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1 : parrello 1.1 #!/usr/bin/perl -w
2 :    
3 :     package SearchHelper;
4 :    
5 :     use strict;
6 :     use Tracer;
7 :     use PageBuilder;
8 :     use Digest::MD5;
9 :     use File::Basename;
10 :     use File::Path;
11 :     use File::stat;
12 :     use LWP::UserAgent;
13 : parrello 1.34 use FIGRules;
14 : parrello 1.1 use Sprout;
15 :     use SFXlate;
16 :     use FIGRules;
17 :     use HTML;
18 :     use BasicLocation;
19 : parrello 1.3 use URI::Escape;
20 :     use PageBuilder;
21 : parrello 1.34 use AliasAnalysis;
22 :     use FreezeThaw qw(freeze thaw);
23 : parrello 1.1
24 :     =head1 Search Helper Base Class
25 :    
26 :     =head2 Introduction
27 :    
28 :     The search helper is a base class for all search objects. It has methods for performing
29 :     all the common tasks required to build and manage a search cache. The subclass must
30 :     provide methods for generating and processing search forms. The base class has the
31 :     following object fields.
32 :    
33 :     =over 4
34 :    
35 :     =item cols
36 :    
37 :     Reference to a list of column header descriptions. If undefined, then the session cache
38 :     file has been opened but nothing has been written to it.
39 :    
40 :     =item fileHandle
41 :    
42 :     File handle for the session cache file.
43 :    
44 :     =item query
45 :    
46 :     CGI query object, which includes the search parameters and the various
47 :     session status variables kept between requests from the user.
48 :    
49 :     =item type
50 :    
51 :     Session type: C<old> if there is an existing cache file from which we are
52 :     displaying search results, or C<new> if the cache file needs to be built.
53 :    
54 :     =item class
55 :    
56 :     Name of the search helper class as it would appear in the CGI query object
57 :     (i.e. without the C<SH> prefix.
58 :    
59 :     =item sprout
60 :    
61 :     Sprout object for accessing the database.
62 :    
63 :     =item message
64 :    
65 :     Message to display if an error has been detected.
66 :    
67 :     =item orgs
68 :    
69 : parrello 1.34 Reference to a hash mapping genome IDs to organism data. (Used to
70 :     improve performance.)
71 : parrello 1.1
72 :     =item name
73 :    
74 :     Name to use for this object's form.
75 :    
76 :     =item scriptQueue
77 :    
78 :     List of JavaScript statements to be executed after the form is closed.
79 :    
80 : parrello 1.3 =item genomeHash
81 :    
82 :     Cache of the genome group hash used to build genome selection controls.
83 :    
84 :     =item genomeParms
85 :    
86 :     List of the parameters that are used to select multiple genomes.
87 :    
88 : parrello 1.1 =back
89 :    
90 : parrello 1.2 =head2 Adding a new Search Tool
91 :    
92 :     To add a new search tool to the system, you must
93 :    
94 :     =over 4
95 :    
96 :     =item 1
97 :    
98 :     Choose a class name for your search tool.
99 :    
100 :     =item 2
101 :    
102 :     Create a new subclass of this object and implement each of the virtual methods. The
103 : parrello 1.34 name of the subclass must be C<SH>I<className>, where I<className> is the
104 :     type of search.
105 : parrello 1.2
106 :     =item 3
107 :    
108 :     Create an include file among the web server pages that describes how to use
109 :     the search tool. The include file must be in the B<includes> directory, and
110 :     its name must be C<SearchHelp_>I<className>C<.inc>.
111 :    
112 :     =item 4
113 :    
114 : parrello 1.34 If your search produces a result for which a helper does not exist, you
115 :     must create a new subclass of B<ResultHelper>. Its name must be
116 :     C<RH>I<className>, where I<className> is the type of result.
117 : parrello 1.2
118 :     =back
119 :    
120 :     =head3 Building a Search Form
121 :    
122 :     All search forms are three-column tables. In general, you want one form
123 :     variable per table row. The first column should contain the label and
124 :     the second should contain the form control for specifying the variable
125 :     value. If the control is wide, you should use C<colspan="2"> to give it
126 :     extra room. B<Do not> specify a width in any of your table cells, as
127 :     width management is handled by this class.
128 :    
129 :     The general code for creating the form should be
130 :    
131 :     sub Form {
132 :     my ($self) = @_;
133 :     # Get the CGI object.
134 :     my $cgi = @self->Q();
135 :     # Start the form.
136 :     my $retVal = $self->FormStart("form title");
137 :     # Assemble the table rows.
138 :     my @rows = ();
139 :     ... push table row Html into @rows ...
140 :     push @rows, $self->SubmitRow();
141 :     ... push more Html into @rows ...
142 :     # Build the table from the rows.
143 :     $retVal .= $self->MakeTable(\@rows);
144 :     # Close the form.
145 :     $retVal .= $self->FormEnd();
146 :     # Return the form Html.
147 :     return $retVal;
148 :     }
149 :    
150 :     Several helper methods are provided for particular purposes.
151 :    
152 : parrello 1.3 L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
153 :     L</GetGenomes> to retrieve all the genomes passed in for a specified parameter
154 :     name. Note that as an assist to people working with GET-style links, if no
155 :     genomes are specified and the incoming request style is GET, all genomes will
156 :     be returned.
157 : parrello 1.2
158 :     L</QueueFormScript> allows you to queue JavaScript statements for execution
159 :     after the form is fully generated. If you are using very complicated
160 :     form controls, the L</QueueFormScript> method allows you to perform
161 :     JavaScript initialization. The L</NmpdrGenomeMenu> control uses this
162 :     facility to display a list of the pre-selected genomes.
163 :    
164 :     Finally, when generating the code for your controls, be sure to use any incoming
165 :     query parameters as default values so that the search request is persistent.
166 :    
167 :     =head3 Finding Search Results
168 :    
169 : parrello 1.34 The L</Find> method is used to create the search results. The basic code
170 :     structure would work as follows.
171 : parrello 1.2
172 :     sub Find {
173 :     my ($self) = @_;
174 :     # Get the CGI and Sprout objects.
175 :     my $cgi = $self->Q();
176 :     my $sprout = $self->DB();
177 :     # Declare the return variable. If it remains undefined, the caller will
178 :     # know that an error occurred.
179 :     my $retVal;
180 :     ... validate the parameters ...
181 :     if (... invalid parameters...) {
182 :     $self->SetMessage(...appropriate message...);
183 : parrello 1.34 } else {
184 :     # Determine the result type.
185 :     my $rhelp = SearchHelper::GetHelper($self, RH => $resultType);
186 : parrello 1.38 # Specify the columns.
187 : parrello 1.34 $self->DefaultColumns($rhelp);
188 :     # You may want to add extra columns. $name is the column name and
189 :     # $loc is its location. The other parameters take their names from the
190 :     # corresponding column methods.
191 :     $rhelp->AddExtraColumn($name => $loc, style => $style, download => $flag,
192 :     title => $title);
193 :     # Some searches require optional columns that are configured by the
194 :     # user or by the search query itself. There are some special methods
195 :     # for this in the result helpers, but there's also the direct approach
196 :     # shown below.
197 :     $rhelp->AddOptionalColumn($name => $loc);
198 : parrello 1.2 # Initialize the session file.
199 : parrello 1.34 $self->OpenSession($rhelp);
200 : parrello 1.2 # Initialize the result counter.
201 :     $retVal = 0;
202 : parrello 1.34 ... set up to loop through the results ...
203 :     while (...more results...) {
204 :     ...compute extra columns and call PutExtraColumns...
205 :     $rhelp->PutData($sortKey, $objectID, $record);
206 :     $retVal++;
207 : parrello 1.2 }
208 : parrello 1.9 # Close the session file.
209 :     $self->CloseSession();
210 : parrello 1.2 }
211 :     # Return the result count.
212 :     return $retVal;
213 :     }
214 :    
215 :     A Find method is of course much more complicated than generating a form, and there
216 : parrello 1.34 are variations on the above theme.
217 : parrello 1.2
218 : parrello 1.28 In addition to the finding and filtering, it is necessary to send status messages
219 :     to the output so that the user does not get bored waiting for results. The L</PrintLine>
220 :     method performs this function. The single parameter should be text to be
221 :     output to the browser. In general, you'll invoke it as follows.
222 :    
223 :     $self->PrintLine("...my message text...<br />");
224 :    
225 :     The break tag is optional. When the Find method gets control, a paragraph will
226 :     have been started so that everything is XHTML-compliant.
227 :    
228 : parrello 1.2 The L</Find> method must return C<undef> if the search parameters are invalid. If this
229 :     is the case, then a message describing the problem should be passed to the framework
230 :     by calling L</SetMessage>. If the parameters are valid, then the method must return
231 :     the number of items found.
232 :    
233 : parrello 1.1 =cut
234 :    
235 :     # This counter is used to insure every form on the page has a unique name.
236 :     my $formCount = 0;
237 : parrello 1.16 # This counter is used to generate unique DIV IDs.
238 :     my $divCount = 0;
239 : parrello 1.1
240 :     =head2 Public Methods
241 :    
242 :     =head3 new
243 :    
244 : parrello 1.38 my $shelp = SearchHelper->new($cgi);
245 : parrello 1.1
246 :     Construct a new SearchHelper object.
247 :    
248 :     =over 4
249 :    
250 : parrello 1.19 =item cgi
251 : parrello 1.1
252 :     The CGI query object for the current script.
253 :    
254 :     =back
255 :    
256 :     =cut
257 :    
258 :     sub new {
259 :     # Get the parameters.
260 : parrello 1.19 my ($class, $cgi) = @_;
261 : parrello 1.1 # Check for a session ID.
262 : parrello 1.19 my $session_id = $cgi->param("SessionID");
263 : parrello 1.1 my $type = "old";
264 :     if (! $session_id) {
265 : parrello 1.26 Trace("No session ID found.") if T(3);
266 : parrello 1.1 # Here we're starting a new session. We create the session ID and
267 :     # store it in the query object.
268 : parrello 1.34 $session_id = FIGRules::NewSessionID();
269 :     Trace("New session ID is $session_id.") if T(3);
270 : parrello 1.1 $type = "new";
271 : parrello 1.19 $cgi->param(-name => 'SessionID', -value => $session_id);
272 : parrello 1.26 } else {
273 :     Trace("Session ID is $session_id.") if T(3);
274 : parrello 1.1 }
275 : parrello 1.34 Trace("Computing subclass.") if T(3);
276 : parrello 1.1 # Compute the subclass name.
277 : parrello 1.19 my $subClass;
278 :     if ($class =~ /SH(.+)$/) {
279 :     # Here we have a real search class.
280 :     $subClass = $1;
281 :     } else {
282 :     # Here we have a bare class. The bare class cannot search, but it can
283 :     # process search results.
284 :     $subClass = 'SearchHelper';
285 :     }
286 : parrello 1.34 Trace("Subclass name is $subClass.") if T(3);
287 : parrello 1.1 # Insure everybody knows we're in Sprout mode.
288 : parrello 1.19 $cgi->param(-name => 'SPROUT', -value => 1);
289 : parrello 1.1 # Generate the form name.
290 :     my $formName = "$class$formCount";
291 :     $formCount++;
292 : parrello 1.34 Trace("Creating helper.") if T(3);
293 : parrello 1.1 # Create the shelp object. It contains the query object (with the session ID)
294 :     # as well as an indicator as to whether or not the session is new, plus the
295 : parrello 1.2 # class name and a placeholder for the Sprout object.
296 : parrello 1.1 my $retVal = {
297 : parrello 1.19 query => $cgi,
298 : parrello 1.1 type => $type,
299 :     class => $subClass,
300 : parrello 1.2 sprout => undef,
301 : parrello 1.1 orgs => {},
302 :     name => $formName,
303 :     scriptQueue => [],
304 : parrello 1.3 genomeList => undef,
305 :     genomeParms => [],
306 : parrello 1.1 };
307 :     # Bless and return it.
308 :     bless $retVal, $class;
309 :     return $retVal;
310 :     }
311 :    
312 :     =head3 Q
313 :    
314 : parrello 1.38 my $query = $shelp->Q();
315 : parrello 1.1
316 :     Return the CGI query object.
317 :    
318 :     =cut
319 :    
320 :     sub Q {
321 :     # Get the parameters.
322 :     my ($self) = @_;
323 :     # Return the result.
324 :     return $self->{query};
325 :     }
326 :    
327 : parrello 1.9
328 :    
329 : parrello 1.1 =head3 DB
330 :    
331 : parrello 1.38 my $sprout = $shelp->DB();
332 : parrello 1.1
333 :     Return the Sprout database object.
334 :    
335 :     =cut
336 :    
337 :     sub DB {
338 :     # Get the parameters.
339 :     my ($self) = @_;
340 : parrello 1.2 # Insure we have a database.
341 :     my $retVal = $self->{sprout};
342 :     if (! defined $retVal) {
343 :     $retVal = SFXlate->new_sprout_only();
344 :     $self->{sprout} = $retVal;
345 :     }
346 : parrello 1.1 # Return the result.
347 : parrello 1.2 return $retVal;
348 : parrello 1.1 }
349 :    
350 :     =head3 IsNew
351 :    
352 : parrello 1.38 my $flag = $shelp->IsNew();
353 : parrello 1.1
354 :     Return TRUE if this is a new session, FALSE if this is an old session. An old
355 :     session already has search results ready to process.
356 :    
357 :     =cut
358 :    
359 :     sub IsNew {
360 :     # Get the parameters.
361 :     my ($self) = @_;
362 :     # Return the result.
363 :     return ($self->{type} eq 'new');
364 :     }
365 :    
366 :     =head3 ID
367 :    
368 : parrello 1.38 my $sessionID = $shelp->ID();
369 : parrello 1.1
370 :     Return the current session ID.
371 :    
372 :     =cut
373 :    
374 :     sub ID {
375 :     # Get the parameters.
376 :     my ($self) = @_;
377 :     # Return the result.
378 :     return $self->Q()->param("SessionID");
379 :     }
380 :    
381 :     =head3 FormName
382 :    
383 : parrello 1.38 my $name = $shelp->FormName();
384 : parrello 1.1
385 :     Return the name of the form this helper object will generate.
386 :    
387 :     =cut
388 :    
389 :     sub FormName {
390 :     # Get the parameters.
391 :     my ($self) = @_;
392 :     # Return the result.
393 :     return $self->{name};
394 :     }
395 :    
396 :     =head3 QueueFormScript
397 :    
398 : parrello 1.38 $shelp->QueueFormScript($statement);
399 : parrello 1.1
400 :     Add the specified statement to the queue of JavaScript statements that are to be
401 :     executed when the form has been fully defined. This is necessary because until
402 :     the closing </FORM> tag is emitted, the form elements cannot be referenced by
403 :     name. When generating the statement, you can refer to the variable C<thisForm>
404 :     in order to reference the form in progress. Thus,
405 :    
406 :     thisForm.simLimit.value = 1e-10;
407 :    
408 :     would set the value of the form element C<simLimit> in the current form to
409 :     C<1e-10>.
410 :    
411 :     =over 4
412 :    
413 :     =item statement
414 :    
415 :     JavaScript statement to be queued for execution after the form is built.
416 :     The trailing semi-colon is required. Theoretically, you could include
417 :     multiple statements separated by semi-colons, but one at a time works
418 :     just as well.
419 :    
420 :     =back
421 :    
422 :     =cut
423 :    
424 :     sub QueueFormScript {
425 :     # Get the parameters.
426 :     my ($self, $statement) = @_;
427 :     # Push the statement onto the script queue.
428 :     push @{$self->{scriptQueue}}, $statement;
429 :     }
430 :    
431 :     =head3 FormStart
432 :    
433 : parrello 1.38 my $html = $shelp->FormStart($title);
434 : parrello 1.1
435 :     Return the initial section of a form designed to perform another search of the
436 :     same type. The form header is included along with hidden fields to persist the
437 :     tracing, sprout status, and search class.
438 :    
439 :     A call to L</FormEnd> is required to close the form.
440 :    
441 :     =over 4
442 :    
443 :     =item title
444 :    
445 :     Title to be used for the form.
446 :    
447 :     =item RETURN
448 :    
449 :     Returns the initial HTML for the search form.
450 :    
451 :     =back
452 :    
453 :     =cut
454 :    
455 :     sub FormStart {
456 :     # Get the parameters.
457 :     my ($self, $title) = @_;
458 :     # Get the CGI object.
459 :     my $cgi = $self->Q();
460 : parrello 1.18 # Start the form. Note we use the override option on the Class value, in
461 :     # case the Advanced button was used.
462 : parrello 1.1 my $retVal = "<div class=\"search\">\n" .
463 :     $cgi->start_form(-method => 'POST',
464 : parrello 1.41 -action => "$FIG_Config::cgi_url/SearchSkeleton.cgi",
465 : parrello 1.1 -name => $self->FormName()) .
466 :     $cgi->hidden(-name => 'Class',
467 : parrello 1.18 -value => $self->{class},
468 :     -override => 1) .
469 : parrello 1.1 $cgi->hidden(-name => 'SPROUT',
470 :     -value => 1) .
471 : parrello 1.37 $cgi->h3("$title" . Hint($self->{class}, "Click here for more information."));
472 : parrello 1.1 # Put in an anchor tag in case there's a table of contents.
473 :     my $anchorName = $self->FormName();
474 :     $retVal .= "<a name=\"$anchorName\"></a>\n";
475 :     # Return the result.
476 :     return $retVal;
477 :     }
478 :    
479 :     =head3 FormEnd
480 :    
481 : parrello 1.38 my $htmlText = $shelp->FormEnd();
482 : parrello 1.1
483 :     Return the HTML text for closing a search form. This closes both the C<form> and
484 :     C<div> tags.
485 :    
486 :     =cut
487 :    
488 :     sub FormEnd {
489 :     # Get the parameters.
490 :     my ($self) = @_;
491 :     # Declare the return variable, closing the form and the DIV block.
492 :     my $retVal = "</form></div>\n";
493 :     # Now we flush out the statement queue.
494 :     my @statements = @{$self->{scriptQueue}};
495 :     if (@statements > 0) {
496 :     # Switch to JavaScript and set the "thisForm" variable.
497 :     $retVal .= "<SCRIPT language=\"JavaScript\">\n" .
498 :     " thisForm = document.$self->{name};\n";
499 :     # Unroll the statements.
500 :     while (@statements > 0) {
501 :     my $statement = shift @statements;
502 :     $retVal .= " $statement\n";
503 :     }
504 :     # Close the JavaScript.
505 :     $retVal .= "</SCRIPT>\n";
506 :     }
507 :     # Return the result.
508 :     return $retVal;
509 :     }
510 :    
511 :     =head3 SetMessage
512 :    
513 : parrello 1.38 $shelp->SetMessage($msg);
514 : parrello 1.1
515 :     Store the specified text as the result message. The result message is displayed
516 :     if an invalid parameter value is specified.
517 :    
518 :     =over 4
519 :    
520 :     =item msg
521 :    
522 :     Text of the result message to be displayed.
523 :    
524 :     =back
525 :    
526 :     =cut
527 :    
528 :     sub SetMessage {
529 :     # Get the parameters.
530 :     my ($self, $msg) = @_;
531 :     # Store the message.
532 :     $self->{message} = $msg;
533 :     }
534 :    
535 :     =head3 Message
536 :    
537 : parrello 1.38 my $text = $shelp->Message();
538 : parrello 1.1
539 :     Return the result message. The result message is displayed if an invalid parameter
540 :     value is specified.
541 :    
542 :     =cut
543 :    
544 :     sub Message {
545 :     # Get the parameters.
546 :     my ($self) = @_;
547 :     # Return the result.
548 :     return $self->{message};
549 :     }
550 :    
551 :     =head3 OpenSession
552 :    
553 : parrello 1.38 $shelp->OpenSession($rhelp);
554 : parrello 1.34
555 :     Set up the session cache file and write out the column headers.
556 :     This method should not be called until all the columns have
557 :     been configured, including the extra columns.
558 :    
559 :     =over 4
560 :    
561 :     =item rhelp
562 :    
563 :     Result helper for formatting the output. This has the column
564 :     headers stored in it.
565 : parrello 1.1
566 : parrello 1.34 =back
567 : parrello 1.1
568 :     =cut
569 :    
570 :     sub OpenSession {
571 :     # Get the parameters.
572 : parrello 1.34 my ($self, $rhelp) = @_;
573 :     # Insure the result helper is valid.
574 :     if (! defined($rhelp)) {
575 :     Confess("No result type specified for $self->{class}.");
576 :     } elsif(! $rhelp->isa('ResultHelper')) {
577 :     Confess("Invalid result type specified for $self->{class}.");
578 :     } else {
579 :     # Get the column headers and write them out.
580 :     my $colHdrs = $rhelp->GetColumnHeaders();
581 :     Trace(scalar(@{$colHdrs}) . " column headers written to output.") if T(3);
582 :     $self->WriteColumnHeaders(@{$colHdrs});
583 :     }
584 : parrello 1.1 }
585 :    
586 :     =head3 GetCacheFileName
587 :    
588 : parrello 1.38 my $fileName = $shelp->GetCacheFileName();
589 : parrello 1.1
590 :     Return the name to be used for this session's cache file.
591 :    
592 :     =cut
593 :    
594 :     sub GetCacheFileName {
595 :     # Get the parameters.
596 :     my ($self) = @_;
597 :     # Return the result.
598 :     return $self->GetTempFileName('cache');
599 :     }
600 :    
601 :     =head3 GetTempFileName
602 :    
603 : parrello 1.38 my $fileName = $shelp->GetTempFileName($type);
604 : parrello 1.1
605 :     Return the name to be used for a temporary file of the specified type. The
606 :     name is computed from the session name with the type as a suffix.
607 :    
608 :     =over 4
609 :    
610 :     =item type
611 :    
612 :     Type of temporary file to be generated.
613 :    
614 :     =item RETURN
615 :    
616 :     Returns a file name generated from the session name and the specified type.
617 :    
618 :     =back
619 :    
620 :     =cut
621 :    
622 :     sub GetTempFileName {
623 :     # Get the parameters.
624 :     my ($self, $type) = @_;
625 :     # Compute the file name. Note it gets stuffed in the FIG temporary
626 :     # directory.
627 : parrello 1.34 my $retVal = FIGRules::GetTempFileName(sessionID => $self->ID(), extension => $type);
628 : parrello 1.1 # Return the result.
629 :     return $retVal;
630 :     }
631 :    
632 :     =head3 WriteColumnHeaders
633 :    
634 : parrello 1.38 $shelp->WriteColumnHeaders(@colNames);
635 : parrello 1.1
636 :     Write out the column headers for the current search session. The column headers
637 :     are sent to the cache file, and then the cache is re-opened as a sort pipe and
638 :     the handle saved.
639 :    
640 :     =over 4
641 :    
642 :     =item colNames
643 :    
644 : parrello 1.34 A list of column names in the desired presentation order. For extra columns,
645 :     the column name is the hash supplied as the column definition.
646 : parrello 1.1
647 :     =back
648 :    
649 :     =cut
650 :    
651 :     sub WriteColumnHeaders {
652 :     # Get the parameters.
653 :     my ($self, @colNames) = @_;
654 :     # Get the cache file name and open it for output.
655 :     my $fileName = $self->GetCacheFileName();
656 :     my $handle1 = Open(undef, ">$fileName");
657 : parrello 1.34 # Freeze the column headers.
658 :     my @colHdrs = map { freeze($_) } @colNames;
659 : parrello 1.1 # Write the column headers and close the file.
660 : parrello 1.34 Tracer::PutLine($handle1, \@colHdrs);
661 : parrello 1.1 close $handle1;
662 :     # Now open the sort pipe and save the file handle. Note how we append the
663 :     # sorted data to the column header row already in place. The output will
664 :     # contain a sort key followed by the real columns. The sort key is
665 :     # hacked off before going to the output file.
666 :     $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");
667 :     }
668 :    
669 : parrello 1.34 =head3 ReadColumnHeaders
670 :    
671 : parrello 1.38 my @colHdrs = $shelp->ReadColumnHeaders($fh);
672 : parrello 1.34
673 :     Read the column headers from the specified file handle. The column headers are
674 :     frozen strings intermixed with frozen hash references. The strings represent
675 :     column names defined in the result helper. The hash references represent the
676 :     definitions of the extra columns.
677 :    
678 :     =over 4
679 :    
680 :     =item fh
681 :    
682 :     File handle from which the column headers are to be read.
683 :    
684 :     =item RETURN
685 :    
686 :     Returns a list of the column headers pulled from the specified file's first line.
687 :    
688 :     =back
689 :    
690 :     =cut
691 :    
692 :     sub ReadColumnHeaders {
693 :     # Get the parameters.
694 :     my ($self, $fh) = @_;
695 :     # Read and thaw the columns.
696 :     my @retVal = map { thaw($_) } Tracer::GetLine($fh);
697 :     # Return them to the caller.
698 :     return @retVal;
699 :     }
700 :    
701 : parrello 1.1 =head3 WriteColumnData
702 :    
703 : parrello 1.38 $shelp->WriteColumnData($key, @colValues);
704 : parrello 1.1
705 :     Write a row of column values to the current search session. It is assumed that
706 :     the session file is already open for output.
707 :    
708 :     =over 4
709 :    
710 :     =item key
711 :    
712 :     Sort key.
713 :    
714 :     =item colValues
715 :    
716 :     List of column values to write to the search result cache file for this session.
717 :    
718 :     =back
719 :    
720 :     =cut
721 :    
722 :     sub WriteColumnData {
723 :     # Get the parameters.
724 :     my ($self, $key, @colValues) = @_;
725 :     # Write them to the cache file.
726 :     Tracer::PutLine($self->{fileHandle}, [$key, @colValues]);
727 : parrello 1.32 Trace("Column data is " . join("; ", $key, @colValues) . ".") if T(4);
728 : parrello 1.1 }
729 :    
730 :     =head3 CloseSession
731 :    
732 : parrello 1.38 $shelp->CloseSession();
733 : parrello 1.1
734 :     Close the session file.
735 :    
736 :     =cut
737 :    
738 :     sub CloseSession {
739 :     # Get the parameters.
740 :     my ($self) = @_;
741 :     # Check for an open session file.
742 :     if (defined $self->{fileHandle}) {
743 :     # We found one, so close it.
744 : parrello 1.9 Trace("Closing session file.") if T(2);
745 : parrello 1.1 close $self->{fileHandle};
746 : parrello 1.28 # Tell the user.
747 :     my $cgi = $self->Q();
748 :     $self->PrintLine("Output formatting complete.<br />");
749 : parrello 1.1 }
750 :     }
751 :    
752 :     =head3 OrganismData
753 :    
754 : parrello 1.38 my ($orgName, $group) = $shelp->Organism($genomeID);
755 : parrello 1.1
756 :     Return the name and status of the organism corresponding to the specified genome ID.
757 :     For performance reasons, this information is cached in a special hash table, so we
758 :     only compute it once per run.
759 :    
760 :     =over 4
761 :    
762 :     =item genomeID
763 :    
764 :     ID of the genome whose name is desired.
765 :    
766 :     =item RETURN
767 :    
768 : parrello 1.32 Returns a list of three items. The first item in the list is the organism name,
769 : parrello 1.1 and the second is the name of the NMPDR group, or an empty string if the
770 : parrello 1.32 organism is not in an NMPDR group. The third item is the organism's domain.
771 : parrello 1.1
772 :     =back
773 :    
774 :     =cut
775 :    
776 :     sub OrganismData {
777 :     # Get the parameters.
778 :     my ($self, $genomeID) = @_;
779 :     # Declare the return variables.
780 : parrello 1.32 my ($orgName, $group, $domain);
781 : parrello 1.1 # Check the cache.
782 :     my $cache = $self->{orgs};
783 :     if (exists $cache->{$genomeID}) {
784 : parrello 1.32 ($orgName, $group, $domain) = @{$cache->{$genomeID}};
785 : parrello 1.36 Trace("Cached organism $genomeID has group \"$group\".") if T(4);
786 : parrello 1.1 } else {
787 :     # Here we have to use the database.
788 :     my $sprout = $self->DB();
789 : parrello 1.36 my ($genus, $species, $strain, $newGroup, $taxonomy) = $sprout->GetEntityValues('Genome', $genomeID,
790 : parrello 1.32 ['Genome(genus)', 'Genome(species)',
791 :     'Genome(unique-characterization)',
792 :     'Genome(primary-group)',
793 :     'Genome(taxonomy)']);
794 : parrello 1.10 # Format and cache the name and display group.
795 : parrello 1.36 Trace("Caching organism $genomeID with group \"$newGroup\".") if T(4);
796 :     ($orgName, $group, $domain) = $self->SaveOrganismData($newGroup, $genomeID, $genus, $species,
797 : parrello 1.32 $strain, $taxonomy);
798 : parrello 1.36 Trace("Returning group $group.") if T(4);
799 : parrello 1.1 }
800 :     # Return the result.
801 : parrello 1.32 return ($orgName, $group, $domain);
802 : parrello 1.1 }
803 :    
804 :     =head3 Organism
805 :    
806 : parrello 1.38 my $orgName = $shelp->Organism($genomeID);
807 : parrello 1.1
808 :     Return the name of the relevant organism. The name is computed from the genus,
809 :     species, and unique characterization. A cache is used to improve performance.
810 :    
811 :     =over 4
812 :    
813 :     =item genomeID
814 :    
815 :     ID of the genome whose name is desired.
816 :    
817 :     =item RETURN
818 :    
819 :     Returns the display name of the specified organism.
820 :    
821 :     =back
822 :    
823 :     =cut
824 :    
825 :     sub Organism {
826 :     # Get the parameters.
827 :     my ($self, $genomeID) = @_;
828 :     # Get the organism data.
829 : parrello 1.32 my ($retVal) = $self->OrganismData($genomeID);
830 : parrello 1.1 # Return the result.
831 :     return $retVal;
832 :     }
833 :    
834 :     =head3 ComputeFASTA
835 :    
836 : parrello 1.42 my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth, $comments);
837 : parrello 1.1
838 : parrello 1.32 Parse a sequence input and convert it into a FASTA string of the desired type with
839 :     the desired flanking width.
840 : parrello 1.1
841 :     =over 4
842 :    
843 :     =item desiredType
844 :    
845 : parrello 1.34 C<dna> to return a DNA sequence, C<prot> to return a protein sequence, C<dnaPattern>
846 :     to return a DNA search pattern, C<protPattern> to return a protein search pattern.
847 : parrello 1.1
848 :     =item sequence
849 :    
850 :     Sequence to return. It may be a DNA or protein sequence in FASTA form or a feature ID.
851 :     If a feature ID is specified, the feature's DNA or translation will be returned. The
852 :     feature ID is recognized by the presence of a vertical bar in the input. Otherwise,
853 :     if the input does not begin with a greater-than sign (FASTA label line), a default label
854 :     line will be provided.
855 :    
856 : parrello 1.32 =item flankingWidth
857 :    
858 :     If the DNA FASTA of a feature is desired, the number of base pairs to either side of the
859 :     feature that should be included. Currently we can't do this for Proteins because the
860 :     protein translation of a feature doesn't always match the DNA and is taken directly
861 :     from the database.
862 :    
863 : parrello 1.42 =item comments
864 :    
865 :     Comment string to be added to the FASTA header.
866 :    
867 : parrello 1.1 =item RETURN
868 :    
869 :     Returns a string in FASTA format representing the content of the desired sequence with
870 :     an appropriate label. If the input is invalid, a message will be stored and we will
871 :     return C<undef>. Note that the output will include a trailing new-line.
872 :    
873 :     =back
874 :    
875 :     =cut
876 :    
877 :     sub ComputeFASTA {
878 :     # Get the parameters.
879 : parrello 1.42 my ($self, $desiredType, $sequence, $flankingWidth, $comment) = @_;
880 : parrello 1.1 # Declare the return variable. If an error occurs, it will remain undefined.
881 :     my $retVal;
882 : parrello 1.11 # This variable will be cleared if an error is detected.
883 :     my $okFlag = 1;
884 : parrello 1.1 # Create variables to hold the FASTA label and data.
885 :     my ($fastaLabel, $fastaData);
886 : parrello 1.18 Trace("FASTA desired type is $desiredType.") if T(4);
887 : parrello 1.29 # Check for a feature specification. The smoking gun for that is a vertical bar.
888 : parrello 1.1 if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
889 :     # Here we have a feature ID in $1. We'll need the Sprout object to process
890 :     # it.
891 :     my $fid = $1;
892 : parrello 1.11 Trace("Feature ID for fasta is $fid.") if T(3);
893 : parrello 1.1 my $sprout = $self->DB();
894 :     # Get the FIG ID. Note that we only use the first feature found. We are not
895 :     # supposed to have redundant aliases, though we may have an ID that doesn't
896 :     # exist.
897 :     my ($figID) = $sprout->FeaturesByAlias($fid);
898 :     if (! $figID) {
899 : parrello 1.17 $self->SetMessage("No gene found with the ID \"$fid\".");
900 : parrello 1.11 $okFlag = 0;
901 : parrello 1.1 } else {
902 : parrello 1.29 # Set the FASTA label. The ID is the first favored alias.
903 :     my $favored = $self->Q()->param('FavoredAlias') || 'fig';
904 :     my $favorLen = length $favored;
905 :     ($fastaLabel) = grep { substr($_, 0, $favorLen) eq $favored } $sprout->FeatureAliases($fid);
906 :     if (! $fastaLabel) {
907 :     # In an emergency, fall back to the original ID.
908 :     $fastaLabel = $fid;
909 :     }
910 : parrello 1.42 # Add any specified comments.
911 :     if ($comment) {
912 :     $fastaLabel .= " $comment";
913 :     }
914 : parrello 1.1 # Now proceed according to the sequence type.
915 : parrello 1.33 if ($desiredType =~ /prot/) {
916 : parrello 1.1 # We want protein, so get the translation.
917 :     $fastaData = $sprout->FeatureTranslation($figID);
918 : parrello 1.11 Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
919 : parrello 1.34 } elsif ($desiredType =~ /dna/) {
920 : parrello 1.32 # We want DNA, so get the DNA sequence. This is a two-step process. First, we get the
921 :     # locations.
922 : parrello 1.1 my @locList = $sprout->FeatureLocation($figID);
923 : parrello 1.32 if ($flankingWidth > 0) {
924 :     # Here we need to add flanking data. Convert the locations to a list
925 :     # of location objects.
926 :     my @locObjects = map { BasicLocation->new($_) } @locList;
927 :     # Initialize the return variable. We will put the DNA in here segment by segment.
928 :     $fastaData = "";
929 :     # Now we widen each location by the flanking width and stash the results. This
930 :     # requires getting the contig length for each contig so we don't fall off the end.
931 :     for my $locObject (@locObjects) {
932 :     Trace("Current location is " . $locObject->String . ".") if T(4);
933 :     # Remember the current start and length.
934 :     my ($start, $len) = ($locObject->Left, $locObject->Length);
935 :     # Get the contig length.
936 :     my $contigLen = $sprout->ContigLength($locObject->Contig);
937 :     # Widen the location and get its DNA.
938 :     $locObject->Widen($flankingWidth, $contigLen);
939 :     my $fastaSegment = $sprout->DNASeq([$locObject->String()]);
940 :     # Now we need to do some case changing. The main DNA is upper case and
941 :     # the flanking DNA is lower case.
942 :     my $leftFlank = $start - $locObject->Left;
943 :     my $rightFlank = $leftFlank + $len;
944 :     Trace("Wide location is " . $locObject->String . ". Flanks are $leftFlank and $rightFlank. Contig len is $contigLen.") if T(4);
945 :     my $fancyFastaSegment = lc(substr($fastaSegment, 0, $leftFlank)) .
946 :     uc(substr($fastaSegment, $leftFlank, $rightFlank - $leftFlank)) .
947 :     lc(substr($fastaSegment, $rightFlank));
948 :     $fastaData .= $fancyFastaSegment;
949 :     }
950 :     } else {
951 :     # Here we have just the raw sequence.
952 :     $fastaData = $sprout->DNASeq(\@locList);
953 :     }
954 :     Trace((length $fastaData) . " characters returned for DNA of $fastaLabel.") if T(3);
955 : parrello 1.1 }
956 :     }
957 :     } else {
958 : parrello 1.11 Trace("Analyzing FASTA sequence.") if T(4);
959 : parrello 1.1 # Here we are expecting a FASTA. We need to see if there's a label.
960 : parrello 1.11 if ($sequence =~ /^>[\n\s]*(\S[^\n]*)\n(.+)$/s) {
961 :     Trace("Label \"$1\" found in match to sequence:\n$sequence") if T(4);
962 : parrello 1.1 # Here we have a label, so we split it from the data.
963 :     $fastaLabel = $1;
964 :     $fastaData = $2;
965 :     } else {
966 : parrello 1.11 Trace("No label found in match to sequence:\n$sequence") if T(4);
967 : parrello 1.1 # Here we have no label, so we create one and use the entire sequence
968 :     # as data.
969 : parrello 1.34 $fastaLabel = "$desiredType sequence specified by user";
970 : parrello 1.1 $fastaData = $sequence;
971 :     }
972 : parrello 1.34 # If we are not doing a pattern search, we need to clean the junk out of the sequence.
973 :     if ($desiredType !~ /pattern/i) {
974 :     $fastaData =~ s/\n//g;
975 :     $fastaData =~ s/\s+//g;
976 :     }
977 : parrello 1.18 # Finally, verify that it's DNA if we're doing DNA stuff.
978 : parrello 1.34 if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {
979 : parrello 1.24 $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
980 : parrello 1.11 $okFlag = 0;
981 : parrello 1.1 }
982 :     }
983 : parrello 1.11 Trace("FASTA data sequence: $fastaData") if T(4);
984 :     # Only proceed if no error was detected.
985 :     if ($okFlag) {
986 : parrello 1.33 if ($desiredType =~ /pattern/i) {
987 : parrello 1.34 # For a scan, there is no label and no breakup.
988 : parrello 1.33 $retVal = $fastaData;
989 :     } else {
990 :     # We need to format the sequence into 60-byte chunks. We use the infamous
991 :     # grep-split trick. The split, because of the presence of the parentheses,
992 :     # includes the matched delimiters in the output list. The grep strips out
993 :     # the empty list items that appear between the so-called delimiters, since
994 :     # the delimiters are what we want.
995 :     my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
996 :     $retVal = join("\n", ">$fastaLabel", @chunks, "");
997 :     }
998 : parrello 1.1 }
999 :     # Return the result.
1000 :     return $retVal;
1001 :     }
1002 :    
1003 : parrello 1.16 =head3 SubsystemTree
1004 :    
1005 : parrello 1.38 my $tree = SearchHelper::SubsystemTree($sprout, %options);
1006 : parrello 1.16
1007 :     This method creates a subsystem selection tree suitable for passing to
1008 :     L</SelectionTree>. Each leaf node in the tree will have a link to the
1009 :     subsystem display page. In addition, each node can have a radio button. The
1010 :     radio button alue is either C<classification=>I<string>, where I<string> is
1011 :     a classification string, or C<id=>I<string>, where I<string> is a subsystem ID.
1012 :     Thus, it can either be used to filter by a group of related subsystems or a
1013 :     single subsystem.
1014 :    
1015 :     =over 4
1016 :    
1017 :     =item sprout
1018 :    
1019 :     Sprout database object used to get the list of subsystems.
1020 :    
1021 :     =item options
1022 :    
1023 :     Hash containing options for building the tree.
1024 :    
1025 :     =item RETURN
1026 :    
1027 :     Returns a reference to a tree list suitable for passing to L</SelectionTree>.
1028 :    
1029 :     =back
1030 :    
1031 :     The supported options are as follows.
1032 :    
1033 :     =over 4
1034 :    
1035 :     =item radio
1036 :    
1037 :     TRUE if the tree should be configured for radio buttons. The default is FALSE.
1038 :    
1039 :     =item links
1040 :    
1041 :     TRUE if the tree should be configured for links. The default is TRUE.
1042 :    
1043 :     =back
1044 :    
1045 :     =cut
1046 :    
1047 :     sub SubsystemTree {
1048 :     # Get the parameters.
1049 :     my ($sprout, %options) = @_;
1050 :     # Process the options.
1051 :     my $optionThing = Tracer::GetOptions({ radio => 0, links => 1 }, \%options);
1052 :     # Read in the subsystems.
1053 :     my @subs = $sprout->GetAll(['Subsystem'], "ORDER BY Subsystem(classification), Subsystem(id)", [],
1054 :     ['Subsystem(classification)', 'Subsystem(id)']);
1055 : parrello 1.26 # Put any unclassified subsystems at the end. They will always be at the beginning, so if one
1056 :     # is at the end, ALL subsystems are unclassified and we don't bother.
1057 :     if ($#subs >= 0 && $subs[$#subs]->[0] ne '') {
1058 :     while ($subs[0]->[0] eq '') {
1059 :     my $classLess = shift @subs;
1060 :     push @subs, $classLess;
1061 :     }
1062 :     }
1063 : parrello 1.41 # Get the seedviewer URL.
1064 :     my $svURL = $FIG_Config::linkinSV || "$FIG_Config::cgi_url/seedviewer.cgi";
1065 :     Trace("Seed Viewer URL is $svURL.") if T(3);
1066 : parrello 1.16 # Declare the return variable.
1067 :     my @retVal = ();
1068 :     # Each element in @subs represents a leaf node, so as we loop through it we will be
1069 :     # producing one leaf node at a time. The leaf node is represented as a 2-tuple. The
1070 :     # first element is a semi-colon-delimited list of the classifications for the
1071 :     # subsystem. There will be a stack of currently-active classifications, which we will
1072 :     # compare to the incoming classifications from the end backward. A new classification
1073 :     # requires starting a new branch. A different classification requires closing an old
1074 :     # branch and starting a new one. Each classification in the stack will also contain
1075 :     # that classification's current branch. We'll add a fake classification at the
1076 :     # beginning that we can use to represent the tree as a whole.
1077 :     my $rootName = '<root>';
1078 :     # Create the classification stack. Note the stack is a pair of parallel lists,
1079 :     # one containing names and the other containing content.
1080 :     my @stackNames = ($rootName);
1081 :     my @stackContents = (\@retVal);
1082 :     # Add a null entry at the end of the subsystem list to force an unrolling.
1083 : parrello 1.27 push @subs, ['', undef];
1084 : parrello 1.16 # Loop through the subsystems.
1085 :     for my $sub (@subs) {
1086 :     # Pull out the classification list and the subsystem ID.
1087 :     my ($classString, $id) = @{$sub};
1088 :     Trace("Processing class \"$classString\" and subsystem $id.") if T(4);
1089 :     # Convert the classification string to a list with the root classification in
1090 :     # the front.
1091 :     my @classList = ($rootName, split($FIG_Config::splitter, $classString));
1092 :     # Find the leftmost point at which the class list differs from the stack.
1093 :     my $matchPoint = 0;
1094 :     while ($matchPoint <= $#stackNames && $matchPoint <= $#classList &&
1095 :     $stackNames[$matchPoint] eq $classList[$matchPoint]) {
1096 :     $matchPoint++;
1097 :     }
1098 :     Trace("Match point is $matchPoint. Stack length is " . scalar(@stackNames) .
1099 :     ". Class List length is " . scalar(@classList) . ".") if T(4);
1100 :     # Unroll the stack to the matchpoint.
1101 :     while ($#stackNames >= $matchPoint) {
1102 :     my $popped = pop @stackNames;
1103 :     pop @stackContents;
1104 :     Trace("\"$popped\" popped from stack.") if T(4);
1105 :     }
1106 :     # Start branches for any new classifications.
1107 :     while ($#stackNames < $#classList) {
1108 :     # The branch for a new classification contains its radio button
1109 :     # data and then a list of children. So, at this point, if radio buttons
1110 :     # are desired, we put them into the content.
1111 :     my $newLevel = scalar(@stackNames);
1112 :     my @newClassContent = ();
1113 :     if ($optionThing->{radio}) {
1114 :     my $newClassString = join($FIG_Config::splitter, @classList[1..$newLevel]);
1115 :     push @newClassContent, { value => "classification=$newClassString%" };
1116 :     }
1117 :     # The new classification node is appended to its parent's content
1118 :     # and then pushed onto the stack. First, we need the node name.
1119 :     my $nodeName = $classList[$newLevel];
1120 :     # Add the classification to its parent. This makes it part of the
1121 :     # tree we'll be returning to the user.
1122 :     push @{$stackContents[$#stackNames]}, $nodeName, \@newClassContent;
1123 :     # Push the classification onto the stack.
1124 :     push @stackContents, \@newClassContent;
1125 :     push @stackNames, $nodeName;
1126 :     Trace("\"$nodeName\" pushed onto stack.") if T(4);
1127 :     }
1128 :     # Now the stack contains all our parent branches. We add the subsystem to
1129 :     # the branch at the top of the stack, but only if it's NOT the dummy node.
1130 :     if (defined $id) {
1131 :     # Compute the node name from the ID.
1132 :     my $nodeName = $id;
1133 :     $nodeName =~ s/_/ /g;
1134 :     # Create the node's leaf hash. This depends on the value of the radio
1135 :     # and link options.
1136 :     my $nodeContent = {};
1137 :     if ($optionThing->{links}) {
1138 :     # Compute the link value.
1139 :     my $linkable = uri_escape($id);
1140 : parrello 1.41 $nodeContent->{link} = "$svURL?page=Subsystems;subsystem=$linkable";
1141 : parrello 1.16 }
1142 :     if ($optionThing->{radio}) {
1143 :     # Compute the radio value.
1144 :     $nodeContent->{value} = "id=$id";
1145 :     }
1146 :     # Push the node into its parent branch.
1147 :     Trace("\"$nodeName\" added to node list.") if T(4);
1148 :     push @{$stackContents[$#stackNames]}, $nodeName, $nodeContent;
1149 :     }
1150 :     }
1151 :     # Return the result.
1152 :     return \@retVal;
1153 :     }
1154 :    
1155 :    
1156 : parrello 1.1 =head3 NmpdrGenomeMenu
1157 :    
1158 : parrello 1.38 my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows);
1159 : parrello 1.1
1160 :     This method creates a hierarchical HTML menu for NMPDR genomes organized by category. The
1161 :     category indicates the low-level NMPDR group. Organizing the genomes in this way makes it
1162 :     easier to select all genomes from a particular category.
1163 :    
1164 :     =over 4
1165 :    
1166 :     =item menuName
1167 :    
1168 :     Name to give to the menu.
1169 :    
1170 : parrello 1.3 =item multiple
1171 : parrello 1.1
1172 : parrello 1.3 TRUE if the user is allowed to select multiple genomes, else FALSE.
1173 : parrello 1.1
1174 :     =item selected
1175 :    
1176 :     Reference to a list containing the IDs of the genomes to be pre-selected. If the menu
1177 :     is not intended to allow multiple selections, the list should be a singleton. If the
1178 :     list is empty, nothing will be pre-selected.
1179 :    
1180 : parrello 1.3 =item rows (optional)
1181 :    
1182 :     Number of rows to display. If omitted, the default is 1 for a single-select list
1183 :     and 10 for a multi-select list.
1184 :    
1185 : parrello 1.8 =item crossMenu (optional)
1186 :    
1187 : parrello 1.41 This is currently not supported.
1188 : parrello 1.8
1189 : parrello 1.1 =item RETURN
1190 :    
1191 :     Returns the HTML text to generate a C<SELECT> menu inside a form.
1192 :    
1193 :     =back
1194 :    
1195 :     =cut
1196 :    
1197 :     sub NmpdrGenomeMenu {
1198 :     # Get the parameters.
1199 : parrello 1.8 my ($self, $menuName, $multiple, $selected, $rows, $cross) = @_;
1200 : parrello 1.1 # Get the Sprout and CGI objects.
1201 :     my $sprout = $self->DB();
1202 :     my $cgi = $self->Q();
1203 : parrello 1.3 # Compute the row count.
1204 :     if (! defined $rows) {
1205 :     $rows = ($multiple ? 10 : 1);
1206 :     }
1207 : parrello 1.41 # Get a comma-delimited list of the preselected genomes.
1208 :     my $preselected = "";
1209 :     if ($selected) {
1210 :     $preselected = join(", ", @$selected);
1211 :     }
1212 :     # Ask Sprout for a genome menu.
1213 :     my $retVal = $sprout->GenomeMenu(name => $menuName,
1214 :     multiSelect => $multiple,
1215 :     selected => $preselected,
1216 :     size => $rows);
1217 : parrello 1.1 # Return the result.
1218 :     return $retVal;
1219 :     }
1220 :    
1221 : parrello 1.3 =head3 PropertyMenu
1222 :    
1223 : parrello 1.38 my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force);
1224 : parrello 1.3
1225 :     Generate a property name dropdown menu.
1226 :    
1227 :     =over 4
1228 :    
1229 :     =item menuName
1230 :    
1231 :     Name to give to the menu.
1232 :    
1233 :     =item selected
1234 :    
1235 :     Value of the property name to pre-select.
1236 :    
1237 :     =item force (optional)
1238 :    
1239 :     If TRUE, then the user will be forced to choose a property name. If FALSE,
1240 :     then an additional menu choice will be provided to select nothing.
1241 :    
1242 :     =item RETURN
1243 :    
1244 :     Returns a dropdown menu box that allows the user to select a property name. An additional
1245 :     selection entry will be provided for selecting no property name
1246 :    
1247 :     =back
1248 :    
1249 :     =cut
1250 :    
1251 :     sub PropertyMenu {
1252 :     # Get the parameters.
1253 :     my ($self, $menuName, $selected, $force) = @_;
1254 :     # Get the CGI and Sprout objects.
1255 :     my $sprout = $self->DB();
1256 :     my $cgi = $self->Q();
1257 :     # Create the property name list.
1258 :     my @propNames = ();
1259 :     if (! $force) {
1260 :     push @propNames, "";
1261 :     }
1262 :     # Get all the property names, putting them after the null choice if one exists.
1263 :     push @propNames, $sprout->GetChoices('Property', 'property-name');
1264 :     # Create a menu from them.
1265 :     my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,
1266 :     -default => $selected);
1267 :     # Return the result.
1268 :     return $retVal;
1269 :     }
1270 :    
1271 : parrello 1.1 =head3 MakeTable
1272 :    
1273 : parrello 1.38 my $htmlText = $shelp->MakeTable(\@rows);
1274 : parrello 1.1
1275 :     Create a table from a group of table rows. The table rows must be fully pre-formatted: in
1276 :     other words, each must have the TR and TD tags included.
1277 :    
1278 :     The purpose of this method is to provide a uniform look for search form tables. It is
1279 :     almost impossible to control a table using styles, so rather than have a table style,
1280 :     we create the TABLE tag in this method. Note also that the first TD or TH in each row will
1281 :     be updated with an explicit width so the forms look pretty when they are all on one
1282 :     page.
1283 :    
1284 :     =over 4
1285 :    
1286 :     =item rows
1287 :    
1288 :     Reference to a list of table rows. Each table row must be in HTML form with all
1289 : parrello 1.29 the TR and TD tags set up. The first TD or TH tag in the first non-colspanned row
1290 :     will be modified to set the width. Everything else will be left as is.
1291 : parrello 1.1
1292 :     =item RETURN
1293 :    
1294 :     Returns the full HTML for a table in the approved NMPDR Search Form style.
1295 :    
1296 :     =back
1297 :    
1298 :     =cut
1299 :    
1300 :     sub MakeTable {
1301 :     # Get the parameters.
1302 :     my ($self, $rows) = @_;
1303 :     # Get the CGI object.
1304 :     my $cgi = $self->Q();
1305 : parrello 1.29 # The first column of the first row must have its width fixed.
1306 :     # This flag will be set to FALSE when that happens.
1307 :     my $needWidth = 1;
1308 : parrello 1.1 # modifier becase we only want to change the first tag. Also, if a width
1309 :     # is already specified on the first column bad things will happen.
1310 :     for my $row (@{$rows}) {
1311 : parrello 1.29 # See if this row needs a width.
1312 :     if ($needWidth && $row =~ /<(td|th) ([^>]+)>/i) {
1313 :     # Here we have a first cell and its tag parameters are in $2.
1314 :     my $elements = $2;
1315 :     if ($elements !~ /colspan/i) {
1316 :     Trace("No colspan tag found in element \'$elements\'.") if T(3);
1317 :     # Here there's no colspan, so we plug in the width. We
1318 :     # eschew the "g" modifier on the substitution because we
1319 :     # only want to update the first cell.
1320 :     $row =~ s/(<(td|th))/$1 width="150"/i;
1321 :     # Denote we don't need this any more.
1322 :     $needWidth = 0;
1323 :     }
1324 :     }
1325 : parrello 1.1 }
1326 :     # Create the table.
1327 :     my $retVal = $cgi->table({border => 2, cellspacing => 2,
1328 :     width => 700, class => 'search'},
1329 :     @{$rows});
1330 :     # Return the result.
1331 :     return $retVal;
1332 :     }
1333 :    
1334 :     =head3 SubmitRow
1335 :    
1336 : parrello 1.38 my $htmlText = $shelp->SubmitRow($caption);
1337 : parrello 1.1
1338 :     Returns the HTML text for the row containing the page size control
1339 :     and the submit button. All searches should have this row somewhere
1340 :     near the top of the form.
1341 :    
1342 : parrello 1.18 =over 4
1343 :    
1344 :     =item caption (optional)
1345 :    
1346 :     Caption to be put on the search button. The default is C<Go>.
1347 :    
1348 :     =item RETURN
1349 :    
1350 :     Returns a table row containing the controls for submitting the search
1351 :     and tuning the results.
1352 :    
1353 :     =back
1354 :    
1355 : parrello 1.1 =cut
1356 :    
1357 :     sub SubmitRow {
1358 :     # Get the parameters.
1359 : parrello 1.18 my ($self, $caption) = @_;
1360 : parrello 1.1 my $cgi = $self->Q();
1361 : parrello 1.18 # Compute the button caption.
1362 :     my $realCaption = (defined $caption ? $caption : 'Go');
1363 : parrello 1.3 # Get the current page size.
1364 :     my $pageSize = $cgi->param('PageSize');
1365 : parrello 1.34 # Get the current feature ID type.
1366 :     my $aliasType = $self->GetPreferredAliasType();
1367 :     # Create the rows.
1368 : parrello 1.37 my $retVal = $cgi->Tr($cgi->td("Identifier Type "),
1369 :     $cgi->td({ colspan => 2 },
1370 :     $cgi->popup_menu(-name => 'AliasType',
1371 :     -values => ['FIG', AliasAnalysis::AliasTypes() ],
1372 :     -default => $aliasType) .
1373 : parrello 1.40 Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .
1374 : parrello 1.34 "\n" .
1375 :     $cgi->Tr($cgi->td("Results/Page"),
1376 : parrello 1.1 $cgi->td($cgi->popup_menu(-name => 'PageSize',
1377 : parrello 1.7 -values => [10, 25, 50, 100, 1000],
1378 : parrello 1.25 -default => $pageSize)),
1379 : parrello 1.1 $cgi->td($cgi->submit(-class => 'goButton',
1380 :     -name => 'Search',
1381 : parrello 1.18 -value => $realCaption)));
1382 : parrello 1.1 # Return the result.
1383 :     return $retVal;
1384 :     }
1385 : parrello 1.2
1386 : parrello 1.3 =head3 GetGenomes
1387 :    
1388 : parrello 1.38 my @genomeList = $shelp->GetGenomes($parmName);
1389 : parrello 1.3
1390 :     Return the list of genomes specified by the specified CGI query parameter.
1391 :     If the request method is POST, then the list of genome IDs is returned
1392 :     without preamble. If the request method is GET and the parameter is not
1393 :     specified, then it is treated as a request for all genomes. This makes it
1394 :     easier for web pages to link to a search that wants to specify all genomes.
1395 :    
1396 :     =over 4
1397 :    
1398 :     =item parmName
1399 :    
1400 :     Name of the parameter containing the list of genomes. This will be the
1401 :     first parameter passed to the L</NmpdrGenomeMenu> call that created the
1402 :     genome selection control on the form.
1403 :    
1404 :     =item RETURN
1405 :    
1406 :     Returns a list of the genomes to process.
1407 :    
1408 :     =back
1409 :    
1410 :     =cut
1411 :    
1412 :     sub GetGenomes {
1413 :     # Get the parameters.
1414 :     my ($self, $parmName) = @_;
1415 :     # Get the CGI query object.
1416 :     my $cgi = $self->Q();
1417 :     # Get the list of genome IDs in the request header.
1418 :     my @retVal = $cgi->param($parmName);
1419 :     Trace("Genome list for $parmName is (" . join(", ", @retVal) . ") with method " . $cgi->request_method() . ".") if T(3);
1420 :     # Check for the special GET case.
1421 :     if ($cgi->request_method() eq "GET" && ! @retVal) {
1422 :     # Here the caller wants all the genomes.
1423 :     my $sprout = $self->DB();
1424 :     @retVal = $sprout->Genomes();
1425 :     }
1426 :     # Return the result.
1427 :     return @retVal;
1428 :     }
1429 :    
1430 :     =head3 ComputeSearchURL
1431 :    
1432 : parrello 1.38 my $url = $shelp->ComputeSearchURL(%overrides);
1433 : parrello 1.3
1434 :     Compute the GET-style URL for the current search. In order for this to work, there
1435 :     must be a copy of the search form on the current page. This will always be the
1436 :     case if the search is coming from C<SearchSkeleton.cgi>.
1437 :    
1438 :     A little expense is involved in order to make the URL as smart as possible. The
1439 :     main complication is that if the user specified all genomes, we'll want to
1440 :     remove the parameter entirely from a get-style URL.
1441 :    
1442 : parrello 1.19 =over 4
1443 :    
1444 :     =item overrides
1445 :    
1446 :     Hash containing override values for the parameters, where the parameter name is
1447 :     the key and the parameter value is the override value. If the override value is
1448 :     C<undef>, the parameter will be deleted from the result.
1449 :    
1450 :     =item RETURN
1451 :    
1452 :     Returns a GET-style URL for invoking the search with the specified overrides.
1453 :    
1454 :     =back
1455 :    
1456 : parrello 1.3 =cut
1457 :    
1458 :     sub ComputeSearchURL {
1459 :     # Get the parameters.
1460 : parrello 1.19 my ($self, %overrides) = @_;
1461 : parrello 1.3 # Get the database and CGI query object.
1462 :     my $cgi = $self->Q();
1463 :     my $sprout = $self->DB();
1464 :     # Start with the full URL.
1465 : parrello 1.41 my $retVal = "$FIG_Config::cgi_url/SearchSkeleton.cgi";
1466 : parrello 1.3 # Get all the query parameters in a hash.
1467 :     my %parms = $cgi->Vars();
1468 :     # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
1469 :     # characters separating the individual values. We have to convert those to lists. In addition,
1470 :     # the multiple-selection genome parameters and the feature type parameter must be checked to
1471 :     # determine whether or not they can be removed from the URL. First, we get a list of the
1472 :     # genome parameters and a list of all genomes. Note that we only need the list if a
1473 :     # multiple-selection genome parameter has been found on the form.
1474 :     my %genomeParms = map { $_ => 1 } @{$self->{genomeParms}};
1475 :     my @genomeList;
1476 :     if (keys %genomeParms) {
1477 :     @genomeList = $sprout->Genomes();
1478 :     }
1479 :     # Create a list to hold the URL parameters we find.
1480 :     my @urlList = ();
1481 :     # Now loop through the parameters in the hash, putting them into the output URL.
1482 :     for my $parmKey (keys %parms) {
1483 :     # Get a list of the parameter values. If there's only one, we'll end up with
1484 :     # a singleton list, but that's okay.
1485 :     my @values = split (/\0/, $parms{$parmKey});
1486 :     # Check for special cases.
1487 : parrello 1.26 if (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF)) {
1488 : parrello 1.3 # These are bookkeeping parameters we don't need to start a search.
1489 :     @values = ();
1490 :     } elsif ($parmKey =~ /_SearchThing$/) {
1491 :     # Here the value coming in is from a genome control's search thing. It does
1492 :     # not affect the results of the search, so we clear it.
1493 :     @values = ();
1494 :     } elsif ($genomeParms{$parmKey}) {
1495 :     # Here we need to see if the user wants all the genomes. If he does,
1496 :     # we erase all the values just like with features.
1497 :     my $allFlag = $sprout->IsAllGenomes(\@values, \@genomeList);
1498 :     if ($allFlag) {
1499 :     @values = ();
1500 :     }
1501 : parrello 1.19 } elsif (exists $overrides{$parmKey}) {
1502 :     # Here the value is being overridden, so we skip it for now.
1503 :     @values = ();
1504 : parrello 1.3 }
1505 :     # If we still have values, create the URL parameters.
1506 :     if (@values) {
1507 :     push @urlList, map { "$parmKey=" . uri_escape($_) } @values;
1508 :     }
1509 :     }
1510 : parrello 1.19 # Now do the overrides.
1511 :     for my $overKey (keys %overrides) {
1512 :     # Only use this override if it's not a delete marker.
1513 :     if (defined $overrides{$overKey}) {
1514 :     push @urlList, "$overKey=" . uri_escape($overrides{$overKey});
1515 :     }
1516 :     }
1517 : parrello 1.3 # Add the parameters to the URL.
1518 :     $retVal .= "?" . join(";", @urlList);
1519 :     # Return the result.
1520 :     return $retVal;
1521 :     }
1522 :    
1523 : parrello 1.9 =head3 AdvancedClassList
1524 :    
1525 : parrello 1.38 my @classes = SearchHelper::AdvancedClassList();
1526 : parrello 1.9
1527 :     Return a list of advanced class names. This list is used to generate the directory
1528 :     of available searches on the search page.
1529 :    
1530 : parrello 1.34 We do a file search to accomplish this, but to pull it off we need to look at %INC.
1531 : parrello 1.9
1532 :     =cut
1533 :    
1534 :     sub AdvancedClassList {
1535 : parrello 1.34 # Determine the search helper module directory.
1536 :     my $libDirectory = $INC{'SearchHelper.pm'};
1537 :     $libDirectory =~ s/SearchHelper\.pm//;
1538 :     # Read it, keeping only the helper modules.
1539 :     my @modules = grep { /^SH\w+\.pm/ } Tracer::OpenDir($libDirectory, 0);
1540 :     # Convert the file names to search types.
1541 :     my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } @modules;
1542 :     # Return the result in alphabetical order.
1543 : parrello 1.30 return sort @retVal;
1544 : parrello 1.9 }
1545 :    
1546 : parrello 1.16 =head3 SelectionTree
1547 :    
1548 : parrello 1.38 my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options);
1549 : parrello 1.16
1550 :     Display a selection tree.
1551 :    
1552 :     This method creates the HTML for a tree selection control. The tree is implemented as a set of
1553 :     nested HTML unordered lists. Each selectable element of the tree will contain a radio button. In
1554 :     addition, some of the tree nodes can contain hyperlinks.
1555 :    
1556 :     The tree itself is passed in as a multi-level list containing node names followed by
1557 :     contents. Each content element is a reference to a similar list. The first element of
1558 :     each list may be a hash reference. If so, it should contain one or both of the following
1559 :     keys.
1560 :    
1561 :     =over 4
1562 :    
1563 :     =item link
1564 :    
1565 :     The navigation URL to be popped up if the user clicks on the node name.
1566 :    
1567 :     =item value
1568 :    
1569 :     The form value to be returned if the user selects the tree node.
1570 :    
1571 :     =back
1572 :    
1573 :     The presence of a C<link> key indicates the node name will be hyperlinked. The presence of
1574 :     a C<value> key indicates the node name will have a radio button. If a node has no children,
1575 :     you may pass it a hash reference instead of a list reference.
1576 :    
1577 :     The following example shows the hash for a three-level tree with links on the second level and
1578 :     radio buttons on the third.
1579 :    
1580 :     [ Objects => [
1581 :     Entities => [
1582 :     {link => "../docs/WhatIsAnEntity.html"},
1583 :     Genome => {value => 'GenomeData'},
1584 :     Feature => {value => 'FeatureData'},
1585 :     Contig => {value => 'ContigData'},
1586 :     ],
1587 :     Relationships => [
1588 :     {link => "../docs/WhatIsARelationShip.html"},
1589 :     HasFeature => {value => 'GenomeToFeature'},
1590 :     IsOnContig => {value => 'FeatureToContig'},
1591 :     ]
1592 :     ]
1593 :     ]
1594 :    
1595 :     Note how each leaf of the tree has a hash reference for its value, while the branch nodes
1596 :     all have list references.
1597 :    
1598 :     This next example shows how to set up a taxonomy selection field. The value returned
1599 :     by the tree control will be the taxonomy string for the selected node ready for use
1600 :     in a LIKE-style SQL filter. Only the single branch ending in campylobacter is shown for
1601 :     reasons of space.
1602 :    
1603 :     [ All => [
1604 :     {value => "%"},
1605 :     Bacteria => [
1606 :     {value => "Bacteria%"},
1607 :     Proteobacteria => [
1608 :     {value => "Bacteria; Proteobacteria%"},
1609 :     Epsilonproteobacteria => [
1610 :     {value => "Bacteria; Proteobacteria;Epsilonproteobacteria%"},
1611 :     Campylobacterales => [
1612 :     {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales%"},
1613 : parrello 1.38 Campylobacteraceae =>
1614 : parrello 1.16 {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae%"},
1615 :     ...
1616 :     ]
1617 :     ...
1618 :     ]
1619 :     ...
1620 :     ]
1621 :     ...
1622 :     ]
1623 :     ...
1624 :     ]
1625 :     ]
1626 :    
1627 :    
1628 :     This method of tree storage allows the caller to control the order in which the tree nodes
1629 :     are displayed and to completely control value selection and use of hyperlinks. It is, however
1630 :     a bit complicated. Eventually, tree-building classes will be provided to simplify things.
1631 :    
1632 :     The parameters to this method are as follows.
1633 :    
1634 :     =over 4
1635 :    
1636 :     =item cgi
1637 :    
1638 :     CGI object used to generate the HTML.
1639 :    
1640 :     =item tree
1641 :    
1642 :     Reference to a hash describing a tree. See the description above.
1643 :    
1644 :     =item options
1645 :    
1646 :     Hash containing options for the tree display.
1647 :    
1648 :     =back
1649 :    
1650 :     The allowable options are as follows
1651 :    
1652 :     =over 4
1653 :    
1654 :     =item nodeImageClosed
1655 :    
1656 :     URL of the image to display next to the tree nodes when they are collapsed. Clicking
1657 : parrello 1.41 on the image will expand a section of the tree. The default is C<plus.gif>.
1658 : parrello 1.16
1659 :     =item nodeImageOpen
1660 :    
1661 :     URL of the image to display next to the tree nodes when they are expanded. Clicking
1662 : parrello 1.41 on the image will collapse a section of the tree. The default is C<minus.gif>.
1663 : parrello 1.16
1664 :     =item style
1665 :    
1666 :     Style to use for the tree. The default is C<tree>. Because the tree style is implemented
1667 :     as nested lists, the key components of this style are the definitions for the C<ul> and
1668 :     C<li> tags. The default style file contains the following definitions.
1669 :    
1670 :     .tree ul {
1671 : parrello 1.38 margin-left: 0; padding-left: 22px
1672 : parrello 1.16 }
1673 :     .tree li {
1674 :     list-style-type: none;
1675 :     }
1676 :    
1677 :     The default image is 22 pixels wide, so in the above scheme each tree level is indented from its
1678 :     parent by the width of the node image. This use of styles limits the things we can do in formatting
1679 :     the tree, but it has the advantage of vastly simplifying the tree creation.
1680 :    
1681 :     =item name
1682 :    
1683 :     Field name to give to the radio buttons in the tree. The default is C<selection>.
1684 :    
1685 :     =item target
1686 :    
1687 :     Frame target for links. The default is C<_self>.
1688 :    
1689 :     =item selected
1690 :    
1691 :     If specified, the value of the radio button to be pre-selected.
1692 :    
1693 :     =back
1694 :    
1695 :     =cut
1696 :    
1697 :     sub SelectionTree {
1698 :     # Get the parameters.
1699 :     my ($cgi, $tree, %options) = @_;
1700 :     # Get the options.
1701 :     my $optionThing = Tracer::GetOptions({ name => 'selection',
1702 : parrello 1.41 nodeImageClosed => "$FIG_Config::cgi_url/Html/plus.gif",
1703 :     nodeImageOpen => "$FIG_Config::cgi_url/Html/minus.gif",
1704 : parrello 1.16 style => 'tree',
1705 :     target => '_self',
1706 :     selected => undef},
1707 :     \%options);
1708 :     # Declare the return variable. We'll do the standard thing with creating a list
1709 :     # of HTML lines and rolling them together at the end.
1710 :     my @retVal = ();
1711 :     # Only proceed if the tree is present.
1712 :     if (defined($tree)) {
1713 :     # Validate the tree.
1714 :     if (ref $tree ne 'ARRAY') {
1715 :     Confess("Selection tree is not a list reference.");
1716 :     } elsif (scalar @{$tree} == 0) {
1717 :     # The tree is empty, so we do nothing.
1718 :     } elsif ($tree->[0] eq 'HASH') {
1719 :     Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");
1720 :     } else {
1721 :     # Here we have a real tree. Apply the tree style.
1722 :     push @retVal, $cgi->start_div({ class => $optionThing->{style} });
1723 :     # Give us a DIV ID.
1724 :     my $divID = GetDivID($optionThing->{name});
1725 :     # Show the tree.
1726 :     push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
1727 :     # Close the DIV block.
1728 :     push @retVal, $cgi->end_div();
1729 :     }
1730 :     }
1731 :     # Return the result.
1732 :     return join("\n", @retVal, "");
1733 :     }
1734 :    
1735 :     =head3 ShowBranch
1736 :    
1737 : parrello 1.38 my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType);
1738 : parrello 1.16
1739 : parrello 1.38 This is a recursive method that displays a branch of the tree.
1740 : parrello 1.16
1741 :     =over 4
1742 :    
1743 :     =item cgi
1744 :    
1745 :     CGI object used to format HTML.
1746 :    
1747 :     =item label
1748 :    
1749 :     Label of this tree branch. It is only used in error messages.
1750 :    
1751 :     =item id
1752 :    
1753 :     ID to be given to this tree branch. The ID is used in the code that expands and collapses
1754 :     tree nodes.
1755 :    
1756 :     =item branch
1757 :    
1758 :     Reference to a list containing the content of the tree branch. The list contains an optional
1759 :     hash reference that is ignored and the list of children, each child represented by a name
1760 :     and then its contents. The contents could by a hash reference (indicating the attributes
1761 :     of a leaf node), or another tree branch.
1762 :    
1763 :     =item options
1764 :    
1765 :     Options from the original call to L</SelectionTree>.
1766 :    
1767 :     =item displayType
1768 :    
1769 :     C<block> if the contents of this list are to be displayed, C<none> if they are to be
1770 :     hidden.
1771 :    
1772 :     =item RETURN
1773 :    
1774 :     Returns one or more HTML lines that can be used to display the tree branch.
1775 :    
1776 :     =back
1777 :    
1778 :     =cut
1779 :    
1780 :     sub ShowBranch {
1781 :     # Get the parameters.
1782 :     my ($cgi, $label, $id, $branch, $options, $displayType) = @_;
1783 :     # Declare the return variable.
1784 :     my @retVal = ();
1785 :     # Start the branch.
1786 :     push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });
1787 :     # Check for the hash and choose the start location accordingly.
1788 :     my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
1789 :     # Get the list length.
1790 :     my $i1 = scalar(@{$branch});
1791 :     # Verify we have an even number of elements.
1792 :     if (($i1 - $i0) % 2 != 0) {
1793 :     Trace("Branch elements are from $i0 to $i1.") if T(3);
1794 :     Confess("Odd number of elements in tree branch $label.");
1795 :     } else {
1796 :     # Loop through the elements.
1797 :     for (my $i = $i0; $i < $i1; $i += 2) {
1798 :     # Get this node's label and contents.
1799 :     my ($myLabel, $myContent) = ($branch->[$i], $branch->[$i+1]);
1800 :     # Get an ID for this node's children (if any).
1801 :     my $myID = GetDivID($options->{name});
1802 :     # Now we need to find the list of children and the options hash.
1803 :     # This is a bit ugly because we allow the shortcut of a hash without an
1804 :     # enclosing list. First, we need some variables.
1805 :     my $attrHash = {};
1806 :     my @childHtml = ();
1807 :     my $hasChildren = 0;
1808 :     if (! ref $myContent) {
1809 :     Confess("Invalid tree definition. Scalar found as content of node \"$myLabel\".");
1810 :     } elsif (ref $myContent eq 'HASH') {
1811 :     # Here the node is a leaf and its content contains the link/value hash.
1812 :     $attrHash = $myContent;
1813 :     } elsif (ref $myContent eq 'ARRAY') {
1814 :     # Here the node may be a branch. Its content is a list.
1815 :     my $len = scalar @{$myContent};
1816 :     if ($len >= 1) {
1817 :     # Here the first element of the list could by the link/value hash.
1818 :     if (ref $myContent->[0] eq 'HASH') {
1819 :     $attrHash = $myContent->[0];
1820 :     # If there's data in the list besides the hash, it's our child list.
1821 :     # We can pass the entire thing as the child list, because the hash
1822 :     # is ignored.
1823 :     if ($len > 1) {
1824 :     $hasChildren = 1;
1825 :     }
1826 :     } else {
1827 :     $hasChildren = 1;
1828 :     }
1829 :     # If we have children, create the child list with a recursive call.
1830 :     if ($hasChildren) {
1831 :     Trace("Processing children of $myLabel.") if T(4);
1832 : parrello 1.42 push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'block');
1833 : parrello 1.27 Trace("Children of $myLabel finished.") if T(4);
1834 : parrello 1.16 }
1835 :     }
1836 :     }
1837 :     # Okay, it's time to pause and take stock. We have the label of the current node
1838 :     # in $myLabel, its attributes in $attrHash, and if it is NOT a leaf node, we
1839 :     # have a child list in @childHtml. If it IS a leaf node, $hasChildren is 0.
1840 :     # Compute the image HTML. It's tricky, because we have to deal with the open and
1841 :     # closed images.
1842 :     my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
1843 :     my $image = $images[$hasChildren];
1844 :     my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});
1845 :     if ($hasChildren) {
1846 :     # If there are children, we wrap the image in a toggle hyperlink.
1847 :     $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
1848 :     $prefixHtml);
1849 :     }
1850 :     # Now the radio button, if any. Note we use "defined" in case the user wants the
1851 :     # value to be 0.
1852 :     if (defined $attrHash->{value}) {
1853 :     # Due to a glitchiness in the CGI stuff, we have to build the attribute
1854 :     # hash for the "input" method. If the item is pre-selected, we add
1855 :     # "checked => undef" to the hash. Otherwise, we can't have "checked"
1856 :     # at all.
1857 :     my $radioParms = { type => 'radio',
1858 :     name => $options->{name},
1859 :     value => $attrHash->{value},
1860 :     };
1861 :     if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
1862 :     $radioParms->{checked} = undef;
1863 :     }
1864 :     $prefixHtml .= $cgi->input($radioParms);
1865 :     }
1866 :     # Next, we format the label.
1867 :     my $labelHtml = $myLabel;
1868 : parrello 1.27 Trace("Formatting tree node for \"$myLabel\".") if T(4);
1869 : parrello 1.16 # Apply a hyperlink if necessary.
1870 :     if (defined $attrHash->{link}) {
1871 :     $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },
1872 :     $labelHtml);
1873 :     }
1874 :     # Finally, roll up the child HTML. If there are no children, we'll get a null string
1875 :     # here.
1876 :     my $childHtml = join("\n", @childHtml);
1877 :     # Now we have all the pieces, so we can put them together.
1878 :     push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");
1879 :     }
1880 :     }
1881 :     # Close the tree branch.
1882 :     push @retVal, $cgi->end_ul();
1883 :     # Return the result.
1884 :     return @retVal;
1885 :     }
1886 :    
1887 :     =head3 GetDivID
1888 :    
1889 : parrello 1.38 my $idString = SearchHelper::GetDivID($name);
1890 : parrello 1.16
1891 :     Return a new HTML ID string.
1892 :    
1893 :     =over 4
1894 :    
1895 :     =item name
1896 :    
1897 :     Name to be prefixed to the ID string.
1898 :    
1899 :     =item RETURN
1900 :    
1901 :     Returns a hopefully-unique ID string.
1902 :    
1903 :     =back
1904 :    
1905 :     =cut
1906 :    
1907 :     sub GetDivID {
1908 :     # Get the parameters.
1909 :     my ($name) = @_;
1910 :     # Compute the ID.
1911 :     my $retVal = "elt_$name$divCount";
1912 :     # Increment the counter to make sure this ID is not re-used.
1913 :     $divCount++;
1914 :     # Return the result.
1915 :     return $retVal;
1916 :     }
1917 :    
1918 : parrello 1.31 =head3 PrintLine
1919 :    
1920 : parrello 1.38 $shelp->PrintLine($message);
1921 : parrello 1.31
1922 :     Print a line of CGI output. This is used during the operation of the B<Find> method while
1923 :     searching, so the user sees progress in real-time.
1924 :    
1925 :     =over 4
1926 :    
1927 :     =item message
1928 :    
1929 :     HTML text to display.
1930 :    
1931 :     =back
1932 :    
1933 :     =cut
1934 :    
1935 :     sub PrintLine {
1936 :     # Get the parameters.
1937 :     my ($self, $message) = @_;
1938 :     # Send them to the output.
1939 :     print "$message\n";
1940 :     }
1941 :    
1942 : parrello 1.34 =head3 GetHelper
1943 : parrello 1.13
1944 : parrello 1.38 my $shelp = SearchHelper::GetHelper($parm, $type => $className);
1945 : parrello 1.1
1946 : parrello 1.34 Return a helper object with the given class name. If no such class exists, an
1947 :     error will be thrown.
1948 : parrello 1.1
1949 :     =over 4
1950 :    
1951 : parrello 1.34 =item parm
1952 : parrello 1.1
1953 : parrello 1.34 Parameter to pass to the constructor. This is a CGI object for a search helper
1954 :     and a search helper object for the result helper.
1955 : parrello 1.3
1956 :     =item type
1957 :    
1958 : parrello 1.34 Type of helper: C<RH> for a result helper and C<SH> for a search helper.
1959 : parrello 1.3
1960 : parrello 1.34 =item className
1961 : parrello 1.3
1962 : parrello 1.34 Class name for the helper object, without the preceding C<SH> or C<RH>. This is
1963 :     identical to what the script expects for the C<Class> or C<ResultType> parameter.
1964 : parrello 1.3
1965 :     =item RETURN
1966 :    
1967 : parrello 1.34 Returns a helper object for the specified class.
1968 : parrello 1.3
1969 :     =back
1970 :    
1971 :     =cut
1972 :    
1973 : parrello 1.34 sub GetHelper {
1974 : parrello 1.3 # Get the parameters.
1975 : parrello 1.34 my ($parm, $type, $className) = @_;
1976 : parrello 1.3 # Declare the return variable.
1977 : parrello 1.34 my $retVal;
1978 :     # Try to create the helper.
1979 :     eval {
1980 :     # Load it into memory. If it's already there nothing will happen here.
1981 :     my $realName = "$type$className";
1982 :     Trace("Requiring helper $realName.") if T(3);
1983 :     require "$realName.pm";
1984 :     Trace("Constructing helper object.") if T(3);
1985 :     # Construct the object.
1986 :     $retVal = eval("$realName->new(\$parm)");
1987 :     # Commit suicide if it didn't work.
1988 :     if (! defined $retVal) {
1989 :     die "Could not find a $type handler of type $className.";
1990 :     }
1991 :     };
1992 :     # Check for errors.
1993 :     if ($@) {
1994 :     Confess("Error retrieving $type$className: $@");
1995 : parrello 1.3 }
1996 :     # Return the result.
1997 :     return $retVal;
1998 :     }
1999 :    
2000 : parrello 1.10 =head3 SaveOrganismData
2001 :    
2002 : parrello 1.38 my ($name, $displayGroup, $domain) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy);
2003 : parrello 1.10
2004 :     Format the name of an organism and the display version of its group name. The incoming
2005 :     data should be the relevant fields from the B<Genome> record in the database. The
2006 :     data will also be stored in the genome cache for later use in posting search results.
2007 :    
2008 :     =over 4
2009 :    
2010 :     =item group
2011 :    
2012 :     Name of the genome's group as it appears in the database.
2013 :    
2014 :     =item genomeID
2015 :    
2016 :     ID of the relevant genome.
2017 :    
2018 :     =item genus
2019 :    
2020 :     Genus of the genome's organism. If undefined or null, it will be assumed the genome is not
2021 :     in the database. In this case, the organism name is derived from the genomeID and the group
2022 :     is automatically the supporting-genomes group.
2023 :    
2024 :     =item species
2025 :    
2026 :     Species of the genome's organism.
2027 :    
2028 :     =item strain
2029 :    
2030 :     Strain of the species represented by the genome.
2031 :    
2032 : parrello 1.32 =item taxonomy
2033 :    
2034 :     Taxonomy of the species represented by the genome.
2035 :    
2036 : parrello 1.10 =item RETURN
2037 :    
2038 : parrello 1.32 Returns a three-element list. The first element is the formatted genome name. The second
2039 :     element is the display name of the genome's group. The third is the genome's domain.
2040 : parrello 1.10
2041 :     =back
2042 :    
2043 :     =cut
2044 :    
2045 :     sub SaveOrganismData {
2046 :     # Get the parameters.
2047 : parrello 1.32 my ($self, $group, $genomeID, $genus, $species, $strain, $taxonomy) = @_;
2048 : parrello 1.10 # Declare the return values.
2049 :     my ($name, $displayGroup);
2050 :     # If the organism does not exist, format an unknown name and a blank group.
2051 :     if (! defined($genus)) {
2052 :     $name = "Unknown Genome $genomeID";
2053 :     $displayGroup = "";
2054 :     } else {
2055 :     # It does exist, so format the organism name.
2056 :     $name = "$genus $species";
2057 :     if ($strain) {
2058 :     $name .= " $strain";
2059 :     }
2060 :     # Compute the display group. This is currently the same as the incoming group
2061 :     # name unless it's the supporting group, which is nulled out.
2062 :     $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2063 : parrello 1.36 Trace("Group = $displayGroup, translated from \"$group\".") if T(4);
2064 : parrello 1.10 }
2065 : parrello 1.32 # Compute the domain from the taxonomy.
2066 :     my ($domain) = split /\s*;\s*/, $taxonomy, 2;
2067 : parrello 1.10 # Cache the group and organism data.
2068 :     my $cache = $self->{orgs};
2069 : parrello 1.32 $cache->{$genomeID} = [$name, $displayGroup, $domain];
2070 : parrello 1.10 # Return the result.
2071 : parrello 1.32 return ($name, $displayGroup, $domain);
2072 : parrello 1.10 }
2073 :    
2074 : parrello 1.16 =head3 ValidateKeywords
2075 :    
2076 : parrello 1.38 my $okFlag = $shelp->ValidateKeywords($keywordString, $required);
2077 : parrello 1.16
2078 :     Insure that a keyword string is reasonably valid. If it is invalid, a message will be
2079 :     set.
2080 :    
2081 :     =over 4
2082 :    
2083 :     =item keywordString
2084 :    
2085 :     Keyword string specified as a parameter to the current search.
2086 :    
2087 :     =item required
2088 :    
2089 :     TRUE if there must be at least one keyword specified, else FALSE.
2090 :    
2091 :     =item RETURN
2092 :    
2093 :     Returns TRUE if the keyword string is valid, else FALSE. Note that a null keyword string
2094 :     is acceptable if the I<$required> parameter is not specified.
2095 :    
2096 :     =back
2097 :    
2098 :     =cut
2099 :    
2100 :     sub ValidateKeywords {
2101 :     # Get the parameters.
2102 :     my ($self, $keywordString, $required) = @_;
2103 :     # Declare the return variable.
2104 :     my $retVal = 0;
2105 :     my @wordList = split /\s+/, $keywordString;
2106 :     # Right now our only real worry is a list of all minus words. The problem with it is that
2107 :     # it will return an incorrect result.
2108 :     my @plusWords = grep { $_ =~ /^[^\-]/ } @wordList;
2109 :     if (! @wordList) {
2110 :     if ($required) {
2111 :     $self->SetMessage("No search words specified.");
2112 : parrello 1.22 } else {
2113 :     $retVal = 1;
2114 : parrello 1.16 }
2115 :     } elsif (! @plusWords) {
2116 :     $self->SetMessage("At least one keyword must be positive. All the keywords entered are preceded by minus signs.");
2117 :     } else {
2118 :     $retVal = 1;
2119 :     }
2120 :     # Return the result.
2121 :     return $retVal;
2122 :     }
2123 :    
2124 : parrello 1.30 =head3 TuningParameters
2125 :    
2126 : parrello 1.38 my $options = $shelp->TuningParameters(%parmHash);
2127 : parrello 1.30
2128 :     Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2129 :     to their default values. The parameters and their values will be returned as a hash reference.
2130 :    
2131 :     =over 4
2132 :    
2133 :     =item parmHash
2134 :    
2135 :     Hash mapping parameter names to their default values.
2136 :    
2137 :     =item RETURN
2138 :    
2139 :     Returns a reference to a hash containing the parameter names mapped to their actual values.
2140 :    
2141 :     =back
2142 :    
2143 :     =cut
2144 :    
2145 :     sub TuningParameters {
2146 :     # Get the parameters.
2147 :     my ($self, %parmHash) = @_;
2148 :     # Declare the return variable.
2149 :     my $retVal = {};
2150 :     # Get the CGI Query Object.
2151 :     my $cgi = $self->Q();
2152 :     # Loop through the parameter names.
2153 :     for my $parm (keys %parmHash) {
2154 :     # Get the incoming value for this parameter.
2155 :     my $value = $cgi->param($parm);
2156 :     # Zero might be a valid value, so we do an is-defined check rather than an OR.
2157 :     if (defined($value)) {
2158 :     $retVal->{$parm} = $value;
2159 :     } else {
2160 :     $retVal->{$parm} = $parmHash{$parm};
2161 :     }
2162 :     }
2163 :     # Return the result.
2164 :     return $retVal;
2165 :     }
2166 :    
2167 : parrello 1.34 =head3 GetPreferredAliasType
2168 :    
2169 : parrello 1.38 my $type = $shelp->GetPreferredAliasType();
2170 : parrello 1.34
2171 :     Return the preferred alias type for the current session. This information is stored
2172 :     in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>
2173 :     (which indicates the FIG ID).
2174 :    
2175 :     =cut
2176 :    
2177 :     sub GetPreferredAliasType {
2178 :     # Get the parameters.
2179 :     my ($self) = @_;
2180 :     # Determine the preferred type.
2181 :     my $cgi = $self->Q();
2182 :     my $retVal = $cgi->param('AliasType') || 'FIG';
2183 :     # Return it.
2184 :     return $retVal;
2185 :     }
2186 :    
2187 : parrello 1.4 =head2 Virtual Methods
2188 :    
2189 :     =head3 Form
2190 :    
2191 : parrello 1.38 my $html = $shelp->Form();
2192 : parrello 1.4
2193 :     Generate the HTML for a form to request a new search.
2194 :    
2195 :     =head3 Find
2196 :    
2197 : parrello 1.38 my $resultCount = $shelp->Find();
2198 : parrello 1.4
2199 :     Conduct a search based on the current CGI query parameters. The search results will
2200 :     be written to the session cache file and the number of results will be
2201 :     returned. If the search parameters are invalid, a result count of C<undef> will be
2202 :     returned and a result message will be stored in this object describing the problem.
2203 :    
2204 : parrello 1.34 =cut
2205 :    
2206 :     sub Find {
2207 :     # Get the parameters.
2208 :     my ($self) = @_;
2209 :     $self->Message("Call to pure virtual Find method in helper of type " . ref($self) . ".");
2210 :     return undef;
2211 :     }
2212 :    
2213 : parrello 1.4 =head3 Description
2214 :    
2215 : parrello 1.38 my $htmlText = $shelp->Description();
2216 : parrello 1.4
2217 :     Return a description of this search. The description is used for the table of contents
2218 :     on the main search tools page. It may contain HTML, but it should be character-level,
2219 :     not block-level, since the description is going to appear in a list.
2220 :    
2221 :     =cut
2222 :    
2223 : parrello 1.34 sub Description {
2224 : parrello 1.4 # Get the parameters.
2225 : parrello 1.34 my ($self) = @_;
2226 :     $self->Message("Call to pure virtual Description method in helper of type " . ref($self) . ".");
2227 :     return "Unknown search type";
2228 : parrello 1.4 }
2229 : parrello 1.9
2230 : parrello 1.31 =head3 SearchTitle
2231 :    
2232 : parrello 1.38 my $titleHtml = $shelp->SearchTitle();
2233 : parrello 1.31
2234 :     Return the display title for this search. The display title appears above the search results.
2235 :     If no result is returned, no title will be displayed. The result should be an html string
2236 :     that can be legally put inside a block tag such as C<h3> or C<p>.
2237 :    
2238 :     =cut
2239 :    
2240 :     sub SearchTitle {
2241 :     # Get the parameters.
2242 :     my ($self) = @_;
2243 :     # Declare the return variable.
2244 : parrello 1.34 my $retVal = "";
2245 : parrello 1.31 # Return it.
2246 :     return $retVal;
2247 :     }
2248 :    
2249 : parrello 1.34 =head3 DefaultColumns
2250 : parrello 1.28
2251 : parrello 1.38 $shelp->DefaultColumns($rhelp);
2252 : parrello 1.28
2253 : parrello 1.34 Store the default columns in the result helper. The default action is just to ask
2254 :     the result helper for its default columns, but this may be changed by overriding
2255 :     this method.
2256 : parrello 1.28
2257 :     =over 4
2258 :    
2259 : parrello 1.34 =item rhelp
2260 : parrello 1.28
2261 : parrello 1.34 Result helper object in which the column list should be stored.
2262 : parrello 1.28
2263 :     =back
2264 :    
2265 :     =cut
2266 :    
2267 : parrello 1.34 sub DefaultColumns {
2268 : parrello 1.28 # Get the parameters.
2269 : parrello 1.34 my ($self, $rhelp) = @_;
2270 :     # Get the default columns from the result helper.
2271 :     my @cols = $rhelp->DefaultResultColumns();
2272 :     # Store them back.
2273 :     $rhelp->SetColumns(@cols);
2274 : parrello 1.28 }
2275 :    
2276 : parrello 1.34 =head3 Hint
2277 : parrello 1.32
2278 : parrello 1.38 my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
2279 : parrello 1.32
2280 : parrello 1.34 Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2281 :     This HTML can be put in forms to provide a useful hinting mechanism.
2282 : parrello 1.32
2283 :     =over 4
2284 :    
2285 : parrello 1.37 =item wikiPage
2286 :    
2287 : parrello 1.39 Name of the wiki page to be popped up when the hint mark is clicked.
2288 : parrello 1.37
2289 : parrello 1.34 =item hintText
2290 : parrello 1.32
2291 : parrello 1.34 Text to display for the hint. It is raw html, but may not contain any double quotes.
2292 : parrello 1.32
2293 :     =item RETURN
2294 :    
2295 : parrello 1.34 Returns the html for the hint facility. The resulting html shows a small button-like thing that
2296 :     uses the standard FIG popup technology.
2297 : parrello 1.32
2298 :     =back
2299 :    
2300 :     =cut
2301 :    
2302 : parrello 1.34 sub Hint {
2303 :     # Get the parameters.
2304 : parrello 1.37 my ($wikiPage, $hintText) = @_;
2305 : parrello 1.41 # Ask Sprout to draw the hint button for us.
2306 :     return Sprout::Hint($wikiPage, $hintText);
2307 : parrello 1.32 }
2308 :    
2309 :    
2310 : parrello 1.38 1;

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