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1 : parrello 1.1 #!/usr/bin/perl -w
2 :    
3 :     package CustomAttributes;
4 :    
5 :     require Exporter;
6 :     use ERDB;
7 : parrello 1.4 @ISA = qw(ERDB);
8 : parrello 1.1 use strict;
9 :     use Tracer;
10 :     use ERDBLoad;
11 : parrello 1.13 use Stats;
12 : parrello 1.1
13 :     =head1 Custom SEED Attribute Manager
14 :    
15 :     =head2 Introduction
16 :    
17 :     The Custom SEED Attributes Manager allows the user to upload and retrieve
18 :     custom data for SEED objects. It uses the B<ERDB> database system to
19 : parrello 1.10 store the attributes.
20 :    
21 :     Attributes are organized by I<attribute key>. Attribute values are
22 :     assigned to I<objects>. In the real world, objects have types and IDs;
23 :     however, to the attribute database only the ID matters. This will create
24 :     a problem if we have a single ID that applies to two objects of different
25 :     types, but it is more consistent with the original attribute implementation
26 : parrello 1.11 in the SEED (which this implementation replaces).
27 : parrello 1.10
28 : parrello 1.11 The actual attribute values are stored as a relationship between the attribute
29 :     keys and the objects. There can be multiple values for a single key/object pair.
30 : parrello 1.1
31 :     The full suite of ERDB retrieval capabilities is provided. In addition,
32 :     custom methods are provided specific to this application. To get all
33 : parrello 1.6 the values of the attribute C<essential> in a specified B<Feature>, you
34 : parrello 1.1 would code
35 :    
36 : parrello 1.10 my @values = $attrDB->GetAttributes($fid, 'essential');
37 : parrello 1.1
38 : parrello 1.10 where I<$fid> contains the ID of the desired feature.
39 : parrello 1.1
40 : parrello 1.10 New attribute keys must be defined before they can be used. A web interface
41 :     is provided for this purpose.
42 : parrello 1.1
43 : parrello 1.18 Major attribute activity is recorded in a log (C<attributes.log>) in the
44 :     C<$FIG_Config::var> directory. The log reports the user name, time, and
45 :     the details of the operation. The user name will almost always be unknown,
46 :     except when it is specified in this object's constructor (see L</new>).
47 :    
48 : parrello 1.1 =head2 FIG_Config Parameters
49 :    
50 :     The following configuration parameters are used to manage custom attributes.
51 :    
52 :     =over 4
53 :    
54 :     =item attrDbms
55 :    
56 :     Type of database manager used: C<mysql> for MySQL or C<pg> for PostGres.
57 :    
58 :     =item attrDbName
59 :    
60 :     Name of the attribute database.
61 :    
62 :     =item attrHost
63 :    
64 :     Name of the host server for the database. If omitted, the current host
65 :     is used.
66 :    
67 :     =item attrUser
68 :    
69 :     User name for logging in to the database.
70 :    
71 :     =item attrPass
72 :    
73 :     Password for logging in to the database.
74 :    
75 :     =item attrPort
76 :    
77 :     TCP/IP port for accessing the database.
78 :    
79 :     =item attrSock
80 :    
81 :     Socket name used to access the database. If omitted, the default socket
82 :     will be used.
83 :    
84 :     =item attrDBD
85 :    
86 :     Fully-qualified file name for the database definition XML file. This file
87 :     functions as data to the attribute management process, so if the data is
88 :     moved, this file must go with it.
89 :    
90 :     =back
91 :    
92 :     =head2 Public Methods
93 :    
94 :     =head3 new
95 :    
96 : parrello 1.18 C<< my $attrDB = CustomAttributes->new(%options); >>
97 : parrello 1.1
98 : parrello 1.18 Construct a new CustomAttributes object. The following options are
99 :     supported.
100 : parrello 1.3
101 :     =over 4
102 :    
103 :     =item splitter
104 :    
105 :     Value to be used to split attribute values into sections in the
106 : parrello 1.18 L</Fig Replacement Methods>. The default is a double colon C<::>,
107 :     and should only be overridden in extreme circumstances.
108 :    
109 :     =item user
110 :    
111 :     Name of the current user. This will appear in the attribute log.
112 : parrello 1.3
113 :     =back
114 : parrello 1.1
115 :     =cut
116 :    
117 :     sub new {
118 :     # Get the parameters.
119 : parrello 1.18 my ($class, %options) = @_;
120 : parrello 1.1 # Connect to the database.
121 :     my $dbh = DBKernel->new($FIG_Config::attrDbms, $FIG_Config::attrDbName,
122 :     $FIG_Config::attrUser, $FIG_Config::attrPass,
123 :     $FIG_Config::attrPort, $FIG_Config::attrHost,
124 :     $FIG_Config::attrSock);
125 :     # Create the ERDB object.
126 :     my $xmlFileName = $FIG_Config::attrDBD;
127 :     my $retVal = ERDB::new($class, $dbh, $xmlFileName);
128 : parrello 1.3 # Store the splitter value.
129 : parrello 1.18 $retVal->{splitter} = $options{splitter} || '::';
130 :     # Store the user name.
131 :     $retVal->{user} = $options{user} || '<unknown>';
132 :     Trace("User $retVal->{user} selected for attribute object.") if T(3);
133 : parrello 1.1 # Return the result.
134 :     return $retVal;
135 :     }
136 :    
137 : parrello 1.10 =head3 StoreAttributeKey
138 :    
139 :     C<< $attrDB->StoreAttributeKey($attributeName, $type, $notes, \@groups); >>
140 :    
141 :     Create or update an attribute for the database.
142 :    
143 :     =over 4
144 : parrello 1.1
145 :     =item attributeName
146 :    
147 :     Name of the attribute. It must be a valid ERDB field name, consisting entirely of
148 :     letters, digits, and hyphens, with a letter at the beginning. If it does not
149 :     exist already, it will be created.
150 :    
151 :     =item type
152 :    
153 :     Data type of the attribute. This must be a valid ERDB data type name.
154 :    
155 :     =item notes
156 :    
157 :     Descriptive notes about the attribute. It is presumed to be raw text, not HTML.
158 :    
159 : parrello 1.10 =item groups
160 : parrello 1.1
161 : parrello 1.10 Reference to a list of the groups to which the attribute should be associated.
162 :     This will replace any groups to which the attribute is currently attached.
163 : parrello 1.1
164 :     =back
165 :    
166 :     =cut
167 :    
168 : parrello 1.3 sub StoreAttributeKey {
169 : parrello 1.1 # Get the parameters.
170 : parrello 1.10 my ($self, $attributeName, $type, $notes, $groups) = @_;
171 : parrello 1.8 # Declare the return variable.
172 :     my $retVal;
173 : parrello 1.1 # Get the data type hash.
174 :     my %types = ERDB::GetDataTypes();
175 :     # Validate the initial input values.
176 :     if (! ERDB::ValidateFieldName($attributeName)) {
177 :     Confess("Invalid attribute name \"$attributeName\" specified.");
178 :     } elsif (! $notes || length($notes) < 25) {
179 :     Confess("Missing or incomplete description for $attributeName.");
180 :     } elsif (! exists $types{$type}) {
181 :     Confess("Invalid data type \"$type\" for $attributeName.");
182 :     } else {
183 : parrello 1.18 # Create a variable to hold the action to be displayed for the log (Add or Update).
184 :     my $action;
185 : parrello 1.10 # Okay, we're ready to begin. See if this key exists.
186 :     my $attribute = $self->GetEntity('AttributeKey', $attributeName);
187 :     if (defined($attribute)) {
188 :     # It does, so we do an update.
189 : parrello 1.18 $action = "Update Key";
190 : parrello 1.10 $self->UpdateEntity('AttributeKey', $attributeName,
191 :     { description => $notes, 'data-type' => $type });
192 :     # Detach the key from its current groups.
193 :     $self->Disconnect('IsInGroup', 'AttributeKey', $attributeName);
194 :     } else {
195 :     # It doesn't, so we do an insert.
196 : parrello 1.18 $action = "Insert Key";
197 : parrello 1.10 $self->InsertObject('AttributeKey', { id => $attributeName,
198 :     description => $notes, 'data-type' => $type });
199 : parrello 1.8 }
200 : parrello 1.10 # Attach the key to the specified groups. (We presume the groups already
201 :     # exist.)
202 :     for my $group (@{$groups}) {
203 :     $self->InsertObject('IsInGroup', { 'from-link' => $attributeName,
204 :     'to-link' => $group });
205 : parrello 1.1 }
206 : parrello 1.18 # Log the operation.
207 :     $self->LogOperation($action, $attributeName, "Group list is " . join(" ", @{$groups}));
208 : parrello 1.1 }
209 :     }
210 :    
211 : parrello 1.3 =head3 LoadAttributeKey
212 : parrello 1.1
213 : parrello 1.10 C<< my $stats = $attrDB->LoadAttributeKey($keyName, $fh, $keyCol, $dataCol, %options); >>
214 : parrello 1.1
215 :     Load the specified attribute from the specified file. The file should be a
216 :     tab-delimited file with internal tab and new-line characters escaped. This is
217 :     the typical TBL-style file used by most FIG applications. One of the columns
218 : parrello 1.10 in the input file must contain the appropriate object id value and the other the
219 : parrello 1.1 corresponding attribute value.
220 :    
221 :     =over 4
222 :    
223 : parrello 1.10 =item keyName
224 : parrello 1.1
225 : parrello 1.10 Key of the attribute to load.
226 : parrello 1.1
227 :     =item fh
228 :    
229 :     Open file handle for the input file.
230 :    
231 : parrello 1.10 =item idCol
232 : parrello 1.1
233 : parrello 1.10 Index (0-based) of the column containing the ID field. The ID field should
234 : parrello 1.1 contain the ID of an instance of the named entity.
235 :    
236 :     =item dataCol
237 :    
238 :     Index (0-based) of the column containing the data value field.
239 :    
240 : parrello 1.10 =item options
241 :    
242 :     Hash specifying the options for this load.
243 :    
244 : parrello 1.1 =item RETURN
245 :    
246 :     Returns a statistics object for the load process.
247 :    
248 :     =back
249 :    
250 : parrello 1.10 The available options are as follows.
251 :    
252 :     =over 4
253 :    
254 :     =item erase
255 :    
256 :     If TRUE, the key's values will all be erased before loading. (Doing so
257 :     makes for a faster load.)
258 :    
259 :     =back
260 :    
261 : parrello 1.1 =cut
262 :    
263 : parrello 1.3 sub LoadAttributeKey {
264 : parrello 1.1 # Get the parameters.
265 : parrello 1.10 my ($self, $keyName, $fh, $idCol, $dataCol, %options) = @_;
266 : parrello 1.1 # Create the return variable.
267 : parrello 1.18 my $retVal = Stats->new("lineIn", "shortLine");
268 :     # Compute the minimum number of fields required in each input line. The user specifies two
269 :     # columns, and we need to make sure both columns are in every record.
270 : parrello 1.10 my $minCols = ($idCol < $dataCol ? $idCol : $idCol) + 1;
271 :     # Insure the attribute key exists.
272 :     my $found = $self->GetEntity('AttributeKey', $keyName);
273 :     if (! defined $found) {
274 :     Confess("Attribute key \"$keyName\" not found in database.");
275 : parrello 1.1 } else {
276 : parrello 1.11 # Erase the key's current values.
277 :     $self->EraseAttribute($keyName);
278 :     # Save a list of the object IDs we need to add.
279 :     my %objectIDs = ();
280 : parrello 1.10 # Loop through the input file.
281 :     while (! eof $fh) {
282 :     # Get the next line of the file.
283 :     my @fields = Tracer::GetLine($fh);
284 :     $retVal->Add(lineIn => 1);
285 :     # Now we need to validate the line.
286 :     if (scalar(@fields) < $minCols) {
287 :     $retVal->Add(shortLine => 1);
288 :     } else {
289 :     # It's valid, so get the ID and value.
290 :     my ($id, $value) = ($fields[$idCol], $fields[$dataCol]);
291 :     # Denote we're using this input line.
292 :     $retVal->Add(lineUsed => 1);
293 : parrello 1.11 # Now we insert the attribute.
294 : parrello 1.15 $self->InsertObject('HasValueFor', { from => $keyName, to => $id,
295 :     value => $value });
296 : parrello 1.11 $retVal->Add(newValue => 1);
297 : parrello 1.1 }
298 :     }
299 : parrello 1.18 # Log this operation.
300 :     $self->LogOperation("Load Key", $keyName, $retVal->Display());
301 : parrello 1.1 }
302 :     # Return the statistics.
303 :     return $retVal;
304 :     }
305 :    
306 :    
307 : parrello 1.3 =head3 DeleteAttributeKey
308 :    
309 : parrello 1.10 C<< my $stats = $attrDB->DeleteAttributeKey($attributeName); >>
310 : parrello 1.1
311 :     Delete an attribute from the custom attributes database.
312 :    
313 :     =over 4
314 :    
315 : parrello 1.10 =item attributeName
316 : parrello 1.1
317 : parrello 1.10 Name of the attribute to delete.
318 : parrello 1.1
319 : parrello 1.10 =item RETURN
320 : parrello 1.1
321 : parrello 1.10 Returns a statistics object describing the effects of the deletion.
322 : parrello 1.1
323 :     =back
324 :    
325 :     =cut
326 :    
327 : parrello 1.3 sub DeleteAttributeKey {
328 : parrello 1.1 # Get the parameters.
329 : parrello 1.10 my ($self, $attributeName) = @_;
330 :     # Delete the attribute key.
331 :     my $retVal = $self->Delete('AttributeKey', $attributeName);
332 : parrello 1.18 # Log this operation.
333 :     $self->LogOperation("Delete Key", $attributeName, "Key will no longer be available for use by anyone.");
334 : parrello 1.10 # Return the result.
335 :     return $retVal;
336 :    
337 :     }
338 :    
339 :     =head3 NewName
340 :    
341 :     C<< my $text = CustomAttributes::NewName(); >>
342 :    
343 :     Return the string used to indicate the user wants to add a new attribute.
344 :    
345 :     =cut
346 :    
347 :     sub NewName {
348 :     return "(new)";
349 : parrello 1.1 }
350 :    
351 :     =head3 ControlForm
352 :    
353 : parrello 1.10 C<< my $formHtml = $attrDB->ControlForm($cgi, $name, \%keys); >>
354 : parrello 1.1
355 :     Return a form that can be used to control the creation and modification of
356 : parrello 1.10 attributes. Only a subset of the attribute keys will be displayed, as
357 :     determined by the incoming list.
358 : parrello 1.1
359 :     =over 4
360 :    
361 :     =item cgi
362 :    
363 :     CGI query object used to create HTML.
364 :    
365 :     =item name
366 :    
367 :     Name to give to the form. This should be unique for the web page.
368 :    
369 : parrello 1.10 =item keys
370 :    
371 :     Reference to a hash mapping attribute keys to n-tuples. Each tuple will contain the
372 :     attribute's data type, its description, and a list of the groups in which it participates.
373 :    
374 : parrello 1.1 =item RETURN
375 :    
376 : parrello 1.10 Returns the HTML for a form that can be used to submit instructions to the C<Attributes.cgi> script
377 :     for loading, creating, displaying, changing, or deleting an attribute. Note that only the form
378 :     controls are generated. The form tags are left to the caller.
379 : parrello 1.1
380 :     =back
381 :    
382 :     =cut
383 :    
384 :     sub ControlForm {
385 :     # Get the parameters.
386 : parrello 1.10 my ($self, $cgi, $name, $keys) = @_;
387 : parrello 1.1 # Declare the return list.
388 :     my @retVal = ();
389 :     # We'll put the controls in a table. Nothing else ever seems to look nice.
390 :     push @retVal, $cgi->start_table({ border => 2, cellpadding => 2 });
391 :     # The first row is for selecting the field name.
392 :     push @retVal, $cgi->Tr($cgi->th("Select a Field"),
393 : parrello 1.10 $cgi->td($self->FieldMenu($cgi, 10, 'fieldName', $keys,
394 :     new => 1,
395 :     notes => "document.$name.notes.value",
396 :     type => "document.$name.dataType.value",
397 :     groups => "document.$name.groups")));
398 : parrello 1.1 # Now we set up a dropdown for the data types. The values will be the
399 :     # data type names, and the labels will be the descriptions.
400 :     my %types = ERDB::GetDataTypes();
401 :     my %labelMap = map { $_ => $types{$_}->{notes} } keys %types;
402 :     my $typeMenu = $cgi->popup_menu(-name => 'dataType',
403 :     -values => [sort keys %types],
404 : parrello 1.10 -labels => \%labelMap,
405 :     -default => 'string');
406 :     # Allow the user to specify a new field name. This is required if the
407 :     # user has selected the "(new)" marker. We put a little scriptlet in here that
408 :     # selects the (new) marker when the user enters the field.
409 :     push @retVal, "<script language=\"javaScript\">";
410 :     my $fieldField = "document.$name.fieldName";
411 :     my $newName = "\"" . NewName() . "\"";
412 :     push @retVal, $cgi->Tr($cgi->th("New Field Name"),
413 :     $cgi->td($cgi->textfield(-name => 'newName',
414 :     -size => 30,
415 :     -value => "",
416 :     -onFocus => "setIfEmpty($fieldField, $newName);")),
417 :     );
418 : parrello 1.1 push @retVal, $cgi->Tr($cgi->th("Data type"),
419 :     $cgi->td($typeMenu));
420 :     # The next row is for the notes.
421 :     push @retVal, $cgi->Tr($cgi->th("Description"),
422 :     $cgi->td($cgi->textarea(-name => 'notes',
423 :     -rows => 6,
424 :     -columns => 80))
425 :     );
426 : parrello 1.10 # Now we have the groups, which are implemented as a checkbox group.
427 :     my @groups = $self->GetGroups();
428 :     push @retVal, $cgi->Tr($cgi->th("Groups"),
429 :     $cgi->td($cgi->checkbox_group(-name=>'groups',
430 :     -values=> \@groups))
431 :     );
432 : parrello 1.1 # If the user wants to upload new values for the field, then we have
433 :     # an upload file name and column indicators.
434 :     push @retVal, $cgi->Tr($cgi->th("Upload Values"),
435 :     $cgi->td($cgi->filefield(-name => 'newValueFile',
436 :     -size => 20) .
437 :     " Key&nbsp;" .
438 :     $cgi->textfield(-name => 'keyCol',
439 :     -size => 3,
440 :     -default => 0) .
441 :     " Value&nbsp;" .
442 :     $cgi->textfield(-name => 'valueCol',
443 :     -size => 3,
444 :     -default => 1)
445 :     ),
446 :     );
447 : parrello 1.10 # Now the three buttons: STORE, SHOW, and DELETE.
448 : parrello 1.1 push @retVal, $cgi->Tr($cgi->th("&nbsp;"),
449 :     $cgi->td({align => 'center'},
450 :     $cgi->submit(-name => 'Delete', -value => 'DELETE') . " " .
451 : parrello 1.7 $cgi->submit(-name => 'Store', -value => 'STORE') . " " .
452 :     $cgi->submit(-name => 'Show', -value => 'SHOW')
453 : parrello 1.1 )
454 :     );
455 :     # Close the table and the form.
456 :     push @retVal, $cgi->end_table();
457 :     # Return the assembled HTML.
458 :     return join("\n", @retVal, "");
459 :     }
460 :    
461 : parrello 1.11 =head3 LoadAttributesFrom
462 :    
463 :     C<< my $stats = $attrDB->LoadAttributesFrom($fileName, %options); >>
464 :    
465 :     Load attributes from the specified tab-delimited file. Each line of the file must
466 :     contain an object ID in the first column, an attribute key name in the second
467 :     column, and attribute values in the remaining columns. The attribute values will
468 :     be assembled into a single value using the splitter code.
469 :    
470 :     =over 4
471 :    
472 :     =item fileName
473 :    
474 :     Name of the file from which to load the attributes.
475 :    
476 :     =item options
477 :    
478 :     Hash of options for modifying the load process.
479 :    
480 :     =item RETURN
481 :    
482 :     Returns a statistics object describing the load.
483 :    
484 :     =back
485 :    
486 :     Permissible option values are as follows.
487 :    
488 :     =over 4
489 :    
490 :     =item append
491 :    
492 :     If TRUE, then the attributes will be appended to existing data; otherwise, the
493 :     first time a key name is encountered, it will be erased.
494 :    
495 :     =back
496 :    
497 :     =cut
498 :    
499 :     sub LoadAttributesFrom {
500 :     # Get the parameters.
501 :     my ($self, $fileName, %options) = @_;
502 :     # Declare the return variable.
503 :     my $retVal = Stats->new('keys', 'values');
504 :     # Check for append mode.
505 :     my $append = ($options{append} ? 1 : 0);
506 :     # Create a hash of key names found.
507 :     my %keyHash = ();
508 :     # Open the file for input.
509 :     my $fh = Open(undef, "<$fileName");
510 :     # Loop through the file.
511 :     while (! eof $fh) {
512 :     my ($id, $key, @values) = Tracer::GetLine($fh);
513 :     $retVal->Add(linesIn => 1);
514 :     # Do some validation.
515 :     if (! defined($id)) {
516 :     # We ignore blank lines.
517 :     $retVal->Add(blankLines => 1);
518 :     } elsif (! defined($key)) {
519 :     # An ID without a key is a serious error.
520 :     my $lines = $retVal->Ask('linesIn');
521 :     Confess("Line $lines in $fileName has no attribute key.");
522 :     } else {
523 :     # Now we need to check for a new key.
524 :     if (! exists $keyHash{$key}) {
525 :     # This is a new key. Verify that it exists.
526 :     if (! $self->Exists('AttributeKey', $key)) {
527 :     my $line = $retVal->Ask('linesIn');
528 :     Confess("Attribute \"$key\" on line $line of $fileName not found in database.");
529 :     } else {
530 :     # Make sure we know this is no longer a new key.
531 :     $keyHash{$key} = 1;
532 :     $retVal->Add(keys => 1);
533 :     # If this is NOT append mode, erase the key.
534 :     if (! $append) {
535 :     $self->EraseAttribute($key);
536 :     }
537 :     }
538 :     Trace("Key $key found.") if T(3);
539 :     }
540 :     # Now we know the key is valid. Add this value.
541 :     $self->AddAttribute($id, $key, @values);
542 :     my $progress = $retVal->Add(values => 1);
543 :     Trace("$progress values loaded.") if T(3) && ($progress % 1000 == 0);
544 :    
545 :     }
546 :     }
547 :     # Return the result.
548 :     return $retVal;
549 :     }
550 :    
551 : parrello 1.13 =head3 BackupKeys
552 :    
553 :     C<< my $stats = $attrDB->BackupKeys($fileName, %options); >>
554 :    
555 :     Backup the attribute key information from the attribute database.
556 :    
557 :     =over 4
558 :    
559 :     =item fileName
560 :    
561 :     Name of the output file.
562 :    
563 :     =item options
564 :    
565 :     Options for modifying the backup process.
566 :    
567 :     =item RETURN
568 :    
569 :     Returns a statistics object for the backup.
570 :    
571 :     =back
572 :    
573 :     Currently there are no options. The backup is straight to a text file in
574 :     tab-delimited format. Each key is backup up to two lines. The first line
575 :     is all of the data from the B<AttributeKey> table. The second is a
576 :     tab-delimited list of all the groups.
577 :    
578 :     =cut
579 :    
580 :     sub BackupKeys {
581 :     # Get the parameters.
582 :     my ($self, $fileName, %options) = @_;
583 :     # Declare the return variable.
584 :     my $retVal = Stats->new();
585 :     # Open the output file.
586 :     my $fh = Open(undef, ">$fileName");
587 :     # Set up to read the keys.
588 :     my $keyQuery = $self->Get(['AttributeKey'], "", []);
589 :     # Loop through the keys.
590 :     while (my $keyData = $keyQuery->Fetch()) {
591 :     $retVal->Add(key => 1);
592 :     # Get the fields.
593 :     my ($id, $type, $description) = $keyData->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
594 :     'AttributeKey(description)']);
595 :     # Escape any tabs or new-lines in the description.
596 :     my $escapedDescription = Tracer::Escape($description);
597 :     # Write the key data to the output.
598 :     Tracer::PutLine($fh, [$id, $type, $escapedDescription]);
599 :     # Get the key's groups.
600 :     my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?", [$id],
601 :     'IsInGroup(to-link)');
602 :     $retVal->Add(memberships => scalar(@groups));
603 :     # Write them to the output. Note we put a marker at the beginning to insure the line
604 :     # is nonempty.
605 :     Tracer::PutLine($fh, ['#GROUPS', @groups]);
606 :     }
607 : parrello 1.18 # Log the operation.
608 :     $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
609 : parrello 1.13 # Return the result.
610 :     return $retVal;
611 :     }
612 :    
613 :     =head3 RestoreKeys
614 :    
615 :     C<< my $stats = $attrDB->RestoreKeys($fileName, %options); >>
616 :    
617 :     Restore the attribute keys and groups from a backup file.
618 :    
619 :     =over 4
620 :    
621 :     =item fileName
622 :    
623 :     Name of the file containing the backed-up keys. Each key has a pair of lines,
624 :     one containing the key data and one listing its groups.
625 :    
626 :     =back
627 :    
628 :     =cut
629 :    
630 :     sub RestoreKeys {
631 :     # Get the parameters.
632 :     my ($self, $fileName, %options) = @_;
633 :     # Declare the return variable.
634 :     my $retVal = Stats->new();
635 :     # Set up a hash to hold the group IDs.
636 :     my %groups = ();
637 :     # Open the file.
638 :     my $fh = Open(undef, "<$fileName");
639 :     # Loop until we're done.
640 :     while (! eof $fh) {
641 :     # Get a key record.
642 :     my ($id, $dataType, $description) = Tracer::GetLine($fh);
643 :     if ($id eq '#GROUPS') {
644 :     Confess("Group record found when key record expected.");
645 :     } elsif (! defined($description)) {
646 :     Confess("Invalid format found for key record.");
647 :     } else {
648 :     $retVal->Add("keyIn" => 1);
649 :     # Add this key to the database.
650 :     $self->InsertObject('AttributeKey', { id => $id, 'data-type' => $dataType,
651 :     description => Tracer::UnEscape($description) });
652 :     Trace("Attribute $id stored.") if T(3);
653 :     # Get the group line.
654 :     my ($marker, @groups) = Tracer::GetLine($fh);
655 :     if (! defined($marker)) {
656 :     Confess("End of file found where group record expected.");
657 :     } elsif ($marker ne '#GROUPS') {
658 :     Confess("Group record not found after key record.");
659 :     } else {
660 :     $retVal->Add(memberships => scalar(@groups));
661 :     # Connect the groups.
662 :     for my $group (@groups) {
663 :     # Find out if this is a new group.
664 :     if (! $groups{$group}) {
665 :     $retVal->Add(newGroup => 1);
666 :     # Add the group.
667 :     $self->InsertObject('AttributeGroup', { id => $group });
668 :     Trace("Group $group created.") if T(3);
669 :     # Make sure we know it's not new.
670 :     $groups{$group} = 1;
671 :     }
672 :     # Connect the group to our key.
673 :     $self->InsertObject('IsInGroup', { 'from-link' => $id, 'to-link' => $group });
674 :     }
675 :     Trace("$id added to " . scalar(@groups) . " groups.") if T(3);
676 :     }
677 :     }
678 :     }
679 : parrello 1.18 # Log the operation.
680 :     $self->LogOperation("Backup Keys", $fileName, $retVal->Display());
681 : parrello 1.13 # Return the result.
682 :     return $retVal;
683 :     }
684 :    
685 :    
686 : parrello 1.11 =head3 BackupAllAttributes
687 :    
688 :     C<< my $stats = $attrDB->BackupAllAttributes($fileName, %options); >>
689 :    
690 :     Backup all of the attributes to a file. The attributes will be stored in a
691 :     tab-delimited file suitable for reloading via L</LoadAttributesFrom>.
692 :    
693 :     =over 4
694 :    
695 :     =item fileName
696 :    
697 :     Name of the file to which the attribute data should be backed up.
698 :    
699 :     =item options
700 :    
701 :     Hash of options for the backup.
702 :    
703 :     =item RETURN
704 :    
705 :     Returns a statistics object describing the backup.
706 :    
707 :     =back
708 :    
709 :     Currently there are no options defined.
710 :    
711 :     =cut
712 :    
713 :     sub BackupAllAttributes {
714 :     # Get the parameters.
715 :     my ($self, $fileName, %options) = @_;
716 :     # Declare the return variable.
717 :     my $retVal = Stats->new();
718 :     # Get a list of the keys.
719 :     my @keys = $self->GetFlat(['AttributeKey'], "", [], 'AttributeKey(id)');
720 :     Trace(scalar(@keys) . " keys found during backup.") if T(2);
721 :     # Open the file for output.
722 : parrello 1.12 my $fh = Open(undef, ">$fileName");
723 : parrello 1.11 # Loop through the keys.
724 :     for my $key (@keys) {
725 :     Trace("Backing up attribute $key.") if T(3);
726 :     $retVal->Add(keys => 1);
727 :     # Loop through this key's values.
728 : parrello 1.12 my $query = $self->Get(['HasValueFor'], "HasValueFor(from-link) = ?", [$key]);
729 : parrello 1.11 my $valuesFound = 0;
730 :     while (my $line = $query->Fetch()) {
731 :     $valuesFound++;
732 :     # Get this row's data.
733 : parrello 1.13 my @row = $line->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
734 : parrello 1.11 'HasValueFor(value)']);
735 :     # Write it to the file.
736 :     Tracer::PutLine($fh, \@row);
737 :     }
738 :     Trace("$valuesFound values backed up for key $key.") if T(3);
739 :     $retVal->Add(values => $valuesFound);
740 :     }
741 : parrello 1.18 # Log the operation.
742 :     $self->LogOperation("Backup Data", $fileName, $retVal->Display());
743 : parrello 1.11 # Return the result.
744 :     return $retVal;
745 :     }
746 :    
747 : parrello 1.1 =head3 FieldMenu
748 :    
749 : parrello 1.10 C<< my $menuHtml = $attrDB->FieldMenu($cgi, $height, $name, $keys, %options); >>
750 : parrello 1.1
751 :     Return the HTML for a menu to select an attribute field. The menu will
752 :     be a standard SELECT/OPTION thing which is called "popup menu" in the
753 :     CGI package, but actually looks like a list. The list will contain
754 : parrello 1.10 one selectable row per field.
755 : parrello 1.1
756 :     =over 4
757 :    
758 :     =item cgi
759 :    
760 :     CGI query object used to generate HTML.
761 :    
762 :     =item height
763 :    
764 :     Number of lines to display in the list.
765 :    
766 :     =item name
767 :    
768 :     Name to give to the menu. This is the name under which the value will
769 :     appear when the form is submitted.
770 :    
771 : parrello 1.10 =item keys
772 :    
773 :     Reference to a hash mapping each attribute key name to a list reference,
774 :     the list itself consisting of the attribute data type, its description,
775 :     and a list of its groups.
776 :    
777 :     =item options
778 :    
779 :     Hash containing options that modify the generation of the menu.
780 :    
781 :     =item RETURN
782 :    
783 :     Returns the HTML to create a form field that can be used to select an
784 :     attribute from the custom attributes system.
785 :    
786 :     =back
787 :    
788 :     The permissible options are as follows.
789 :    
790 :     =over 4
791 :    
792 :     =item new
793 : parrello 1.1
794 :     If TRUE, then extra rows will be provided to allow the user to select
795 :     a new attribute. In other words, the user can select an existing
796 :     attribute, or can choose a C<(new)> marker to indicate a field to
797 :     be created in the parent entity.
798 :    
799 : parrello 1.10 =item notes
800 : parrello 1.1
801 :     If specified, the name of a variable for displaying the notes attached
802 :     to the field. This must be in Javascript form ready for assignment.
803 :     So, for example, if you have a variable called C<notes> that
804 :     represents a paragraph element, you should code C<notes.innerHTML>.
805 :     If it actually represents a form field you should code C<notes.value>.
806 :     If an C<innerHTML> coding is used, the text will be HTML-escaped before
807 :     it is copied in. Specifying this parameter generates Javascript for
808 :     displaying the field description when a field is selected.
809 :    
810 : parrello 1.10 =item type
811 : parrello 1.1
812 :     If specified, the name of a variable for displaying the field's
813 :     data type. Data types are a much more controlled vocabulary than
814 :     notes, so there is no worry about HTML translation. Instead, the
815 :     raw value is put into the specified variable. Otherwise, the same
816 :     rules apply to this value that apply to I<$noteControl>.
817 :    
818 : parrello 1.10 =item groups
819 : parrello 1.1
820 : parrello 1.10 If specified, the name of a multiple-selection list control (also called
821 :     a popup menu) which shall be used to display the selected groups.
822 : parrello 1.1
823 :     =back
824 :    
825 :     =cut
826 :    
827 :     sub FieldMenu {
828 :     # Get the parameters.
829 : parrello 1.10 my ($self, $cgi, $height, $name, $keys, %options) = @_;
830 :     # Reformat the list of keys.
831 :     my %keys = %{$keys};
832 :     # Add the (new) key, if needed.
833 :     if ($options{new}) {
834 :     $keys{NewName()} = ["string", ""];
835 : parrello 1.1 }
836 : parrello 1.10 # Get a sorted list of key.
837 :     my @keys = sort keys %keys;
838 :     # We need to create the name for the onChange function. This function
839 : parrello 1.1 # may not do anything, but we need to know the name to generate the HTML
840 :     # for the menu.
841 :     my $changeName = "${name}_setNotes";
842 :     my $retVal = $cgi->popup_menu({name => $name,
843 :     size => $height,
844 :     onChange => "$changeName(this.value)",
845 : parrello 1.10 values => \@keys,
846 :     });
847 : parrello 1.1 # Create the change function.
848 :     $retVal .= "\n<script language=\"javascript\">\n";
849 :     $retVal .= " function $changeName(fieldValue) {\n";
850 : parrello 1.10 # The function only has a body if we have a control to store data about the
851 :     # attribute.
852 :     if ($options{notes} || $options{type} || $options{groups}) {
853 : parrello 1.1 # Check to see if we're storing HTML or text into the note control.
854 : parrello 1.10 my $noteControl = $options{notes};
855 : parrello 1.1 my $htmlMode = ($noteControl && $noteControl =~ /innerHTML$/);
856 :     # We use a CASE statement based on the newly-selected field value. The
857 :     # field description will be stored in the JavaScript variable "myText"
858 :     # and the data type in "myType". Note the default data type is a normal
859 :     # string, but the default notes is an empty string.
860 :     $retVal .= " var myText = \"\";\n";
861 :     $retVal .= " var myType = \"string\";\n";
862 :     $retVal .= " switch (fieldValue) {\n";
863 : parrello 1.10 # Loop through the keys.
864 :     for my $key (@keys) {
865 :     # Generate this case.
866 :     $retVal .= " case \"$key\" :\n";
867 :     # Here we either want to update the note display, the
868 :     # type display, the group list, or a combination of them.
869 :     my ($type, $notes, @groups) = @{$keys{$key}};
870 :     if ($noteControl) {
871 :     # Insure it's in the proper form.
872 :     if ($htmlMode) {
873 :     $notes = ERDB::HTMLNote($notes);
874 : parrello 1.1 }
875 : parrello 1.10 # Escape it for use as a string literal.
876 :     $notes =~ s/\n/\\n/g;
877 :     $notes =~ s/"/\\"/g;
878 :     $retVal .= " myText = \"$notes\";\n";
879 :     }
880 :     if ($options{type}) {
881 :     # Here we want the type updated.
882 :     $retVal .= " myType = \"$type\";\n";
883 :     }
884 :     if ($options{groups}) {
885 :     # Here we want the groups shown. Get a list of this attribute's groups.
886 :     # We'll search through this list for each group to see if it belongs with
887 :     # our attribute.
888 :     my $groupLiteral = "=" . join("=", @groups) . "=";
889 :     # Now we need some variables containing useful code for the javascript. It's
890 :     # worth knowing we go through a bit of pain to insure $groupField[i] isn't
891 :     # parsed as an array element.
892 :     my $groupField = $options{groups};
893 :     my $currentField = $groupField . "[i]";
894 :     # Do the javascript.
895 :     $retVal .= " var groupList = \"$groupLiteral\";\n";
896 :     $retVal .= " for (var i = 0; i < $groupField.length; i++) {\n";
897 :     $retVal .= " var srchString = \"=\" + $currentField.value + \"=\";\n";
898 :     $retVal .= " var srchLoc = groupList.indexOf(srchString);\n";
899 :     $retVal .= " $currentField.checked = (srchLoc >= 0);\n";
900 :     $retVal .= " }\n";
901 : parrello 1.1 }
902 : parrello 1.10 # Close this case.
903 :     $retVal .= " break;\n";
904 : parrello 1.1 }
905 :     # Close the CASE statement and make the appropriate assignments.
906 :     $retVal .= " }\n";
907 :     if ($noteControl) {
908 :     $retVal .= " $noteControl = myText;\n";
909 :     }
910 : parrello 1.10 if ($options{type}) {
911 :     $retVal .= " $options{type} = myType;\n";
912 : parrello 1.1 }
913 :     }
914 :     # Terminate the change function.
915 :     $retVal .= " }\n";
916 :     $retVal .= "</script>\n";
917 :     # Return the result.
918 :     return $retVal;
919 :     }
920 :    
921 : parrello 1.10 =head3 GetGroups
922 : parrello 1.3
923 : parrello 1.10 C<< my @groups = $attrDB->GetGroups(); >>
924 : parrello 1.3
925 : parrello 1.10 Return a list of the available groups.
926 : parrello 1.3
927 :     =cut
928 :    
929 : parrello 1.10 sub GetGroups {
930 : parrello 1.3 # Get the parameters.
931 : parrello 1.10 my ($self) = @_;
932 :     # Get the groups.
933 :     my @retVal = $self->GetFlat(['AttributeGroup'], "", [], 'AttributeGroup(id)');
934 :     # Return them.
935 :     return @retVal;
936 : parrello 1.3 }
937 :    
938 : parrello 1.10 =head3 GetAttributeData
939 : parrello 1.3
940 : parrello 1.10 C<< my %keys = $attrDB->GetAttributeData($type, @list); >>
941 : parrello 1.3
942 : parrello 1.10 Return attribute data for the selected attributes. The attribute
943 :     data is a hash mapping each attribute key name to a n-tuple containing the
944 :     data type, the description, and the groups. This is the same format expected in
945 :     the L</FieldMenu> and L</ControlForm> methods for the list of attributes to display.
946 : parrello 1.3
947 :     =over 4
948 :    
949 : parrello 1.10 =item type
950 : parrello 1.4
951 : parrello 1.10 Type of attribute criterion: C<name> for attributes whose names begin with the
952 :     specified string, or C<group> for attributes in the specified group.
953 : parrello 1.4
954 : parrello 1.10 =item list
955 : parrello 1.4
956 : parrello 1.10 List containing the names of the groups or keys for the desired attributes.
957 : parrello 1.4
958 :     =item RETURN
959 :    
960 : parrello 1.10 Returns a hash mapping each attribute key name to its data type, description, and
961 :     parent groups.
962 : parrello 1.4
963 :     =back
964 :    
965 :     =cut
966 :    
967 : parrello 1.10 sub GetAttributeData {
968 : parrello 1.4 # Get the parameters.
969 : parrello 1.10 my ($self, $type, @list) = @_;
970 :     # Set up a hash to store the attribute data.
971 :     my %retVal = ();
972 :     # Loop through the list items.
973 :     for my $item (@list) {
974 :     # Set up a query for the desired attributes.
975 :     my $query;
976 :     if ($type eq 'name') {
977 :     # Here we're doing a generic name search. We need to escape it and then tack
978 :     # on a %.
979 :     my $parm = $item;
980 :     $parm =~ s/_/\\_/g;
981 :     $parm =~ s/%/\\%/g;
982 :     $parm .= "%";
983 :     # Ask for matching attributes. (Note that if the user passed in a null string
984 :     # he'll get everything.)
985 :     $query = $self->Get(['AttributeKey'], "AttributeKey(id) LIKE ?", [$parm]);
986 :     } elsif ($type eq 'group') {
987 :     $query = $self->Get(['IsInGroup', 'AttributeKey'], "IsInGroup(to-link) = ?", [$item]);
988 : parrello 1.4 } else {
989 : parrello 1.10 Confess("Unknown attribute query type \"$type\".");
990 :     }
991 :     while (my $row = $query->Fetch()) {
992 :     # Get this attribute's data.
993 :     my ($key, $type, $notes) = $row->Values(['AttributeKey(id)', 'AttributeKey(data-type)',
994 :     'AttributeKey(description)']);
995 :     # If it's new, get its groups and add it to the return hash.
996 :     if (! exists $retVal{$key}) {
997 :     my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(from-link) = ?",
998 :     [$key], 'IsInGroup(to-link)');
999 :     $retVal{$key} = [$type, $notes, @groups];
1000 : parrello 1.4 }
1001 :     }
1002 :     }
1003 :     # Return the result.
1004 : parrello 1.10 return %retVal;
1005 : parrello 1.4 }
1006 :    
1007 : parrello 1.18 =head3 LogOperation
1008 :    
1009 :     C<< $ca->LogOperation($action, $target, $description); >>
1010 :    
1011 :     Write an operation description to the attribute activity log (C<$FIG_Config::var/attributes.log>).
1012 :    
1013 :     =over 4
1014 :    
1015 :     =item action
1016 :    
1017 :     Action being logged (e.g. C<Delete Group> or C<Load Key>).
1018 :    
1019 :     =item target
1020 :    
1021 :     ID of the key or group affected.
1022 :    
1023 :     =item description
1024 :    
1025 :     Short description of the action.
1026 :    
1027 :     =back
1028 :    
1029 :     =cut
1030 :    
1031 :     sub LogOperation {
1032 :     # Get the parameters.
1033 :     my ($self, $action, $target, $description) = @_;
1034 :     # Get the user ID.
1035 :     my $user = $self->{user};
1036 :     # Get a timestamp.
1037 :     my $timeString = Tracer::Now();
1038 :     # Open the log file for appending.
1039 :     my $oh = Open(undef, ">>$FIG_Config::var/attributes.log");
1040 :     # Write the data to it.
1041 :     Tracer::PutLine($oh, [$timeString, $user, $action, $target, $description]);
1042 :     # Close the log file.
1043 :     close $oh;
1044 :     }
1045 :    
1046 : parrello 1.15 =head2 Internal Utility Methods
1047 :    
1048 :     =head3 _KeywordString
1049 :    
1050 :     C<< my $keywordString = $ca->_KeywordString($key, $value); >>
1051 :    
1052 :     Compute the keyword string for a specified key/value pair. This consists of the
1053 :     key name and value converted to lower case with underscores translated to spaces.
1054 :    
1055 :     This method is for internal use only. It is called whenever we need to update or
1056 :     insert a B<HasValueFor> record.
1057 :    
1058 :     =over 4
1059 :    
1060 :     =item key
1061 :    
1062 :     Name of the relevant attribute key.
1063 :    
1064 :     =item target
1065 :    
1066 :     ID of the target object to which this key/value pair will be associated.
1067 :    
1068 :     =item value
1069 :    
1070 :     The value to store for this key/object combination.
1071 :    
1072 :     =item RETURN
1073 :    
1074 :     Returns the value that should be stored as the keyword string for the specified
1075 :     key/value pair.
1076 :    
1077 :     =back
1078 :    
1079 :     =cut
1080 :    
1081 :     sub _KeywordString {
1082 :     # Get the parameters.
1083 :     my ($self, $key, $value) = @_;
1084 :     # Get a copy of the key name and convert underscores to spaces.
1085 :     my $keywordString = $key;
1086 :     $keywordString =~ s/_/ /g;
1087 :     # Add the value convert it all to lower case.
1088 :     my $retVal = lc "$keywordString $value";
1089 :     # Return the result.
1090 :     return $retVal;
1091 :     }
1092 :    
1093 :     =head3 _QueryResults
1094 :    
1095 :     C<< my @attributeList = $attrDB->_QueryResults($query, @values); >>
1096 :    
1097 :     Match the results of a B<HasValueFor> query against value criteria and return
1098 :     the results. This is an internal method that splits the values coming back
1099 :     and matches the sections against the specified section patterns. It serves
1100 :     as the back end to L</GetAttributes> and L</FindAttributes>.
1101 :    
1102 :     =over 4
1103 :    
1104 :     =item query
1105 :    
1106 :     A query object that will return the desired B<HasValueFor> records.
1107 :    
1108 :     =item values
1109 :    
1110 :     List of the desired attribute values, section by section. If C<undef>
1111 :     or an empty string is specified, all values in that section will match. A
1112 :     generic match can be requested by placing a percent sign (C<%>) at the end.
1113 :     In that case, all values that match up to and not including the percent sign
1114 :     will match. You may also specify a regular expression enclosed
1115 :     in slashes. All values that match the regular expression will be returned. For
1116 :     performance reasons, only values have this extra capability.
1117 :    
1118 :     =item RETURN
1119 :    
1120 :     Returns a list of tuples. The first element in the tuple is an object ID, the
1121 :     second is an attribute key, and the remaining elements are the sections of
1122 :     the attribute value. All of the tuples will match the criteria set forth in
1123 :     the parameter list.
1124 :    
1125 :     =back
1126 :    
1127 :     =cut
1128 :    
1129 :     sub _QueryResults {
1130 :     # Get the parameters.
1131 :     my ($self, $query, @values) = @_;
1132 :     # Declare the return value.
1133 :     my @retVal = ();
1134 :     # Get the number of value sections we have to match.
1135 :     my $sectionCount = scalar(@values);
1136 :     # Loop through the assignments found.
1137 :     while (my $row = $query->Fetch()) {
1138 :     # Get the current row's data.
1139 :     my ($id, $key, $valueString) = $row->Values(['HasValueFor(to-link)', 'HasValueFor(from-link)',
1140 :     'HasValueFor(value)']);
1141 :     # Break the value into sections.
1142 :     my @sections = split($self->{splitter}, $valueString);
1143 :     # Match each section against the incoming values. We'll assume we're
1144 :     # okay unless we learn otherwise.
1145 :     my $matching = 1;
1146 :     for (my $i = 0; $i < $sectionCount && $matching; $i++) {
1147 :     # We need to check to see if this section is generic.
1148 :     my $value = $values[$i];
1149 :     Trace("Current value pattern is \"$value\".") if T(4);
1150 :     if (substr($value, -1, 1) eq '%') {
1151 :     Trace("Generic match used.") if T(4);
1152 :     # Here we have a generic match.
1153 :     my $matchLen = length($values[$i] - 1);
1154 :     $matching = substr($sections[$i], 0, $matchLen) eq
1155 :     substr($values[$i], 0, $matchLen);
1156 :     } elsif ($value =~ m#^/(.+)/[a-z]*$#) {
1157 :     Trace("Regular expression detected.") if T(4);
1158 :     # Here we have a regular expression match.
1159 :     my $section = $sections[$i];
1160 :     $matching = eval("\$section =~ $value");
1161 :     } else {
1162 :     # Here we have a strict match.
1163 :     Trace("Strict match used.") if T(4);
1164 :     $matching = ($sections[$i] eq $values[$i]);
1165 :     }
1166 :     }
1167 :     # If we match, output this row to the return list.
1168 :     if ($matching) {
1169 :     push @retVal, [$id, $key, @sections];
1170 :     }
1171 :     }
1172 :     # Return the rows found.
1173 :     return @retVal;
1174 :     }
1175 :    
1176 : parrello 1.3 =head2 FIG Method Replacements
1177 :    
1178 :     The following methods are used by B<FIG.pm> to replace the previous attribute functionality.
1179 : parrello 1.10 Some of the old functionality is no longer present: controlled vocabulary is no longer
1180 : parrello 1.3 supported and there is no longer any searching by URL. Fortunately, neither of these
1181 :     capabilities were used in the old system.
1182 :    
1183 : parrello 1.4 The methods here are the only ones supported by the B<RemoteCustomAttributes> object.
1184 :     The idea is that these methods represent attribute manipulation allowed by all users, while
1185 :     the others are only for privileged users with access to the attribute server.
1186 :    
1187 : parrello 1.3 In the previous implementation, an attribute had a value and a URL. In the new implementation,
1188 :     there is only a value. In this implementation, each attribute has only a value. These
1189 :     methods will treat the value as a list with the individual elements separated by the
1190 :     value of the splitter parameter on the constructor (L</new>). The default is double
1191 :     colons C<::>.
1192 :    
1193 : parrello 1.10 So, for example, an old-style keyword with a value of C<essential> and a URL of
1194 : parrello 1.3 C<http://www.sciencemag.org/cgi/content/abstract/293/5538/2266> using the default
1195 :     splitter value would be stored as
1196 :    
1197 :     essential::http://www.sciencemag.org/cgi/content/abstract/293/5538/2266
1198 :    
1199 :     The best performance is achieved by searching for a particular key for a specified
1200 :     feature or genome.
1201 :    
1202 :     =head3 GetAttributes
1203 :    
1204 : parrello 1.10 C<< my @attributeList = $attrDB->GetAttributes($objectID, $key, @values); >>
1205 : parrello 1.3
1206 :     In the database, attribute values are sectioned into pieces using a splitter
1207 :     value specified in the constructor (L</new>). This is not a requirement of
1208 :     the attribute system as a whole, merely a convenience for the purpose of
1209 : parrello 1.10 these methods. If a value has multiple sections, each section
1210 :     is matched against the corresponding criterion in the I<@valuePatterns> list.
1211 : parrello 1.3
1212 :     This method returns a series of tuples that match the specified criteria. Each tuple
1213 :     will contain an object ID, a key, and one or more values. The parameters to this
1214 : parrello 1.10 method therefore correspond structurally to the values expected in each tuple. In
1215 :     addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any
1216 :     of the parameters. So, for example,
1217 : parrello 1.3
1218 : parrello 1.10 my @attributeList = $attrDB->GetAttributes('fig|100226.1.peg.1004', 'structure%', 1, 2);
1219 : parrello 1.3
1220 :     would return something like
1221 :    
1222 :     ['fig}100226.1.peg.1004', 'structure', 1, 2]
1223 :     ['fig}100226.1.peg.1004', 'structure1', 1, 2]
1224 :     ['fig}100226.1.peg.1004', 'structure2', 1, 2]
1225 :     ['fig}100226.1.peg.1004', 'structureA', 1, 2]
1226 :    
1227 : parrello 1.10 Use of C<undef> in any position acts as a wild card (all values). You can also specify
1228 :     a list reference in the ID column. Thus,
1229 :    
1230 :     my @attributeList = $attrDB->GetAttributes(['100226.1', 'fig|100226.1.%'], 'PUBMED');
1231 :    
1232 :     would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its
1233 :     features.
1234 : parrello 1.3
1235 :     In addition to values in multiple sections, a single attribute key can have multiple
1236 :     values, so even
1237 :    
1238 : parrello 1.10 my @attributeList = $attrDB->GetAttributes($peg, 'virulent');
1239 : parrello 1.3
1240 :     which has no wildcard in the key or the object ID, may return multiple tuples.
1241 :    
1242 : parrello 1.10 Value matching in this system works very poorly, because of the way multiple values are
1243 :     stored. For the object ID and key name, we create queries that filter for the desired
1244 :     results. For the values, we do a comparison after the attributes are retrieved from the
1245 :     database. As a result, queries in which filter only on value end up reading the entire
1246 :     attribute table to find the desired results.
1247 : parrello 1.3
1248 :     =over 4
1249 :    
1250 :     =item objectID
1251 :    
1252 : parrello 1.10 ID of object whose attributes are desired. If the attributes are desired for multiple
1253 :     objects, this parameter can be specified as a list reference. If the attributes are
1254 :     desired for all objects, specify C<undef> or an empty string. Finally, you can specify
1255 :     attributes for a range of object IDs by putting a percent sign (C<%>) at the end.
1256 : parrello 1.3
1257 :     =item key
1258 :    
1259 : parrello 1.10 Attribute key name. A value of C<undef> or an empty string will match all
1260 :     attribute keys. If the values are desired for multiple keys, this parameter can be
1261 :     specified as a list reference. Finally, you can specify attributes for a range of
1262 :     keys by putting a percent sign (C<%>) at the end.
1263 : parrello 1.3
1264 : parrello 1.10 =item values
1265 : parrello 1.3
1266 :     List of the desired attribute values, section by section. If C<undef>
1267 : parrello 1.10 or an empty string is specified, all values in that section will match. A
1268 :     generic match can be requested by placing a percent sign (C<%>) at the end.
1269 :     In that case, all values that match up to and not including the percent sign
1270 : parrello 1.14 will match. You may also specify a regular expression enclosed
1271 :     in slashes. All values that match the regular expression will be returned. For
1272 :     performance reasons, only values have this extra capability.
1273 : parrello 1.3
1274 :     =item RETURN
1275 :    
1276 :     Returns a list of tuples. The first element in the tuple is an object ID, the
1277 :     second is an attribute key, and the remaining elements are the sections of
1278 :     the attribute value. All of the tuples will match the criteria set forth in
1279 :     the parameter list.
1280 :    
1281 :     =back
1282 :    
1283 :     =cut
1284 :    
1285 :     sub GetAttributes {
1286 : parrello 1.4 # Get the parameters.
1287 : parrello 1.10 my ($self, $objectID, $key, @values) = @_;
1288 :     # We will create one big honking query. The following hash will build the filter
1289 :     # clause and a parameter list.
1290 : parrello 1.11 my %data = ('HasValueFor(from-link)' => $key, 'HasValueFor(to-link)' => $objectID);
1291 : parrello 1.10 my @filter = ();
1292 :     my @parms = ();
1293 :     # This next loop goes through the different fields that can be specified in the
1294 :     # parameter list and generates filters for each.
1295 :     for my $field (keys %data) {
1296 :     # Accumulate filter information for this field. We will OR together all the
1297 :     # elements accumulated to create the final result.
1298 :     my @fieldFilter = ();
1299 :     # Get the specified data from the caller.
1300 :     my $fieldPattern = $data{$field};
1301 :     # Only proceed if the pattern is one that won't match everything.
1302 :     if (defined($fieldPattern) && $fieldPattern ne "" && $fieldPattern ne "%") {
1303 :     # Convert the pattern to an array.
1304 :     my @patterns = ();
1305 :     if (ref $fieldPattern eq 'ARRAY') {
1306 :     push @patterns, @{$fieldPattern};
1307 :     } else {
1308 :     push @patterns, $fieldPattern;
1309 :     }
1310 :     # Only proceed if the array is nonempty. The loop will work fine if the
1311 :     # array is empty, but when we build the filter string at the end we'll
1312 :     # get "()" in the filter list, which will result in an SQL syntax error.
1313 :     if (@patterns) {
1314 :     # Loop through the individual patterns.
1315 :     for my $pattern (@patterns) {
1316 :     # Check for a generic request.
1317 :     if (substr($pattern, -1, 1) ne '%') {
1318 :     # Here we have a normal request.
1319 :     push @fieldFilter, "$field = ?";
1320 :     push @parms, $pattern;
1321 :     } else {
1322 :     # Here we have a generate request, so we will use the LIKE operator to
1323 :     # filter the field to this value pattern.
1324 :     push @fieldFilter, "$field LIKE ?";
1325 :     # We must convert the pattern value to an SQL match pattern. First
1326 : parrello 1.11 # we get a copy of it.
1327 :     my $actualPattern = $pattern;
1328 : parrello 1.10 # Now we escape the underscores. Underscores are an SQL wild card
1329 :     # character, but they are used frequently in key names and object IDs.
1330 : parrello 1.11 $actualPattern =~ s/_/\\_/g;
1331 : parrello 1.10 # Add the escaped pattern to the bound parameter list.
1332 :     push @parms, $actualPattern;
1333 :     }
1334 :     }
1335 :     # Form the filter for this field.
1336 :     my $fieldFilterString = join(" OR ", @fieldFilter);
1337 :     push @filter, "($fieldFilterString)";
1338 :     }
1339 :     }
1340 :     }
1341 :     # Now @filter contains one or more filter strings and @parms contains the parameter
1342 :     # values to bind to them.
1343 :     my $actualFilter = join(" AND ", @filter);
1344 :     # Now we're ready to make our query.
1345 : parrello 1.11 my $query = $self->Get(['HasValueFor'], $actualFilter, \@parms);
1346 : parrello 1.15 # Format the results.
1347 :     my @retVal = $self->_QueryResults($query, @values);
1348 : parrello 1.10 # Return the rows found.
1349 : parrello 1.3 return @retVal;
1350 :     }
1351 :    
1352 :     =head3 AddAttribute
1353 :    
1354 :     C<< $attrDB->AddAttribute($objectID, $key, @values); >>
1355 :    
1356 :     Add an attribute key/value pair to an object. This method cannot add a new key, merely
1357 :     add a value to an existing key. Use L</StoreAttributeKey> to create a new key.
1358 :    
1359 :     =over 4
1360 :    
1361 :     =item objectID
1362 :    
1363 : parrello 1.10 ID of the object to which the attribute is to be added.
1364 : parrello 1.3
1365 :     =item key
1366 :    
1367 : parrello 1.10 Attribute key name.
1368 : parrello 1.3
1369 :     =item values
1370 :    
1371 :     One or more values to be associated with the key. The values are joined together with
1372 :     the splitter value before being stored as field values. This enables L</GetAttributes>
1373 :     to split them apart during retrieval. The splitter value defaults to double colons C<::>.
1374 :    
1375 :     =back
1376 :    
1377 :     =cut
1378 :    
1379 :     sub AddAttribute {
1380 :     # Get the parameters.
1381 : parrello 1.4 my ($self, $objectID, $key, @values) = @_;
1382 : parrello 1.3 # Don't allow undefs.
1383 :     if (! defined($objectID)) {
1384 :     Confess("No object ID specified for AddAttribute call.");
1385 :     } elsif (! defined($key)) {
1386 :     Confess("No attribute key specified for AddAttribute call.");
1387 :     } elsif (! @values) {
1388 :     Confess("No values specified in AddAttribute call for key $key.");
1389 :     } else {
1390 : parrello 1.11 # Okay, now we have some reason to believe we can do this. Form the values
1391 :     # into a scalar.
1392 : parrello 1.3 my $valueString = join($self->{splitter}, @values);
1393 : parrello 1.11 # Connect the object to the key.
1394 :     $self->InsertObject('HasValueFor', { 'from-link' => $key,
1395 :     'to-link' => $objectID,
1396 :     'value' => $valueString,
1397 :     });
1398 : parrello 1.3 }
1399 : parrello 1.10 # Return a one, indicating success. We do this for backward compatability.
1400 : parrello 1.3 return 1;
1401 :     }
1402 :    
1403 :     =head3 DeleteAttribute
1404 :    
1405 :     C<< $attrDB->DeleteAttribute($objectID, $key, @values); >>
1406 :    
1407 :     Delete the specified attribute key/value combination from the database.
1408 :    
1409 :     =over 4
1410 :    
1411 :     =item objectID
1412 :    
1413 : parrello 1.10 ID of the object whose attribute is to be deleted.
1414 : parrello 1.3
1415 :     =item key
1416 :    
1417 : parrello 1.10 Attribute key name.
1418 : parrello 1.3
1419 :     =item values
1420 :    
1421 : parrello 1.10 One or more values associated with the key. If no values are specified, then all values
1422 :     will be deleted. Otherwise, only a matching value will be deleted.
1423 : parrello 1.3
1424 :     =back
1425 :    
1426 :     =cut
1427 :    
1428 :     sub DeleteAttribute {
1429 :     # Get the parameters.
1430 : parrello 1.4 my ($self, $objectID, $key, @values) = @_;
1431 : parrello 1.3 # Don't allow undefs.
1432 :     if (! defined($objectID)) {
1433 :     Confess("No object ID specified for DeleteAttribute call.");
1434 :     } elsif (! defined($key)) {
1435 :     Confess("No attribute key specified for DeleteAttribute call.");
1436 : parrello 1.11 } elsif (scalar(@values) == 0) {
1437 : parrello 1.16 # Here we erase the entire key for this object.
1438 :     $self->DeleteRow('HasValueFor', $key, $objectID);
1439 : parrello 1.3 } else {
1440 : parrello 1.11 # Here we erase the matching values.
1441 :     my $valueString = join($self->{splitter}, @values);
1442 :     $self->DeleteRow('HasValueFor', $key, $objectID, { value => $valueString });
1443 : parrello 1.3 }
1444 :     # Return a one. This is for backward compatability.
1445 :     return 1;
1446 :     }
1447 :    
1448 : parrello 1.16 =head3 DeleteMatchingAttributes
1449 :    
1450 :     C<< my @deleted = $attrDB->DeleteMatchingAttributes($objectID, $key, @values); >>
1451 :    
1452 :     Delete all attributes that match the specified criteria. This is equivalent to
1453 :     calling L</GetAttributes> and then invoking L</DeleteAttribute> for each
1454 :     row found.
1455 :    
1456 :     =over 4
1457 :    
1458 :     =item objectID
1459 :    
1460 :     ID of object whose attributes are to be deleted. If the attributes for multiple
1461 :     objects are to be deleted, this parameter can be specified as a list reference. If
1462 :     attributes are to be deleted for all objects, specify C<undef> or an empty string.
1463 :     Finally, you can delete attributes for a range of object IDs by putting a percent
1464 :     sign (C<%>) at the end.
1465 :    
1466 :     =item key
1467 :    
1468 :     Attribute key name. A value of C<undef> or an empty string will match all
1469 :     attribute keys. If the values are to be deletedfor multiple keys, this parameter can be
1470 :     specified as a list reference. Finally, you can delete attributes for a range of
1471 :     keys by putting a percent sign (C<%>) at the end.
1472 :    
1473 :     =item values
1474 :    
1475 :     List of the desired attribute values, section by section. If C<undef>
1476 :     or an empty string is specified, all values in that section will match. A
1477 :     generic match can be requested by placing a percent sign (C<%>) at the end.
1478 :     In that case, all values that match up to and not including the percent sign
1479 :     will match. You may also specify a regular expression enclosed
1480 :     in slashes. All values that match the regular expression will be deleted. For
1481 :     performance reasons, only values have this extra capability.
1482 :    
1483 :     =item RETURN
1484 :    
1485 :     Returns a list of tuples for the attributes that were deleted, in the
1486 :     same form as L</GetAttributes>.
1487 :    
1488 :     =back
1489 :    
1490 :     =cut
1491 :    
1492 :     sub DeleteMatchingAttributes {
1493 :     # Get the parameters.
1494 :     my ($self, $objectID, $key, @values) = @_;
1495 :     # Get the matching attributes.
1496 :     my @retVal = $self->GetAttributes($objectID, $key, @values);
1497 :     # Loop through the attributes, deleting them.
1498 :     for my $tuple (@retVal) {
1499 :     $self->DeleteAttribute(@{$tuple});
1500 :     }
1501 : parrello 1.18 # Log this operation.
1502 :     my $count = @retVal;
1503 :     $self->LogOperation("Mass Delete", $key, "$count matching attributes deleted.");
1504 : parrello 1.16 # Return the deleted attributes.
1505 :     return @retVal;
1506 :     }
1507 :    
1508 : parrello 1.3 =head3 ChangeAttribute
1509 :    
1510 :     C<< $attrDB->ChangeAttribute($objectID, $key, \@oldValues, \@newValues); >>
1511 :    
1512 :     Change the value of an attribute key/value pair for an object.
1513 :    
1514 :     =over 4
1515 :    
1516 :     =item objectID
1517 :    
1518 :     ID of the genome or feature to which the attribute is to be changed. In general, an ID that
1519 :     starts with C<fig|> is treated as a feature ID, and an ID that is all digits and periods
1520 :     is treated as a genome ID. For IDs of other types, this parameter should be a reference
1521 :     to a 2-tuple consisting of the entity type name followed by the object ID.
1522 :    
1523 :     =item key
1524 :    
1525 :     Attribute key name. This corresponds to the name of a field in the database.
1526 :    
1527 :     =item oldValues
1528 :    
1529 :     One or more values identifying the key/value pair to change.
1530 :    
1531 :     =item newValues
1532 :    
1533 :     One or more values to be put in place of the old values.
1534 :    
1535 :     =back
1536 :    
1537 :     =cut
1538 :    
1539 :     sub ChangeAttribute {
1540 :     # Get the parameters.
1541 : parrello 1.4 my ($self, $objectID, $key, $oldValues, $newValues) = @_;
1542 : parrello 1.3 # Don't allow undefs.
1543 :     if (! defined($objectID)) {
1544 :     Confess("No object ID specified for ChangeAttribute call.");
1545 :     } elsif (! defined($key)) {
1546 :     Confess("No attribute key specified for ChangeAttribute call.");
1547 :     } elsif (! defined($oldValues) || ref $oldValues ne 'ARRAY') {
1548 :     Confess("No old values specified in ChangeAttribute call for key $key.");
1549 :     } elsif (! defined($newValues) || ref $newValues ne 'ARRAY') {
1550 :     Confess("No new values specified in ChangeAttribute call for key $key.");
1551 :     } else {
1552 : parrello 1.10 # We do the change as a delete/add.
1553 : parrello 1.3 $self->DeleteAttribute($objectID, $key, @{$oldValues});
1554 :     $self->AddAttribute($objectID, $key, @{$newValues});
1555 :     }
1556 :     # Return a one. We do this for backward compatability.
1557 :     return 1;
1558 :     }
1559 :    
1560 : parrello 1.7 =head3 EraseAttribute
1561 :    
1562 : parrello 1.11 C<< $attrDB->EraseAttribute($key); >>
1563 : parrello 1.7
1564 :     Erase all values for the specified attribute key. This does not remove the
1565 :     key from the database; it merely removes all the values.
1566 :    
1567 :     =over 4
1568 :    
1569 :     =item key
1570 :    
1571 :     Key to erase.
1572 :    
1573 :     =back
1574 :    
1575 :     =cut
1576 :    
1577 :     sub EraseAttribute {
1578 :     # Get the parameters.
1579 : parrello 1.10 my ($self, $key) = @_;
1580 : parrello 1.16 # Delete everything connected to the key.
1581 :     $self->Disconnect('HasValueFor', 'AttributeKey', $key);
1582 : parrello 1.18 # Log the operation.
1583 :     $self->LogOperation("Erase Data", $key);
1584 : parrello 1.7 # Return a 1, for backward compatability.
1585 :     return 1;
1586 :     }
1587 :    
1588 : parrello 1.9 =head3 GetAttributeKeys
1589 :    
1590 : parrello 1.10 C<< my @keyList = $attrDB->GetAttributeKeys($groupName); >>
1591 : parrello 1.9
1592 : parrello 1.10 Return a list of the attribute keys for a particular group.
1593 : parrello 1.9
1594 :     =over 4
1595 :    
1596 : parrello 1.10 =item groupName
1597 : parrello 1.9
1598 : parrello 1.10 Name of the group whose keys are desired.
1599 : parrello 1.9
1600 :     =item RETURN
1601 :    
1602 : parrello 1.10 Returns a list of the attribute keys for the specified group.
1603 : parrello 1.9
1604 :     =back
1605 :    
1606 :     =cut
1607 :    
1608 :     sub GetAttributeKeys {
1609 :     # Get the parameters.
1610 : parrello 1.10 my ($self, $groupName) = @_;
1611 :     # Get the attributes for the specified group.
1612 :     my @groups = $self->GetFlat(['IsInGroup'], "IsInGroup(to-link) = ?", [$groupName],
1613 :     'IsInGroup(from-link)');
1614 : parrello 1.9 # Return the keys.
1615 : parrello 1.10 return sort @groups;
1616 : parrello 1.9 }
1617 :    
1618 : parrello 1.1 1;

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