fieldThing") if T(2);
808 : parrello 1.18 $dbh->create_table(tbl => $relationName, flds => $fieldThing, estimates => $estimation);
809 : parrello 1.10 Trace("Relation $relationName created in database.") if T(2);
810 : parrello 1.70 # If we want to build the indexes, we do it here. Note that the full-text search
811 :     # index will not be built until the table has been loaded.
812 : parrello 1.10 if ($indexFlag) {
813 :     $self->CreateIndex($relationName);
814 :     }
815 : parrello 1.1 }
816 :    
817 : parrello 1.31 =head3 VerifyFields
818 :    
819 :     C<< my $count = $erdb->VerifyFields($relName, \@fieldList); >>
820 :    
821 :     Run through the list of proposed field values, insuring that all the character fields are
822 :     below the maximum length. If any fields are too long, they will be truncated in place.
823 :    
824 :     =over 4
825 :    
826 :     =item relName
827 :    
828 :     Name of the relation for which the specified fields are destined.
829 :    
830 :     =item fieldList
831 :    
832 :     Reference to a list, in order, of the fields to be put into the relation.
833 :    
834 :     =item RETURN
835 :    
836 :     Returns the number of fields truncated.
837 :    
838 :     =back
839 :    
840 :     =cut
841 :    
842 :     sub VerifyFields {
843 :     # Get the parameters.
844 :     my ($self, $relName, $fieldList) = @_;
845 :     # Initialize the return value.
846 :     my $retVal = 0;
847 :     # Get the relation definition.
848 :     my $relData = $self->_FindRelation($relName);
849 :     # Get the list of field descriptors.
850 :     my $fieldTypes = $relData->{Fields};
851 :     my $fieldCount = scalar @{$fieldTypes};
852 :     # Loop through the two lists.
853 :     for (my $i = 0; $i < $fieldCount; $i++) {
854 :     # Get the type of the current field.
855 :     my $fieldType = $fieldTypes->[$i]->{type};
856 :     # If it's a character field, verify the length.
857 :     if ($fieldType =~ /string/) {
858 :     my $maxLen = $TypeTable{$fieldType}->{maxLen};
859 :     my $oldString = $fieldList->[$i];
860 :     if (length($oldString) > $maxLen) {
861 :     # Here it's too big, so we truncate it.
862 :     Trace("Truncating field $i in relation $relName to $maxLen characters from \"$oldString\".") if T(1);
863 :     $fieldList->[$i] = substr $oldString, 0, $maxLen;
864 :     $retVal++;
865 :     }
866 :     }
867 :     }
868 :     # Return the truncation count.
869 :     return $retVal;
870 :     }
871 :    
872 : parrello 1.42 =head3 DigestFields
873 :    
874 :     C<< $erdb->DigestFields($relName, $fieldList); >>
875 :    
876 :     Digest the strings in the field list that correspond to data type C<hash-string> in the
877 :     specified relation.
878 :    
879 :     =over 4
880 :    
881 :     =item relName
882 :    
883 :     Name of the relation to which the fields belong.
884 :    
885 :     =item fieldList
886 :    
887 :     List of field contents to be loaded into the relation.
888 :    
889 :     =back
890 :    
891 :     =cut
892 :     #: Return Type ;
893 :     sub DigestFields {
894 :     # Get the parameters.
895 :     my ($self, $relName, $fieldList) = @_;
896 :     # Get the relation definition.
897 :     my $relData = $self->_FindRelation($relName);
898 :     # Get the list of field descriptors.
899 :     my $fieldTypes = $relData->{Fields};
900 :     my $fieldCount = scalar @{$fieldTypes};
901 :     # Loop through the two lists.
902 :     for (my $i = 0; $i < $fieldCount; $i++) {
903 :     # Get the type of the current field.
904 :     my $fieldType = $fieldTypes->[$i]->{type};
905 :     # If it's a hash string, digest it in place.
906 :     if ($fieldType eq 'hash-string') {
907 : parrello 1.46 $fieldList->[$i] = $self->DigestKey($fieldList->[$i]);
908 : parrello 1.42 }
909 :     }
910 :     }
911 :    
912 : parrello 1.46 =head3 DigestKey
913 :    
914 :     C<< my $digested = $erdb->DigestKey($keyValue); >>
915 :    
916 :     Return the digested value of a symbolic key. The digested value can then be plugged into a
917 :     key-based search into a table with key-type hash-string.
918 :    
919 :     Currently the digesting process is independent of the database structure, but that may not
920 :     always be the case, so this is an instance method instead of a static method.
921 :    
922 :     =over 4
923 :    
924 :     =item keyValue
925 :    
926 :     Key value to digest.
927 :    
928 :     =item RETURN
929 :    
930 : parrello 1.56 Digested value of the key.
931 : parrello 1.46
932 :     =back
933 :    
934 :     =cut
935 :    
936 :     sub DigestKey {
937 :     # Get the parameters.
938 :     my ($self, $keyValue) = @_;
939 :     # Compute the digest.
940 :     my $retVal = md5_base64($keyValue);
941 :     # Return the result.
942 :     return $retVal;
943 :     }
944 :    
945 : parrello 1.1 =head3 CreateIndex
946 :    
947 : parrello 1.18 C<< $erdb->CreateIndex($relationName); >>
948 : parrello 1.1
949 :     Create the indexes for a relation. If a table is being loaded from a large source file (as
950 : parrello 1.12 is the case in L</LoadTable>), it is sometimes best to create the indexes after the load.
951 :     If that is the case, then L</CreateTable> should be called with the index flag set to
952 :     FALSE, and this method used after the load to create the indexes for the table.
953 : parrello 1.1
954 :     =cut
955 :    
956 :     sub CreateIndex {
957 : parrello 1.10 # Get the parameters.
958 :     my ($self, $relationName) = @_;
959 :     # Get the relation's descriptor.
960 :     my $relationData = $self->_FindRelation($relationName);
961 :     # Get the database handle.
962 :     my $dbh = $self->{_dbh};
963 :     # Now we need to create this relation's indexes. We do this by looping through its index table.
964 :     my $indexHash = $relationData->{Indexes};
965 :     for my $indexName (keys %{$indexHash}) {
966 :     my $indexData = $indexHash->{$indexName};
967 :     # Get the index's field list.
968 : parrello 1.75 my @rawFields = @{$indexData->{IndexFields}};
969 :     # Get a hash of the relation's field types.
970 :     my %types = map { $_->{name} => $_->{type} } @{$relationData->{Fields}};
971 : parrello 1.78 # We need to check for text fields so we can append a length limitation for them. To do
972 : parrello 1.75 # that, we need the relation's field list.
973 :     my $relFields = $relationData->{Fields};
974 :     for (my $i = 0; $i <= $#rawFields; $i++) {
975 :     # Get the field type.
976 :     my $field = $rawFields[$i];
977 :     my $type = $types{$field};
978 :     # Ask if it requires using prefix notation for the index.
979 :     my $mod = $TypeTable{$type}->{indexMod};
980 :     Trace("Field $field ($i) in $relationName has type $type and indexMod $mod.") if T(3);
981 :     if ($mod) {
982 :     # Append the prefix length to the field name,
983 :     $rawFields[$i] .= "($mod)";
984 :     }
985 :     }
986 :     my @fieldList = _FixNames(@rawFields);
987 : parrello 1.10 my $flds = join(', ', @fieldList);
988 :     # Get the index's uniqueness flag.
989 : parrello 1.70 my $unique = (exists $indexData->{Unique} ? 'unique' : undef);
990 : parrello 1.10 # Create the index.
991 : parrello 1.24 my $rv = $dbh->create_index(idx => $indexName, tbl => $relationName,
992 : parrello 1.70 flds => $flds, kind => $unique);
993 : parrello 1.24 if ($rv) {
994 :     Trace("Index created: $indexName for $relationName ($flds)") if T(1);
995 :     } else {
996 :     Confess("Error creating index $indexName for $relationName using ($flds): " . $dbh->error_message());
997 :     }
998 : parrello 1.10 }
999 : parrello 1.1 }
1000 :    
1001 : parrello 1.75 =head3 GetSecondaryFields
1002 :    
1003 :     C<< my %fieldTuples = $erdb->GetSecondaryFields($entityName); >>
1004 :    
1005 :     This method will return a list of the name and type of each of the secondary
1006 :     fields for a specified entity. Secondary fields are stored in two-column tables
1007 :     in addition to the primary entity table. This enables the field to have no value
1008 :     or to have multiple values.
1009 :    
1010 :     =over 4
1011 :    
1012 :     =item entityName
1013 :    
1014 :     Name of the entity whose secondary fields are desired.
1015 :    
1016 :     =item RETURN
1017 :    
1018 :     Returns a hash mapping the field names to their field types.
1019 :    
1020 :     =back
1021 :    
1022 :     =cut
1023 :    
1024 :     sub GetSecondaryFields {
1025 :     # Get the parameters.
1026 :     my ($self, $entityName) = @_;
1027 :     # Declare the return variable.
1028 :     my %retVal = ();
1029 :     # Look for the entity.
1030 :     my $table = $self->GetFieldTable($entityName);
1031 :     # Loop through the fields, pulling out the secondaries.
1032 :     for my $field (sort keys %{$table}) {
1033 :     if ($table->{$field}->{relation} ne $entityName) {
1034 :     # Here we have a secondary field.
1035 :     $retVal{$field} = $table->{$field}->{type};
1036 :     }
1037 :     }
1038 :     # Return the result.
1039 :     return %retVal;
1040 :     }
1041 :    
1042 :     =head3 GetFieldRelationName
1043 :    
1044 :     C<< my $name = $erdb->GetFieldRelationName($objectName, $fieldName); >>
1045 :    
1046 :     Return the name of the relation containing a specified field.
1047 :    
1048 :     =over 4
1049 :    
1050 :     =item objectName
1051 :    
1052 :     Name of the entity or relationship containing the field.
1053 :    
1054 :     =item fieldName
1055 :    
1056 :     Name of the relevant field in that entity or relationship.
1057 :    
1058 :     =item RETURN
1059 :    
1060 :     Returns the name of the database relation containing the field, or C<undef> if
1061 :     the field does not exist.
1062 :    
1063 :     =back
1064 :    
1065 :     =cut
1066 :    
1067 :     sub GetFieldRelationName {
1068 :     # Get the parameters.
1069 :     my ($self, $objectName, $fieldName) = @_;
1070 :     # Declare the return variable.
1071 :     my $retVal;
1072 :     # Get the object field table.
1073 :     my $table = $self->GetFieldTable($objectName);
1074 :     # Only proceed if the field exists.
1075 :     if (exists $table->{$fieldName}) {
1076 :     # Determine the name of the relation that contains this field.
1077 :     $retVal = $table->{$fieldName}->{relation};
1078 :     }
1079 :     # Return the result.
1080 :     return $retVal;
1081 :     }
1082 :    
1083 :     =head3 DeleteValue
1084 :    
1085 :     C<< my $numDeleted = $erdb->DeleteValue($entityName, $id, $fieldName, $fieldValue); >>
1086 :    
1087 :     Delete secondary field values from the database. This method can be used to delete all
1088 :     values of a specified field for a particular entity instance, or only a single value.
1089 :    
1090 :     Secondary fields are stored in two-column relations separate from an entity's primary
1091 :     table, and as a result a secondary field can legitimately have no value or multiple
1092 :     values. Therefore, it makes sense to talk about deleting secondary fields where it
1093 :     would not make sense for primary fields.
1094 :    
1095 :     =over 4
1096 :    
1097 :     =item entityName
1098 :    
1099 :     Name of the entity from which the fields are to be deleted.
1100 :    
1101 :     =item id
1102 :    
1103 :     ID of the entity instance to be processed. If the instance is not found, this
1104 : parrello 1.76 method will have no effect. If C<undef> is specified, all values for all of
1105 :     the entity instances will be deleted.
1106 : parrello 1.75
1107 :     =item fieldName
1108 :    
1109 :     Name of the field whose values are to be deleted.
1110 :    
1111 :     =item fieldValue (optional)
1112 :    
1113 :     Value to be deleted. If not specified, then all values of the specified field
1114 :     will be deleted for the entity instance. If specified, then only the values which
1115 :     match this parameter will be deleted.
1116 :    
1117 :     =item RETURN
1118 :    
1119 :     Returns the number of rows deleted.
1120 :    
1121 :     =back
1122 :    
1123 :     =cut
1124 :    
1125 :     sub DeleteValue {
1126 :     # Get the parameters.
1127 :     my ($self, $entityName, $id, $fieldName, $fieldValue) = @_;
1128 :     # Declare the return value.
1129 :     my $retVal = 0;
1130 :     # We need to set up an SQL command to do the deletion. First, we
1131 :     # find the name of the field's relation.
1132 :     my $table = $self->GetFieldTable($entityName);
1133 :     my $field = $table->{$fieldName};
1134 :     my $relation = $field->{relation};
1135 :     # Make sure this is a secondary field.
1136 :     if ($relation eq $entityName) {
1137 :     Confess("Cannot delete values of $fieldName for $entityName.");
1138 :     } else {
1139 :     # Set up the SQL command to delete all values.
1140 : parrello 1.76 my $sql = "DELETE FROM $relation";
1141 :     # Build the filter.
1142 :     my @filters = ();
1143 :     my @parms = ();
1144 :     # Check for a filter by ID.
1145 :     if (defined $id) {
1146 :     push @filters, "id = ?";
1147 :     push @parms, $id;
1148 :     }
1149 :     # Check for a filter by value.
1150 : parrello 1.75 if (defined $fieldValue) {
1151 : parrello 1.76 push @filters, "$fieldName = ?";
1152 : parrello 1.75 push @parms, $fieldValue;
1153 :     }
1154 : parrello 1.76 # Append the filters to the command.
1155 :     if (@filters) {
1156 :     $sql .= " WHERE " . join(" AND ", @filters);
1157 :     }
1158 : parrello 1.75 # Execute the command.
1159 :     my $dbh = $self->{_dbh};
1160 :     $retVal = $dbh->SQL($sql, 0, @parms);
1161 :     }
1162 :     # Return the result.
1163 :     return $retVal;
1164 :     }
1165 :    
1166 : parrello 1.1 =head3 LoadTables
1167 :    
1168 : parrello 1.18 C<< my $stats = $erdb->LoadTables($directoryName, $rebuild); >>
1169 : parrello 1.1
1170 :     This method will load the database tables from a directory. The tables must already have been created
1171 :     in the database. (This can be done by calling L</CreateTables>.) The caller passes in a directory name;
1172 :     all of the relations to be loaded must have a file in the directory with the same name as the relation
1173 :     (optionally with a suffix of C<.dtx>). Each file must be a tab-delimited table of field values. Each
1174 :     line of the file will be loaded as a row of the target relation table. The field values should be in
1175 :     the same order as the fields in the relation tables generated by L</ShowMetaData>. The old data is
1176 :     erased before the new data is loaded in.
1177 :    
1178 :     A certain amount of translation automatically takes place. Ctrl-M characters are deleted, and
1179 :     tab and new-line characters inside a field are escaped as C<\t> and C<\n>, respectively. Dates must
1180 :     be entered as a Unix timestamp, that is, as an integer number of seconds since the base epoch.
1181 :    
1182 :     =over 4
1183 :    
1184 :     =item directoryName
1185 :    
1186 :     Name of the directory containing the relation files to be loaded.
1187 :    
1188 :     =item rebuild
1189 :    
1190 :     TRUE if the tables should be dropped and rebuilt, else FALSE. This is, unfortunately, the
1191 :     only way to erase existing data in the tables, since the TRUNCATE command is not supported
1192 :     by all of the DB engines we use.
1193 :    
1194 :     =item RETURN
1195 :    
1196 :     Returns a statistical object describing the number of records read and a list of the error messages.
1197 :    
1198 :     =back
1199 :    
1200 :     =cut
1201 :    
1202 :     sub LoadTables {
1203 : parrello 1.10 # Get the parameters.
1204 :     my ($self, $directoryName, $rebuild) = @_;
1205 :     # Start the timer.
1206 :     my $startTime = gettimeofday;
1207 :     # Clean any trailing slash from the directory name.
1208 :     $directoryName =~ s!/\\$!!;
1209 :     # Declare the return variable.
1210 :     my $retVal = Stats->new();
1211 : parrello 1.23 # Get the relation names.
1212 :     my @relNames = $self->GetTableNames();
1213 :     for my $relationName (@relNames) {
1214 :     # Try to load this relation.
1215 :     my $result = $self->_LoadRelation($directoryName, $relationName, $rebuild);
1216 : parrello 1.10 # Accumulate the statistics.
1217 :     $retVal->Accumulate($result);
1218 :     }
1219 :     # Add the duration of the load to the statistical object.
1220 :     $retVal->Add('duration', gettimeofday - $startTime);
1221 :     # Return the accumulated statistics.
1222 :     return $retVal;
1223 : parrello 1.1 }
1224 :    
1225 : parrello 1.23
1226 : parrello 1.1 =head3 GetTableNames
1227 :    
1228 : parrello 1.18 C<< my @names = $erdb->GetTableNames; >>
1229 : parrello 1.1
1230 :     Return a list of the relations required to implement this database.
1231 :    
1232 :     =cut
1233 :    
1234 :     sub GetTableNames {
1235 : parrello 1.10 # Get the parameters.
1236 :     my ($self) = @_;
1237 :     # Get the relation list from the metadata.
1238 :     my $relationTable = $self->{_metaData}->{RelationTable};
1239 :     # Return the relation names.
1240 :     return keys %{$relationTable};
1241 : parrello 1.1 }
1242 :    
1243 :     =head3 GetEntityTypes
1244 :    
1245 : parrello 1.18 C<< my @names = $erdb->GetEntityTypes; >>
1246 : parrello 1.1
1247 :     Return a list of the entity type names.
1248 :    
1249 :     =cut
1250 :    
1251 :     sub GetEntityTypes {
1252 : parrello 1.10 # Get the database object.
1253 :     my ($self) = @_;
1254 :     # Get the entity list from the metadata object.
1255 :     my $entityList = $self->{_metaData}->{Entities};
1256 :     # Return the list of entity names in alphabetical order.
1257 :     return sort keys %{$entityList};
1258 : parrello 1.1 }
1259 :    
1260 : parrello 1.73 =head3 GetDataTypes
1261 :    
1262 :     C<< my %types = ERDB::GetDataTypes(); >>
1263 :    
1264 :     Return a table of ERDB data types. The table returned is a hash of hashes.
1265 :     The keys of the big hash are the datatypes. Each smaller hash has several
1266 :     values used to manage the data. The most interesting is the SQL type (key
1267 :     C<sqlType>) and the descriptive node (key C<notes>).
1268 :    
1269 :     Note that changing the values in the smaller hashes will seriously break
1270 :     things, so this data should be treated as read-only.
1271 :    
1272 :     =cut
1273 :    
1274 :     sub GetDataTypes {
1275 :     return %TypeTable;
1276 :     }
1277 :    
1278 :    
1279 : parrello 1.20 =head3 IsEntity
1280 :    
1281 :     C<< my $flag = $erdb->IsEntity($entityName); >>
1282 :    
1283 :     Return TRUE if the parameter is an entity name, else FALSE.
1284 :    
1285 :     =over 4
1286 :    
1287 :     =item entityName
1288 :    
1289 :     Object name to be tested.
1290 :    
1291 :     =item RETURN
1292 :    
1293 :     Returns TRUE if the specified string is an entity name, else FALSE.
1294 :    
1295 :     =back
1296 :    
1297 :     =cut
1298 :    
1299 :     sub IsEntity {
1300 :     # Get the parameters.
1301 :     my ($self, $entityName) = @_;
1302 :     # Test to see if it's an entity.
1303 :     return exists $self->{_metaData}->{Entities}->{$entityName};
1304 :     }
1305 :    
1306 : parrello 1.1 =head3 Get
1307 :    
1308 : parrello 1.45 C<< my $query = $erdb->Get(\@objectNames, $filterClause, \@params); >>
1309 : parrello 1.1
1310 :     This method returns a query object for entities of a specified type using a specified filter.
1311 :     The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each
1312 :     field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the
1313 :     following call requests all B<Genome> objects for the genus specified in the variable
1314 :     $genus.
1315 :    
1316 : parrello 1.45 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>
1317 : parrello 1.1
1318 :     The WHERE clause contains a single question mark, so there is a single additional
1319 :     parameter representing the parameter value. It would also be possible to code
1320 :    
1321 : parrello 1.18 C<< $query = $erdb->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>
1322 : parrello 1.1
1323 :     however, this version of the call would generate a syntax error if there were any quote
1324 :     characters inside the variable C<$genus>.
1325 :    
1326 :     The use of the strange parenthesized notation for field names enables us to distinguish
1327 :     hyphens contained within field names from minus signs that participate in the computation
1328 :     of the WHERE clause. All of the methods that manipulate fields will use this same notation.
1329 :    
1330 :     It is possible to specify multiple entity and relationship names in order to retrieve more than
1331 :     one object's data at the same time, which allows highly complex joined queries. For example,
1332 :    
1333 : parrello 1.45 C<< $query = $erdb->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>
1334 : parrello 1.1
1335 :     If multiple names are specified, then the query processor will automatically determine a
1336 :     join path between the entities and relationships. The algorithm used is very simplistic.
1337 : parrello 1.39 In particular, if a relationship is recursive, the path is determined by the order in which
1338 :     the entity and the relationship appear. For example, consider a recursive relationship
1339 :     B<IsParentOf> which relates B<People> objects to other B<People> objects. If the join path is
1340 : parrello 1.1 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,
1341 :     the join path is C<['IsParentOf', 'People']>, then the people returned will be children.
1342 :    
1343 : parrello 1.39 If an entity or relationship is mentioned twice, the name for the second occurrence will
1344 :     be suffixed with C<2>, the third occurrence will be suffixed with C<3>, and so forth. So,
1345 :     for example, if we have C<['Feature', 'HasContig', 'Contig', 'HasContig']>, then the
1346 :     B<to-link> field of the first B<HasContig> is specified as C<HasContig(to-link)>, while
1347 :     the B<to-link> field of the second B<HasContig> is specified as C<HasContig2(to-link)>.
1348 :    
1349 : parrello 1.1 =over 4
1350 :    
1351 :     =item objectNames
1352 :    
1353 :     List containing the names of the entity and relationship objects to be retrieved.
1354 :    
1355 :     =item filterClause
1356 :    
1357 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1358 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1359 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1360 :     in the filter clause should be added to the parameter list as additional parameters. The
1361 :     fields in a filter clause can come from primary entity relations, relationship relations,
1362 :     or secondary entity relations; however, all of the entities and relationships involved must
1363 :     be included in the list of object names.
1364 :    
1365 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
1366 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
1367 :     particular genus and sorts them by species name.
1368 :    
1369 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
1370 :    
1371 : parrello 1.30 Note that the case is important. Only an uppercase "ORDER BY" with a single space will
1372 :     be processed. The idea is to make it less likely to find the verb by accident.
1373 :    
1374 : parrello 1.1 The rules for field references in a sort order are the same as those for field references in the
1375 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
1376 :     relation.
1377 :    
1378 : parrello 1.39 Finally, you can limit the number of rows returned by adding a LIMIT clause. The LIMIT must
1379 :     be the last thing in the filter clause, and it contains only the word "LIMIT" followed by
1380 :     a positive number. So, for example
1381 :    
1382 :     C<< "Genome(genus) = ? ORDER BY Genome(species) LIMIT 10" >>
1383 :    
1384 :     will only return the first ten genomes for the specified genus. The ORDER BY clause is not
1385 :     required. For example, to just get the first 10 genomes in the B<Genome> table, you could
1386 :     use
1387 :    
1388 :     C<< "LIMIT 10" >>
1389 :    
1390 : parrello 1.45 =item params
1391 : parrello 1.1
1392 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
1393 : parrello 1.1
1394 :     =item RETURN
1395 :    
1396 :     Returns a B<DBQuery> that can be used to iterate through all of the results.
1397 :    
1398 :     =back
1399 :    
1400 :     =cut
1401 :    
1402 :     sub Get {
1403 : parrello 1.10 # Get the parameters.
1404 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
1405 :     # Process the SQL stuff.
1406 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1407 :     $self->_SetupSQL($objectNames, $filterClause);
1408 :     # Create the query.
1409 :     my $command = "SELECT DISTINCT " . join(".*, ", @{$mappedNameListRef}) .
1410 :     ".* $suffix";
1411 :     my $sth = $self->_GetStatementHandle($command, $params);
1412 : parrello 1.39 # Now we create the relation map, which enables DBQuery to determine the order, name
1413 :     # and mapped name for each object in the query.
1414 :     my @relationMap = ();
1415 : parrello 1.45 for my $mappedName (@{$mappedNameListRef}) {
1416 :     push @relationMap, [$mappedName, $mappedNameHashRef->{$mappedName}];
1417 : parrello 1.39 }
1418 : parrello 1.10 # Return the statement object.
1419 : parrello 1.39 my $retVal = DBQuery::_new($self, $sth, \@relationMap);
1420 : parrello 1.10 return $retVal;
1421 : parrello 1.1 }
1422 :    
1423 : parrello 1.78
1424 :    
1425 : parrello 1.70 =head3 Search
1426 :    
1427 :     C<< my $query = $erdb->Search($searchExpression, $idx, \@objectNames, $filterClause, \@params); >>
1428 :    
1429 :     Perform a full text search with filtering. The search will be against a specified object
1430 :     in the object name list. That object will get an extra field containing the search
1431 :     relevance. Note that except for the search expression, the parameters of this method are
1432 :     the same as those for L</Get> and follow the same rules.
1433 :    
1434 :     =over 4
1435 :    
1436 :     =item searchExpression
1437 :    
1438 : parrello 1.75 Boolean search expression for the text fields of the target object. The default mode for
1439 :     a Boolean search expression is OR, but we want the default to be AND, so we will
1440 :     add a C<+> operator to each word with no other operator before it.
1441 : parrello 1.70
1442 :     =item idx
1443 :    
1444 :     Index in the I<$objectNames> list of the table to be searched in full-text mode.
1445 :    
1446 :     =item objectNames
1447 :    
1448 :     List containing the names of the entity and relationship objects to be retrieved.
1449 :    
1450 :     =item filterClause
1451 :    
1452 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1453 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
1454 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
1455 :     in the filter clause should be added to the parameter list as additional parameters. The
1456 :     fields in a filter clause can come from primary entity relations, relationship relations,
1457 :     or secondary entity relations; however, all of the entities and relationships involved must
1458 :     be included in the list of object names.
1459 :    
1460 :     =item params
1461 :    
1462 :     Reference to a list of parameter values to be substituted into the filter clause.
1463 :    
1464 :     =item RETURN
1465 :    
1466 :     Returns a query object for the specified search.
1467 :    
1468 :     =back
1469 :    
1470 :     =cut
1471 :    
1472 :     sub Search {
1473 :     # Get the parameters.
1474 :     my ($self, $searchExpression, $idx, $objectNames, $filterClause, $params) = @_;
1475 :     # Declare the return variable.
1476 :     my $retVal;
1477 : parrello 1.72 # Create a safety copy of the parameter list. Note we have to be careful to insure
1478 :     # a parameter list exists before we copy it.
1479 :     my @myParams = ();
1480 :     if (defined $params) {
1481 :     @myParams = @{$params};
1482 :     }
1483 : parrello 1.70 # Get the first object's structure so we have access to the searchable fields.
1484 :     my $object1Name = $objectNames->[$idx];
1485 :     my $object1Structure = $self->_GetStructure($object1Name);
1486 :     # Get the field list.
1487 :     if (! exists $object1Structure->{searchFields}) {
1488 :     Confess("No searchable index for $object1Name.");
1489 :     } else {
1490 :     # Get the field list.
1491 :     my @fields = @{$object1Structure->{searchFields}};
1492 : parrello 1.71 # Clean the search expression.
1493 :     my $actualKeywords = $self->CleanKeywords($searchExpression);
1494 : parrello 1.75 # Prefix a "+" to each uncontrolled word. This converts the default
1495 :     # search mode from OR to AND.
1496 : parrello 1.80 $actualKeywords =~ s/(^|\s)(\w|")/$1\+$2/g;
1497 : parrello 1.72 Trace("Actual keywords for search are\n$actualKeywords") if T(3);
1498 : parrello 1.70 # We need two match expressions, one for the filter clause and one in the
1499 :     # query itself. Both will use a parameter mark, so we need to push the
1500 :     # search expression onto the front of the parameter list twice.
1501 : parrello 1.71 unshift @myParams, $actualKeywords, $actualKeywords;
1502 : parrello 1.70 # Build the match expression.
1503 :     my @matchFilterFields = map { "$object1Name." . _FixName($_) } @fields;
1504 :     my $matchClause = "MATCH (" . join(", ", @matchFilterFields) . ") AGAINST (? IN BOOLEAN MODE)";
1505 :     # Process the SQL stuff.
1506 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) =
1507 :     $self->_SetupSQL($objectNames, $filterClause, $matchClause);
1508 :     # Create the query. Note that the match clause is inserted at the front of
1509 :     # the select fields.
1510 :     my $command = "SELECT DISTINCT $matchClause, " . join(".*, ", @{$mappedNameListRef}) .
1511 :     ".* $suffix";
1512 :     my $sth = $self->_GetStatementHandle($command, \@myParams);
1513 :     # Now we create the relation map, which enables DBQuery to determine the order, name
1514 :     # and mapped name for each object in the query.
1515 :     my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef);
1516 :     # Return the statement object.
1517 :     $retVal = DBQuery::_new($self, $sth, \@relationMap, $object1Name);
1518 :     }
1519 :     return $retVal;
1520 :     }
1521 :    
1522 : parrello 1.45 =head3 GetFlat
1523 :    
1524 :     C<< my @list = $erdb->GetFlat(\@objectNames, $filterClause, \@parameterList, $field); >>
1525 :    
1526 :     This is a variation of L</GetAll> that asks for only a single field per record and
1527 :     returns a single flattened list.
1528 :    
1529 :     =over 4
1530 :    
1531 :     =item objectNames
1532 :    
1533 :     List containing the names of the entity and relationship objects to be retrieved.
1534 :    
1535 :     =item filterClause
1536 :    
1537 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
1538 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
1539 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
1540 :     parameter list as additional parameters. The fields in a filter clause can come from primary
1541 :     entity relations, relationship relations, or secondary entity relations; however, all of the
1542 :     entities and relationships involved must be included in the list of object names.
1543 :    
1544 :     =item parameterList
1545 :    
1546 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
1547 :    
1548 :     =item field
1549 :    
1550 :     Name of the field to be used to get the elements of the list returned.
1551 :    
1552 :     =item RETURN
1553 :    
1554 :     Returns a list of values.
1555 :    
1556 :     =back
1557 :    
1558 :     =cut
1559 :     #: Return Type @;
1560 :     sub GetFlat {
1561 :     # Get the parameters.
1562 :     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
1563 :     # Construct the query.
1564 :     my $query = $self->Get($objectNames, $filterClause, $parameterList);
1565 :     # Create the result list.
1566 :     my @retVal = ();
1567 :     # Loop through the records, adding the field values found to the result list.
1568 :     while (my $row = $query->Fetch()) {
1569 :     push @retVal, $row->Value($field);
1570 :     }
1571 :     # Return the list created.
1572 :     return @retVal;
1573 :     }
1574 :    
1575 : parrello 1.73 =head3 SpecialFields
1576 :    
1577 :     C<< my %specials = $erdb->SpecialFields($entityName); >>
1578 :    
1579 :     Return a hash mapping special fields in the specified entity to the value of their
1580 :     C<special> attribute. This enables the subclass to get access to the special field
1581 :     attributes without needed to plumb the internal ERDB data structures.
1582 :    
1583 :     =over 4
1584 :    
1585 :     =item entityName
1586 :    
1587 :     Name of the entity whose special fields are desired.
1588 :    
1589 :     =item RETURN
1590 :    
1591 :     Returns a hash. The keys of the hash are the special field names, and the values
1592 :     are the values from each special field's C<special> attribute.
1593 :    
1594 :     =back
1595 :    
1596 :     =cut
1597 :    
1598 :     sub SpecialFields {
1599 :     # Get the parameters.
1600 :     my ($self, $entityName) = @_;
1601 :     # Declare the return variable.
1602 :     my %retVal = ();
1603 :     # Find the entity's data structure.
1604 : parrello 1.75 my $entityData = $self->{_metaData}->{Entities}->{$entityName};
1605 : parrello 1.73 # Loop through its fields, adding each special field to the return hash.
1606 :     my $fieldHash = $entityData->{Fields};
1607 :     for my $fieldName (keys %{$fieldHash}) {
1608 :     my $fieldData = $fieldHash->{$fieldName};
1609 :     if (exists $fieldData->{special}) {
1610 :     $retVal{$fieldName} = $fieldData->{special};
1611 :     }
1612 :     }
1613 :     # Return the result.
1614 :     return %retVal;
1615 :     }
1616 :    
1617 : parrello 1.32 =head3 Delete
1618 :    
1619 : parrello 1.78 C<< my $stats = $erdb->Delete($entityName, $objectID, %options); >>
1620 : parrello 1.32
1621 :     Delete an entity instance from the database. The instance is deleted along with all entity and
1622 : parrello 1.77 relationship instances dependent on it. The definition of I<dependence> is recursive.
1623 :    
1624 :     An object is always dependent on itself. An object is dependent if it is a 1-to-many or many-to-many
1625 :     relationship connected to a dependent entity or if it is the "to" entity connected to a 1-to-many
1626 : parrello 1.32 dependent relationship.
1627 :    
1628 :     =over 4
1629 :    
1630 :     =item entityName
1631 :    
1632 :     Name of the entity type for the instance being deleted.
1633 :    
1634 :     =item objectID
1635 :    
1636 :     ID of the entity instance to be deleted. If the ID contains a wild card character (C<%>),
1637 :     then it is presumed to by a LIKE pattern.
1638 :    
1639 : parrello 1.78 =item options
1640 : parrello 1.32
1641 : parrello 1.78 A hash detailing the options for this delete operation.
1642 : parrello 1.32
1643 :     =item RETURN
1644 :    
1645 :     Returns a statistics object indicating how many records of each particular table were
1646 :     deleted.
1647 :    
1648 :     =back
1649 :    
1650 : parrello 1.78 The permissible options for this method are as follows.
1651 :    
1652 :     =over 4
1653 :    
1654 :     =item testMode
1655 :    
1656 :     If TRUE, then the delete statements will be traced, but no changes will be made to the database.
1657 :    
1658 :     =item keepRoot
1659 :    
1660 :     If TRUE, then the entity instances will not be deleted, only the dependent records.
1661 :    
1662 :     =back
1663 :    
1664 : parrello 1.32 =cut
1665 :     #: Return Type $%;
1666 :     sub Delete {
1667 :     # Get the parameters.
1668 : parrello 1.78 my ($self, $entityName, $objectID, %options) = @_;
1669 : parrello 1.32 # Declare the return variable.
1670 :     my $retVal = Stats->new();
1671 :     # Get the DBKernel object.
1672 :     my $db = $self->{_dbh};
1673 :     # We're going to generate all the paths branching out from the starting entity. One of
1674 :     # the things we have to be careful about is preventing loops. We'll use a hash to
1675 :     # determine if we've hit a loop.
1676 :     my %alreadyFound = ();
1677 : parrello 1.33 # These next lists will serve as our result stack. We start by pushing object lists onto
1678 : parrello 1.32 # the stack, and then popping them off to do the deletes. This means the deletes will
1679 :     # start with the longer paths before getting to the shorter ones. That, in turn, makes
1680 :     # sure we don't delete records that might be needed to forge relationships back to the
1681 : parrello 1.33 # original item. We have two lists-- one for TO-relationships, and one for
1682 :     # FROM-relationships and entities.
1683 :     my @fromPathList = ();
1684 :     my @toPathList = ();
1685 : parrello 1.78 # This final list is used to remember what work still needs to be done. We push paths
1686 : parrello 1.32 # onto the list, then pop them off to extend the paths. We prime it with the starting
1687 :     # point. Note that we will work hard to insure that the last item on a path in the
1688 : parrello 1.75 # to-do list is always an entity.
1689 : parrello 1.32 my @todoList = ([$entityName]);
1690 :     while (@todoList) {
1691 :     # Get the current path.
1692 :     my $current = pop @todoList;
1693 :     # Copy it into a list.
1694 :     my @stackedPath = @{$current};
1695 :     # Pull off the last item on the path. It will always be an entity.
1696 : parrello 1.78 my $myEntityName = pop @stackedPath;
1697 : parrello 1.32 # Add it to the alreadyFound list.
1698 : parrello 1.78 $alreadyFound{$myEntityName} = 1;
1699 :     # Figure out if we need to delete this entity.
1700 :     if ($myEntityName ne $entityName || ! $options{keepRoot}) {
1701 :     # Get the entity data.
1702 :     my $entityData = $self->_GetStructure($myEntityName);
1703 :     # Loop through the entity's relations. A DELETE command will be needed for each of them.
1704 :     my $relations = $entityData->{Relations};
1705 :     for my $relation (keys %{$relations}) {
1706 :     my @augmentedList = (@stackedPath, $relation);
1707 :     push @fromPathList, \@augmentedList;
1708 :     }
1709 : parrello 1.32 }
1710 :     # Now we need to look for relationships connected to this entity.
1711 :     my $relationshipList = $self->{_metaData}->{Relationships};
1712 :     for my $relationshipName (keys %{$relationshipList}) {
1713 :     my $relationship = $relationshipList->{$relationshipName};
1714 :     # Check the FROM field. We're only interested if it's us.
1715 : parrello 1.78 if ($relationship->{from} eq $myEntityName) {
1716 : parrello 1.32 # Add the path to this relationship.
1717 : parrello 1.78 my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1718 : parrello 1.33 push @fromPathList, \@augmentedList;
1719 : parrello 1.32 # Check the arity. If it's MM we're done. If it's 1M
1720 :     # and the target hasn't been seen yet, we want to
1721 :     # stack the entity for future processing.
1722 :     if ($relationship->{arity} eq '1M') {
1723 :     my $toEntity = $relationship->{to};
1724 :     if (! exists $alreadyFound{$toEntity}) {
1725 :     # Here we have a new entity that's dependent on
1726 :     # the current entity, so we need to stack it.
1727 :     my @stackList = (@augmentedList, $toEntity);
1728 : parrello 1.33 push @fromPathList, \@stackList;
1729 : parrello 1.34 } else {
1730 :     Trace("$toEntity ignored because it occurred previously.") if T(4);
1731 : parrello 1.32 }
1732 :     }
1733 :     }
1734 :     # Now check the TO field. In this case only the relationship needs
1735 : parrello 1.33 # deletion.
1736 : parrello 1.78 if ($relationship->{to} eq $myEntityName) {
1737 :     my @augmentedList = (@stackedPath, $myEntityName, $relationshipName);
1738 : parrello 1.33 push @toPathList, \@augmentedList;
1739 : parrello 1.32 }
1740 :     }
1741 :     }
1742 :     # Create the first qualifier for the WHERE clause. This selects the
1743 :     # keys of the primary entity records to be deleted. When we're deleting
1744 : parrello 1.78 # from a dependent table, we construct a join path from the first qualifier
1745 : parrello 1.32 # to the table containing the dependent records to delete.
1746 :     my $qualifier = ($objectID =~ /%/ ? "LIKE ?" : "= ?");
1747 : parrello 1.33 # We need to make two passes. The first is through the to-list, and
1748 :     # the second through the from-list. The from-list is second because
1749 :     # the to-list may need to pass through some of the entities the
1750 :     # from-list would delete.
1751 :     my %stackList = ( from_link => \@fromPathList, to_link => \@toPathList );
1752 :     # Now it's time to do the deletes. We do it in two passes.
1753 :     for my $keyName ('to_link', 'from_link') {
1754 :     # Get the list for this key.
1755 :     my @pathList = @{$stackList{$keyName}};
1756 : parrello 1.34 Trace(scalar(@pathList) . " entries in path list for $keyName.") if T(3);
1757 : parrello 1.33 # Loop through this list.
1758 :     while (my $path = pop @pathList) {
1759 :     # Get the table whose rows are to be deleted.
1760 :     my @pathTables = @{$path};
1761 : parrello 1.37 # Start the DELETE statement. We need to call DBKernel because the
1762 :     # syntax of a DELETE-USING varies among DBMSs.
1763 : parrello 1.33 my $target = $pathTables[$#pathTables];
1764 : parrello 1.37 my $stmt = $db->SetUsing(@pathTables);
1765 : parrello 1.33 # Now start the WHERE. The first thing is the ID field from the starting table. That
1766 :     # starting table will either be the entity relation or one of the entity's
1767 :     # sub-relations.
1768 :     $stmt .= " WHERE $pathTables[0].id $qualifier";
1769 :     # Now we run through the remaining entities in the path, connecting them up.
1770 :     for (my $i = 1; $i <= $#pathTables; $i += 2) {
1771 :     # Connect the current relationship to the preceding entity.
1772 :     my ($entity, $rel) = @pathTables[$i-1,$i];
1773 :     # The style of connection depends on the direction of the relationship.
1774 : parrello 1.35 $stmt .= " AND $entity.id = $rel.$keyName";
1775 : parrello 1.32 if ($i + 1 <= $#pathTables) {
1776 :     # Here there's a next entity, so connect that to the relationship's
1777 :     # to-link.
1778 :     my $entity2 = $pathTables[$i+1];
1779 : parrello 1.35 $stmt .= " AND $rel.to_link = $entity2.id";
1780 : parrello 1.32 }
1781 :     }
1782 : parrello 1.33 # Now we have our desired DELETE statement.
1783 : parrello 1.78 if ($options{testMode}) {
1784 : parrello 1.33 # Here the user wants to trace without executing.
1785 :     Trace($stmt) if T(0);
1786 :     } else {
1787 : parrello 1.77 # Here we can delete. Note that the SQL method dies with a confession
1788 : parrello 1.33 # if an error occurs, so we just go ahead and do it.
1789 : parrello 1.36 Trace("Executing delete from $target using '$objectID'.") if T(3);
1790 :     my $rv = $db->SQL($stmt, 0, $objectID);
1791 : parrello 1.33 # Accumulate the statistics for this delete. The only rows deleted
1792 :     # are from the target table, so we use its name to record the
1793 :     # statistic.
1794 :     $retVal->Add($target, $rv);
1795 :     }
1796 : parrello 1.32 }
1797 :     }
1798 :     # Return the result.
1799 :     return $retVal;
1800 :     }
1801 :    
1802 : parrello 1.78 =head3 Disconnect
1803 :    
1804 :     C<< $erdb->Disconnect($relationshipName, $originEntityName, $originEntityID); >>
1805 :    
1806 :     Disconnect an entity instance from all the objects to which it is related. This
1807 :     will delete each relationship instance that connects to the specified entity.
1808 :    
1809 :     =over 4
1810 :    
1811 :     =item relationshipName
1812 :    
1813 :     Name of the relationship whose instances are to be deleted.
1814 :    
1815 :     =item originEntityName
1816 :    
1817 :     Name of the entity that is to be disconnected.
1818 :    
1819 :     =item originEntityID
1820 :    
1821 :     ID of the entity that is to be disconnected.
1822 :    
1823 :     =back
1824 :    
1825 :     =cut
1826 :    
1827 :     sub Disconnect {
1828 :     # Get the parameters.
1829 :     my ($self, $relationshipName, $originEntityName, $originEntityID) = @_;
1830 :     # Get the relationship descriptor.
1831 :     my $structure = $self->_GetStructure($relationshipName);
1832 :     # Insure we have a relationship.
1833 :     if (! exists $structure->{from}) {
1834 :     Confess("$relationshipName is not a relationship in the database.");
1835 :     } else {
1836 :     # Get the database handle.
1837 :     my $dbh = $self->{_dbh};
1838 :     # We'll set this value to 1 if we find our entity.
1839 :     my $found = 0;
1840 :     # Loop through the ends of the relationship.
1841 :     for my $dir ('from', 'to') {
1842 :     if ($structure->{$dir} eq $originEntityName) {
1843 :     # Delete all relationship instances on this side of the entity instance.
1844 :     $dbh->SQL("DELETE FROM $relationshipName WHERE ${dir}_link = ?", 0, $originEntityID);
1845 :     $found = 1;
1846 :     }
1847 :     }
1848 :     # Insure we found the entity on at least one end.
1849 :     if (! $found) {
1850 :     Confess("Entity \"$originEntityName\" does not use $relationshipName.");
1851 :     }
1852 :     }
1853 :     }
1854 :    
1855 : parrello 1.79 =head3 DeleteRow
1856 :    
1857 :     C<< $erdb->DeleteRow($relationshipName, $fromLink, $toLink, \%values); >>
1858 :    
1859 :     Delete a row from a relationship. In most cases, only the from-link and to-link are
1860 :     needed; however, for relationships with intersection data values can be specified
1861 :     for the other fields using a hash.
1862 :    
1863 :     =over 4
1864 :    
1865 :     =item relationshipName
1866 :    
1867 :     Name of the relationship from which the row is to be deleted.
1868 :    
1869 :     =item fromLink
1870 :    
1871 :     ID of the entity instance in the From direction.
1872 :    
1873 :     =item toLink
1874 :    
1875 :     ID of the entity instance in the To direction.
1876 :    
1877 :     =item values
1878 :    
1879 :     Reference to a hash of other values to be used for filtering the delete.
1880 :    
1881 :     =back
1882 :    
1883 :     =cut
1884 :    
1885 :     sub DeleteRow {
1886 :     # Get the parameters.
1887 :     my ($self, $relationshipName, $fromLink, $toLink, $values) = @_;
1888 :     # Create a hash of all the filter information.
1889 :     my %filter = ('from-link' => $fromLink, 'to-link' => $toLink);
1890 :     if (defined $values) {
1891 :     for my $key (keys %{$values}) {
1892 :     $filter{$key} = $values->{$key};
1893 :     }
1894 :     }
1895 :     # Build an SQL statement out of the hash.
1896 :     my @filters = ();
1897 :     my @parms = ();
1898 :     for my $key (keys %filter) {
1899 :     push @filters, _FixName($key) . " = ?";
1900 :     push @parms, $filter{$key};
1901 :     }
1902 :     Trace("Parms for delete row are " . join(", ", map { "\"$_\"" } @parms) . ".") if T(SQL => 4);
1903 :     my $command = "DELETE FROM $relationshipName WHERE " .
1904 :     join(" AND ", @filters);
1905 :     # Execute it.
1906 :     my $dbh = $self->{_dbh};
1907 :     $dbh->SQL($command, undef, @parms);
1908 :     }
1909 :    
1910 : parrello 1.70 =head3 SortNeeded
1911 :    
1912 :     C<< my $parms = $erdb->SortNeeded($relationName); >>
1913 :    
1914 :     Return the pipe command for the sort that should be applied to the specified
1915 :     relation when creating the load file.
1916 :    
1917 :     For example, if the load file should be sorted ascending by the first
1918 :     field, this method would return
1919 :    
1920 :     sort -k1 -t"\t"
1921 :    
1922 :     If the first field is numeric, the method would return
1923 :    
1924 :     sort -k1n -t"\t"
1925 :    
1926 :     Unfortunately, due to a bug in the C<sort> command, we cannot eliminate duplicate
1927 :     keys using a sort.
1928 :    
1929 :     =over 4
1930 :    
1931 :     =item relationName
1932 :    
1933 :     Name of the relation to be examined.
1934 :    
1935 :     =item
1936 :    
1937 :     Returns the sort command to use for sorting the relation, suitable for piping.
1938 :    
1939 :     =back
1940 :    
1941 :     =cut
1942 :     #: Return Type $;
1943 :     sub SortNeeded {
1944 :     # Get the parameters.
1945 :     my ($self, $relationName) = @_;
1946 :     # Declare a descriptor to hold the names of the key fields.
1947 :     my @keyNames = ();
1948 :     # Get the relation structure.
1949 :     my $relationData = $self->_FindRelation($relationName);
1950 :     # Find out if the relation is a primary entity relation,
1951 :     # a relationship relation, or a secondary entity relation.
1952 :     my $entityTable = $self->{_metaData}->{Entities};
1953 :     my $relationshipTable = $self->{_metaData}->{Relationships};
1954 :     if (exists $entityTable->{$relationName}) {
1955 :     # Here we have a primary entity relation.
1956 :     push @keyNames, "id";
1957 :     } elsif (exists $relationshipTable->{$relationName}) {
1958 :     # Here we have a relationship. We sort using the FROM index.
1959 :     my $relationshipData = $relationshipTable->{$relationName};
1960 : parrello 1.75 my $index = $relationData->{Indexes}->{idxFrom};
1961 : parrello 1.70 push @keyNames, @{$index->{IndexFields}};
1962 :     } else {
1963 :     # Here we have a secondary entity relation, so we have a sort on the ID field.
1964 :     push @keyNames, "id";
1965 :     }
1966 :     # Now we parse the key names into sort parameters. First, we prime the return
1967 :     # string.
1968 :     my $retVal = "sort -t\"\t\" ";
1969 :     # Get the relation's field list.
1970 :     my @fields = @{$relationData->{Fields}};
1971 :     # Loop through the keys.
1972 :     for my $keyData (@keyNames) {
1973 :     # Get the key and the ordering.
1974 :     my ($keyName, $ordering);
1975 :     if ($keyData =~ /^([^ ]+) DESC/) {
1976 :     ($keyName, $ordering) = ($1, "descending");
1977 :     } else {
1978 :     ($keyName, $ordering) = ($keyData, "ascending");
1979 :     }
1980 :     # Find the key's position and type.
1981 :     my $fieldSpec;
1982 :     for (my $i = 0; $i <= $#fields && ! $fieldSpec; $i++) {
1983 :     my $thisField = $fields[$i];
1984 :     if ($thisField->{name} eq $keyName) {
1985 :     # Get the sort modifier for this field type. The modifier
1986 :     # decides whether we're using a character, numeric, or
1987 :     # floating-point sort.
1988 :     my $modifier = $TypeTable{$thisField->{type}}->{sort};
1989 :     # If the index is descending for this field, denote we want
1990 :     # to reverse the sort order on this field.
1991 :     if ($ordering eq 'descending') {
1992 :     $modifier .= "r";
1993 :     }
1994 :     # Store the position and modifier into the field spec, which
1995 :     # will stop the inner loop. Note that the field number is
1996 :     # 1-based in the sort command, so we have to increment the
1997 :     # index.
1998 :     $fieldSpec = ($i + 1) . $modifier;
1999 :     }
2000 :     }
2001 :     # Add this field to the sort command.
2002 :     $retVal .= " -k$fieldSpec";
2003 :     }
2004 :     # Return the result.
2005 :     return $retVal;
2006 :     }
2007 :    
2008 : parrello 1.6 =head3 GetList
2009 :    
2010 : parrello 1.45 C<< my @dbObjects = $erdb->GetList(\@objectNames, $filterClause, \@params); >>
2011 : parrello 1.6
2012 :     Return a list of object descriptors for the specified objects as determined by the
2013 :     specified filter clause.
2014 :    
2015 :     This method is essentially the same as L</Get> except it returns a list of objects rather
2016 : parrello 1.7 than a query object that can be used to get the results one record at a time.
2017 : parrello 1.6
2018 :     =over 4
2019 :    
2020 :     =item objectNames
2021 :    
2022 :     List containing the names of the entity and relationship objects to be retrieved.
2023 :    
2024 :     =item filterClause
2025 :    
2026 :     WHERE clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2027 :     be parameterized with parameter markers (C<?>). Each field used in the WHERE clause must be
2028 :     specified in the standard form B<I<objectName>(I<fieldName>)>. Any parameters specified
2029 :     in the filter clause should be added to the parameter list as additional parameters. The
2030 :     fields in a filter clause can come from primary entity relations, relationship relations,
2031 :     or secondary entity relations; however, all of the entities and relationships involved must
2032 :     be included in the list of object names.
2033 :    
2034 :     The filter clause can also specify a sort order. To do this, simply follow the filter string
2035 :     with an ORDER BY clause. For example, the following filter string gets all genomes for a
2036 :     particular genus and sorts them by species name.
2037 :    
2038 :     C<< "Genome(genus) = ? ORDER BY Genome(species)" >>
2039 :    
2040 :     The rules for field references in a sort order are the same as those for field references in the
2041 :     filter clause in general; however, odd things may happen if a sort field is from a secondary
2042 :     relation.
2043 :    
2044 : parrello 1.45 =item params
2045 : parrello 1.6
2046 : parrello 1.45 Reference to a list of parameter values to be substituted into the filter clause.
2047 : parrello 1.6
2048 :     =item RETURN
2049 :    
2050 :     Returns a list of B<DBObject>s that satisfy the query conditions.
2051 :    
2052 :     =back
2053 :    
2054 :     =cut
2055 :     #: Return Type @%
2056 :     sub GetList {
2057 :     # Get the parameters.
2058 : parrello 1.45 my ($self, $objectNames, $filterClause, $params) = @_;
2059 : parrello 1.10 # Declare the return variable.
2060 :     my @retVal = ();
2061 :     # Perform the query.
2062 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, $params);
2063 : parrello 1.10 # Loop through the results.
2064 :     while (my $object = $query->Fetch) {
2065 :     push @retVal, $object;
2066 :     }
2067 : parrello 1.6 # Return the result.
2068 :     return @retVal;
2069 :     }
2070 :    
2071 : parrello 1.45 =head3 GetCount
2072 :    
2073 :     C<< my $count = $erdb->GetCount(\@objectNames, $filter, \@params); >>
2074 :    
2075 :     Return the number of rows found by a specified query. This method would
2076 :     normally be used to count the records in a single table. For example, in a
2077 :     genetics database
2078 :    
2079 :     my $count = $erdb->GetCount(['Genome'], 'Genome(genus-species) LIKE ?', ['homo %']);
2080 :    
2081 :     would return the number of genomes for the genus I<homo>. It is conceivable, however,
2082 :     to use it to return records based on a join. For example,
2083 :    
2084 : parrello 1.47 my $count = $erdb->GetCount(['HasFeature', 'Genome'], 'Genome(genus-species) LIKE ?',
2085 : parrello 1.45 ['homo %']);
2086 :    
2087 :     would return the number of features for genomes in the genus I<homo>. Note that
2088 :     only the rows from the first table are counted. If the above command were
2089 :    
2090 :     my $count = $erdb->GetCount(['Genome', 'Feature'], 'Genome(genus-species) LIKE ?',
2091 :     ['homo %']);
2092 :    
2093 :     it would return the number of genomes, not the number of genome/feature pairs.
2094 :    
2095 :     =over 4
2096 :    
2097 :     =item objectNames
2098 :    
2099 :     Reference to a list of the objects (entities and relationships) included in the
2100 :     query.
2101 :    
2102 :     =item filter
2103 :    
2104 :     A filter clause for restricting the query. The rules are the same as for the L</Get>
2105 :     method.
2106 :    
2107 :     =item params
2108 :    
2109 :     Reference to a list of the parameter values to be substituted for the parameter marks
2110 :     in the filter.
2111 :    
2112 :     =item RETURN
2113 :    
2114 :     Returns a count of the number of records in the first table that would satisfy
2115 :     the query.
2116 :    
2117 :     =back
2118 :    
2119 :     =cut
2120 :    
2121 :     sub GetCount {
2122 :     # Get the parameters.
2123 :     my ($self, $objectNames, $filter, $params) = @_;
2124 : parrello 1.66 # Insure the params argument is an array reference if the caller left it off.
2125 :     if (! defined($params)) {
2126 :     $params = [];
2127 :     }
2128 : parrello 1.45 # Declare the return variable.
2129 :     my $retVal;
2130 : parrello 1.47 # Find out if we're counting an entity or a relationship.
2131 :     my $countedField;
2132 :     if ($self->IsEntity($objectNames->[0])) {
2133 :     $countedField = "id";
2134 :     } else {
2135 :     # For a relationship we count the to-link because it's usually more
2136 :     # numerous. Note we're automatically converting to the SQL form
2137 :     # of the field name (to_link vs. to-link).
2138 :     $countedField = "to_link";
2139 :     }
2140 : parrello 1.45 # Create the SQL command suffix to get the desired records.
2141 :     my ($suffix, $mappedNameListRef, $mappedNameHashRef) = $self->_SetupSQL($objectNames,
2142 :     $filter);
2143 :     # Prefix it with text telling it we want a record count.
2144 :     my $firstObject = $mappedNameListRef->[0];
2145 : parrello 1.47 my $command = "SELECT COUNT($firstObject.$countedField) $suffix";
2146 : parrello 1.45 # Prepare and execute the command.
2147 :     my $sth = $self->_GetStatementHandle($command, $params);
2148 :     # Get the count value.
2149 :     ($retVal) = $sth->fetchrow_array();
2150 :     # Check for a problem.
2151 :     if (! defined($retVal)) {
2152 :     if ($sth->err) {
2153 :     # Here we had an SQL error.
2154 :     Confess("Error retrieving row count: " . $sth->errstr());
2155 :     } else {
2156 :     # Here we have no result.
2157 :     Confess("No result attempting to retrieve row count.");
2158 :     }
2159 :     }
2160 :     # Return the result.
2161 :     return $retVal;
2162 :     }
2163 :    
2164 : parrello 1.1 =head3 ComputeObjectSentence
2165 :    
2166 : parrello 1.18 C<< my $sentence = $erdb->ComputeObjectSentence($objectName); >>
2167 : parrello 1.1
2168 :     Check an object name, and if it is a relationship convert it to a relationship sentence.
2169 :    
2170 :     =over 4
2171 :    
2172 :     =item objectName
2173 :    
2174 :     Name of the entity or relationship.
2175 :    
2176 :     =item RETURN
2177 :    
2178 :     Returns a string containing the entity name or a relationship sentence.
2179 :    
2180 :     =back
2181 :    
2182 :     =cut
2183 :    
2184 :     sub ComputeObjectSentence {
2185 : parrello 1.10 # Get the parameters.
2186 :     my ($self, $objectName) = @_;
2187 :     # Set the default return value.
2188 :     my $retVal = $objectName;
2189 :     # Look for the object as a relationship.
2190 :     my $relTable = $self->{_metaData}->{Relationships};
2191 :     if (exists $relTable->{$objectName}) {
2192 :     # Get the relationship sentence.
2193 :     $retVal = _ComputeRelationshipSentence($objectName, $relTable->{$objectName});
2194 :     }
2195 :     # Return the result.
2196 :     return $retVal;
2197 : parrello 1.1 }
2198 :    
2199 :     =head3 DumpRelations
2200 :    
2201 : parrello 1.18 C<< $erdb->DumpRelations($outputDirectory); >>
2202 : parrello 1.1
2203 :     Write the contents of all the relations to tab-delimited files in the specified directory.
2204 :     Each file will have the same name as the relation dumped, with an extension of DTX.
2205 :    
2206 :     =over 4
2207 :    
2208 :     =item outputDirectory
2209 :    
2210 :     Name of the directory into which the relation files should be dumped.
2211 :    
2212 :     =back
2213 :    
2214 :     =cut
2215 :    
2216 :     sub DumpRelations {
2217 : parrello 1.10 # Get the parameters.
2218 :     my ($self, $outputDirectory) = @_;
2219 :     # Now we need to run through all the relations. First, we loop through the entities.
2220 :     my $metaData = $self->{_metaData};
2221 :     my $entities = $metaData->{Entities};
2222 :     for my $entityName (keys %{$entities}) {
2223 :     my $entityStructure = $entities->{$entityName};
2224 :     # Get the entity's relations.
2225 :     my $relationList = $entityStructure->{Relations};
2226 :     # Loop through the relations, dumping them.
2227 :     for my $relationName (keys %{$relationList}) {
2228 :     my $relation = $relationList->{$relationName};
2229 :     $self->_DumpRelation($outputDirectory, $relationName, $relation);
2230 :     }
2231 :     }
2232 :     # Next, we loop through the relationships.
2233 :     my $relationships = $metaData->{Relationships};
2234 :     for my $relationshipName (keys %{$relationships}) {
2235 :     my $relationshipStructure = $relationships->{$relationshipName};
2236 :     # Dump this relationship's relation.
2237 :     $self->_DumpRelation($outputDirectory, $relationshipName, $relationshipStructure->{Relations}->{$relationshipName});
2238 :     }
2239 : parrello 1.1 }
2240 :    
2241 : parrello 1.51 =head3 InsertValue
2242 :    
2243 :     C<< $erdb->InsertValue($entityID, $fieldName, $value); >>
2244 :    
2245 :     This method will insert a new value into the database. The value must be one
2246 :     associated with a secondary relation, since primary values cannot be inserted:
2247 :     they occur exactly once. Secondary values, on the other hand, can be missing
2248 :     or multiply-occurring.
2249 :    
2250 :     =over 4
2251 :    
2252 :     =item entityID
2253 :    
2254 :     ID of the object that is to receive the new value.
2255 :    
2256 :     =item fieldName
2257 :    
2258 :     Field name for the new value-- this includes the entity name, since
2259 :     field names are of the format I<objectName>C<(>I<fieldName>C<)>.
2260 :    
2261 :     =item value
2262 :    
2263 :     New value to be put in the field.
2264 :    
2265 :     =back
2266 :    
2267 :     =cut
2268 :    
2269 :     sub InsertValue {
2270 :     # Get the parameters.
2271 :     my ($self, $entityID, $fieldName, $value) = @_;
2272 :     # Parse the entity name and the real field name.
2273 :     if ($fieldName =~ /^([^(]+)\(([^)]+)\)/) {
2274 :     my $entityName = $1;
2275 :     my $fieldTitle = $2;
2276 :     # Get its descriptor.
2277 :     if (!$self->IsEntity($entityName)) {
2278 :     Confess("$entityName is not a valid entity.");
2279 :     } else {
2280 :     my $entityData = $self->{_metaData}->{Entities}->{$entityName};
2281 :     # Find the relation containing this field.
2282 :     my $fieldHash = $entityData->{Fields};
2283 : parrello 1.52 if (! exists $fieldHash->{$fieldTitle}) {
2284 : parrello 1.51 Confess("$fieldTitle not found in $entityName.");
2285 :     } else {
2286 :     my $relation = $fieldHash->{$fieldTitle}->{relation};
2287 :     if ($relation eq $entityName) {
2288 :     Confess("Cannot do InsertValue on primary field $fieldTitle of $entityName.");
2289 :     } else {
2290 :     # Now we can create an INSERT statement.
2291 :     my $dbh = $self->{_dbh};
2292 :     my $fixedName = _FixName($fieldTitle);
2293 : parrello 1.53 my $statement = "INSERT INTO $relation (id, $fixedName) VALUES(?, ?)";
2294 : parrello 1.51 # Execute the command.
2295 :     $dbh->SQL($statement, 0, $entityID, $value);
2296 :     }
2297 :     }
2298 :     }
2299 :     } else {
2300 :     Confess("$fieldName is not a valid field name.");
2301 :     }
2302 :     }
2303 :    
2304 : parrello 1.1 =head3 InsertObject
2305 :    
2306 : parrello 1.78 C<< $erdb->InsertObject($objectType, \%fieldHash); >>
2307 : parrello 1.1
2308 :     Insert an object into the database. The object is defined by a type name and then a hash
2309 :     of field names to values. Field values in the primary relation are represented by scalars.
2310 :     (Note that for relationships, the primary relation is the B<only> relation.)
2311 :     Field values for the other relations comprising the entity are always list references. For
2312 :     example, the following line inserts an inactive PEG feature named C<fig|188.1.peg.1> with aliases
2313 :     C<ZP_00210270.1> and C<gi|46206278>.
2314 :    
2315 : parrello 1.18 C<< $erdb->InsertObject('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>
2316 : parrello 1.1
2317 :     The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2318 :     property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2319 :    
2320 : parrello 1.57 C<< $erdb->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2321 : parrello 1.1
2322 :     =over 4
2323 :    
2324 :     =item newObjectType
2325 :    
2326 :     Type name of the object to insert.
2327 :    
2328 :     =item fieldHash
2329 :    
2330 :     Hash of field names to values.
2331 :    
2332 :     =back
2333 :    
2334 :     =cut
2335 :    
2336 :     sub InsertObject {
2337 : parrello 1.10 # Get the parameters.
2338 :     my ($self, $newObjectType, $fieldHash) = @_;
2339 :     # Denote that so far we appear successful.
2340 :     my $retVal = 1;
2341 :     # Get the database handle.
2342 :     my $dbh = $self->{_dbh};
2343 :     # Get the relation list.
2344 :     my $relationTable = $self->_GetRelationTable($newObjectType);
2345 :     # Loop through the relations. We'll build insert statements for each one. If a relation is
2346 :     # secondary, we may end up generating multiple insert statements. If an error occurs, we
2347 :     # stop the loop.
2348 :     my @relationList = keys %{$relationTable};
2349 :     for (my $i = 0; $retVal && $i <= $#relationList; $i++) {
2350 :     my $relationName = $relationList[$i];
2351 :     my $relationDefinition = $relationTable->{$relationName};
2352 :     # Get the relation's fields. For each field we will collect a value in the corresponding
2353 :     # position of the @valueList array. If one of the fields is missing, we will add it to the
2354 :     # @missing list.
2355 :     my @fieldList = @{$relationDefinition->{Fields}};
2356 :     my @fieldNameList = ();
2357 :     my @valueList = ();
2358 :     my @missing = ();
2359 :     my $recordCount = 1;
2360 :     for my $fieldDescriptor (@fieldList) {
2361 :     # Get the field name and save it. Note we need to fix it up so the hyphens
2362 :     # are converted to underscores.
2363 :     my $fieldName = $fieldDescriptor->{name};
2364 :     push @fieldNameList, _FixName($fieldName);
2365 :     # Look for the named field in the incoming structure. Note that we are looking
2366 :     # for the real field name, not the fixed-up one!
2367 :     if (exists $fieldHash->{$fieldName}) {
2368 :     # Here we found the field. Stash it in the value list.
2369 :     my $value = $fieldHash->{$fieldName};
2370 :     push @valueList, $value;
2371 :     # If the value is a list, we may need to increment the record count.
2372 :     if (ref $value eq "ARRAY") {
2373 :     my $thisCount = @{$value};
2374 :     if ($recordCount == 1) {
2375 :     # Here we have our first list, so we save its count.
2376 :     $recordCount = $thisCount;
2377 :     } elsif ($recordCount != $thisCount) {
2378 :     # Here we have a second list, so its length has to match the
2379 :     # previous lists.
2380 :     Trace("Field $value in new $newObjectType object has an invalid list length $thisCount. Expected $recordCount.") if T(0);
2381 :     $retVal = 0;
2382 :     }
2383 :     }
2384 :     } else {
2385 :     # Here the field is not present. Flag it as missing.
2386 :     push @missing, $fieldName;
2387 :     }
2388 :     }
2389 :     # If we are the primary relation, add the new-record flag.
2390 :     if ($relationName eq $newObjectType) {
2391 :     push @valueList, 1;
2392 :     push @fieldNameList, "new_record";
2393 :     }
2394 :     # Only proceed if there are no missing fields.
2395 :     if (@missing > 0) {
2396 :     Trace("Relation $relationName for $newObjectType skipped due to missing fields: " .
2397 :     join(' ', @missing)) if T(1);
2398 :     } else {
2399 :     # Build the INSERT statement.
2400 :     my $statement = "INSERT INTO $relationName (" . join (', ', @fieldNameList) .
2401 :     ") VALUES (";
2402 :     # Create a marker list of the proper size and put it in the statement.
2403 :     my @markers = ();
2404 :     while (@markers < @fieldNameList) { push @markers, '?'; }
2405 :     $statement .= join(', ', @markers) . ")";
2406 :     # We have the insert statement, so prepare it.
2407 :     my $sth = $dbh->prepare_command($statement);
2408 :     Trace("Insert statement prepared: $statement") if T(3);
2409 :     # Now we loop through the values. If a value is scalar, we use it unmodified. If it's
2410 :     # a list, we use the current element. The values are stored in the @parameterList array.
2411 :     my $done = 0;
2412 :     for (my $i = 0; $i < $recordCount; $i++) {
2413 :     # Clear the parameter list array.
2414 :     my @parameterList = ();
2415 :     # Loop through the values.
2416 :     for my $value (@valueList) {
2417 :     # Check to see if this is a scalar value.
2418 :     if (ref $value eq "ARRAY") {
2419 :     # Here we have a list value. Pull the current entry.
2420 :     push @parameterList, $value->[$i];
2421 :     } else {
2422 :     # Here we have a scalar value. Use it unmodified.
2423 :     push @parameterList, $value;
2424 :     }
2425 :     }
2426 :     # Execute the INSERT statement with the specified parameter list.
2427 :     $retVal = $sth->execute(@parameterList);
2428 :     if (!$retVal) {
2429 :     my $errorString = $sth->errstr();
2430 : parrello 1.78 Confess("Error inserting into $relationName: $errorString");
2431 : parrello 1.10 }
2432 :     }
2433 :     }
2434 :     }
2435 : parrello 1.78 # Return a 1 for backward compatability.
2436 :     return 1;
2437 :     }
2438 :    
2439 :     =head3 UpdateEntity
2440 :    
2441 :     C<< $erdb->UpdateEntity($entityName, $id, \%fields); >>
2442 :    
2443 :     Update the values of an entity. This is an unprotected update, so it should only be
2444 :     done if the database resides on a database server.
2445 :    
2446 :     =over 4
2447 :    
2448 :     =item entityName
2449 :    
2450 :     Name of the entity to update. (This is the entity type.)
2451 :    
2452 :     =item id
2453 :    
2454 :     ID of the entity to update. If no entity exists with this ID, an error will be thrown.
2455 :    
2456 :     =item fields
2457 :    
2458 :     Reference to a hash mapping field names to their new values. All of the fields named
2459 :     must be in the entity's primary relation, and they cannot any of them be the ID field.
2460 :    
2461 :     =back
2462 :    
2463 :     =cut
2464 :    
2465 :     sub UpdateEntity {
2466 :     # Get the parameters.
2467 :     my ($self, $entityName, $id, $fields) = @_;
2468 :     # Get a list of the field names being updated.
2469 :     my @fieldList = keys %{$fields};
2470 :     # Verify that the fields exist.
2471 :     my $checker = $self->GetFieldTable($entityName);
2472 :     for my $field (@fieldList) {
2473 :     if ($field eq 'id') {
2474 :     Confess("Cannot update the ID field for entity $entityName.");
2475 :     } elsif ($checker->{$field}->{relation} ne $entityName) {
2476 :     Confess("Cannot find $field in primary relation of $entityName.");
2477 :     }
2478 :     }
2479 :     # Build the SQL statement.
2480 :     my @sets = ();
2481 :     my @valueList = ();
2482 :     for my $field (@fieldList) {
2483 :     push @sets, _FixName($field) . " = ?";
2484 :     push @valueList, $fields->{$field};
2485 :     }
2486 :     my $command = "UPDATE $entityName SET " . join(", ", @sets) . " WHERE id = ?";
2487 :     # Add the ID to the list of binding values.
2488 :     push @valueList, $id;
2489 :     # Call SQL to do the work.
2490 :     my $rows = $self->{_dbh}->SQL($command, 0, @valueList);
2491 :     # Check for errors.
2492 :     if ($rows == 0) {
2493 :     Confess("Entity $id of type $entityName not found.");
2494 :     }
2495 : parrello 1.1 }
2496 :    
2497 :     =head3 LoadTable
2498 :    
2499 : parrello 1.78 C<< my $results = $erdb->LoadTable($fileName, $relationName, $truncateFlag); >>
2500 : parrello 1.1
2501 : parrello 1.9 Load data from a tab-delimited file into a specified table, optionally re-creating the table
2502 :     first.
2503 : parrello 1.1
2504 :     =over 4
2505 :    
2506 :     =item fileName
2507 :    
2508 :     Name of the file from which the table data should be loaded.
2509 :    
2510 :     =item relationName
2511 :    
2512 :     Name of the relation to be loaded. This is the same as the table name.
2513 :    
2514 :     =item truncateFlag
2515 :    
2516 :     TRUE if the table should be dropped and re-created, else FALSE
2517 :    
2518 :     =item RETURN
2519 :    
2520 : parrello 1.28 Returns a statistical object containing a list of the error messages.
2521 : parrello 1.1
2522 :     =back
2523 :    
2524 :     =cut
2525 :     sub LoadTable {
2526 : parrello 1.10 # Get the parameters.
2527 :     my ($self, $fileName, $relationName, $truncateFlag) = @_;
2528 :     # Create the statistical return object.
2529 :     my $retVal = _GetLoadStats();
2530 :     # Trace the fact of the load.
2531 :     Trace("Loading table $relationName from $fileName") if T(2);
2532 :     # Get the database handle.
2533 :     my $dbh = $self->{_dbh};
2534 : parrello 1.22 # Get the input file size.
2535 :     my $fileSize = -s $fileName;
2536 : parrello 1.10 # Get the relation data.
2537 :     my $relation = $self->_FindRelation($relationName);
2538 :     # Check the truncation flag.
2539 :     if ($truncateFlag) {
2540 :     Trace("Creating table $relationName") if T(2);
2541 : parrello 1.19 # Compute the row count estimate. We take the size of the load file,
2542 :     # divide it by the estimated row size, and then multiply by 1.5 to
2543 :     # leave extra room. We postulate a minimum row count of 1000 to
2544 :     # prevent problems with incoming empty load files.
2545 :     my $rowSize = $self->EstimateRowSize($relationName);
2546 :     my $estimate = FIG::max($fileSize * 1.5 / $rowSize, 1000);
2547 : parrello 1.10 # Re-create the table without its index.
2548 : parrello 1.19 $self->CreateTable($relationName, 0, $estimate);
2549 : parrello 1.10 # If this is a pre-index DBMS, create the index here.
2550 :     if ($dbh->{_preIndex}) {
2551 :     eval {
2552 :     $self->CreateIndex($relationName);
2553 :     };
2554 :     if ($@) {
2555 :     $retVal->AddMessage($@);
2556 :     }
2557 :     }
2558 :     }
2559 : parrello 1.3 # Load the table.
2560 : parrello 1.10 my $rv;
2561 :     eval {
2562 : parrello 1.20 $rv = $dbh->load_table(file => $fileName, tbl => $relationName);
2563 : parrello 1.10 };
2564 :     if (!defined $rv) {
2565 : parrello 1.3 $retVal->AddMessage($@) if ($@);
2566 : parrello 1.73 $retVal->AddMessage("Table load failed for $relationName using $fileName: " . $dbh->error_message);
2567 : parrello 1.10 Trace("Table load failed for $relationName.") if T(1);
2568 :     } else {
2569 : parrello 1.22 # Here we successfully loaded the table.
2570 :     $retVal->Add("tables");
2571 :     my $size = -s $fileName;
2572 :     Trace("$size bytes loaded into $relationName.") if T(2);
2573 : parrello 1.10 # If we're rebuilding, we need to create the table indexes.
2574 : parrello 1.70 if ($truncateFlag) {
2575 :     # Indexes are created here for PostGres. For PostGres, indexes are
2576 :     # best built at the end. For MySQL, the reverse is true.
2577 :     if (! $dbh->{_preIndex}) {
2578 :     eval {
2579 :     $self->CreateIndex($relationName);
2580 :     };
2581 :     if ($@) {
2582 :     $retVal->AddMessage($@);
2583 :     }
2584 :     }
2585 :     # The full-text index (if any) is always built last, even for MySQL.
2586 :     # First we need to see if this table has a full-text index. Only
2587 :     # primary relations are allowed that privilege.
2588 : parrello 1.81 Trace("Checking for full-text index on $relationName.") if T(2);
2589 : parrello 1.70 if ($self->_IsPrimary($relationName)) {
2590 :     # Get the relation's entity/relationship structure.
2591 :     my $structure = $self->_GetStructure($relationName);
2592 : parrello 1.81 Trace("Checking for search fields in $relationName.") if T(3);
2593 : parrello 1.70 # Check for a searchable fields list.
2594 :     if (exists $structure->{searchFields}) {
2595 :     # Here we know that we need to create a full-text search index.
2596 :     # Get an SQL-formatted field name list.
2597 : parrello 1.81 my $fields = join(", ", _FixNames(@{$structure->{searchFields}}));
2598 : parrello 1.70 # Create the index.
2599 : parrello 1.75 $dbh->create_index(tbl => $relationName, idx => "search_idx",
2600 : parrello 1.70 flds => $fields, kind => 'fulltext');
2601 : parrello 1.81 Trace("Index created for $fields in $relationName.") if T(2);
2602 : parrello 1.70 }
2603 : parrello 1.10 }
2604 :     }
2605 :     }
2606 : parrello 1.20 # Analyze the table to improve performance.
2607 : parrello 1.61 Trace("Analyzing and compacting $relationName.") if T(3);
2608 : olson 1.16 $dbh->vacuum_it($relationName);
2609 : parrello 1.61 Trace("$relationName load completed.") if T(3);
2610 : parrello 1.10 # Return the statistics.
2611 :     return $retVal;
2612 : parrello 1.1 }
2613 :    
2614 : parrello 1.73 =head3 DropRelation
2615 : parrello 1.1
2616 : parrello 1.73 C<< $erdb->DropRelation($relationName); >>
2617 : parrello 1.1
2618 : parrello 1.73 Physically drop a relation from the database.
2619 : parrello 1.1
2620 :     =over 4
2621 :    
2622 : parrello 1.73 =item relationName
2623 : parrello 1.1
2624 : parrello 1.73 Name of the relation to drop. If it does not exist, this method will have
2625 :     no effect.
2626 : parrello 1.1
2627 :     =back
2628 :    
2629 :     =cut
2630 :    
2631 : parrello 1.73 sub DropRelation {
2632 : parrello 1.10 # Get the parameters.
2633 : parrello 1.73 my ($self, $relationName) = @_;
2634 :     # Get the database handle.
2635 :     my $dbh = $self->{_dbh};
2636 :     # Drop the relation. The method used here has no effect if the relation
2637 :     # does not exist.
2638 : parrello 1.74 Trace("Invoking DB Kernel to drop $relationName.") if T(3);
2639 :     $dbh->drop_table(tbl => $relationName);
2640 : parrello 1.1 }
2641 :    
2642 : parrello 1.78 =head3 MatchSqlPattern
2643 :    
2644 :     C<< my $matched = ERDB::MatchSqlPattern($value, $pattern); >>
2645 :    
2646 :     Determine whether or not a specified value matches an SQL pattern. An SQL
2647 :     pattern has two wild card characters: C<%> that matches multiple characters,
2648 :     and C<_> that matches a single character. These can be escaped using a
2649 :     backslash (C<\>). We pull this off by converting the SQL pattern to a
2650 :     PERL regular expression. As per SQL rules, the match is case-insensitive.
2651 :    
2652 :     =over 4
2653 :    
2654 :     =item value
2655 :    
2656 :     Value to be matched against the pattern. Note that an undefined or empty
2657 :     value will not match anything.
2658 :    
2659 :     =item pattern
2660 :    
2661 :     SQL pattern against which to match the value. An undefined or empty pattern will
2662 :     match everything.
2663 :    
2664 :     =item RETURN
2665 :    
2666 :     Returns TRUE if the value and pattern match, else FALSE.
2667 :    
2668 :     =back
2669 :    
2670 :     =cut
2671 :    
2672 :     sub MatchSqlPattern {
2673 :     # Get the parameters.
2674 :     my ($value, $pattern) = @_;
2675 :     # Declare the return variable.
2676 :     my $retVal;
2677 :     # Insure we have a pattern.
2678 :     if (! defined($pattern) || $pattern eq "") {
2679 :     $retVal = 1;
2680 :     } else {
2681 :     # Break the pattern into pieces around the wildcard characters. Because we
2682 :     # use parentheses in the split function's delimiter expression, we'll get
2683 :     # list elements for the delimiters as well as the rest of the string.
2684 :     my @pieces = split /([_%]|\\[_%])/, $pattern;
2685 :     # Check some fast special cases.
2686 :     if ($pattern eq '%') {
2687 :     # A null pattern matches everything.
2688 :     $retVal = 1;
2689 :     } elsif (@pieces == 1) {
2690 :     # No wildcards, so we have a literal comparison. Note we're case-insensitive.
2691 :     $retVal = (lc($value) eq lc($pattern));
2692 :     } elsif (@pieces == 2 && $pieces[1] eq '%') {
2693 :     # A wildcard at the end, so we have a substring match. This is also case-insensitive.
2694 :     $retVal = (lc(substr($value, 0, length($pieces[0]))) eq lc($pieces[0]));
2695 :     } else {
2696 :     # Okay, we have to do it the hard way. Convert each piece to a PERL pattern.
2697 :     my $realPattern = "";
2698 :     for my $piece (@pieces) {
2699 :     # Determine the type of piece.
2700 :     if ($piece eq "") {
2701 :     # Empty pieces are ignored.
2702 :     } elsif ($piece eq "%") {
2703 :     # Here we have a multi-character wildcard. Note that it can match
2704 :     # zero or more characters.
2705 :     $realPattern .= ".*"
2706 :     } elsif ($piece eq "_") {
2707 :     # Here we have a single-character wildcard.
2708 :     $realPattern .= ".";
2709 :     } elsif ($piece eq "\\%" || $piece eq "\\_") {
2710 :     # This is an escape sequence (which is a rare thing, actually).
2711 :     $realPattern .= substr($piece, 1, 1);
2712 :     } else {
2713 :     # Here we have raw text.
2714 :     $realPattern .= quotemeta($piece);
2715 :     }
2716 :     }
2717 :     # Do the match.
2718 :     $retVal = ($value =~ /^$realPattern$/i ? 1 : 0);
2719 :     }
2720 :     }
2721 :     # Return the result.
2722 :     return $retVal;
2723 :     }
2724 :    
2725 : parrello 1.6 =head3 GetEntity
2726 :    
2727 : parrello 1.18 C<< my $entityObject = $erdb->GetEntity($entityType, $ID); >>
2728 : parrello 1.6
2729 :     Return an object describing the entity instance with a specified ID.
2730 :    
2731 :     =over 4
2732 :    
2733 :     =item entityType
2734 :    
2735 :     Entity type name.
2736 :    
2737 :     =item ID
2738 :    
2739 :     ID of the desired entity.
2740 :    
2741 :     =item RETURN
2742 :    
2743 :     Returns a B<DBObject> representing the desired entity instance, or an undefined value if no
2744 :     instance is found with the specified key.
2745 :    
2746 :     =back
2747 :    
2748 :     =cut
2749 :    
2750 :     sub GetEntity {
2751 : parrello 1.10 # Get the parameters.
2752 :     my ($self, $entityType, $ID) = @_;
2753 :     # Create a query.
2754 : parrello 1.45 my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);
2755 : parrello 1.10 # Get the first (and only) object.
2756 :     my $retVal = $query->Fetch();
2757 :     # Return the result.
2758 :     return $retVal;
2759 : parrello 1.6 }
2760 :    
2761 : parrello 1.69 =head3 GetChoices
2762 :    
2763 :     C<< my @values = $erdb->GetChoices($entityName, $fieldName); >>
2764 :    
2765 :     Return a list of all the values for the specified field that are represented in the
2766 :     specified entity.
2767 :    
2768 :     Note that if the field is not indexed, then this will be a very slow operation.
2769 :    
2770 :     =over 4
2771 :    
2772 :     =item entityName
2773 :    
2774 :     Name of an entity in the database.
2775 :    
2776 :     =item fieldName
2777 :    
2778 :     Name of a field belonging to the entity. This is a raw field name without
2779 :     the standard parenthesized notation used in most calls.
2780 :    
2781 :     =item RETURN
2782 :    
2783 :     Returns a list of the distinct values for the specified field in the database.
2784 :    
2785 :     =back
2786 :    
2787 :     =cut
2788 :    
2789 :     sub GetChoices {
2790 :     # Get the parameters.
2791 :     my ($self, $entityName, $fieldName) = @_;
2792 :     # Declare the return variable.
2793 :     my @retVal;
2794 :     # Get the entity data structure.
2795 :     my $entityData = $self->_GetStructure($entityName);
2796 :     # Get the field.
2797 :     my $fieldHash = $entityData->{Fields};
2798 :     if (! exists $fieldHash->{$fieldName}) {
2799 :     Confess("$fieldName not found in $entityName.");
2800 :     } else {
2801 :     # Get the name of the relation containing the field.
2802 :     my $relation = $fieldHash->{$fieldName}->{relation};
2803 :     # Fix up the field name.
2804 :     my $realName = _FixName($fieldName);
2805 :     # Get the database handle.
2806 :     my $dbh = $self->{_dbh};
2807 :     # Query the database.
2808 :     my $results = $dbh->SQL("SELECT DISTINCT $realName FROM $relation");
2809 :     # Clean the results. They are stored as a list of lists, and we just want the one list.
2810 :     @retVal = sort map { $_->[0] } @{$results};
2811 :     }
2812 :     # Return the result.
2813 :     return @retVal;
2814 :     }
2815 :    
2816 : parrello 1.6 =head3 GetEntityValues
2817 :    
2818 : parrello 1.18 C<< my @values = $erdb->GetEntityValues($entityType, $ID, \@fields); >>
2819 : parrello 1.6
2820 : parrello 1.68 Return a list of values from a specified entity instance. If the entity instance
2821 :     does not exist, an empty list is returned.
2822 : parrello 1.6
2823 :     =over 4
2824 :    
2825 :     =item entityType
2826 :    
2827 :     Entity type name.
2828 :    
2829 :     =item ID
2830 :    
2831 :     ID of the desired entity.
2832 :    
2833 :     =item fields
2834 :    
2835 :     List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.
2836 :    
2837 :     =item RETURN
2838 :    
2839 :     Returns a flattened list of the values of the specified fields for the specified entity.
2840 :    
2841 :     =back
2842 :    
2843 :     =cut
2844 :    
2845 :     sub GetEntityValues {
2846 : parrello 1.10 # Get the parameters.
2847 :     my ($self, $entityType, $ID, $fields) = @_;
2848 :     # Get the specified entity.
2849 :     my $entity = $self->GetEntity($entityType, $ID);
2850 :     # Declare the return list.
2851 :     my @retVal = ();
2852 :     # If we found the entity, push the values into the return list.
2853 :     if ($entity) {
2854 :     push @retVal, $entity->Values($fields);
2855 :     }
2856 :     # Return the result.
2857 :     return @retVal;
2858 : parrello 1.6 }
2859 : parrello 1.1
2860 : parrello 1.7 =head3 GetAll
2861 :    
2862 : parrello 1.18 C<< my @list = $erdb->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>
2863 : parrello 1.7
2864 :     Return a list of values taken from the objects returned by a query. The first three
2865 :     parameters correspond to the parameters of the L</Get> method. The final parameter is
2866 :     a list of the fields desired from each record found by the query. The field name
2867 :     syntax is the standard syntax used for fields in the B<ERDB> system--
2868 :     B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity
2869 :     or relationship and I<fieldName> is the name of the field.
2870 :    
2871 :     The list returned will be a list of lists. Each element of the list will contain
2872 :     the values returned for the fields specified in the fourth parameter. If one of the
2873 :     fields specified returns multiple values, they are flattened in with the rest. For
2874 :     example, the following call will return a list of the features in a particular
2875 :     spreadsheet cell, and each feature will be represented by a list containing the
2876 :     feature ID followed by all of its aliases.
2877 :    
2878 : parrello 1.78 C<< @query = $erdb->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>
2879 : parrello 1.7
2880 :     =over 4
2881 :    
2882 :     =item objectNames
2883 :    
2884 :     List containing the names of the entity and relationship objects to be retrieved.
2885 :    
2886 :     =item filterClause
2887 :    
2888 :     WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
2889 :     be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
2890 :     B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the
2891 :     parameter list as additional parameters. The fields in a filter clause can come from primary
2892 :     entity relations, relationship relations, or secondary entity relations; however, all of the
2893 :     entities and relationships involved must be included in the list of object names.
2894 :    
2895 :     =item parameterList
2896 :    
2897 :     List of the parameters to be substituted in for the parameters marks in the filter clause.
2898 :    
2899 :     =item fields
2900 :    
2901 :     List of the fields to be returned in each element of the list returned.
2902 :    
2903 :     =item count
2904 :    
2905 :     Maximum number of records to return. If omitted or 0, all available records will be returned.
2906 :    
2907 :     =item RETURN
2908 :    
2909 :     Returns a list of list references. Each element of the return list contains the values for the
2910 :     fields specified in the B<fields> parameter.
2911 :    
2912 :     =back
2913 :    
2914 :     =cut
2915 :     #: Return Type @@;
2916 :     sub GetAll {
2917 : parrello 1.10 # Get the parameters.
2918 :     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2919 :     # Translate the parameters from a list reference to a list. If the parameter
2920 :     # list is a scalar we convert it into a singleton list.
2921 :     my @parmList = ();
2922 :     if (ref $parameterList eq "ARRAY") {
2923 : parrello 1.45 Trace("GetAll parm list is an array.") if T(4);
2924 : parrello 1.10 @parmList = @{$parameterList};
2925 :     } else {
2926 : parrello 1.45 Trace("GetAll parm list is a scalar: $parameterList.") if T(4);
2927 : parrello 1.10 push @parmList, $parameterList;
2928 :     }
2929 : parrello 1.30 # Insure the counter has a value.
2930 :     if (!defined $count) {
2931 :     $count = 0;
2932 :     }
2933 :     # Add the row limit to the filter clause.
2934 :     if ($count > 0) {
2935 :     $filterClause .= " LIMIT $count";
2936 :     }
2937 : parrello 1.10 # Create the query.
2938 : parrello 1.45 my $query = $self->Get($objectNames, $filterClause, \@parmList);
2939 : parrello 1.10 # Set up a counter of the number of records read.
2940 :     my $fetched = 0;
2941 :     # Loop through the records returned, extracting the fields. Note that if the
2942 :     # counter is non-zero, we stop when the number of records read hits the count.
2943 :     my @retVal = ();
2944 :     while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {
2945 :     my @rowData = $row->Values($fields);
2946 :     push @retVal, \@rowData;
2947 :     $fetched++;
2948 :     }
2949 : parrello 1.54 Trace("$fetched rows returned in GetAll.") if T(SQL => 4);
2950 : parrello 1.10 # Return the resulting list.
2951 :     return @retVal;
2952 : parrello 1.7 }
2953 :    
2954 : parrello 1.55 =head3 Exists
2955 :    
2956 :     C<< my $found = $sprout->Exists($entityName, $entityID); >>
2957 :    
2958 :     Return TRUE if an entity exists, else FALSE.
2959 :    
2960 :     =over 4
2961 :    
2962 :     =item entityName
2963 :    
2964 :     Name of the entity type (e.g. C<Feature>) relevant to the existence check.
2965 :    
2966 :     =item entityID
2967 :    
2968 :     ID of the entity instance whose existence is to be checked.
2969 :    
2970 :     =item RETURN
2971 :    
2972 :     Returns TRUE if the entity instance exists, else FALSE.
2973 :    
2974 :     =back
2975 :    
2976 :     =cut
2977 :     #: Return Type $;
2978 :     sub Exists {
2979 :     # Get the parameters.
2980 :     my ($self, $entityName, $entityID) = @_;
2981 :     # Check for the entity instance.
2982 :     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2983 :     my $testInstance = $self->GetEntity($entityName, $entityID);
2984 :     # Return an existence indicator.
2985 :     my $retVal = ($testInstance ? 1 : 0);
2986 :     return $retVal;
2987 :     }
2988 :    
2989 : parrello 1.18 =head3 EstimateRowSize
2990 :    
2991 :     C<< my $rowSize = $erdb->EstimateRowSize($relName); >>
2992 :    
2993 :     Estimate the row size of the specified relation. The estimated row size is computed by adding
2994 :     up the average length for each data type.
2995 :    
2996 :     =over 4
2997 :    
2998 :     =item relName
2999 :    
3000 :     Name of the relation whose estimated row size is desired.
3001 :    
3002 :     =item RETURN
3003 :    
3004 :     Returns an estimate of the row size for the specified relation.
3005 :    
3006 :     =back
3007 :    
3008 :     =cut
3009 :     #: Return Type $;
3010 :     sub EstimateRowSize {
3011 :     # Get the parameters.
3012 :     my ($self, $relName) = @_;
3013 :     # Declare the return variable.
3014 :     my $retVal = 0;
3015 :     # Find the relation descriptor.
3016 :     my $relation = $self->_FindRelation($relName);
3017 :     # Get the list of fields.
3018 :     for my $fieldData (@{$relation->{Fields}}) {
3019 :     # Get the field type and add its length.
3020 :     my $fieldLen = $TypeTable{$fieldData->{type}}->{avgLen};
3021 :     $retVal += $fieldLen;
3022 :     }
3023 :     # Return the result.
3024 :     return $retVal;
3025 :     }
3026 :    
3027 : parrello 1.38 =head3 GetFieldTable
3028 :    
3029 :     C<< my $fieldHash = $self->GetFieldTable($objectnName); >>
3030 :    
3031 :     Get the field structure for a specified entity or relationship.
3032 :    
3033 :     =over 4
3034 :    
3035 :     =item objectName
3036 :    
3037 :     Name of the desired entity or relationship.
3038 :    
3039 :     =item RETURN
3040 :    
3041 :     The table containing the field descriptors for the specified object.
3042 :    
3043 :     =back
3044 :    
3045 :     =cut
3046 :    
3047 :     sub GetFieldTable {
3048 :     # Get the parameters.
3049 :     my ($self, $objectName) = @_;
3050 :     # Get the descriptor from the metadata.
3051 :     my $objectData = $self->_GetStructure($objectName);
3052 :     # Return the object's field table.
3053 :     return $objectData->{Fields};
3054 :     }
3055 :    
3056 : parrello 1.73 =head3 SplitKeywords
3057 :    
3058 :     C<< my @keywords = ERDB::SplitKeywords($keywordString); >>
3059 :    
3060 :     This method returns a list of the positive keywords in the specified
3061 :     keyword string. All of the operators will have been stripped off,
3062 :     and if the keyword is preceded by a minus operator (C<->), it will
3063 :     not be in the list returned. The idea here is to get a list of the
3064 :     keywords the user wants to see. The list will be processed to remove
3065 :     duplicates.
3066 :    
3067 :     It is possible to create a string that confuses this method. For example
3068 :    
3069 :     frog toad -frog
3070 :    
3071 :     would return both C<frog> and C<toad>. If this is a problem we can deal
3072 :     with it later.
3073 :    
3074 :     =over 4
3075 :    
3076 :     =item keywordString
3077 :    
3078 :     The keyword string to be parsed.
3079 :    
3080 :     =item RETURN
3081 :    
3082 :     Returns a list of the words in the keyword string the user wants to
3083 :     see.
3084 :    
3085 :     =back
3086 :    
3087 :     =cut
3088 :    
3089 :     sub SplitKeywords {
3090 :     # Get the parameters.
3091 :     my ($keywordString) = @_;
3092 :     # Make a safety copy of the string. (This helps during debugging.)
3093 :     my $workString = $keywordString;
3094 :     # Convert operators we don't care about to spaces.
3095 :     $workString =~ tr/+"()<>/ /;
3096 :     # Split the rest of the string along space boundaries. Note that we
3097 :     # eliminate any words that are zero length or begin with a minus sign.
3098 :     my @wordList = grep { $_ && substr($_, 0, 1) ne "-" } split /\s+/, $workString;
3099 :     # Use a hash to remove duplicates.
3100 :     my %words = map { $_ => 1 } @wordList;
3101 :     # Return the result.
3102 :     return sort keys %words;
3103 :     }
3104 :    
3105 :     =head3 ValidateFieldName
3106 :    
3107 :     C<< my $okFlag = ERDB::ValidateFieldName($fieldName); >>
3108 :    
3109 :     Return TRUE if the specified field name is valid, else FALSE. Valid field names must
3110 :     be hyphenated words subject to certain restrictions.
3111 :    
3112 :     =over 4
3113 :    
3114 :     =item fieldName
3115 :    
3116 :     Field name to be validated.
3117 :    
3118 :     =item RETURN
3119 :    
3120 :     Returns TRUE if the field name is valid, else FALSE.
3121 :    
3122 :     =back
3123 :    
3124 :     =cut
3125 :    
3126 :     sub ValidateFieldName {
3127 :     # Get the parameters.
3128 :     my ($fieldName) = @_;
3129 :     # Declare the return variable. The field name is valid until we hear
3130 :     # differently.
3131 :     my $retVal = 1;
3132 : parrello 1.78 # Compute the maximum name length.
3133 :     my $maxLen = $TypeTable{'name-string'}->{maxLen};
3134 : parrello 1.73 # Look for bad stuff in the name.
3135 :     if ($fieldName =~ /--/) {
3136 :     # Here we have a doubled minus sign.
3137 :     Trace("Field name $fieldName has a doubled hyphen.") if T(1);
3138 :     $retVal = 0;
3139 :     } elsif ($fieldName !~ /^[A-Za-z]/) {
3140 :     # Here the field name is missing the initial letter.
3141 :     Trace("Field name $fieldName does not begin with a letter.") if T(1);
3142 :     $retVal = 0;
3143 : parrello 1.78 } elsif (length($fieldName) > $maxLen) {
3144 :     # Here the field name is too long.
3145 :     Trace("Maximum field name length is $maxLen. Field name must be truncated to " . substr($fieldName,0, $maxLen) . ".");
3146 : parrello 1.73 } else {
3147 : parrello 1.75 # Strip out the minus signs. Everything remaining must be a letter,
3148 :     # underscore, or digit.
3149 : parrello 1.73 my $strippedName = $fieldName;
3150 :     $strippedName =~ s/-//g;
3151 : parrello 1.75 if ($strippedName !~ /^(\w|\d)+$/) {
3152 : parrello 1.73 Trace("Field name $fieldName contains illegal characters.") if T(1);
3153 :     $retVal = 0;
3154 :     }
3155 :     }
3156 :     # Return the result.
3157 :     return $retVal;
3158 :     }
3159 :    
3160 :     =head3 ReadMetaXML
3161 :    
3162 :     C<< my $rawMetaData = ERDB::ReadDBD($fileName); >>
3163 :    
3164 :     This method reads a raw database definition XML file and returns it.
3165 :     Normally, the metadata used by the ERDB system has been processed and
3166 :     modified to make it easier to load and retrieve the data; however,
3167 :     this method can be used to get the data in its raw form.
3168 :    
3169 :     =over 4
3170 :    
3171 :     =item fileName
3172 :    
3173 :     Name of the XML file to read.
3174 :    
3175 :     =item RETURN
3176 :    
3177 :     Returns a hash reference containing the raw XML data from the specified file.
3178 :    
3179 :     =back
3180 :    
3181 :     =cut
3182 :    
3183 :     sub ReadMetaXML {
3184 :     # Get the parameters.
3185 :     my ($fileName) = @_;
3186 :     # Read the XML.
3187 :     my $retVal = XML::Simple::XMLin($fileName, %XmlOptions, %XmlInOpts);
3188 :     Trace("XML metadata loaded from file $fileName.") if T(1);
3189 :     # Return the result.
3190 :     return $retVal;
3191 :     }
3192 :    
3193 :     =head3 GetEntityFieldHash
3194 :    
3195 :     C<< my $fieldHashRef = ERDB::GetEntityFieldHash($structure, $entityName); >>
3196 :    
3197 :     Get the field hash of the named entity in the specified raw XML structure.
3198 :     The field hash may not exist, in which case we need to create it.
3199 :    
3200 :     =over 4
3201 :    
3202 :     =item structure
3203 :    
3204 :     Raw XML structure defininng the database. This is not the run-time XML used by
3205 :     an ERDB object, since that has all sorts of optimizations built-in.
3206 :    
3207 :     =item entityName
3208 :    
3209 :     Name of the entity whose field structure is desired.
3210 :    
3211 :     =item RETURN
3212 :    
3213 :     Returns the field hash used to define the entity's fields.
3214 :    
3215 :     =back
3216 :    
3217 :     =cut
3218 :    
3219 :     sub GetEntityFieldHash {
3220 :     # Get the parameters.
3221 :     my ($structure, $entityName) = @_;
3222 :     # Get the entity structure.
3223 :     my $entityData = $structure->{Entities}->{$entityName};
3224 :     # Look for a field structure.
3225 :     my $retVal = $entityData->{Fields};
3226 :     # If it doesn't exist, create it.
3227 :     if (! defined($retVal)) {
3228 :     $entityData->{Fields} = {};
3229 :     $retVal = $entityData->{Fields};
3230 :     }
3231 :     # Return the result.
3232 :     return $retVal;
3233 :     }
3234 :    
3235 :     =head3 WriteMetaXML
3236 :    
3237 :     C<< ERDB::WriteMetaXML($structure, $fileName); >>
3238 :    
3239 :     Write the metadata XML to a file. This method is the reverse of L</ReadMetaXML>, and is
3240 :     used to update the database definition. It must be used with care, however, since it
3241 :     will only work on a raw structure, not on the processed structure created by an ERDB
3242 :     constructor.
3243 :    
3244 :     =over 4
3245 :    
3246 :     =item structure
3247 :    
3248 :     XML structure to be written to the file.
3249 :    
3250 :     =item fileName
3251 :    
3252 :     Name of the output file to which the updated XML should be stored.
3253 :    
3254 :     =back
3255 :    
3256 :     =cut
3257 :    
3258 :     sub WriteMetaXML {
3259 :     # Get the parameters.
3260 :     my ($structure, $fileName) = @_;
3261 :     # Compute the output.
3262 :     my $fileString = XML::Simple::XMLout($structure, %XmlOptions, %XmlOutOpts);
3263 :     # Write it to the file.
3264 :     my $xmlOut = Open(undef, ">$fileName");
3265 :     print $xmlOut $fileString;
3266 :     }
3267 :    
3268 :    
3269 :     =head3 HTMLNote
3270 :    
3271 :     Convert a note or comment to HTML by replacing some bulletin-board codes with HTML. The codes
3272 :     supported are C<[b]> for B<bold>, C<[i]> for I<italics>, and C<[p]> for a new paragraph.
3273 :     Except for C<[p]>, all the codes are closed by slash-codes. So, for
3274 :     example, C<[b]Feature[/b]> displays the string C<Feature> in boldface.
3275 :    
3276 :     C<< my $realHtml = ERDB::HTMLNote($dataString); >>
3277 :    
3278 :     =over 4
3279 :    
3280 :     =item dataString
3281 :    
3282 :     String to convert to HTML.
3283 :    
3284 :     =item RETURN
3285 :    
3286 :     An HTML string derived from the input string.
3287 :    
3288 :     =back
3289 :    
3290 :     =cut
3291 :    
3292 :     sub HTMLNote {
3293 :     # Get the parameter.
3294 :     my ($dataString) = @_;
3295 :     # HTML-escape the text.
3296 :     my $retVal = CGI::escapeHTML($dataString);
3297 :     # Substitute the bulletin board codes.
3298 :     $retVal =~ s!\[(/?[bi])\]!<$1>!g;
3299 :     $retVal =~ s!\[p\]!</p><p>!g;
3300 :     # Return the result.
3301 :     return $retVal;
3302 :     }
3303 :    
3304 :    
3305 : parrello 1.48 =head2 Data Mining Methods
3306 :    
3307 : parrello 1.38 =head3 GetUsefulCrossValues
3308 :    
3309 :     C<< my @attrNames = $sprout->GetUsefulCrossValues($sourceEntity, $relationship); >>
3310 :    
3311 :     Return a list of the useful attributes that would be returned by a B<Cross> call
3312 :     from an entity of the source entity type through the specified relationship. This
3313 :     means it will return the fields of the target entity type and the intersection data
3314 :     fields in the relationship. Only primary table fields are returned. In other words,
3315 :     the field names returned will be for fields where there is always one and only one
3316 :     value.
3317 :    
3318 :     =over 4
3319 :    
3320 :     =item sourceEntity
3321 :    
3322 :     Name of the entity from which the relationship crossing will start.
3323 :    
3324 :     =item relationship
3325 :    
3326 :     Name of the relationship being crossed.
3327 :    
3328 :     =item RETURN
3329 :    
3330 :     Returns a list of field names in Sprout field format (I<objectName>C<(>I<fieldName>C<)>.
3331 :    
3332 :     =back
3333 :    
3334 :     =cut
3335 :     #: Return Type @;
3336 :     sub GetUsefulCrossValues {
3337 :     # Get the parameters.
3338 :     my ($self, $sourceEntity, $relationship) = @_;
3339 :     # Declare the return variable.
3340 :     my @retVal = ();
3341 :     # Determine the target entity for the relationship. This is whichever entity is not
3342 :     # the source entity. So, if the source entity is the FROM, we'll get the name of
3343 :     # the TO, and vice versa.
3344 :     my $relStructure = $self->_GetStructure($relationship);
3345 :     my $targetEntityType = ($relStructure->{from} eq $sourceEntity ? "to" : "from");
3346 :     my $targetEntity = $relStructure->{$targetEntityType};
3347 :     # Get the field table for the entity.
3348 :     my $entityFields = $self->GetFieldTable($targetEntity);
3349 :     # The field table is a hash. The hash key is the field name. The hash value is a structure.
3350 :     # For the entity fields, the key aspect of the target structure is that the {relation} value
3351 :     # must match the entity name.
3352 :     my @fieldList = map { "$targetEntity($_)" } grep { $entityFields->{$_}->{relation} eq $targetEntity }
3353 :     keys %{$entityFields};
3354 :     # Push the fields found onto the return variable.
3355 :     push @retVal, sort @fieldList;
3356 :     # Get the field table for the relationship.
3357 :     my $relationshipFields = $self->GetFieldTable($relationship);
3358 :     # Here we have a different rule. We want all the fields other than "from-link" and "to-link".
3359 :     # This may end up being an empty set.
3360 :     my @fieldList2 = map { "$relationship($_)" } grep { $_ ne "from-link" && $_ ne "to-link" }
3361 :     keys %{$relationshipFields};
3362 :     # Push these onto the return list.
3363 :     push @retVal, sort @fieldList2;
3364 :     # Return the result.
3365 :     return @retVal;
3366 :     }
3367 :    
3368 : parrello 1.48 =head3 FindColumn
3369 :    
3370 :     C<< my $colIndex = ERDB::FindColumn($headerLine, $columnIdentifier); >>
3371 :    
3372 :     Return the location a desired column in a data mining header line. The data
3373 :     mining header line is a tab-separated list of column names. The column
3374 :     identifier is either the numerical index of a column or the actual column
3375 :     name.
3376 :    
3377 :     =over 4
3378 :    
3379 :     =item headerLine
3380 :    
3381 :     The header line from a data mining command, which consists of a tab-separated
3382 :     list of column names.
3383 :    
3384 :     =item columnIdentifier
3385 :    
3386 :     Either the ordinal number of the desired column (1-based), or the name of the
3387 :     desired column.
3388 :    
3389 :     =item RETURN
3390 :    
3391 :     Returns the array index (0-based) of the desired column.
3392 :    
3393 :     =back
3394 :    
3395 :     =cut
3396 :    
3397 :     sub FindColumn {
3398 :     # Get the parameters.
3399 :     my ($headerLine, $columnIdentifier) = @_;
3400 :     # Declare the return variable.
3401 :     my $retVal;
3402 :     # Split the header line into column names.
3403 :     my @headers = ParseColumns($headerLine);
3404 :     # Determine whether we have a number or a name.
3405 :     if ($columnIdentifier =~ /^\d+$/) {
3406 :     # Here we have a number. Subtract 1 and validate the result.
3407 :     $retVal = $columnIdentifier - 1;
3408 :     if ($retVal < 0 || $retVal > $#headers) {
3409 :     Confess("Invalid column identifer \"$columnIdentifier\": value out of range.");
3410 :     }
3411 :     } else {
3412 :     # Here we have a name. We need to find it in the list.
3413 :     for (my $i = 0; $i <= $#headers && ! defined($retVal); $i++) {
3414 :     if ($headers[$i] eq $columnIdentifier) {
3415 :     $retVal = $i;
3416 :     }
3417 :     }
3418 :     if (! defined($retVal)) {
3419 :     Confess("Invalid column identifier \"$columnIdentifier\": value not found.");
3420 :     }
3421 :     }
3422 :     # Return the result.
3423 :     return $retVal;
3424 :     }
3425 :    
3426 :     =head3 ParseColumns
3427 :    
3428 : parrello 1.50 C<< my @columns = ERDB::ParseColumns($line); >>
3429 : parrello 1.48
3430 :     Convert the specified data line to a list of columns.
3431 :    
3432 :     =over 4
3433 :    
3434 :     =item line
3435 :    
3436 :     A data mining input, consisting of a tab-separated list of columns terminated by a
3437 :     new-line.
3438 :    
3439 :     =item RETURN
3440 :    
3441 :     Returns a list consisting of the column values.
3442 :    
3443 :     =back
3444 :    
3445 :     =cut
3446 :    
3447 :     sub ParseColumns {
3448 :     # Get the parameters.
3449 : parrello 1.50 my ($line) = @_;
3450 : parrello 1.48 # Chop off the line-end.
3451 :     chomp $line;
3452 :     # Split it into a list.
3453 :     my @retVal = split(/\t/, $line);
3454 :     # Return the result.
3455 :     return @retVal;
3456 :     }
3457 :    
3458 : parrello 1.71 =head2 Virtual Methods
3459 :    
3460 :     =head3 CleanKeywords
3461 :    
3462 :     C<< my $cleanedString = $erdb->CleanKeywords($searchExpression); >>
3463 :    
3464 :     Clean up a search expression or keyword list. This is a virtual method that may
3465 :     be overridden by the subclass. The base-class method removes extra spaces
3466 :     and converts everything to lower case.
3467 :    
3468 :     =over 4
3469 :    
3470 :     =item searchExpression
3471 :    
3472 :     Search expression or keyword list to clean. Note that a search expression may
3473 :     contain boolean operators which need to be preserved. This includes leading
3474 :     minus signs.
3475 :    
3476 :     =item RETURN
3477 :    
3478 :     Cleaned expression or keyword list.
3479 :    
3480 :     =back
3481 :    
3482 :     =cut
3483 :    
3484 :     sub CleanKeywords {
3485 :     # Get the parameters.
3486 :     my ($self, $searchExpression) = @_;
3487 :     # Lower-case the expression and copy it into the return variable. Note that we insure we
3488 :     # don't accidentally end up with an undefined value.
3489 :     my $retVal = lc($searchExpression || "");
3490 :     # Remove extra spaces.
3491 :     $retVal =~ s/\s+/ /g;
3492 :     $retVal =~ s/(^\s+)|(\s+$)//g;
3493 :     # Return the result.
3494 :     return $retVal;
3495 :     }
3496 :    
3497 : parrello 1.73 =head3 GetSourceObject
3498 :    
3499 :     C<< my $source = $erdb->GetSourceObject($entityName); >>
3500 :    
3501 :     Return the object to be used in loading special attributes of the specified entity. The
3502 :     algorithm for loading special attributes is stored in the C<DataGen> elements of the
3503 :     XML
3504 :    
3505 : parrello 1.1 =head2 Internal Utility Methods
3506 :    
3507 : parrello 1.70 =head3 _RelationMap
3508 :    
3509 :     C<< my @relationMap = _RelationMap($mappedNameHashRef, $mappedNameListRef); >>
3510 :    
3511 :     Create the relation map for an SQL query. The relation map is used by B<DBObject>
3512 :     to determine how to interpret the results of the query.
3513 :    
3514 :     =over 4
3515 :    
3516 :     =item mappedNameHashRef
3517 :    
3518 :     Reference to a hash that maps modified object names to real object names.
3519 :    
3520 :     =item mappedNameListRef
3521 :    
3522 :     Reference to a list of modified object names in the order they appear in the
3523 :     SELECT list.
3524 :    
3525 :     =item RETURN
3526 :    
3527 :     Returns a list of 2-tuples. Each tuple consists of an object name as used in the
3528 :     query followed by the actual name of that object. This enables the B<DBObject> to
3529 :     determine the order of the tables in the query and which object name belongs to each
3530 :     mapped object name. Most of the time these two values are the same; however, if a
3531 :     relation occurs twice in the query, the relation name in the field list and WHERE
3532 :     clause will use a mapped name (generally the actual relation name with a numeric
3533 :     suffix) that does not match the actual relation name.
3534 :    
3535 :     =back
3536 :    
3537 :     =cut
3538 :    
3539 :     sub _RelationMap {
3540 :     # Get the parameters.
3541 :     my ($mappedNameHashRef, $mappedNameListRef) = @_;
3542 :     # Declare the return variable.
3543 :     my @retVal = ();
3544 :     # Build the map.
3545 :     for my $mappedName (@{$mappedNameListRef}) {
3546 :     push @retVal, [$mappedName, $mappedNameHashRef->{$mappedName}];
3547 :     }
3548 :     # Return it.
3549 :     return @retVal;
3550 :     }
3551 :    
3552 :    
3553 :     =head3 _SetupSQL
3554 : parrello 1.45
3555 :     Process a list of object names and a filter clause so that they can be used to
3556 :     build an SQL statement. This method takes in a reference to a list of object names
3557 :     and a filter clause. It will return a corrected filter clause, a list of mapped
3558 :     names and the mapped name hash.
3559 :    
3560 :     This is an instance method.
3561 :    
3562 :     =over 4
3563 :    
3564 :     =item objectNames
3565 :    
3566 :     Reference to a list of the object names to be included in the query.
3567 :    
3568 :     =item filterClause
3569 :    
3570 :     A string containing the WHERE clause for the query (without the C<WHERE>) and also
3571 :     optionally the C<ORDER BY> and C<LIMIT> clauses.
3572 :    
3573 : parrello 1.70 =item matchClause
3574 :    
3575 :     An optional full-text search clause. If specified, it will be inserted at the
3576 :     front of the WHERE clause. It should already be SQL-formatted; that is, the
3577 :     field names should be in the form I<table>C<.>I<fieldName>.
3578 :    
3579 : parrello 1.45 =item RETURN
3580 :    
3581 :     Returns a three-element list. The first element is the SQL statement suffix, beginning
3582 :     with the FROM clause. The second element is a reference to a list of the names to be
3583 :     used in retrieving the fields. The third element is a hash mapping the names to the
3584 :     objects they represent.
3585 :    
3586 :     =back
3587 :    
3588 :     =cut
3589 :    
3590 :     sub _SetupSQL {
3591 : parrello 1.70 my ($self, $objectNames, $filterClause, $matchClause) = @_;
3592 : parrello 1.45 # Adjust the list of object names to account for multiple occurrences of the
3593 :     # same object. We start with a hash table keyed on object name that will
3594 :     # return the object suffix. The first time an object is encountered it will
3595 :     # not be found in the hash. The next time the hash will map the object name
3596 :     # to 2, then 3, and so forth.
3597 :     my %objectHash = ();
3598 :     # This list will contain the object names as they are to appear in the
3599 :     # FROM list.
3600 :     my @fromList = ();
3601 :     # This list contains the suffixed object name for each object. It is exactly
3602 :     # parallel to the list in the $objectNames parameter.
3603 :     my @mappedNameList = ();
3604 :     # Finally, this hash translates from a mapped name to its original object name.
3605 :     my %mappedNameHash = ();
3606 :     # Now we create the lists. Note that for every single name we push something into
3607 :     # @fromList and @mappedNameList. This insures that those two arrays are exactly
3608 :     # parallel to $objectNames.
3609 :     for my $objectName (@{$objectNames}) {
3610 :     # Get the next suffix for this object.
3611 :     my $suffix = $objectHash{$objectName};
3612 :     if (! $suffix) {
3613 :     # Here we are seeing the object for the first time. The object name
3614 :     # is used as is.
3615 :     push @mappedNameList, $objectName;
3616 :     push @fromList, $objectName;
3617 :     $mappedNameHash{$objectName} = $objectName;
3618 :     # Denote the next suffix will be 2.
3619 :     $objectHash{$objectName} = 2;
3620 :     } else {
3621 :     # Here we've seen the object before. We construct a new name using
3622 :     # the suffix from the hash and update the hash.
3623 :     my $mappedName = "$objectName$suffix";
3624 :     $objectHash{$objectName} = $suffix + 1;
3625 :     # The FROM list has the object name followed by the mapped name. This
3626 :     # tells SQL it's still the same table, but we're using a different name
3627 :     # for it to avoid confusion.
3628 :     push @fromList, "$objectName $mappedName";
3629 :     # The mapped-name list contains the real mapped name.
3630 :     push @mappedNameList, $mappedName;
3631 :     # Finally, enable us to get back from the mapped name to the object name.
3632 :     $mappedNameHash{$mappedName} = $objectName;
3633 :     }
3634 :     }
3635 :     # Begin the SELECT suffix. It starts with
3636 :     #
3637 :     # FROM name1, name2, ... nameN
3638 :     #
3639 :     my $suffix = "FROM " . join(', ', @fromList);
3640 : parrello 1.70 # Now for the WHERE. First, we need a place for the filter string.
3641 :     my $filterString = "";
3642 :     # We will also keep a list of conditions to add to the WHERE clause in order to link
3643 :     # entities and relationships as well as primary relations to secondary ones.
3644 :     my @joinWhere = ();
3645 : parrello 1.45 # Check for a filter clause.
3646 :     if ($filterClause) {
3647 :     # Here we have one, so we convert its field names and add it to the query. First,
3648 :     # We create a copy of the filter string we can work with.
3649 : parrello 1.70 $filterString = $filterClause;
3650 : parrello 1.45 # Next, we sort the object names by length. This helps protect us from finding
3651 :     # object names inside other object names when we're doing our search and replace.
3652 :     my @sortedNames = sort { length($b) - length($a) } @mappedNameList;
3653 :     # The final preparatory step is to create a hash table of relation names. The
3654 :     # table begins with the relation names already in the SELECT command. We may
3655 :     # need to add relations later if there is filtering on a field in a secondary
3656 :     # relation. The secondary relations are the ones that contain multiply-
3657 :     # occurring or optional fields.
3658 :     my %fromNames = map { $_ => 1 } @sortedNames;
3659 :     # We are ready to begin. We loop through the object names, replacing each
3660 :     # object name's field references by the corresponding SQL field reference.
3661 :     # Along the way, if we find a secondary relation, we will need to add it
3662 :     # to the FROM clause.
3663 :     for my $mappedName (@sortedNames) {
3664 :     # Get the length of the object name plus 2. This is the value we add to the
3665 :     # size of the field name to determine the size of the field reference as a
3666 :     # whole.
3667 :     my $nameLength = 2 + length $mappedName;
3668 :     # Get the real object name for this mapped name.
3669 :     my $objectName = $mappedNameHash{$mappedName};
3670 :     Trace("Processing $mappedName for object $objectName.") if T(4);
3671 :     # Get the object's field list.
3672 :     my $fieldList = $self->GetFieldTable($objectName);
3673 :     # Find the field references for this object.
3674 :     while ($filterString =~ m/$mappedName\(([^)]*)\)/g) {
3675 :     # At this point, $1 contains the field name, and the current position
3676 :     # is set immediately after the final parenthesis. We pull out the name of
3677 :     # the field and the position and length of the field reference as a whole.
3678 :     my $fieldName = $1;
3679 :     my $len = $nameLength + length $fieldName;
3680 :     my $pos = pos($filterString) - $len;
3681 :     # Insure the field exists.
3682 :     if (!exists $fieldList->{$fieldName}) {
3683 :     Confess("Field $fieldName not found for object $objectName.");
3684 :     } else {
3685 :     Trace("Processing $fieldName at position $pos.") if T(4);
3686 :     # Get the field's relation.
3687 :     my $relationName = $fieldList->{$fieldName}->{relation};
3688 :     # Now we have a secondary relation. We need to insure it matches the
3689 :     # mapped name of the primary relation. First we peel off the suffix
3690 :     # from the mapped name.
3691 :     my $mappingSuffix = substr $mappedName, length($objectName);
3692 :     # Put the mapping suffix onto the relation name to get the
3693 :     # mapped relation name.
3694 :     my $mappedRelationName = "$relationName$mappingSuffix";
3695 :     # Insure the relation is in the FROM clause.
3696 :     if (!exists $fromNames{$mappedRelationName}) {
3697 :     # Add the relation to the FROM clause.
3698 :     if ($mappedRelationName eq $relationName) {
3699 :     # The name is un-mapped, so we add it without
3700 :     # any frills.
3701 :     $suffix .= ", $relationName";
3702 :     push @joinWhere, "$objectName.id = $relationName.id";
3703 :     } else {
3704 :     # Here we have a mapping situation.
3705 :     $suffix .= ", $relationName $mappedRelationName";
3706 :     push @joinWhere, "$mappedRelationName.id = $mappedName.id";
3707 :     }
3708 :     # Denote we have this relation available for future fields.
3709 :     $fromNames{$mappedRelationName} = 1;
3710 :     }
3711 :     # Form an SQL field reference from the relation name and the field name.
3712 :     my $sqlReference = "$mappedRelationName." . _FixName($fieldName);
3713 :     # Put it into the filter string in place of the old value.
3714 :     substr($filterString, $pos, $len) = $sqlReference;
3715 :     # Reposition the search.
3716 :     pos $filterString = $pos + length $sqlReference;
3717 :     }
3718 :     }
3719 :     }
3720 : parrello 1.70 }
3721 :     # The next step is to join the objects together. We only need to do this if there
3722 :     # is more than one object in the object list. We start with the first object and
3723 :     # run through the objects after it. Note also that we make a safety copy of the
3724 :     # list before running through it, because we shift off the first object before
3725 :     # processing the rest.
3726 :     my @mappedObjectList = @mappedNameList;
3727 :     my $lastMappedObject = shift @mappedObjectList;
3728 :     # Get the join table.
3729 :     my $joinTable = $self->{_metaData}->{Joins};
3730 :     # Loop through the object list.
3731 :     for my $thisMappedObject (@mappedObjectList) {
3732 :     # Look for a join using the real object names.
3733 :     my $lastObject = $mappedNameHash{$lastMappedObject};
3734 :     my $thisObject = $mappedNameHash{$thisMappedObject};
3735 :     my $joinKey = "$lastObject/$thisObject";
3736 :     if (!exists $joinTable->{$joinKey}) {
3737 :     # Here there's no join, so we throw an error.
3738 :     Confess("No join exists to connect from $lastMappedObject to $thisMappedObject.");
3739 :     } else {
3740 :     # Get the join clause.
3741 :     my $unMappedJoin = $joinTable->{$joinKey};
3742 :     # Fix the names.
3743 :     $unMappedJoin =~ s/$lastObject/$lastMappedObject/;
3744 :     $unMappedJoin =~ s/$thisObject/$thisMappedObject/;
3745 :     push @joinWhere, $unMappedJoin;
3746 :     # Save this object as the last object for the next iteration.
3747 :     $lastMappedObject = $thisMappedObject;
3748 :     }
3749 :     }
3750 :     # Now we need to handle the whole ORDER BY / LIMIT thing. The important part
3751 :     # here is we want the filter clause to be empty if there's no WHERE filter.
3752 :     # We'll put the ORDER BY / LIMIT clauses in the following variable.
3753 :     my $orderClause = "";
3754 :     # This is only necessary if we have a filter string in which the ORDER BY
3755 :     # and LIMIT clauses can live.
3756 :     if ($filterString) {
3757 : parrello 1.45 # Locate the ORDER BY or LIMIT verbs (if any). We use a non-greedy
3758 :     # operator so that we find the first occurrence of either verb.
3759 :     if ($filterString =~ m/^(.*?)\s*(ORDER BY|LIMIT)/g) {
3760 :     # Here we have an ORDER BY or LIMIT verb. Split it off of the filter string.
3761 :     my $pos = pos $filterString;
3762 :     $orderClause = $2 . substr($filterString, $pos);
3763 :     $filterString = $1;
3764 :     }
3765 : parrello 1.70 }
3766 :     # All the things that are supposed to be in the WHERE clause of the
3767 :     # SELECT command need to be put into @joinWhere so we can string them
3768 :     # together. We begin with the match clause. This is important,
3769 :     # because the match clause's parameter mark must precede any parameter
3770 :     # marks in the filter string.
3771 :     if ($matchClause) {
3772 :     push @joinWhere, $matchClause;
3773 :     }
3774 :     # Add the filter string. We put it in parentheses to avoid operator
3775 :     # precedence problems with the match clause or the joins.
3776 :     if ($filterString) {
3777 :     Trace("Filter string is \"$filterString\".") if T(4);
3778 :     push @joinWhere, "($filterString)";
3779 :     }
3780 :     # String it all together into a big filter clause.
3781 :     if (@joinWhere) {
3782 :     $suffix .= " WHERE " . join(' AND ', @joinWhere);
3783 :     }
3784 :     # Add the sort or limit clause (if any).
3785 :     if ($orderClause) {
3786 :     $suffix .= " $orderClause";
3787 : parrello 1.45 }
3788 :     # Return the suffix, the mapped name list, and the mapped name hash.
3789 :     return ($suffix, \@mappedNameList, \%mappedNameHash);
3790 :     }
3791 :    
3792 : parrello 1.70 =head3 _GetStatementHandle
3793 : parrello 1.45
3794 :     This method will prepare and execute an SQL query, returning the statement handle.
3795 :     The main reason for doing this here is so that everybody who does SQL queries gets
3796 :     the benefit of tracing.
3797 :    
3798 :     This is an instance method.
3799 :    
3800 :     =over 4
3801 :    
3802 :     =item command
3803 :    
3804 :     Command to prepare and execute.
3805 :    
3806 :     =item params
3807 :    
3808 :     Reference to a list of the values to be substituted in for the parameter marks.
3809 :    
3810 :     =item RETURN
3811 :    
3812 :     Returns a prepared and executed statement handle from which the caller can extract
3813 :     results.
3814 :    
3815 :     =back
3816 :    
3817 :     =cut
3818 :    
3819 :     sub _GetStatementHandle {
3820 :     # Get the parameters.
3821 :     my ($self, $command, $params) = @_;
3822 :     # Trace the query.
3823 :     Trace("SQL query: $command") if T(SQL => 3);
3824 :     Trace("PARMS: '" . (join "', '", @{$params}) . "'") if (T(SQL => 4) && (@{$params} > 0));
3825 :     # Get the database handle.
3826 :     my $dbh = $self->{_dbh};
3827 :     # Prepare the command.
3828 :     my $sth = $dbh->prepare_command($command);
3829 :     # Execute it with the parameters bound in.
3830 : parrello 1.75 $sth->execute(@{$params}) || Confess("SELECT error: " . $sth->errstr());
3831 : parrello 1.45 # Return the statement handle.
3832 :     return $sth;
3833 :     }
3834 :    
3835 : parrello 1.70 =head3 _GetLoadStats
3836 : parrello 1.1
3837 :     Return a blank statistics object for use by the load methods.
3838 :    
3839 :     This is a static method.
3840 :    
3841 :     =cut
3842 :    
3843 : parrello 1.29 sub _GetLoadStats{
3844 : parrello 1.28 return Stats->new();
3845 : parrello 1.1 }
3846 :    
3847 : parrello 1.70 =head3 _DumpRelation
3848 : parrello 1.1
3849 : parrello 1.73 Dump the specified relation to the specified output file in tab-delimited format.
3850 : parrello 1.1
3851 :     This is an instance method.
3852 :    
3853 :     =over 4
3854 :    
3855 :     =item outputDirectory
3856 :    
3857 :     Directory to contain the output file.
3858 :    
3859 :     =item relationName
3860 :    
3861 :     Name of the relation to dump.
3862 :    
3863 :     =item relation
3864 :    
3865 :     Structure describing the relation to be dumped.
3866 :    
3867 :     =back
3868 :    
3869 :     =cut
3870 :    
3871 :     sub _DumpRelation {
3872 : parrello 1.10 # Get the parameters.
3873 :     my ($self, $outputDirectory, $relationName, $relation) = @_;
3874 :     # Open the output file.
3875 :     my $fileName = "$outputDirectory/$relationName.dtx";
3876 :     open(DTXOUT, ">$fileName") || Confess("Could not open dump file $fileName: $!");
3877 :     # Create a query for the specified relation.
3878 :     my $dbh = $self->{_dbh};
3879 :     my $query = $dbh->prepare_command("SELECT * FROM $relationName");
3880 :     # Execute the query.
3881 :     $query->execute() || Confess("SELECT error dumping $relationName.");
3882 :     # Loop through the results.
3883 :     while (my @row = $query->fetchrow) {
3884 :     # Escape any tabs or new-lines in the row text.
3885 :     for my $field (@row) {
3886 :     $field =~ s/\n/\\n/g;
3887 :     $field =~ s/\t/\\t/g;
3888 :     }
3889 :     # Tab-join the row and write it to the output file.
3890 :     my $rowText = join("\t", @row);
3891 :     print DTXOUT "$rowText\n";
3892 :     }
3893 :     # Close the output file.
3894 :     close DTXOUT;
3895 : parrello 1.1 }
3896 :    
3897 : parrello 1.70 =head3 _GetStructure
3898 : parrello 1.1
3899 :     Get the data structure for a specified entity or relationship.
3900 :    
3901 :     This is an instance method.
3902 :    
3903 :     =over 4
3904 :    
3905 :     =item objectName
3906 :    
3907 :     Name of the desired entity or relationship.
3908 :    
3909 :     =item RETURN
3910 :    
3911 :     The descriptor for the specified object.
3912 :    
3913 :     =back
3914 :    
3915 :     =cut
3916 :    
3917 :     sub _GetStructure {
3918 : parrello 1.10 # Get the parameters.
3919 :     my ($self, $objectName) = @_;
3920 :     # Get the metadata structure.
3921 :     my $metadata = $self->{_metaData};
3922 :     # Declare the variable to receive the descriptor.
3923 :     my $retVal;
3924 :     # Get the descriptor from the metadata.
3925 :     if (exists $metadata->{Entities}->{$objectName}) {
3926 :     $retVal = $metadata->{Entities}->{$objectName};
3927 :     } elsif (exists $metadata->{Relationships}->{$objectName}) {
3928 :     $retVal = $metadata->{Relationships}->{$objectName};
3929 :     } else {
3930 :     Confess("Object $objectName not found in database.");
3931 :     }
3932 :     # Return the descriptor.
3933 :     return $retVal;
3934 : parrello 1.1 }
3935 :    
3936 : parrello 1.70
3937 :    
3938 :     =head3 _GetRelationTable
3939 : parrello 1.1
3940 :     Get the list of relations for a specified entity or relationship.
3941 :    
3942 :     This is an instance method.
3943 :    
3944 :     =over 4
3945 :    
3946 :     =item objectName
3947 :    
3948 :     Name of the desired entity or relationship.
3949 :    
3950 :     =item RETURN
3951 :    
3952 :     A table containing the relations for the specified object.
3953 :    
3954 :     =back
3955 :    
3956 :     =cut
3957 :    
3958 :     sub _GetRelationTable {
3959 : parrello 1.10 # Get the parameters.
3960 :     my ($self, $objectName) = @_;
3961 :     # Get the descriptor from the metadata.
3962 :     my $objectData = $self->_GetStructure($objectName);
3963 :     # Return the object's relation list.
3964 :     return $objectData->{Relations};
3965 : parrello 1.1 }
3966 :    
3967 : parrello 1.70 =head3 _ValidateFieldNames
3968 : parrello 1.1
3969 :     Determine whether or not the field names are valid. A description of the problems with the names
3970 :     will be written to the standard error output. If there is an error, this method will abort. This is
3971 :     a static method.
3972 :    
3973 :     =over 4
3974 :    
3975 :     =item metadata
3976 :    
3977 :     Metadata structure loaded from the XML data definition.
3978 :    
3979 :     =back
3980 :    
3981 :     =cut
3982 :    
3983 :     sub _ValidateFieldNames {
3984 : parrello 1.10 # Get the object.
3985 :     my ($metadata) = @_;
3986 :     # Declare the return value. We assume success.
3987 :     my $retVal = 1;
3988 :     # Loop through the sections of the database definition.
3989 :     for my $section ('Entities', 'Relationships') {
3990 :     # Loop through the objects in this section.
3991 :     for my $object (values %{$metadata->{$section}}) {
3992 :     # Loop through the object's fields.
3993 :     for my $fieldName (keys %{$object->{Fields}}) {
3994 : parrello 1.73 # If this field name is invalid, set the return value to zero
3995 :     # so we know we encountered an error.
3996 :     if (! ValidateFieldName($fieldName)) {
3997 : parrello 1.10 $retVal = 0;
3998 :     }
3999 :     }
4000 :     }
4001 :     }
4002 :     # If an error was found, fail.
4003 :     if ($retVal == 0) {
4004 :     Confess("Errors found in field names.");
4005 :     }
4006 : parrello 1.1 }
4007 :    
4008 : parrello 1.70 =head3 _LoadRelation
4009 : parrello 1.1
4010 :     Load a relation from the data in a tab-delimited disk file. The load will only take place if a disk
4011 :     file with the same name as the relation exists in the specified directory.
4012 :    
4013 :     This is an instance method.
4014 :    
4015 :     =over 4
4016 :    
4017 :     =item dbh
4018 :    
4019 :     DBKernel object for accessing the database.
4020 :    
4021 :     =item directoryName
4022 :    
4023 :     Name of the directory containing the tab-delimited data files.
4024 :    
4025 :     =item relationName
4026 :    
4027 :     Name of the relation to load.
4028 :    
4029 :     =item rebuild
4030 :    
4031 :     TRUE if the table should be dropped and re-created before loading.
4032 :    
4033 :     =item RETURN
4034 :    
4035 :     Returns a statistical object describing the number of records read and a list of error messages.
4036 :    
4037 :     =back
4038 :    
4039 :     =cut
4040 :    
4041 :     sub _LoadRelation {
4042 : parrello 1.10 # Get the parameters.
4043 :     my ($self, $directoryName, $relationName, $rebuild) = @_;
4044 :     # Create the file name.
4045 :     my $fileName = "$directoryName/$relationName";
4046 :     # If the file doesn't exist, try adding the .dtx suffix.
4047 :     if (! -e $fileName) {
4048 :     $fileName .= ".dtx";
4049 :     if (! -e $fileName) {
4050 :     $fileName = "";
4051 :     }
4052 :     }
4053 :     # Create the return object.
4054 :     my $retVal = _GetLoadStats();
4055 :     # If a file exists to load the table, its name will be in $fileName. Otherwise, $fileName will
4056 :     # be a null string.
4057 :     if ($fileName ne "") {
4058 :     # Load the relation from the file.
4059 :     $retVal = $self->LoadTable($fileName, $relationName, $rebuild);
4060 :     } elsif ($rebuild) {
4061 :     # Here we are rebuilding, but no file exists, so we just re-create the table.
4062 :     $self->CreateTable($relationName, 1);
4063 :     }
4064 :     # Return the statistics from the load.
4065 :     return $retVal;
4066 : parrello 1.1 }
4067 :    
4068 : parrello 1.73
4069 : parrello 1.70 =head3 _LoadMetaData
4070 : parrello 1.1
4071 :     This method loads the data describing this database from an XML file into a metadata structure.
4072 :     The resulting structure is a set of nested hash tables containing all the information needed to
4073 :     load or use the database. The schema for the XML file is F<ERDatabase.xml>.
4074 :    
4075 :     This is a static method.
4076 :    
4077 :     =over 4
4078 :    
4079 :     =item filename
4080 :    
4081 :     Name of the file containing the database definition.
4082 :    
4083 :     =item RETURN
4084 :    
4085 :     Returns a structure describing the database.
4086 :    
4087 :     =back
4088 :    
4089 :     =cut
4090 :    
4091 :     sub _LoadMetaData {
4092 : parrello 1.10 # Get the parameters.
4093 :     my ($filename) = @_;
4094 : parrello 1.75 Trace("Reading DBD from $filename.") if T(2);
4095 : parrello 1.10 # Slurp the XML file into a variable. Extensive use of options is used to insure we
4096 :     # get the exact structure we want.
4097 : parrello 1.73 my $metadata = ReadMetaXML($filename);
4098 : parrello 1.10 # Before we go any farther, we need to validate the field and object names. If an error is found,
4099 :     # the method below will fail.
4100 :     _ValidateFieldNames($metadata);
4101 :     # Next we need to create a hash table for finding relations. The entities and relationships are
4102 :     # implemented as one or more database relations.
4103 :     my %masterRelationTable = ();
4104 :     # Loop through the entities.
4105 :     my $entityList = $metadata->{Entities};
4106 :     for my $entityName (keys %{$entityList}) {
4107 :     my $entityStructure = $entityList->{$entityName};
4108 :     #
4109 : parrello 1.12 # The first step is to create all the entity's default values. For C<Field> elements,
4110 : parrello 1.10 # the relation name must be added where it is not specified. For relationships,
4111 :     # the B<from-link> and B<to-link> fields must be inserted, and for entities an B<id>
4112 :     # field must be added to each relation. Finally, each field will have a C<PrettySort> attribute
4113 :     # added that can be used to pull the implicit fields to the top when displaying the field
4114 :     # documentation. The PrettySort values are 1-based and indicate in which pass through a
4115 :     # relation's data the field should be displayed-- 1 for the first pass, 2 for the second,
4116 :     # and so on.
4117 :     #
4118 :     # Fix up this entity.
4119 :     _FixupFields($entityStructure, $entityName, 2, 3);
4120 :     # Add the ID field.
4121 :     _AddField($entityStructure, 'id', { type => $entityStructure->{keyType},
4122 :     relation => $entityName,
4123 :     Notes => { content => "Unique identifier for this \[b\]$entityName\[/b\]." },
4124 :     PrettySort => 1});
4125 :     #
4126 :     # The current field list enables us to quickly find the relation containing a particular field.
4127 :     # We also need a list that tells us the fields in each relation. We do this by creating a
4128 :     # Relations structure in the entity structure and collating the fields into it based on their
4129 :     # C<relation> property. There is one tricky bit, which is that every relation has to have the
4130 :     # C<id> field in it. Note also that the field list is put into a C<Fields> member of the
4131 :     # relation's structure so that it looks more like the entity and relationship structures.
4132 :     #
4133 :     # First we need to create the relations list.
4134 :     my $relationTable = { };
4135 :     # Loop through the fields. We use a list of field names to prevent a problem with
4136 :     # the hash table cursor losing its place during the loop.
4137 :     my $fieldList = $entityStructure->{Fields};
4138 :     my @fieldNames = keys %{$fieldList};
4139 :     for my $fieldName (@fieldNames) {
4140 :     my $fieldData = $fieldList->{$fieldName};
4141 :     # Get the current field's relation name.
4142 :     my $relationName = $fieldData->{relation};
4143 :     # Insure the relation exists.
4144 :     if (!exists $relationTable->{$relationName}) {
4145 :     $relationTable->{$relationName} = { Fields => { } };
4146 :     }
4147 :     # Add the field to the relation's field structure.
4148 :     $relationTable->{$relationName}->{Fields}->{$fieldName} = $fieldData;
4149 :     }
4150 :     # Now that we've organized all our fields by relation name we need to do some serious
4151 :     # housekeeping. We must add the C<id> field to every relation and convert each relation
4152 :     # to a list of fields. First, we need the ID field itself.
4153 :     my $idField = $fieldList->{id};
4154 :     # Loop through the relations.
4155 :     for my $relationName (keys %{$relationTable}) {
4156 :     my $relation = $relationTable->{$relationName};
4157 :     # Get the relation's field list.
4158 :     my $relationFieldList = $relation->{Fields};
4159 :     # Add the ID field to it. If the field's already there, it will not make any
4160 :     # difference.
4161 :     $relationFieldList->{id} = $idField;
4162 :     # Convert the field set from a hash into a list using the pretty-sort number.
4163 :     $relation->{Fields} = _ReOrderRelationTable($relationFieldList);
4164 :     # Add the relation to the master table.
4165 :     $masterRelationTable{$relationName} = $relation;
4166 :     }
4167 :     # The indexes come next. The primary relation will have a unique-keyed index based on the ID field.
4168 :     # The other relations must have at least one index that begins with the ID field. In addition, the
4169 :     # metadata may require alternate indexes. We do those alternate indexes first. To begin, we need to
4170 :     # get the entity's field list and index list.
4171 :     my $indexList = $entityStructure->{Indexes};
4172 :     # Loop through the indexes.
4173 :     for my $indexData (@{$indexList}) {
4174 :     # We need to find this index's fields. All of them should belong to the same relation.
4175 :     # The ID field is an exception, since it's in all relations.
4176 :     my $relationName = '0';
4177 :     for my $fieldDescriptor (@{$indexData->{IndexFields}}) {
4178 :     # Get this field's name.
4179 :     my $fieldName = $fieldDescriptor->{name};
4180 :     # Only proceed if it is NOT the ID field.
4181 :     if ($fieldName ne 'id') {
4182 :     # Find the relation containing the current index field.
4183 :     my $thisName = $fieldList->{$fieldName}->{relation};
4184 :     if ($relationName eq '0') {
4185 :     # Here we're looking at the first field, so we save its relation name.
4186 :     $relationName = $thisName;
4187 :     } elsif ($relationName ne $thisName) {
4188 :     # Here we have a field mismatch.
4189 :     Confess("Mixed index: field $fieldName does not belong to relation $relationName.");
4190 :     }
4191 :     }
4192 :     }
4193 :     # Now $relationName is the name of the relation that contains this index. Add the index structure
4194 :     # to the relation.
4195 :     push @{$relationTable->{$relationName}->{Indexes}}, $indexData;
4196 :     }
4197 :     # Now each index has been put in a relation. We need to add the primary index for the primary
4198 :     # relation.
4199 :     push @{$relationTable->{$entityName}->{Indexes}},
4200 :     { IndexFields => [ {name => 'id', order => 'ascending'} ], Unique => 'true',
4201 :     Notes => { content => "Primary index for $entityName." }
4202 :     };
4203 :     # The next step is to insure that each relation has at least one index that begins with the ID field.
4204 :     # After that, we convert each relation's index list to an index table. We first need to loop through
4205 :     # the relations.
4206 :     for my $relationName (keys %{$relationTable}) {
4207 :     my $relation = $relationTable->{$relationName};
4208 :     # Get the relation's index list.
4209 :     my $indexList = $relation->{Indexes};
4210 :     # Insure this relation has an ID index.
4211 :     my $found = 0;
4212 :     for my $index (@{$indexList}) {
4213 :     if ($index->{IndexFields}->[0]->{name} eq "id") {
4214 :     $found = 1;
4215 :     }
4216 :     }
4217 :     if ($found == 0) {
4218 :     push @{$indexList}, { IndexFields => [ {name => 'id', order => 'ascending'} ] };
4219 :     }
4220 :     # Now we need to convert the relation's index list to an index table. We begin by creating
4221 :     # an empty table in the relation structure.
4222 :     $relation->{Indexes} = { };
4223 :     # Loop through the indexes.
4224 :     my $count = 0;
4225 :     for my $index (@{$indexList}) {
4226 :     # Add this index to the index table.
4227 : parrello 1.75 _AddIndex("idx$count", $relation, $index);
4228 : parrello 1.10 # Increment the counter so that the next index has a different name.
4229 :     $count++;
4230 :     }
4231 :     }
4232 :     # Finally, we add the relation structure to the entity.
4233 :     $entityStructure->{Relations} = $relationTable;
4234 :     }
4235 :     # Loop through the relationships. Relationships actually turn out to be much simpler than entities.
4236 :     # For one thing, there is only a single constituent relation.
4237 :     my $relationshipList = $metadata->{Relationships};
4238 :     for my $relationshipName (keys %{$relationshipList}) {
4239 :     my $relationshipStructure = $relationshipList->{$relationshipName};
4240 :     # Fix up this relationship.
4241 :     _FixupFields($relationshipStructure, $relationshipName, 2, 3);
4242 :     # Format a description for the FROM field.
4243 :     my $fromEntity = $relationshipStructure->{from};
4244 :     my $fromComment = "<b>id</b> of the source <b><a href=\"#$fromEntity\">$fromEntity</a></b>.";
4245 :     # Get the FROM entity's key type.
4246 :     my $fromType = $entityList->{$fromEntity}->{keyType};
4247 :     # Add the FROM field.
4248 :     _AddField($relationshipStructure, 'from-link', { type => $fromType,
4249 :     relation => $relationshipName,
4250 :     Notes => { content => $fromComment },
4251 :     PrettySort => 1});
4252 :     # Format a description for the TO field.
4253 :     my $toEntity = $relationshipStructure->{to};
4254 :     my $toComment = "<b>id</b> of the target <b><a href=\"#$toEntity\">$toEntity</a></b>.";
4255 :     # Get the TO entity's key type.
4256 :     my $toType = $entityList->{$toEntity}->{keyType};
4257 :     # Add the TO field.
4258 :     _AddField($relationshipStructure, 'to-link', { type=> $toType,
4259 :     relation => $relationshipName,
4260 :     Notes => { content => $toComment },
4261 :     PrettySort => 1});
4262 :     # Create an index-free relation from the fields.
4263 :     my $thisRelation = { Fields => _ReOrderRelationTable($relationshipStructure->{Fields}),
4264 :     Indexes => { } };
4265 :     $relationshipStructure->{Relations} = { $relationshipName => $thisRelation };
4266 :     # Create the FROM and TO indexes.
4267 :     _CreateRelationshipIndex("From", $relationshipName, $relationshipStructure);
4268 :     _CreateRelationshipIndex("To", $relationshipName, $relationshipStructure);
4269 :     # Add the relation to the master table.
4270 :     $masterRelationTable{$relationshipName} = $thisRelation;
4271 :     }
4272 :     # Now store the master relation table in the metadata structure.
4273 :     $metadata->{RelationTable} = \%masterRelationTable;
4274 :     # Our final task is to create the join table. The join table is a hash that describes all
4275 :     # the join clauses for traveling through the relationships. The join clause is an equality
4276 :     # condition that can be put into a WHERE clause in order to join two objects. Two relationships
4277 :     # can be joined if they share an entity in common; and an entity can be joined to a relationship
4278 :     # if the entity is at either end of the relationship.
4279 :     my %joinTable = ();
4280 :     # Loop through the entities.
4281 :     for my $entityName (keys %{$entityList}) {
4282 :     # Build three lists of the relationships connected to this entity. One will be
4283 :     # for relationships from the entity, one for relationships to the entity, and
4284 :     # one for recursive relationships.
4285 :     my @fromList = ();
4286 :     my @toList = ();
4287 :     my @bothList = ();
4288 : parrello 1.21 Trace("Join table build for $entityName.") if T(metadata => 4);
4289 : parrello 1.10 for my $relationshipName (keys %{$relationshipList}) {
4290 :     my $relationship = $relationshipList->{$relationshipName};
4291 :     # Determine if this relationship has our entity in one of its link fields.
4292 :     my $fromEntity = $relationship->{from};
4293 :     my $toEntity = $relationship->{to};
4294 : parrello 1.41 Trace("Join check for relationship $relationshipName from $fromEntity to $toEntity.") if T(Joins => 4);
4295 : parrello 1.10 if ($fromEntity eq $entityName) {
4296 :     if ($toEntity eq $entityName) {
4297 :     # Here the relationship is recursive.
4298 :     push @bothList, $relationshipName;
4299 : parrello 1.21 Trace("Relationship $relationshipName put in both-list.") if T(metadata => 4);
4300 : parrello 1.10 } else {
4301 :     # Here the relationship comes from the entity.
4302 :     push @fromList, $relationshipName;
4303 : parrello 1.21 Trace("Relationship $relationshipName put in from-list.") if T(metadata => 4);
4304 : parrello 1.10 }
4305 :     } elsif ($toEntity eq $entityName) {
4306 :     # Here the relationship goes to the entity.
4307 :     push @toList, $relationshipName;
4308 : parrello 1.21 Trace("Relationship $relationshipName put in to-list.") if T(metadata => 4);
4309 : parrello 1.10 }
4310 :     }
4311 :     # Create the nonrecursive joins. Note that we build two hashes for running