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1 : gdpusch 1.95 # -*- perl -*-
2 :     ########################################################################
3 : olson 1.30 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 : parrello 1.61 #
8 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 : parrello 1.61 # Public License.
11 : olson 1.30 #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.95 ########################################################################
18 : olson 1.30
19 : olson 1.1 package Tracer;
20 :    
21 : parrello 1.115 use strict;
22 :     use base qw(Exporter);
23 :     use vars qw(@EXPORT @EXPORT_OK);
24 : parrello 1.117 @EXPORT = qw(Trace T TSetup QTrace Confess MemTrace Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25 : parrello 1.97 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26 : gdpusch 1.96 use Carp qw(longmess croak carp);
27 : parrello 1.12 use CGI;
28 : parrello 1.47 use Cwd;
29 : parrello 1.12 use FIG_Config;
30 : parrello 1.9 use PageBuilder;
31 : parrello 1.21 use Digest::MD5;
32 : parrello 1.36 use File::Basename;
33 : parrello 1.37 use File::Path;
34 : parrello 1.48 use File::stat;
35 : parrello 1.59 use LWP::UserAgent;
36 : parrello 1.64 use Time::HiRes 'gettimeofday';
37 : parrello 1.65 use URI::Escape;
38 : parrello 1.74 use Time::Local;
39 : parrello 1.99 use POSIX qw(strftime);
40 :     use Time::Zone;
41 : parrello 1.115 use Fcntl qw(:DEFAULT :flock);
42 :     use Data::Dumper;
43 : parrello 1.99
44 : olson 1.1
45 :     =head1 Tracing and Debugging Helpers
46 :    
47 : parrello 1.72 =head2 Tracing
48 : olson 1.1
49 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
50 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
51 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
52 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
53 :     level is less than or equal to the setup trace level and whose category is activated will
54 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
55 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
56 :     appear.
57 : olson 1.1
58 : parrello 1.72 =head3 Putting Trace Messages in Your Code
59 :    
60 :     To generate a trace message, use the following syntax.
61 :    
62 :     Trace($message) if T(errors => 4);
63 : olson 1.1
64 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
65 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
66 : olson 1.1
67 : parrello 1.72 Trace($message) if T(main => 4);
68 : olson 1.1
69 :     will trace if the trace level is 4 or more.
70 :    
71 :     If the category name is the same as the package name, all you need is the number. So, if the
72 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
73 :     active and the trace level is 2 or more.
74 :    
75 : parrello 1.72 Trace($message) if T(2);
76 :    
77 :     In scripts, where no package name is available, the category defaults to C<main>.
78 :    
79 :     =head3 Custom Tracing
80 :    
81 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
83 :     L</Emergency Tracing> easier to understand.
84 : olson 1.1
85 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86 :     a list of category names, and a destination. The trace level and list of category names are
87 : olson 1.1 specified as a space-delimited string. Thus
88 :    
89 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
90 : olson 1.1
91 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
92 : parrello 1.72 specifies that messages should be sent to the standard output.
93 : parrello 1.12
94 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95 :     level 3 and writes the output to the standard error output. This sort of thing might be
96 :     useful in a CGI environment.
97 :    
98 : parrello 1.72 TSetup('3 *', 'WARN');
99 : olson 1.1
100 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
101 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
102 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
103 :     the page output, they can be gathered together and displayed at the end of the page. This makes
104 :     it easier to debug page formatting problems.
105 :    
106 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
107 :     a file at the same time. To trace to a file, specify the filename with an output character in front
108 :     of it.
109 :    
110 :     TSetup('4 SQL', ">$fileName");
111 :    
112 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113 :     bracket.
114 :    
115 :     TSetup('3 *', "+>$fileName");
116 : parrello 1.4
117 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
118 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
119 :     Thus, debugging information is available and easily retrieved even when the application is
120 :     being used out in the field.
121 :    
122 : parrello 1.72 =head3 Trace Levels
123 :    
124 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
125 :     a suggestion.
126 :    
127 :     =over 4
128 :    
129 : parrello 1.32 =item Error 0
130 : parrello 1.10
131 :     Message indicates an error that may lead to incorrect results or that has stopped the
132 :     application entirely.
133 :    
134 : parrello 1.32 =item Warning 1
135 : parrello 1.10
136 :     Message indicates something that is unexpected but that probably did not interfere
137 :     with program execution.
138 :    
139 : parrello 1.32 =item Notice 2
140 : parrello 1.10
141 :     Message indicates the beginning or end of a major task.
142 :    
143 : parrello 1.32 =item Information 3
144 : parrello 1.10
145 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
146 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
147 :    
148 : parrello 1.32 =item Detail 4
149 : parrello 1.10
150 :     Message indicates a low-level loop iteration.
151 :    
152 :     =back
153 :    
154 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
155 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
156 :     The time stamp is between square brackets and the category name between angle brackets.
157 :     After the category name there is a colon (C<:>) followed by the message text.
158 :     If the square brackets or angle brackets are missing, then the trace management
159 :     utilities assume that they are encountering a set of pre-formatted lines.
160 :    
161 :     Note, however, that this formatting is done automatically by the tracing functions. You
162 :     only need to know about it if you want to parse a trace file.
163 :    
164 :     =head3 Emergency Tracing
165 :    
166 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
167 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169 :     that you specify a tracing key. For command-line tools, the key is
170 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
171 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
172 :     the tracing in your environment without stepping on other users.
173 :    
174 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175 :     generate one for you.
176 :    
177 :     You can activate and de-activate emergency tracing from the debugging control panel, as
178 :     well as display the trace file itself.
179 :    
180 :     To enable emergency tracing in your code, call
181 :    
182 :     ETracing($cgi)
183 :    
184 :     from a web script and
185 :    
186 :     ETracing()
187 :    
188 :     from a command-line script.
189 :    
190 :     The web script will look for the tracing key in the cookies, and the command-line
191 :     script will look for it in the C<TRACING> environment variable. If you are
192 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193 : parrello 1.72 will be configured automatically.
194 :    
195 : olson 1.1 =cut
196 : parrello 1.2
197 : olson 1.1 # Declare the configuration variables.
198 :    
199 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
200 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
201 :     # standard output
202 : parrello 1.3 my %Categories = ( main => 1 );
203 : parrello 1.12 # hash of active category names
204 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
205 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
206 :     # messages
207 :     my @Queue = (); # queued list of trace messages.
208 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
209 : parrello 1.97 my $LastLevel = 0; # level of the last test call
210 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
211 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
212 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
213 : parrello 1.104 my $CommandLine; # Command line passed to StandardSetup
214 : parrello 1.99 umask 2; # Fix the damn umask so everything is group-writable.
215 : olson 1.1
216 : parrello 1.93 =head2 Tracing Methods
217 :    
218 :     =head3 Setups
219 :    
220 :     my $count = Tracer::Setups();
221 :    
222 :     Return the number of times L</TSetup> has been called.
223 :    
224 :     This method allows for the creation of conditional tracing setups where, for example, we
225 :     may want to set up tracing if nobody else has done it before us.
226 :    
227 :     =cut
228 :    
229 :     sub Setups {
230 :     return $SetupCount;
231 :     }
232 : olson 1.1
233 :     =head3 TSetup
234 :    
235 : parrello 1.92 TSetup($categoryList, $target);
236 : olson 1.1
237 :     This method is used to specify the trace options. The options are stored as package data
238 :     and interrogated by the L</Trace> and L</T> methods.
239 :    
240 :     =over 4
241 :    
242 :     =item categoryList
243 :    
244 :     A string specifying the trace level and the categories to be traced, separated by spaces.
245 :     The trace level must come first.
246 :    
247 :     =item target
248 :    
249 :     The destination for the trace output. To send the trace output to a file, specify the file
250 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
251 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
252 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
253 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
254 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
255 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
256 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
257 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
258 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
259 : parrello 1.6 cause tracing to be suppressed.
260 : olson 1.1
261 :     =back
262 :    
263 :     =cut
264 :    
265 :     sub TSetup {
266 : parrello 1.12 # Get the parameters.
267 :     my ($categoryList, $target) = @_;
268 :     # Parse the category list.
269 :     my @categoryData = split /\s+/, $categoryList;
270 :     # Extract the trace level.
271 :     $TraceLevel = shift @categoryData;
272 :     # Presume category-based tracing until we learn otherwise.
273 :     $AllTrace = 0;
274 :     # Build the category hash. Note that if we find a "*", we turn on non-category
275 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
276 : parrello 1.34 %Categories = ( main => 1 );
277 : parrello 1.12 for my $category (@categoryData) {
278 :     if ($category eq '*') {
279 :     $AllTrace = 1;
280 :     } else {
281 : parrello 1.13 $Categories{lc $category} = 1;
282 : parrello 1.12 }
283 :     }
284 :     # Now we need to process the destination information. The most important special
285 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
287 :     # the standard output (tee mode).
288 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
289 :     if ($target =~ m/^\+/) {
290 :     $TeeFlag = 1;
291 :     $target = substr($target, 1);
292 :     }
293 :     if ($target =~ m/^>[^>]/) {
294 : parrello 1.98 # We need to initialize the file (which clears it).
295 : parrello 1.12 open TRACEFILE, $target;
296 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297 : parrello 1.12 close TRACEFILE;
298 : parrello 1.98 # Set to append mode now that the file has been cleared.
299 : parrello 1.12 $Destination = ">$target";
300 :     } else {
301 :     $Destination = $target;
302 :     }
303 :     } else {
304 :     $Destination = uc($target);
305 :     }
306 :     # Increment the setup counter.
307 :     $SetupCount++;
308 : parrello 1.11 }
309 :    
310 : parrello 1.93 =head3 SetLevel
311 : parrello 1.31
312 : parrello 1.93 Tracer::SetLevel($newLevel);
313 : parrello 1.31
314 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
315 : parrello 1.31
316 : parrello 1.93 =over 4
317 : parrello 1.31
318 : parrello 1.93 =item newLevel
319 : parrello 1.31
320 : parrello 1.93 Proposed new trace level.
321 : parrello 1.31
322 : parrello 1.93 =back
323 : parrello 1.31
324 : parrello 1.93 =cut
325 : parrello 1.31
326 : parrello 1.93 sub SetLevel {
327 :     $TraceLevel = $_[0];
328 :     }
329 : parrello 1.31
330 : parrello 1.97 =head3 ParseDate
331 :    
332 :     my $time = Tracer::ParseDate($dateString);
333 :    
334 :     Convert a date into a PERL time number. This method expects a date-like string
335 :     and parses it into a number. The string must be vaguely date-like or it will
336 :     return an undefined value. Our requirement is that a month and day be
337 :     present and that three pieces of the date string (time of day, month and day,
338 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
339 :    
340 :     If a time of day is present, it must be in military time with two digits for
341 :     everything but the hour.
342 : parrello 1.31
343 : parrello 1.97 The year must be exactly four digits.
344 : parrello 1.31
345 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
346 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
347 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
348 :    
349 :     It should be guaranteed that this method will parse the output of the L</Now> function.
350 :    
351 :     The parameters are as follows.
352 : parrello 1.31
353 : parrello 1.93 =over 4
354 : parrello 1.31
355 : parrello 1.93 =item dateString
356 : parrello 1.31
357 : parrello 1.97 The date string to convert.
358 : parrello 1.31
359 : parrello 1.93 =item RETURN
360 : parrello 1.31
361 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
363 : parrello 1.31
364 : parrello 1.93 =back
365 : parrello 1.38
366 : parrello 1.93 =cut
367 : parrello 1.38
368 : parrello 1.97 # Universal month conversion table.
369 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
370 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
371 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
372 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
373 :     May => 4, May => 4, '05' => 4, '5' => 4,
374 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
375 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
376 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
377 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
378 :     Oct => 9, October => 9, '10' => 9,
379 :     Nov => 10, November => 10, '11' => 10,
380 :     Dec => 11, December => 11, '12' => 11
381 :     };
382 :    
383 :     sub ParseDate {
384 : parrello 1.93 # Get the parameters.
385 :     my ($dateString) = @_;
386 :     # Declare the return variable.
387 :     my $retVal;
388 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
389 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390 :     # won't be fooled into thinking the month is Sunday.
391 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
393 :     # Insist that the month and day are valid.
394 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
395 :     # Find the time.
396 :     my ($hour, $min, $sec) = (0, 0, 0);
397 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398 :     ($hour, $min, $sec) = ($1, $2, $3);
399 :     }
400 :     # Find the year.
401 :     my $year;
402 :     if ($dateString =~ /\b(\d{4})\b/) {
403 :     $year = $1;
404 :     } else {
405 :     # Get the default year, which is this one. Note we must convert it to
406 :     # the four-digit value expected by "timelocal".
407 :     (undef, undef, undef, undef, undef, $year) = localtime();
408 :     $year += 1900;
409 :     }
410 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411 :     }
412 : parrello 1.93 }
413 :     # Return the result.
414 :     return $retVal;
415 :     }
416 : parrello 1.31
417 : parrello 1.93 =head3 LogErrors
418 : parrello 1.42
419 : parrello 1.93 Tracer::LogErrors($fileName);
420 : parrello 1.31
421 : parrello 1.93 Route the standard error output to a log file.
422 : parrello 1.31
423 : parrello 1.93 =over 4
424 : parrello 1.31
425 : parrello 1.93 =item fileName
426 : parrello 1.31
427 : parrello 1.93 Name of the file to receive the error output.
428 : parrello 1.31
429 : parrello 1.93 =back
430 : parrello 1.31
431 : parrello 1.93 =cut
432 : parrello 1.84
433 : parrello 1.93 sub LogErrors {
434 :     # Get the file name.
435 :     my ($fileName) = @_;
436 :     # Open the file as the standard error output.
437 :     open STDERR, '>', $fileName;
438 :     }
439 : parrello 1.84
440 : parrello 1.93 =head3 Trace
441 : parrello 1.31
442 : parrello 1.93 Trace($message);
443 : parrello 1.31
444 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
445 :     any prior call to B<TSetup>.
446 : parrello 1.31
447 : parrello 1.93 =over 4
448 : parrello 1.42
449 : parrello 1.93 =item message
450 : parrello 1.42
451 : parrello 1.93 Message to write.
452 : parrello 1.42
453 : parrello 1.93 =back
454 : parrello 1.72
455 : parrello 1.93 =cut
456 : parrello 1.36
457 : parrello 1.93 sub Trace {
458 :     # Get the parameters.
459 :     my ($message) = @_;
460 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
461 :     # new-line stuff ourselves.
462 :     my $stripped = Strip($message);
463 :     # Compute the caller information.
464 :     my ($callPackage, $callFile, $callLine) = caller();
465 :     my $callFileTitle = basename($callFile);
466 :     # Check the caller.
467 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468 : parrello 1.93 # Get the timestamp.
469 :     my $timeStamp = Now();
470 : parrello 1.97 # Build the prefix.
471 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473 : parrello 1.97 # Format the message.
474 :     my $formatted = "$prefix $stripped";
475 : parrello 1.93 # Process according to the destination.
476 :     if ($Destination eq "TEXT") {
477 :     # Write the message to the standard output.
478 :     print "$formatted\n";
479 :     } elsif ($Destination eq "ERROR") {
480 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
481 : parrello 1.93 print STDERR "$formatted\n";
482 : parrello 1.97 } elsif ($Destination eq "WARN") {
483 :     # Emit the message to the standard error output. It is presumed that the
484 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
485 :     # the caller info.
486 :     print STDERR "$callerInfo$stripped\n";
487 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
488 :     # Push the message into the queue.
489 :     push @Queue, "$formatted";
490 :     } elsif ($Destination eq "HTML") {
491 : parrello 1.116 # Convert the message to HTML.
492 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
493 : parrello 1.116 # The stuff after the first line feed should be pre-formatted.
494 :     my @lines = split /\s*\n/, $escapedMessage;
495 :     # Get the normal portion.
496 :     my $line1 = shift @lines;
497 :     print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498 :     if (@lines) {
499 :     print "<pre>" . join("\n", @lines, "<pre>");
500 :     }
501 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
502 :     # Write the trace message to an output file.
503 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504 : parrello 1.111 # Lock the file.
505 :     flock TRACING, LOCK_EX;
506 : parrello 1.93 print TRACING "$formatted\n";
507 :     close TRACING;
508 :     # If the Tee flag is on, echo it to the standard output.
509 :     if ($TeeFlag) {
510 :     print "$formatted\n";
511 :     }
512 :     }
513 :     }
514 : parrello 1.36
515 : parrello 1.117 =head3 MemTrace
516 :    
517 :     MemTrace($message);
518 :    
519 :     Output a trace message that includes memory size information.
520 :    
521 :     =over 4
522 :    
523 :     =item message
524 :    
525 :     Message to display. The message will be followed by a sentence about the memory size.
526 :    
527 :     =back
528 :    
529 :     =cut
530 :    
531 :     sub MemTrace {
532 :     # Get the parameters.
533 :     my ($message) = @_;
534 :     my $memory = GetMemorySize();
535 :     Trace("$message $memory in use.");
536 :     }
537 :    
538 :    
539 : parrello 1.115 =head3 TraceDump
540 :    
541 :     TraceDump($title, $object);
542 :    
543 :     Dump an object to the trace log. This method simply calls the C<Dumper>
544 :     function, but routes the output to the trace log instead of returning it
545 :     as a string. The output is arranged so that it comes out monospaced when
546 :     it appears in an HTML trace dump.
547 :    
548 :     =over 4
549 :    
550 :     =item title
551 :    
552 :     Title to give to the object being dumped.
553 :    
554 :     =item object
555 :    
556 :     Reference to a list, hash, or object to dump.
557 :    
558 :     =back
559 :    
560 :     =cut
561 :    
562 :     sub TraceDump {
563 :     # Get the parameters.
564 :     my ($title, $object) = @_;
565 :     # Trace the object.
566 :     Trace("Object dump for $title:\n" . Dumper($object));
567 :     }
568 :    
569 : parrello 1.93 =head3 T
570 : parrello 1.36
571 : parrello 1.93 my $switch = T($category, $traceLevel);
572 : parrello 1.36
573 : parrello 1.93 or
574 : parrello 1.44
575 : parrello 1.93 my $switch = T($traceLevel);
576 : parrello 1.44
577 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
578 :     is active, else FALSE. If no category is specified, the caller's package name is used.
579 : parrello 1.44
580 : parrello 1.93 =over 4
581 : parrello 1.44
582 : parrello 1.93 =item category
583 : parrello 1.44
584 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
585 :     used.
586 : parrello 1.31
587 : parrello 1.93 =item traceLevel
588 : parrello 1.31
589 : parrello 1.93 Relevant tracing level.
590 : parrello 1.31
591 : parrello 1.93 =item RETURN
592 : parrello 1.31
593 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
594 : parrello 1.31
595 : parrello 1.93 =back
596 : parrello 1.36
597 : parrello 1.93 =cut
598 :    
599 :     sub T {
600 :     # Declare the return variable.
601 :     my $retVal = 0;
602 :     # Only proceed if tracing is turned on.
603 :     if ($Destination ne "NONE") {
604 :     # Get the parameters.
605 :     my ($category, $traceLevel) = @_;
606 :     if (!defined $traceLevel) {
607 :     # Here we have no category, so we need to get the calling package.
608 :     # The calling package is normally the first parameter. If it is
609 :     # omitted, the first parameter will be the tracelevel. So, the
610 :     # first thing we do is shift the so-called category into the
611 :     # $traceLevel variable where it belongs.
612 :     $traceLevel = $category;
613 :     my ($package, $fileName, $line) = caller;
614 :     # If there is no calling package, we default to "main".
615 :     if (!$package) {
616 :     $category = "main";
617 :     } else {
618 :     my @cats = split /::/, $package;
619 :     $category = $cats[$#cats];
620 :     }
621 :     }
622 : parrello 1.97 # Save the category name and level.
623 : parrello 1.93 $LastCategory = $category;
624 : parrello 1.97 $LastLevel = $traceLevel;
625 : parrello 1.93 # Convert it to lower case before we hash it.
626 :     $category = lc $category;
627 : parrello 1.100 # Validate the trace level.
628 : parrello 1.93 if (ref $traceLevel) {
629 :     Confess("Bad trace level.");
630 :     } elsif (ref $TraceLevel) {
631 :     Confess("Bad trace config.");
632 :     }
633 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
634 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
635 : parrello 1.93 }
636 :     # Return the computed result.
637 :     return $retVal;
638 :     }
639 :    
640 :     =head3 QTrace
641 :    
642 :     my $data = QTrace($format);
643 :    
644 :     Return the queued trace data in the specified format.
645 :    
646 :     =over 4
647 :    
648 :     =item format
649 :    
650 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
651 :    
652 :     =back
653 :    
654 :     =cut
655 :    
656 :     sub QTrace {
657 :     # Get the parameter.
658 :     my ($format) = @_;
659 :     # Create the return variable.
660 :     my $retVal = "";
661 :     # Only proceed if there is an actual queue.
662 :     if (@Queue) {
663 :     # Process according to the format.
664 :     if ($format =~ m/^HTML$/i) {
665 :     # Convert the queue into an HTML list.
666 :     $retVal = "<ul>\n";
667 :     for my $line (@Queue) {
668 :     my $escapedLine = CGI::escapeHTML($line);
669 :     $retVal .= "<li>$escapedLine</li>\n";
670 :     }
671 :     $retVal .= "</ul>\n";
672 :     } elsif ($format =~ m/^TEXT$/i) {
673 :     # Convert the queue into a list of text lines.
674 :     $retVal = join("\n", @Queue) . "\n";
675 :     }
676 :     # Clear the queue.
677 :     @Queue = ();
678 :     }
679 :     # Return the formatted list.
680 :     return $retVal;
681 :     }
682 :    
683 :     =head3 Confess
684 :    
685 :     Confess($message);
686 :    
687 :     Trace the call stack and abort the program with the specified message. When used with
688 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
689 :     So, for example
690 :    
691 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
692 :    
693 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
694 :    
695 :     =over 4
696 :    
697 :     =item message
698 :    
699 :     Message to include in the trace.
700 :    
701 :     =back
702 :    
703 :     =cut
704 :    
705 :     sub Confess {
706 :     # Get the parameters.
707 :     my ($message) = @_;
708 : parrello 1.97 # Set up the category and level.
709 :     $LastCategory = "(confess)";
710 :     $LastLevel = 0;
711 : parrello 1.93 # Trace the call stack.
712 :     Cluck($message);
713 :     # Abort the program.
714 :     croak(">>> $message");
715 :     }
716 :    
717 : parrello 1.106 =head3 SaveCGI
718 :    
719 :     Tracer::SaveCGI($cgi);
720 :    
721 :     This method saves the CGI object but does not activate emergency tracing.
722 :     It is used to allow L</Warn> to work in situations where emergency
723 :     tracing is contra-indicated (e.g. the wiki).
724 :    
725 :     =over 4
726 :    
727 :     =item cgi
728 :    
729 :     Active CGI query object.
730 :    
731 :     =back
732 :    
733 :     =cut
734 :    
735 :     sub SaveCGI {
736 :     $SavedCGI = $_[0];
737 :     }
738 :    
739 : parrello 1.99 =head3 Warn
740 :    
741 : parrello 1.106 Warn($message, @options);
742 : parrello 1.99
743 :     This method traces an important message. If an RSS feed is configured
744 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
745 :     then the message will be echoed to the feed. In general, a tracing
746 :     destination of C<WARN> indicates that the caller is running as a web
747 :     service in a production environment; however, this is not a requirement.
748 :    
749 : parrello 1.103 To force warnings into the RSS feed even when the tracing destination
750 :     is not C<WARN>, simply specify the C<Feed> tracing module. This can be
751 :     configured automatically when L</StandardSetup> is used.
752 :    
753 : parrello 1.99 The L</Cluck> method calls this one for its final message. Since
754 :     L</Confess> calls L</Cluck>, this means that any error which is caught
755 :     and confessed will put something in the feed. This insures that someone
756 :     will be alerted relatively quickly when a failure occurs.
757 :    
758 :     =over 4
759 :    
760 :     =item message
761 :    
762 :     Message to be traced.
763 :    
764 : parrello 1.106 =item options
765 :    
766 :     A list containing zero or more options.
767 :    
768 :     =back
769 :    
770 :     The permissible options are as follows.
771 :    
772 :     =over 4
773 :    
774 :     =item noStack
775 :    
776 :     If specified, then the stack trace is not included in the output.
777 :    
778 : parrello 1.99 =back
779 :    
780 :     =cut
781 :    
782 :     sub Warn {
783 :     # Get the parameters.
784 : parrello 1.106 my $message = shift @_;
785 :     my %options = map { $_ => 1 } @_;
786 : parrello 1.107 # Save $@;
787 :     my $savedError = $@;
788 : parrello 1.99 # Trace the message.
789 :     Trace($message);
790 : parrello 1.106 # This will contain the lock handle. If it's defined, it means we need to unlock.
791 :     my $lock;
792 : parrello 1.103 # Check for feed forcing.
793 :     my $forceFeed = exists $Categories{feed};
794 : parrello 1.106 # An error here would be disastrous. Note that if debug mode is specified,
795 :     # we do this stuff even in a test environment.
796 : parrello 1.99 eval {
797 :     # Do we need to put this in the RSS feed?
798 : parrello 1.103 if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
799 : parrello 1.109 # Probably. We need to check first, however, to see if it's from an
800 :     # ignored IP. For non-CGI situations, we default the IP to the self-referent.
801 :     my $key = "127.0.0.1";
802 :     if (defined $SavedCGI) {
803 :     # Get the IP address.
804 :     $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
805 : parrello 1.101 }
806 : parrello 1.109 # Is the IP address in the ignore list?
807 :     my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
808 :     if (! $found) {
809 :     # No. We're good. We now need to compute the date, the link, and the title.
810 :     # First, the date, in a very specific format.
811 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
812 :     (tz_local_offset() / 30);
813 :     # Environment data goes in here. We start with the date.
814 :     my $environment = "$date. ";
815 :     # If we need to recap the message (because it's too long to be a title), we'll
816 :     # put it in here.
817 :     my $recap;
818 :     # Copy the message and remove excess space.
819 :     my $title = $message;
820 :     $title =~ s/\s+/ /gs;
821 :     # If it's too long, we have to split it up.
822 :     if (length $title > 60) {
823 :     # Put the full message in the environment string.
824 :     $recap = $title;
825 :     # Excerpt it as the title.
826 :     $title = substr($title, 0, 50) . "...";
827 :     }
828 :     # If we have a CGI object, then this is a web error. Otherwise, it's
829 :     # command-line.
830 :     if (defined $SavedCGI) {
831 :     # We're in a web service. The environment is the user's IP, and the link
832 :     # is the URL that got us here.
833 :     $environment .= "Event Reported at IP address $key process $$.";
834 :     my $url = $SavedCGI->self_url();
835 :     # We need the user agent string and (if available) the referrer.
836 :     # The referrer will be the link.
837 :     $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
838 :     if ($ENV{HTTP_REFERER}) {
839 :     my $link = $ENV{HTTP_REFERER};
840 :     $environment .= " referred from <a href=\"$link\">$link</a>.";
841 :     } else {
842 :     $environment .= " referrer unknown.";
843 :     }
844 :     # Close off the sentence with the original link.
845 :     $environment .= " URL of event is <a href=\"$url\">$url</a>.";
846 :     } else {
847 :     # No CGI object, so we're a command-line tool. Use the tracing
848 :     # key and the PID as the user identifier, and add the command.
849 :     my $key = EmergencyKey();
850 :     $environment .= "Event Reported by $key process $$.";
851 :     if ($CommandLine) {
852 :     # We're in a StandardSetup script, so we have the real command line.
853 :     $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
854 :     } elsif ($ENV{_}) {
855 :     # We're in a BASH script, so the command has been stored in the _ variable.
856 :     $environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
857 :     }
858 :     }
859 :     # Build a GUID. We use the current time, the title, and the process ID,
860 :     # then digest the result.
861 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
862 :     # Finally, the description. This is a stack trace plus various environmental stuff.
863 :     # The trace is optional.
864 :     my $stackTrace;
865 :     if ($options{noStack}) {
866 :     $stackTrace = "";
867 :     } else {
868 :     my @trace = LongMess();
869 :     # Only proceed if we got something back.
870 :     if (scalar(@trace) > 0) {
871 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
872 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
873 :     }
874 :     }
875 :     # We got the stack trace. Now it's time to put it all together.
876 :     # We have a goofy thing here in that we need to HTML-escape some sections of the description
877 :     # twice. They will be escaped once here, and then once when written by XML::Simple. They are
878 :     # unescaped once when processed by the RSS reader, and stuff in the description is treated as
879 :     # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
880 :     # our <br>s and <pre>s are used to format the description.
881 :     $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
882 :     my $description = "$recap$environment $stackTrace";
883 :     # Okay, we have all the pieces. Create a hash of the new event.
884 :     my $newItem = { title => $title,
885 :     description => $description,
886 :     category => $LastCategory,
887 :     pubDate => $date,
888 :     guid => $guid,
889 :     };
890 :     # We need XML capability for this.
891 :     require XML::Simple;
892 :     # The RSS document goes in here.
893 :     my $rss;
894 :     # Get the name of the RSS file. It's in the FIG temporary directory.
895 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
896 :     # Open the config file and lock it.
897 :     $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
898 :     flock $lock, LOCK_EX;
899 :     # Does it exist?
900 :     if (-s $fileName) {
901 :     # Slurp it in.
902 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
903 : parrello 1.102 } else {
904 : parrello 1.109 my $size = -s $fileName;
905 :     # Create an empty channel.
906 :     $rss = {
907 :     channel => {
908 :     title => 'NMPDR Warning Feed',
909 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
910 :     description => "Important messages regarding the status of the NMPDR.",
911 :     generator => "NMPDR Trace Facility",
912 :     docs => "http://blogs.law.harvard.edu/tech/rss",
913 :     item => []
914 :     },
915 :     };
916 : parrello 1.100 }
917 : parrello 1.109 # Get the channel object.
918 :     my $channel = $rss->{channel};
919 :     # Update the last-build date.
920 :     $channel->{lastBuildDate} = $date;
921 :     # Get the item array.
922 :     my $items = $channel->{item};
923 :     # Insure it has only 100 entries.
924 :     while (scalar @{$items} > 100) {
925 :     pop @{$items};
926 : parrello 1.104 }
927 : parrello 1.109 # Add our new item at the front.
928 :     unshift @{$items}, $newItem;
929 :     # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
930 :     # the requirements for those.
931 :     my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
932 :     # Here we put in the root and declaration. The problem is that the root has to have the version attribute
933 :     # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
934 :     $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
935 :     # We don't use Open here because we can't afford an error.
936 :     if (open XMLOUT, ">$fileName") {
937 :     print XMLOUT $xml;
938 :     close XMLOUT;
939 : parrello 1.106 }
940 : parrello 1.101 }
941 : parrello 1.99 }
942 :     };
943 : parrello 1.103 if ($@) {
944 :     # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
945 :     # (which is a good thing).
946 : parrello 1.102 my $error = $@;
947 : parrello 1.103 Trace("Feed Error: $error") if T(Feed => 0);
948 : parrello 1.102 }
949 : parrello 1.106 # Be sure to unlock.
950 :     if ($lock) {
951 :     flock $lock, LOCK_UN;
952 :     undef $lock;
953 :     }
954 : parrello 1.107 # Restore the error message.
955 :     $@ = $savedError;
956 : parrello 1.99 }
957 :    
958 : parrello 1.106
959 :    
960 :    
961 : parrello 1.93 =head3 Assert
962 :    
963 :     Assert($condition1, $condition2, ... $conditionN);
964 :    
965 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
966 :     the OR operator and the L</Confess> method as a debugging assert.
967 :     So, for example
968 :    
969 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
970 :    
971 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
972 :    
973 :     =cut
974 :     sub Assert {
975 :     my $retVal = 1;
976 :     LOOP: for my $condition (@_) {
977 :     if (! $condition) {
978 :     $retVal = 0;
979 :     last LOOP;
980 :     }
981 :     }
982 :     return $retVal;
983 :     }
984 :    
985 :     =head3 Cluck
986 :    
987 :     Cluck($message);
988 :    
989 :     Trace the call stack. Note that for best results, you should qualify the call with a
990 :     trace condition. For example,
991 :    
992 :     Cluck("Starting record parse.") if T(3);
993 :    
994 :     will only trace the stack if the trace level for the package is 3 or more.
995 :    
996 :     =over 4
997 :    
998 :     =item message
999 :    
1000 :     Message to include in the trace.
1001 :    
1002 :     =back
1003 :    
1004 :     =cut
1005 :    
1006 :     sub Cluck {
1007 :     # Get the parameters.
1008 :     my ($message) = @_;
1009 :     # Trace what's happening.
1010 :     Trace("Stack trace for event: $message");
1011 : parrello 1.99 # Get the stack trace.
1012 :     my @trace = LongMess();
1013 :     # Convert the trace to a series of messages.
1014 :     for my $line (@trace) {
1015 :     # Replace the tab at the beginning with spaces.
1016 :     $line =~ s/^\t/ /;
1017 :     # Trace the line.
1018 :     Trace($line);
1019 :     }
1020 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
1021 :     Warn($message);
1022 :     }
1023 :    
1024 :     =head3 LongMess
1025 :    
1026 :     my @lines = Tracer::LongMess();
1027 :    
1028 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
1029 :     of message strings.
1030 :    
1031 :     =cut
1032 :    
1033 :     sub LongMess {
1034 :     # Declare the return variable.
1035 :     my @retVal = ();
1036 :     my $confession = longmess("");
1037 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
1038 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
1039 :     # Here we have a line worth keeping. Push it onto the result list.
1040 :     push @retVal, $line;
1041 : parrello 1.97 }
1042 : parrello 1.93 }
1043 : parrello 1.99 # Return the result.
1044 :     return @retVal;
1045 : parrello 1.93 }
1046 :    
1047 :     =head3 ETracing
1048 :    
1049 :     ETracing($parameter);
1050 :    
1051 :     Set up emergency tracing. Emergency tracing is tracing that is turned
1052 :     on automatically for any program that calls this method. The emergency
1053 :     tracing parameters are stored in a a file identified by a tracing key.
1054 :     If this method is called with a CGI object, then the tracing key is
1055 :     taken from a cookie. If it is called with no parameters, then the tracing
1056 :     key is taken from an environment variable. If it is called with a string,
1057 :     the tracing key is that string.
1058 :    
1059 :     =over 4
1060 :    
1061 :     =item parameter
1062 :    
1063 :     A parameter from which the tracing key is computed. If it is a scalar,
1064 :     that scalar is used as the tracing key. If it is a CGI object, the
1065 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
1066 :     tracing key is taken from the C<TRACING> environment variable. If it
1067 :     is a CGI object and emergency tracing is not on, the C<Trace> and
1068 :     C<TF> parameters will be used to determine the type of tracing.
1069 :    
1070 :     =back
1071 :    
1072 :     =cut
1073 :    
1074 :     sub ETracing {
1075 :     # Get the parameter.
1076 :     my ($parameter) = @_;
1077 :     # Check for CGI mode.
1078 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
1079 :     $SavedCGI = $parameter;
1080 :     } else {
1081 :     $SavedCGI = undef;
1082 :     }
1083 : parrello 1.93 # Default to no tracing except errors.
1084 :     my ($tracing, $dest) = ("0", "WARN");
1085 :     # Check for emergency tracing.
1086 :     my $tkey = EmergencyKey($parameter);
1087 :     my $emergencyFile = EmergencyFileName($tkey);
1088 :     if (-e $emergencyFile) {
1089 :     # We have the file. Read in the data.
1090 :     my @tracing = GetFile($emergencyFile);
1091 :     # Pull off the time limit.
1092 :     my $expire = shift @tracing;
1093 :     # Convert it to seconds.
1094 :     $expire *= 3600;
1095 :     # Check the file data.
1096 :     my $stat = stat($emergencyFile);
1097 :     my ($now) = gettimeofday;
1098 :     if ($now - $stat->mtime > $expire) {
1099 :     # Delete the expired file.
1100 :     unlink $emergencyFile;
1101 : parrello 1.44 } else {
1102 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
1103 :     # the trace level;
1104 :     $dest = shift @tracing;
1105 :     my $level = shift @tracing;
1106 :     # Convert the destination to a real tracing destination.
1107 :     # temp directory.
1108 :     $dest = EmergencyTracingDest($tkey, $dest);
1109 :     # Insure Tracer is specified.
1110 :     my %moduleHash = map { $_ => 1 } @tracing;
1111 :     $moduleHash{Tracer} = 1;
1112 :     # Set the trace parameter.
1113 :     $tracing = join(" ", $level, sort keys %moduleHash);
1114 : parrello 1.44 }
1115 : parrello 1.99 } elsif (defined $SavedCGI) {
1116 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1117 :     # for tracing from the form parameters.
1118 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1119 : parrello 1.93 # Here the user has requested tracing via a form.
1120 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1121 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1122 : parrello 1.36 }
1123 :     }
1124 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1125 :     TSetup($tracing, $dest);
1126 : parrello 1.94 # Check to see if we're a web script.
1127 : parrello 1.99 if (defined $SavedCGI) {
1128 : parrello 1.94 # Yes we are. Trace the form and environment data.
1129 : parrello 1.99 TraceParms($SavedCGI);
1130 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1131 :     # emitted by the script in its raw form.
1132 :     if (T(Raw => 3)) {
1133 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1134 :     }
1135 : parrello 1.83 }
1136 : parrello 1.31 }
1137 :    
1138 : parrello 1.93 =head3 EmergencyFileName
1139 :    
1140 :     my $fileName = Tracer::EmergencyFileName($tkey);
1141 :    
1142 :     Return the emergency tracing file name. This is the file that specifies
1143 :     the tracing information.
1144 :    
1145 :     =over 4
1146 :    
1147 :     =item tkey
1148 :    
1149 :     Tracing key for the current program.
1150 : parrello 1.11
1151 : parrello 1.93 =item RETURN
1152 : parrello 1.11
1153 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1154 : parrello 1.11
1155 : parrello 1.93 =back
1156 : parrello 1.11
1157 :     =cut
1158 :    
1159 : parrello 1.93 sub EmergencyFileName {
1160 :     # Get the parameters.
1161 :     my ($tkey) = @_;
1162 :     # Compute the emergency tracing file name.
1163 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1164 : olson 1.1 }
1165 :    
1166 : parrello 1.93 =head3 EmergencyFileTarget
1167 : parrello 1.10
1168 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1169 : parrello 1.10
1170 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1171 :     the tracing output for file-based tracing.
1172 : parrello 1.10
1173 : parrello 1.93 =over 4
1174 : parrello 1.10
1175 : parrello 1.93 =item tkey
1176 : parrello 1.10
1177 : parrello 1.93 Tracing key for the current program.
1178 : parrello 1.10
1179 : parrello 1.93 =item RETURN
1180 : parrello 1.10
1181 : parrello 1.93 Returns the name of the file to contain the trace output.
1182 : parrello 1.10
1183 : parrello 1.93 =back
1184 : parrello 1.10
1185 : parrello 1.93 =cut
1186 : parrello 1.10
1187 : parrello 1.93 sub EmergencyFileTarget {
1188 :     # Get the parameters.
1189 :     my ($tkey) = @_;
1190 :     # Compute the emergency tracing file name.
1191 :     return "$FIG_Config::temp/trace$tkey.log";
1192 :     }
1193 : parrello 1.10
1194 : parrello 1.93 =head3 EmergencyTracingDest
1195 : parrello 1.10
1196 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1197 : parrello 1.10
1198 : parrello 1.93 This method converts an emergency tracing destination to a real
1199 :     tracing destination. The main difference is that if the
1200 :     destination is C<FILE> or C<APPEND>, we convert it to file
1201 :     output. If the destination is C<DUAL>, we convert it to file
1202 :     and standard output.
1203 : parrello 1.10
1204 :     =over 4
1205 :    
1206 : parrello 1.93 =item tkey
1207 : parrello 1.10
1208 : parrello 1.93 Tracing key for this environment.
1209 : parrello 1.10
1210 : parrello 1.93 =item myDest
1211 : parrello 1.10
1212 : parrello 1.93 Destination from the emergency tracing file.
1213 : parrello 1.10
1214 :     =item RETURN
1215 :    
1216 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1217 : parrello 1.10
1218 :     =back
1219 :    
1220 :     =cut
1221 :    
1222 : parrello 1.93 sub EmergencyTracingDest {
1223 : parrello 1.12 # Get the parameters.
1224 : parrello 1.93 my ($tkey, $myDest) = @_;
1225 :     # Declare the return variable.
1226 :     my $retVal = $myDest;
1227 :     # Process according to the destination value.
1228 :     if ($myDest eq 'FILE') {
1229 :     $retVal = ">" . EmergencyFileTarget($tkey);
1230 :     } elsif ($myDest eq 'APPEND') {
1231 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1232 :     } elsif ($myDest eq 'DUAL') {
1233 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1234 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1235 :     $retVal = "WARN";
1236 : parrello 1.12 }
1237 : parrello 1.93 # Return the result.
1238 :     return $retVal;
1239 : parrello 1.10 }
1240 :    
1241 : parrello 1.93 =head3 Emergency
1242 :    
1243 :     Emergency($key, $hours, $dest, $level, @modules);
1244 :    
1245 :     Turn on emergency tracing. This method is normally invoked over the web from
1246 :     a debugging console, but it can also be called by the C<trace.pl> script.
1247 :     The caller specifies the duration of the emergency in hours, the desired tracing
1248 :     destination, the trace level, and a list of the trace modules to activate.
1249 :     For the length of the duration, when a program in an environment with the
1250 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1251 :     turned on automatically. See L</TSetup> for more about tracing setup and
1252 :     L</ETracing> for more about emergency tracing.
1253 :    
1254 :     =over 4
1255 : parrello 1.11
1256 : parrello 1.93 =item tkey
1257 : parrello 1.11
1258 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1259 : parrello 1.11
1260 : parrello 1.93 =item hours
1261 : parrello 1.11
1262 : parrello 1.93 Number of hours to keep emergency tracing alive.
1263 : parrello 1.11
1264 : parrello 1.93 =item dest
1265 : parrello 1.11
1266 : parrello 1.93 Tracing destination. If no path information is specified for a file
1267 :     destination, it is put in the FIG temporary directory.
1268 : parrello 1.11
1269 : parrello 1.93 =item level
1270 : parrello 1.11
1271 : parrello 1.93 Tracing level. A higher level means more trace messages.
1272 : parrello 1.11
1273 : parrello 1.93 =item modules
1274 : parrello 1.11
1275 : parrello 1.93 A list of the tracing modules to activate.
1276 : parrello 1.11
1277 :     =back
1278 :    
1279 :     =cut
1280 : parrello 1.93
1281 :     sub Emergency {
1282 : parrello 1.11 # Get the parameters.
1283 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1284 :     # Create the emergency file.
1285 :     my $specFile = EmergencyFileName($tkey);
1286 :     my $outHandle = Open(undef, ">$specFile");
1287 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1288 : parrello 1.11 }
1289 :    
1290 : parrello 1.93 =head3 EmergencyKey
1291 :    
1292 :     my $tkey = EmergencyKey($parameter);
1293 :    
1294 :     Return the Key to be used for emergency tracing. This could be an IP address,
1295 :     a session ID, or a user name, depending on the environment.
1296 : parrello 1.11
1297 : parrello 1.93 =over 4
1298 : parrello 1.11
1299 : parrello 1.93 =item parameter
1300 : parrello 1.11
1301 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1302 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1303 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1304 :     taken from the C<TRACING> environment variable.
1305 : parrello 1.29
1306 : parrello 1.93 =item RETURN
1307 : parrello 1.11
1308 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1309 : parrello 1.11
1310 : parrello 1.93 =back
1311 : parrello 1.11
1312 : parrello 1.93 =cut
1313 : parrello 1.29
1314 : parrello 1.93 sub EmergencyKey {
1315 :     # Get the parameters.
1316 :     my ($parameter) = @_;
1317 :     # Declare the return variable.
1318 :     my $retVal;
1319 :     # Determine the parameter type.
1320 : olson 1.114 if (! defined $parameter || defined($ENV{TRACING})) {
1321 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1322 :     # get the effective login ID.
1323 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1324 : parrello 1.93 } else {
1325 :     my $ptype = ref $parameter;
1326 :     if ($ptype eq 'CGI') {
1327 :     # Here we were invoked from a web page. Look for a cookie.
1328 :     $retVal = $parameter->cookie('IP');
1329 :     } elsif (! $ptype) {
1330 :     # Here the key was passed in.
1331 :     $retVal = $parameter;
1332 :     }
1333 :     }
1334 :     # If no luck finding a key, use the PID.
1335 :     if (! defined $retVal) {
1336 :     $retVal = $$;
1337 :     }
1338 :     # Return the result.
1339 :     return $retVal;
1340 :     }
1341 : parrello 1.11
1342 :    
1343 : parrello 1.93 =head3 TraceParms
1344 : parrello 1.11
1345 : parrello 1.93 Tracer::TraceParms($cgi);
1346 : parrello 1.11
1347 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1348 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1349 : parrello 1.11
1350 : parrello 1.93 =over 4
1351 : parrello 1.11
1352 : parrello 1.93 =item cgi
1353 : parrello 1.31
1354 : parrello 1.93 CGI query object containing the parameters to trace.
1355 : parrello 1.31
1356 : parrello 1.11 =back
1357 :    
1358 :     =cut
1359 : parrello 1.93
1360 :     sub TraceParms {
1361 : parrello 1.11 # Get the parameters.
1362 : parrello 1.93 my ($cgi) = @_;
1363 : parrello 1.94 if (T(CGI => 2)) {
1364 : parrello 1.115 # Here we trace the GET-style URL for the script, but only if it's
1365 :     # relatively small.
1366 :     my $url = $cgi->url(-relative => 1, -query => 1);
1367 :     my $len = length($url);
1368 :     if ($len < 500) {
1369 :     Trace("[URL] $url");
1370 :     } elsif ($len > 2048) {
1371 :     Trace("[URL] URL is too long to use with GET ($len characters).");
1372 :     } else {
1373 :     Trace("[URL] URL length is $len characters.");
1374 :     }
1375 : parrello 1.94 }
1376 : parrello 1.93 if (T(CGI => 3)) {
1377 :     # Here we want to trace the parameter data.
1378 :     my @names = $cgi->param;
1379 :     for my $parmName (sort @names) {
1380 :     # Note we skip the Trace parameters, which are for our use only.
1381 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1382 :     my @values = $cgi->param($parmName);
1383 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1384 : parrello 1.93 }
1385 :     }
1386 :     # Display the request method.
1387 :     my $method = $cgi->request_method();
1388 :     Trace("Method: $method");
1389 :     }
1390 :     if (T(CGI => 4)) {
1391 :     # Here we want the environment data too.
1392 :     for my $envName (sort keys %ENV) {
1393 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1394 : parrello 1.12 }
1395 :     }
1396 : parrello 1.11 }
1397 :    
1398 : parrello 1.94 =head3 TraceImages
1399 :    
1400 :     Tracer::TraceImages($htmlString);
1401 :    
1402 :     Trace information about all of an html document's images. The tracing
1403 :     will be for type "IMG" at level 3. The image's source string
1404 :     will be displayed. This is generally either the URL of the image or
1405 :     raw data for the image itself. If the source is too long, only the first 300
1406 :     characters will be shown at trace level 3. The entire source will be shown,
1407 :     however, at trace level 4. This method is not very smart, and might catch
1408 :     Javascript code, but it is still useful when debugging the arcane
1409 :     behavior of images in multiple browser environments.
1410 :    
1411 :     =over 4
1412 :    
1413 :     =item htmlString
1414 :    
1415 :     HTML text for an outgoing web page.
1416 :    
1417 :     =back
1418 :    
1419 :     =cut
1420 :    
1421 :     sub TraceImages {
1422 :     # Only proceed if we're at the proper trace level.
1423 :     if (T(IMG => 3)) {
1424 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1425 :     # into a variable called "$htmlString". This is because we expect html strings to be
1426 :     # long, and don't want to copy them any more than we have to.
1427 :     Trace(length($_[0]) . " characters in web page.");
1428 :     # Loop through the HTML, culling image tags.
1429 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1430 :     # Extract the source string and determine whether or not it's too long.
1431 :     my $srcString = $1;
1432 :     my $pos = pos($_[0]) - length($srcString);
1433 :     my $excess = length($srcString) - 300;
1434 :     # We'll put the display string in here.
1435 :     my $srcDisplay = $srcString;
1436 :     # If it's a data string, split it at the comma.
1437 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1438 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1439 :     # a long string, however, we only show the first 300 characters.
1440 :     if ($excess > 0 && ! T(IMG => 4)) {
1441 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1442 :     }
1443 :     # Output the trace message.
1444 :     Trace("Image tag at position $pos:\n$srcDisplay");
1445 :     }
1446 :     }
1447 :     }
1448 :    
1449 : parrello 1.93 =head2 Command-Line Utility Methods
1450 : olson 1.1
1451 : parrello 1.93 =head3 SendSMS
1452 : olson 1.1
1453 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1454 : olson 1.1
1455 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1456 :     user name, password, and API ID for the relevant account in the hash reference variable
1457 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1458 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1459 :     is C<2561022>, then the FIG_Config file must contain
1460 : olson 1.1
1461 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1462 :     password => 'silly',
1463 :     api_id => '2561022' };
1464 : olson 1.1
1465 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1466 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1467 :     when you call this method.
1468 : olson 1.1
1469 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1470 : parrello 1.74
1471 : parrello 1.93 =over 4
1472 : parrello 1.74
1473 : parrello 1.93 =item phoneNumber
1474 : parrello 1.74
1475 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1476 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1477 : parrello 1.74
1478 : parrello 1.93 =item msg
1479 : parrello 1.74
1480 : parrello 1.93 Message to send to the specified phone.
1481 : parrello 1.74
1482 :     =item RETURN
1483 :    
1484 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1485 : parrello 1.74
1486 : parrello 1.78 =back
1487 :    
1488 : parrello 1.74 =cut
1489 :    
1490 : parrello 1.93 sub SendSMS {
1491 : parrello 1.74 # Get the parameters.
1492 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1493 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1494 : parrello 1.74 my $retVal;
1495 : parrello 1.93 # Only proceed if we have phone support.
1496 :     if (! defined $FIG_Config::phone) {
1497 :     Trace("Phone support not present in FIG_Config.") if T(1);
1498 :     } else {
1499 :     # Get the phone data.
1500 :     my $parms = $FIG_Config::phone;
1501 :     # Get the Clickatell URL.
1502 :     my $url = "http://api.clickatell.com/http/";
1503 :     # Create the user agent.
1504 :     my $ua = LWP::UserAgent->new;
1505 :     # Request a Clickatell session.
1506 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1507 :     password => $parms->{password},
1508 :     api_id => $parms->{api_id},
1509 :     to => $phoneNumber,
1510 :     text => $msg});
1511 :     # Check for an error.
1512 :     if (! $resp->is_success) {
1513 :     Trace("Alert failed.") if T(1);
1514 :     } else {
1515 :     # Get the message ID.
1516 :     my $rstring = $resp->content;
1517 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1518 :     $retVal = $1;
1519 :     } else {
1520 :     Trace("Phone attempt failed with $rstring") if T(1);
1521 :     }
1522 :     }
1523 : parrello 1.74 }
1524 :     # Return the result.
1525 :     return $retVal;
1526 :     }
1527 :    
1528 : parrello 1.93 =head3 StandardSetup
1529 : olson 1.1
1530 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1531 : olson 1.1
1532 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1533 :     values are a hash of the command-line options and a list of the positional
1534 :     parameters. Tracing is automatically set up and the command-line options are
1535 :     validated.
1536 : olson 1.1
1537 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1538 :     be more easily understood, however, once they are examined individually.
1539 : olson 1.1
1540 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1541 :     special-purpose tracing categories. Most tracing categories are PERL package
1542 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1543 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1544 : olson 1.1
1545 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1546 : olson 1.1
1547 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1548 :     the output. There are two special tracing categories that are automatically
1549 :     handled by this method. In other words, if you used L</TSetup> you would need
1550 :     to include these categories manually, but if you use this method they are turned
1551 :     on automatically.
1552 : parrello 1.5
1553 :     =over 4
1554 :    
1555 : parrello 1.93 =item SQL
1556 : parrello 1.5
1557 : parrello 1.93 Traces SQL commands and activity.
1558 : parrello 1.5
1559 : parrello 1.93 =item Tracer
1560 : parrello 1.5
1561 : parrello 1.93 Traces error messages and call stacks.
1562 : parrello 1.5
1563 :     =back
1564 :    
1565 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1566 :     The trace level is specified using the C<-trace> command-line option. For example,
1567 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1568 :     all tracing at level 3.
1569 : parrello 1.5
1570 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1571 : parrello 1.5
1572 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1573 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1574 :     process ID. You can also specify the C<user> parameter to put a user ID
1575 :     instead of a process ID in the trace file name. So, for example
1576 : olson 1.1
1577 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1578 :     For a genome-by-genome update, use 3.
1579 : olson 1.1
1580 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1581 : olson 1.1
1582 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1583 : olson 1.1
1584 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1585 :     options, their default values, and an explanation of what they mean. Command-line
1586 :     options may be in the form of switches or keywords. In the case of a switch, the
1587 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1588 :     of a keyword, the value is separated from the option name by an equal sign. You
1589 :     can see this last in the command-line example above.
1590 : olson 1.1
1591 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1592 :     prior to calling this method.
1593 : olson 1.1
1594 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1595 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1596 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1597 :     the following code.
1598 : olson 1.1
1599 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1600 :     { safe => [0, "use database transactions"],
1601 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1602 :     start => [' ', "start with this genome"],
1603 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1604 :     "<command> <transactionDirectory> <IDfile>",
1605 :     @ARGV);
1606 : olson 1.1
1607 :    
1608 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1609 :     stores the actual options in a hash that is returned as C<$options>. The
1610 :     positional parameters are returned in C<@parameters>.
1611 : olson 1.1
1612 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1613 : olson 1.1
1614 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1615 : olson 1.1
1616 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1617 :     above command as
1618 : olson 1.1
1619 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1620 : olson 1.1
1621 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1622 :     parameters, and would find themselves in I<@parameters> after executing the
1623 :     above code fragment. The tracing would be set to level 2, and the categories
1624 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1625 :     and C<DocUtils> was included because it came in within the first parameter
1626 :     to this method. The I<$options> hash would be
1627 : olson 1.1
1628 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1629 :     noAlias => 1, start => ' ', tblFiles => 0 }
1630 : olson 1.1
1631 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1632 :     standard tracing setup and command-line parsing. Note that the caller is
1633 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1634 :     are used by this method to control the tracing. If additional tracing features
1635 :     need to be added in the future, they can be processed by this method without
1636 :     upsetting the command-line utilities.
1637 : olson 1.1
1638 : parrello 1.93 If the C<background> option is specified on the command line, then the
1639 :     standard and error outputs will be directed to files in the temporary
1640 :     directory, using the same suffix as the trace file. So, if the command
1641 :     line specified
1642 : olson 1.1
1643 : parrello 1.93 -user=Bruce -background
1644 : olson 1.1
1645 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1646 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1647 :     simplify starting a command in the background.
1648 : olson 1.1
1649 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1650 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1651 :     be used instead of custom tracing. If the user name is not specified,
1652 :     the tracing key is taken from the C<Tracing> environment variable. If there
1653 : parrello 1.103 is no value for that variable, the tracing key will be computed from the active
1654 :     login ID.
1655 :    
1656 :     Since the default situation in StandardSetup is to trace to the standard
1657 :     output, errors that occur in command-line scripts will not generate
1658 :     RSS events. To force the events, use the C<warn> option.
1659 :    
1660 :     TransactFeatures -background -warn register ../xacts IDs.tbl
1661 : olson 1.1
1662 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1663 :     names will be traced at level 0 and the program will exit without processing.
1664 :     This provides a limited help capability. For example, if the user enters
1665 : olson 1.1
1666 : parrello 1.93 TransactFeatures -help
1667 : olson 1.1
1668 : parrello 1.93 he would see the following output.
1669 : olson 1.1
1670 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1671 :     -trace tracing level (default E)
1672 :     -sql trace SQL commands
1673 :     -safe use database transactions
1674 :     -noAlias do not expect aliases in CHANGE transactions
1675 :     -start start with this genome
1676 :     -tblFiles output TBL files containing the corrected IDs
1677 : parrello 1.111 -forked do not erase the trace file before tracing
1678 : olson 1.1
1679 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1680 :     for C<trace> in the incoming options hash. The default value can be overridden,
1681 :     or the tracing to the standard output can be turned off by suffixing a minus
1682 :     sign to the trace level. So, for example,
1683 : olson 1.1
1684 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1685 :     ...
1686 : olson 1.1
1687 : parrello 1.93 would set the default trace level to 0 instead of E, while
1688 : olson 1.1
1689 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1690 :     ...
1691 : olson 1.1
1692 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1693 :     standard output.
1694 : olson 1.1
1695 : parrello 1.93 The parameters to this method are as follows.
1696 : olson 1.1
1697 : parrello 1.93 =over 4
1698 : olson 1.1
1699 : parrello 1.93 =item categories
1700 : parrello 1.2
1701 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1702 :     packages whose internal workings will need to be debugged to get the
1703 :     command working.
1704 : olson 1.1
1705 : parrello 1.93 =item options
1706 : olson 1.1
1707 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1708 :     to their default values and descriptions. The user can override the defaults
1709 :     by specifying the options as command-line switches prefixed by a hyphen.
1710 :     Tracing-related options may be added to this hash. If the C<-h> option is
1711 :     specified on the command line, the option descriptions will be used to
1712 :     explain the options. To turn off tracing to the standard output, add a
1713 :     minus sign to the value for C<trace> (see above).
1714 : olson 1.1
1715 : parrello 1.93 =item parmHelp
1716 : olson 1.1
1717 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1718 :     if the user specifies the C<-h> option.
1719 : olson 1.1
1720 : parrello 1.93 =item argv
1721 : olson 1.1
1722 : parrello 1.93 List of command line parameters, including the option switches, which must
1723 :     precede the positional parameters and be prefixed by a hyphen.
1724 : olson 1.1
1725 :     =item RETURN
1726 :    
1727 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1728 :     maps the command-line option switches to their values. These will either be the
1729 :     default values or overrides specified on the command line. The remaining
1730 :     elements of the list are the position parameters, in order.
1731 : olson 1.1
1732 :     =back
1733 :    
1734 :     =cut
1735 :    
1736 : parrello 1.93 sub StandardSetup {
1737 :     # Get the parameters.
1738 :     my ($categories, $options, $parmHelp, @argv) = @_;
1739 :     # Get the default tracing key.
1740 :     my $tkey = EmergencyKey();
1741 : parrello 1.104 # Save the command line.
1742 :     $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1743 : parrello 1.93 # Add the tracing options.
1744 :     if (! exists $options->{trace}) {
1745 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1746 :     }
1747 : parrello 1.112 if (! exists $options->{forked}) {
1748 :     $options->{forked} = [0, "keep old trace file"];
1749 :     }
1750 : parrello 1.93 $options->{sql} = [0, "turn on SQL tracing"];
1751 :     $options->{help} = [0, "display command-line options"];
1752 :     $options->{user} = [$tkey, "tracing key"];
1753 :     $options->{background} = [0, "spool standard and error output"];
1754 : parrello 1.103 $options->{warn} = [0, "send errors to RSS feed"];
1755 : parrello 1.113 $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1756 : parrello 1.93 # Create a parsing hash from the options hash. The parsing hash
1757 :     # contains the default values rather than the default value
1758 :     # and the description. While we're at it, we'll memorize the
1759 :     # length of the longest option name.
1760 :     my $longestName = 0;
1761 :     my %parseOptions = ();
1762 :     for my $key (keys %{$options}) {
1763 :     if (length $key > $longestName) {
1764 :     $longestName = length $key;
1765 :     }
1766 :     $parseOptions{$key} = $options->{$key}->[0];
1767 :     }
1768 :     # Parse the command line.
1769 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1770 :     # Get the logfile suffix.
1771 :     my $suffix = $retOptions->{user};
1772 : parrello 1.113 # We'll put the trace file name in here. We need it later if background
1773 :     # mode is on.
1774 :     my $traceFileName;
1775 : parrello 1.93 # Now we want to set up tracing. First, we need to know if the user
1776 :     # wants emergency tracing.
1777 :     if ($retOptions->{trace} eq 'E') {
1778 :     ETracing($retOptions->{user});
1779 :     } else {
1780 :     # Here the tracing is controlled from the command line.
1781 :     my @cats = @{$categories};
1782 :     if ($retOptions->{sql}) {
1783 :     push @cats, "SQL";
1784 :     }
1785 : parrello 1.103 if ($retOptions->{warn}) {
1786 :     push @cats, "Feed";
1787 :     }
1788 : parrello 1.93 # Add the default categories.
1789 :     push @cats, "Tracer";
1790 : parrello 1.113 # Check for more tracing groups.
1791 :     if ($retOptions->{moreTracing}) {
1792 :     push @cats, split /,/, $retOptions->{moreTracing};
1793 :     }
1794 : parrello 1.93 # Next, we create the category string by joining the categories.
1795 :     my $cats = join(" ", @cats);
1796 :     # Check to determine whether or not the caller wants to turn off tracing
1797 :     # to the standard output.
1798 :     my $traceLevel = $retOptions->{trace};
1799 :     my $textOKFlag = 1;
1800 :     if ($traceLevel =~ /^(.)-/) {
1801 :     $traceLevel = $1;
1802 :     $textOKFlag = 0;
1803 :     }
1804 :     # Now we set up the trace mode.
1805 :     my $traceMode;
1806 :     # Verify that we can open a file in the FIG temporary directory.
1807 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1808 : parrello 1.111 my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1809 :     if (open TESTTRACE, "$traceFileSpec") {
1810 : parrello 1.93 # Here we can trace to a file.
1811 : parrello 1.111 $traceMode = ">>$traceFileName";
1812 : parrello 1.93 if ($textOKFlag) {
1813 :     # Echo to standard output if the text-OK flag is set.
1814 :     $traceMode = "+$traceMode";
1815 :     }
1816 :     # Close the test file.
1817 :     close TESTTRACE;
1818 :     } else {
1819 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1820 :     warn "Could not open trace file $traceFileName: $!\n";
1821 :     # We trace to the standard output if it's
1822 :     # okay, and the error log otherwise.
1823 : parrello 1.93 if ($textOKFlag) {
1824 :     $traceMode = "TEXT";
1825 : parrello 1.12 } else {
1826 : parrello 1.93 $traceMode = "WARN";
1827 : parrello 1.12 }
1828 :     }
1829 : parrello 1.93 # Now set up the tracing.
1830 :     TSetup("$traceLevel $cats", $traceMode);
1831 :     }
1832 : parrello 1.113 # Check for background mode.
1833 :     if ($retOptions->{background}) {
1834 :     my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1835 :     my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1836 :     # Spool the output.
1837 :     open STDOUT, ">$outFileName";
1838 :     # If we have a trace file, trace the errors to the log. Otherwise,
1839 :     # spool the errors.
1840 :     if (defined $traceFileName) {
1841 :     open STDERR, "| Tracer $traceFileName";
1842 :     } else {
1843 :     open STDERR, ">$errFileName";
1844 :     }
1845 :     # Check for phone support. If we have phone support and a phone number,
1846 :     # we want to turn it on.
1847 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1848 :     $retOptions->{phone} = $ENV{PHONE};
1849 :     }
1850 :     }
1851 : parrello 1.93 # Check for the "help" option. If it is specified, dump the command-line
1852 :     # options and exit the program.
1853 :     if ($retOptions->{help}) {
1854 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1855 :     print "$1 [options] $parmHelp\n";
1856 :     for my $key (sort keys %{$options}) {
1857 :     my $name = Pad($key, $longestName, 0, ' ');
1858 :     my $desc = $options->{$key}->[1];
1859 :     if ($options->{$key}->[0]) {
1860 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1861 :     }
1862 :     print " $name $desc\n";
1863 : parrello 1.36 }
1864 : parrello 1.93 exit(0);
1865 :     }
1866 :     # Trace the options, if applicable.
1867 :     if (T(3)) {
1868 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1869 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1870 : parrello 1.3 }
1871 : parrello 1.93 # Return the parsed parameters.
1872 :     return ($retOptions, @retParameters);
1873 : olson 1.1 }
1874 :    
1875 : parrello 1.93 =head3 ReadOptions
1876 : olson 1.1
1877 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1878 : olson 1.1
1879 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1880 :     format
1881 : olson 1.1
1882 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1883 : olson 1.1
1884 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1885 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1886 :     character is a semi-colon will be ignored. The return hash will map each option name to
1887 :     the corresponding option value.
1888 : olson 1.1
1889 :     =over 4
1890 :    
1891 : parrello 1.93 =item fileName
1892 : olson 1.1
1893 : parrello 1.93 Name of the file containing the option data.
1894 : olson 1.1
1895 :     =item RETURN
1896 :    
1897 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1898 :     value.
1899 : olson 1.1
1900 :     =back
1901 :    
1902 :     =cut
1903 :    
1904 : parrello 1.93 sub ReadOptions {
1905 : parrello 1.12 # Get the parameters.
1906 : parrello 1.93 my ($fileName) = @_;
1907 :     # Open the file.
1908 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1909 :     # Count the number of records read.
1910 :     my ($records, $comments) = 0;
1911 :     # Create the return hash.
1912 :     my %retVal = ();
1913 :     # Loop through the file, accumulating key-value pairs.
1914 :     while (my $line = <CONFIGFILE>) {
1915 :     # Denote we've read a line.
1916 :     $records++;
1917 :     # Determine the line type.
1918 :     if ($line =~ /^\s*[\n\r]/) {
1919 :     # A blank line is a comment.
1920 :     $comments++;
1921 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1922 :     # Here we have an option assignment.
1923 :     retVal{$1} = $2;
1924 :     } elsif ($line =~ /^\s*;/) {
1925 :     # Here we have a text comment.
1926 :     $comments++;
1927 : parrello 1.12 } else {
1928 : parrello 1.93 # Here we have an invalid line.
1929 :     Trace("Invalid option statement in record $records.") if T(0);
1930 : parrello 1.12 }
1931 :     }
1932 : parrello 1.93 # Return the hash created.
1933 :     return %retVal;
1934 : olson 1.1 }
1935 :    
1936 : parrello 1.93 =head3 GetOptions
1937 : parrello 1.9
1938 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1939 : parrello 1.9
1940 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1941 :     as input and uses the data from the second to update the first. If the second does not exist,
1942 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1943 :     exist in the first.
1944 : parrello 1.9
1945 : parrello 1.93 Consider the following example.
1946 : parrello 1.9
1947 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1948 : parrello 1.9
1949 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1950 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1951 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1952 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1953 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1954 : parrello 1.9
1955 : parrello 1.93 {databaseType => 'Oracle'}
1956 : parrello 1.9
1957 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1958 : parrello 1.9
1959 : parrello 1.93 =over 4
1960 : parrello 1.9
1961 : parrello 1.93 =item defaults
1962 : parrello 1.9
1963 : parrello 1.93 Table of default option values.
1964 : parrello 1.9
1965 : parrello 1.93 =item options
1966 : olson 1.1
1967 : parrello 1.93 Table of overrides, if any.
1968 : olson 1.1
1969 :     =item RETURN
1970 :    
1971 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1972 : olson 1.1
1973 :     =back
1974 :    
1975 :     =cut
1976 :    
1977 : parrello 1.93 sub GetOptions {
1978 :     # Get the parameters.
1979 :     my ($defaults, $options) = @_;
1980 :     # Check for overrides.
1981 :     if ($options) {
1982 :     # Loop through the overrides.
1983 :     while (my ($option, $setting) = each %{$options}) {
1984 :     # Insure this override exists.
1985 :     if (!exists $defaults->{$option}) {
1986 :     croak "Unrecognized option $option encountered.";
1987 : parrello 1.12 } else {
1988 : parrello 1.93 # Apply the override.
1989 :     $defaults->{$option} = $setting;
1990 : parrello 1.12 }
1991 :     }
1992 :     }
1993 : parrello 1.93 # Return the merged table.
1994 :     return $defaults;
1995 : olson 1.1 }
1996 :    
1997 : parrello 1.93 =head3 MergeOptions
1998 : olson 1.1
1999 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
2000 : olson 1.1
2001 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
2002 :     second (default) hash, and if a matching key is not found in the first hash, the default
2003 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2004 :     checking and no return value.
2005 : olson 1.1
2006 :     =over 4
2007 :    
2008 : parrello 1.93 =item table
2009 : olson 1.1
2010 : parrello 1.93 Hash table to be updated with the default values.
2011 : olson 1.1
2012 : parrello 1.93 =item defaults
2013 : olson 1.1
2014 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
2015 : olson 1.1
2016 :     =back
2017 :    
2018 :     =cut
2019 :    
2020 : parrello 1.93 sub MergeOptions {
2021 :     # Get the parameters.
2022 :     my ($table, $defaults) = @_;
2023 :     # Loop through the defaults.
2024 :     while (my ($key, $value) = each %{$defaults}) {
2025 :     if (!exists $table->{$key}) {
2026 :     $table->{$key} = $value;
2027 :     }
2028 : parrello 1.12 }
2029 : olson 1.1 }
2030 :    
2031 : parrello 1.111 =head3 UnparseOptions
2032 :    
2033 :     my $optionString = Tracer::UnparseOptions(\%options);
2034 :    
2035 :     Convert an option hash into a command-line string. This will not
2036 :     necessarily be the same text that came in, but it will nonetheless
2037 :     produce the same ultimate result when parsed by L</StandardSetup>.
2038 :    
2039 :     =over 4
2040 :    
2041 :     =item options
2042 :    
2043 :     Reference to a hash of options to convert into an option string.
2044 :    
2045 :     =item RETURN
2046 :    
2047 :     Returns a string that will parse to the same set of options when
2048 :     parsed by L</StandardSetup>.
2049 :    
2050 :     =back
2051 :    
2052 :     =cut
2053 :    
2054 :     sub UnparseOptions {
2055 :     # Get the parameters.
2056 :     my ($options) = @_;
2057 :     # The option segments will be put in here.
2058 :     my @retVal = ();
2059 :     # Loop through the options.
2060 :     for my $key (keys %$options) {
2061 :     # Get the option value.
2062 :     my $value = $options->{$key};
2063 :     # Only use it if it's nonempty.
2064 :     if (defined $value && $value ne "") {
2065 :     my $segment = "--$key=$value";
2066 :     # Quote it if necessary.
2067 :     if ($segment =~ /[ |<>*]/) {
2068 :     $segment = '"' . $segment . '"';
2069 :     }
2070 :     # Add it to the return list.
2071 :     push @retVal, $segment;
2072 :     }
2073 :     }
2074 :     # Return the result.
2075 :     return join(" ", @retVal);
2076 :     }
2077 :    
2078 : parrello 1.93 =head3 ParseCommand
2079 : olson 1.1
2080 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2081 : olson 1.1
2082 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
2083 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2084 :     off and merged into a table of default options. The remainder of the command line is
2085 :     returned as a list of positional arguments. For example, consider the following invocation.
2086 : olson 1.1
2087 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2088 : olson 1.1
2089 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
2090 :     B<errors> and B<logFile>. If @words has the following format
2091 : olson 1.1
2092 : parrello 1.93 -logFile=error.log apple orange rutabaga
2093 : olson 1.1
2094 : parrello 1.93 then at the end of the invocation, C<$options> will be
2095 : olson 1.1
2096 : parrello 1.93 { errors => 0, logFile => 'error.log' }
2097 : olson 1.1
2098 : parrello 1.93 and C<@arguments> will contain
2099 : olson 1.1
2100 : parrello 1.93 apple orange rutabaga
2101 : olson 1.1
2102 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2103 :     support for quote characters. Options can be specified with single or double hyphens.
2104 : parrello 1.54
2105 :     =over 4
2106 :    
2107 : parrello 1.93 =item optionTable
2108 : parrello 1.54
2109 : parrello 1.93 Table of default options.
2110 : parrello 1.54
2111 : parrello 1.93 =item inputList
2112 : parrello 1.54
2113 : parrello 1.93 List of words on the command line.
2114 : parrello 1.54
2115 :     =item RETURN
2116 :    
2117 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2118 : parrello 1.54
2119 :     =back
2120 :    
2121 :     =cut
2122 :    
2123 : parrello 1.93 sub ParseCommand {
2124 : parrello 1.54 # Get the parameters.
2125 : parrello 1.93 my ($optionTable, @inputList) = @_;
2126 :     # Process any options in the input list.
2127 :     my %overrides = ();
2128 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2129 :     # Get the current option.
2130 :     my $arg = shift @inputList;
2131 :     # Pull out the option name.
2132 :     $arg =~ /^--?([^=]*)/g;
2133 :     my $name = $1;
2134 :     # Check for an option value.
2135 :     if ($arg =~ /\G=(.*)$/g) {
2136 :     # Here we have a value for the option.
2137 :     $overrides{$name} = UnEscape($1);
2138 :     } else {
2139 :     # Here there is no value, so we use 1.
2140 :     $overrides{$name} = 1;
2141 :     }
2142 :     }
2143 :     # Merge the options into the defaults.
2144 :     GetOptions($optionTable, \%overrides);
2145 :     # Translate the remaining parameters.
2146 :     my @retVal = ();
2147 :     for my $inputParm (@inputList) {
2148 :     push @retVal, UnEscape($inputParm);
2149 : parrello 1.54 }
2150 : parrello 1.93 # Return the results.
2151 :     return ($optionTable, @retVal);
2152 : parrello 1.54 }
2153 :    
2154 : parrello 1.93
2155 :     =head2 File Utility Methods
2156 :    
2157 : olson 1.1 =head3 GetFile
2158 :    
2159 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2160 : olson 1.1
2161 : parrello 1.35 or
2162 :    
2163 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2164 : parrello 1.35
2165 :     Return the entire contents of a file. In list context, line-ends are removed and
2166 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2167 : olson 1.1
2168 :     =over 4
2169 :    
2170 :     =item fileName
2171 :    
2172 :     Name of the file to read.
2173 :    
2174 :     =item RETURN
2175 :    
2176 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2177 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2178 :     the file, an empty list will be returned.
2179 : olson 1.1
2180 :     =back
2181 :    
2182 :     =cut
2183 :    
2184 :     sub GetFile {
2185 : parrello 1.12 # Get the parameters.
2186 :     my ($fileName) = @_;
2187 :     # Declare the return variable.
2188 :     my @retVal = ();
2189 :     # Open the file for input.
2190 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2191 :     # Read the whole file into the return variable, stripping off any terminator
2192 :     # characters.
2193 :     my $lineCount = 0;
2194 :     while (my $line = <$handle>) {
2195 :     $lineCount++;
2196 :     $line = Strip($line);
2197 :     push @retVal, $line;
2198 :     }
2199 :     # Close it.
2200 :     close $handle;
2201 :     my $actualLines = @retVal;
2202 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2203 : parrello 1.12 # Return the file's contents in the desired format.
2204 : parrello 1.9 if (wantarray) {
2205 : parrello 1.12 return @retVal;
2206 : parrello 1.6 } else {
2207 :     return join "\n", @retVal;
2208 :     }
2209 : olson 1.1 }
2210 :    
2211 : parrello 1.60 =head3 PutFile
2212 :    
2213 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2214 : parrello 1.60
2215 :     Write out a file from a list of lines of text.
2216 :    
2217 :     =over 4
2218 :    
2219 :     =item fileName
2220 :    
2221 :     Name of the output file.
2222 :    
2223 :     =item lines
2224 :    
2225 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2226 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2227 :     modification.
2228 : parrello 1.60
2229 :     =back
2230 :    
2231 :     =cut
2232 :    
2233 :     sub PutFile {
2234 :     # Get the parameters.
2235 :     my ($fileName, $lines) = @_;
2236 :     # Open the output file.
2237 :     my $handle = Open(undef, ">$fileName");
2238 : parrello 1.77 # Count the lines written.
2239 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2240 :     # Here we have a scalar, so we write it raw.
2241 :     print $handle $lines;
2242 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2243 : parrello 1.66 } else {
2244 :     # Write the lines one at a time.
2245 : parrello 1.77 my $count = 0;
2246 : parrello 1.66 for my $line (@{$lines}) {
2247 :     print $handle "$line\n";
2248 : parrello 1.77 $count++;
2249 : parrello 1.66 }
2250 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2251 : parrello 1.60 }
2252 :     # Close the output file.
2253 :     close $handle;
2254 :     }
2255 :    
2256 : parrello 1.93 =head3 ParseRecord
2257 : olson 1.1
2258 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2259 : olson 1.1
2260 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2261 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2262 :     These will automatically be converted.
2263 : olson 1.1
2264 :     =over 4
2265 :    
2266 : parrello 1.93 =item line
2267 :    
2268 :     Line of data containing the tab-delimited fields.
2269 :    
2270 :     =item RETURN
2271 : olson 1.1
2272 : parrello 1.93 Returns a list of the fields found in the data line.
2273 : olson 1.1
2274 :     =back
2275 :    
2276 :     =cut
2277 :    
2278 : parrello 1.93 sub ParseRecord {
2279 : parrello 1.12 # Get the parameter.
2280 : parrello 1.93 my ($line) = @_;
2281 :     # Remove the trailing new-line, if any.
2282 :     chomp $line;
2283 :     # Split the line read into pieces using the tab character.
2284 :     my @retVal = split /\t/, $line;
2285 :     # Trim and fix the escapes in each piece.
2286 :     for my $value (@retVal) {
2287 :     # Trim leading whitespace.
2288 :     $value =~ s/^\s+//;
2289 :     # Trim trailing whitespace.
2290 :     $value =~ s/\s+$//;
2291 :     # Delete the carriage returns.
2292 :     $value =~ s/\r//g;
2293 :     # Convert the escapes into their real values.
2294 :     $value =~ s/\\t/"\t"/ge;
2295 :     $value =~ s/\\n/"\n"/ge;
2296 :     }
2297 :     # Return the result.
2298 :     return @retVal;
2299 :     }
2300 :    
2301 :     =head3 Merge
2302 :    
2303 :     my @mergedList = Tracer::Merge(@inputList);
2304 :    
2305 :     Sort a list of strings and remove duplicates.
2306 :    
2307 :     =over 4
2308 :    
2309 :     =item inputList
2310 :    
2311 :     List of scalars to sort and merge.
2312 :    
2313 :     =item RETURN
2314 :    
2315 :     Returns a list containing the same elements sorted in ascending order with duplicates
2316 :     removed.
2317 :    
2318 :     =back
2319 :    
2320 :     =cut
2321 :    
2322 :     sub Merge {
2323 :     # Get the input list in sort order.
2324 :     my @inputList = sort @_;
2325 :     # Only proceed if the list has at least two elements.
2326 :     if (@inputList > 1) {
2327 :     # Now we want to move through the list splicing out duplicates.
2328 :     my $i = 0;
2329 :     while ($i < @inputList) {
2330 :     # Get the current entry.
2331 :     my $thisEntry = $inputList[$i];
2332 :     # Find out how many elements duplicate the current entry.
2333 :     my $j = $i + 1;
2334 :     my $dup1 = $i + 1;
2335 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2336 :     # If the number is nonzero, splice out the duplicates found.
2337 :     if ($j > $dup1) {
2338 :     splice @inputList, $dup1, $j - $dup1;
2339 : parrello 1.14 }
2340 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2341 :     # at position $i. We push $i forward one position and start again.
2342 :     $i++;
2343 : parrello 1.14 }
2344 : parrello 1.12 }
2345 : parrello 1.93 # Return the merged list.
2346 :     return @inputList;
2347 : olson 1.1 }
2348 :    
2349 : parrello 1.93 =head3 Open
2350 : olson 1.1
2351 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2352 : olson 1.1
2353 : parrello 1.93 Open a file.
2354 : olson 1.1
2355 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2356 :     function. The mode is specified using Unix-like shell information. So, for
2357 :     example,
2358 : olson 1.1
2359 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2360 : olson 1.1
2361 : parrello 1.93 would open for output appended to the specified file, and
2362 : olson 1.1
2363 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2364 : olson 1.1
2365 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2366 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2367 :     code as follows.
2368 : olson 1.1
2369 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2370 : olson 1.1
2371 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2372 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2373 :     failed open will throw an exception and the third parameter will be used to construct
2374 :     an error message. If the parameter is omitted, a standard message is constructed
2375 :     using the file spec.
2376 : olson 1.1
2377 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2378 : olson 1.1
2379 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2380 :     The actual error message from the file system will be captured and appended to the
2381 :     message in any case.
2382 : parrello 1.6
2383 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2384 : parrello 1.6
2385 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2386 :     corresponds to the C++ C<errno> value.
2387 : parrello 1.6
2388 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2389 : parrello 1.6
2390 : parrello 1.93 =over 4
2391 : parrello 1.6
2392 : parrello 1.93 =item fileHandle
2393 : parrello 1.6
2394 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2395 :     and returned as the value of this method.
2396 : olson 1.1
2397 : parrello 1.93 =item fileSpec
2398 : olson 1.1
2399 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2400 : olson 1.1
2401 : parrello 1.93 =item message (optional)
2402 : olson 1.1
2403 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2404 :     will be generated. In either case, the error information from the file system
2405 :     is appended to the message. To specify a conditional open that does not throw
2406 :     an error if it fails, use C<0>.
2407 : olson 1.1
2408 : parrello 1.93 =item RETURN
2409 : olson 1.1
2410 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2411 :     open failed.
2412 : olson 1.1
2413 :     =back
2414 :    
2415 :     =cut
2416 :    
2417 : parrello 1.93 sub Open {
2418 : parrello 1.12 # Get the parameters.
2419 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2420 :     # Attempt to open the file.
2421 :     my $rv = open $fileHandle, $fileSpec;
2422 :     # If the open failed, generate an error message.
2423 :     if (! $rv) {
2424 :     # Save the system error message.
2425 :     my $sysMessage = $!;
2426 :     # See if we need a default message.
2427 :     if (!$message) {
2428 :     # Clean any obvious mode characters and leading spaces from the
2429 :     # filename.
2430 :     my ($fileName) = FindNamePart($fileSpec);
2431 :     $message = "Could not open \"$fileName\"";
2432 :     }
2433 :     # Terminate with an error using the supplied message and the
2434 :     # error message from the file system.
2435 :     Confess("$message: $!");
2436 : parrello 1.12 }
2437 : parrello 1.93 # Return the file handle.
2438 :     return $fileHandle;
2439 : olson 1.1 }
2440 :    
2441 : parrello 1.93 =head3 FindNamePart
2442 :    
2443 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2444 :    
2445 :     Extract the portion of a file specification that contains the file name.
2446 :    
2447 :     A file specification is the string passed to an C<open> call. It specifies the file
2448 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2449 :     method assumes that the file name is whatever follows the first angle bracket
2450 :     sequence. So, for example, in the following strings the file name is
2451 :     C</usr/fig/myfile.txt>.
2452 : parrello 1.5
2453 : parrello 1.93 >>/usr/fig/myfile.txt
2454 :     </usr/fig/myfile.txt
2455 :     | sort -u > /usr/fig/myfile.txt
2456 : parrello 1.5
2457 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2458 :     whole incoming string.
2459 : parrello 1.5
2460 :     =over 4
2461 :    
2462 : parrello 1.93 =item fileSpec
2463 : parrello 1.5
2464 : parrello 1.93 File specification string from which the file name is to be extracted.
2465 : parrello 1.5
2466 :     =item RETURN
2467 :    
2468 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2469 :     the specified string, or the whole string if a file name cannot be found via normal
2470 :     methods. The second element contains the start position of the file name portion and
2471 :     the third element contains the length.
2472 : parrello 1.5
2473 :     =back
2474 :    
2475 :     =cut
2476 : parrello 1.93 #: Return Type $;
2477 :     sub FindNamePart {
2478 :     # Get the parameters.
2479 :     my ($fileSpec) = @_;
2480 :     # Default to the whole input string.
2481 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2482 :     # Parse out the file name if we can.
2483 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2484 :     $retVal = $2;
2485 :     $len = length $retVal;
2486 :     $pos = (length $fileSpec) - (length $3) - $len;
2487 : parrello 1.12 }
2488 : parrello 1.93 # Return the result.
2489 :     return ($retVal, $pos, $len);
2490 : parrello 1.5 }
2491 :    
2492 : parrello 1.93 =head3 OpenDir
2493 : parrello 1.5
2494 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2495 : parrello 1.5
2496 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2497 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2498 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2499 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2500 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2501 :     set, an exception is thrown. So, for example,
2502 : parrello 1.5
2503 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2504 : parrello 1.5
2505 : parrello 1.93 is effectively the same as
2506 : parrello 1.5
2507 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2508 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2509 : parrello 1.5
2510 : parrello 1.93 Similarly, the following code
2511 : parrello 1.5
2512 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2513 : parrello 1.5
2514 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2515 :     automatically returns an empty list if the directory fails to open.
2516 : parrello 1.5
2517 : parrello 1.93 =over 4
2518 : parrello 1.5
2519 : parrello 1.93 =item dirName
2520 : parrello 1.5
2521 : parrello 1.93 Name of the directory to open.
2522 : parrello 1.5
2523 : parrello 1.93 =item filtered
2524 : parrello 1.5
2525 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2526 :     from the list, else FALSE.
2527 : parrello 1.5
2528 : parrello 1.93 =item flag
2529 : parrello 1.5
2530 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2531 : parrello 1.5
2532 : parrello 1.93 =back
2533 : parrello 1.5
2534 : parrello 1.93 =cut
2535 :     #: Return Type @;
2536 :     sub OpenDir {
2537 :     # Get the parameters.
2538 :     my ($dirName, $filtered, $flag) = @_;
2539 :     # Declare the return variable.
2540 :     my @retVal = ();
2541 :     # Open the directory.
2542 :     if (opendir(my $dirHandle, $dirName)) {
2543 :     # The directory opened successfully. Get the appropriate list according to the
2544 :     # strictures of the filter parameter.
2545 :     if ($filtered) {
2546 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2547 :     } else {
2548 :     @retVal = readdir $dirHandle;
2549 :     }
2550 : parrello 1.117 closedir $dirHandle;
2551 : parrello 1.93 } elsif (! $flag) {
2552 :     # Here the directory would not open and it's considered an error.
2553 :     Confess("Could not open directory $dirName.");
2554 :     }
2555 :     # Return the result.
2556 :     return @retVal;
2557 :     }
2558 : parrello 1.5
2559 :    
2560 : parrello 1.93 =head3 Insure
2561 : parrello 1.5
2562 : parrello 1.93 Insure($dirName, $chmod);
2563 : parrello 1.5
2564 : parrello 1.93 Insure a directory is present.
2565 : parrello 1.5
2566 : parrello 1.93 =over 4
2567 : parrello 1.5
2568 : parrello 1.93 =item dirName
2569 : olson 1.1
2570 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2571 : parrello 1.7
2572 : parrello 1.93 =item chmod (optional)
2573 : parrello 1.7
2574 : parrello 1.93 Security privileges to be given to the directory if it is created.
2575 : parrello 1.7
2576 : parrello 1.93 =back
2577 : parrello 1.7
2578 :     =cut
2579 :    
2580 : parrello 1.93 sub Insure {
2581 :     my ($dirName, $chmod) = @_;
2582 :     if (! -d $dirName) {
2583 :     Trace("Creating $dirName directory.") if T(2);
2584 :     eval {
2585 :     mkpath $dirName;
2586 :     # If we have permissions specified, set them here.
2587 :     if (defined($chmod)) {
2588 :     chmod $chmod, $dirName;
2589 :     }
2590 :     };
2591 :     if ($@) {
2592 :     Confess("Error creating $dirName: $@");
2593 :     }
2594 : parrello 1.12 }
2595 : parrello 1.9 }
2596 :    
2597 : parrello 1.93 =head3 ChDir
2598 : parrello 1.9
2599 : parrello 1.93 ChDir($dirName);
2600 : parrello 1.9
2601 : parrello 1.93 Change to the specified directory.
2602 : parrello 1.9
2603 :     =over 4
2604 :    
2605 : parrello 1.93 =item dirName
2606 : parrello 1.9
2607 : parrello 1.93 Name of the directory to which we want to change.
2608 : parrello 1.9
2609 :     =back
2610 :    
2611 :     =cut
2612 :    
2613 : parrello 1.93 sub ChDir {
2614 :     my ($dirName) = @_;
2615 :     if (! -d $dirName) {
2616 :     Confess("Cannot change to directory $dirName: no such directory.");
2617 :     } else {
2618 :     Trace("Changing to directory $dirName.") if T(File => 4);
2619 :     my $okFlag = chdir $dirName;
2620 :     if (! $okFlag) {
2621 :     Confess("Error switching to directory $dirName.");
2622 :     }
2623 :     }
2624 : parrello 1.9 }
2625 :    
2626 : parrello 1.93 =head3 SetPermissions
2627 :    
2628 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2629 : parrello 1.9
2630 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2631 :     In addition, the group ownership will be changed to the specified value.
2632 : parrello 1.9
2633 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2634 :     problems, so it does internal error recovery.
2635 : parrello 1.9
2636 :     =over 4
2637 :    
2638 : parrello 1.93 =item dirName
2639 :    
2640 :     Name of the directory to process.
2641 :    
2642 :     =item group
2643 : parrello 1.9
2644 : parrello 1.93 Name of the group to be assigned.
2645 : parrello 1.9
2646 : parrello 1.93 =item mask
2647 : parrello 1.9
2648 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2649 :     permission bits of any file or directory that does not already have them
2650 :     set to 1.
2651 : parrello 1.9
2652 : parrello 1.93 =item otherMasks
2653 : parrello 1.9
2654 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2655 :     one of the patterns, that directory and all its members and subdirectories
2656 :     will be assigned the new pattern. For example, the following would
2657 : parrello 1.110 assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2658 : parrello 1.9
2659 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2660 : parrello 1.9
2661 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2662 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2663 : parrello 1.22
2664 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2665 :     '^tmp' => 0666);
2666 : parrello 1.9
2667 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2668 :     names are matched, not file names.
2669 : parrello 1.9
2670 :     =back
2671 :    
2672 :     =cut
2673 :    
2674 : parrello 1.93 sub SetPermissions {
2675 : parrello 1.12 # Get the parameters.
2676 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2677 :     # Set up for error recovery.
2678 :     eval {
2679 :     # Switch to the specified directory.
2680 :     ChDir($dirName);
2681 :     # Get the group ID.
2682 :     my $gid = getgrnam($group);
2683 :     # Get the mask for tracing.
2684 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2685 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2686 :     my $fixCount = 0;
2687 :     my $lookCount = 0;
2688 :     # @dirs will be a stack of directories to be processed.
2689 :     my @dirs = (getcwd());
2690 :     while (scalar(@dirs) > 0) {
2691 :     # Get the current directory.
2692 :     my $dir = pop @dirs;
2693 :     # Check for a match to one of the specified directory names. To do
2694 :     # that, we need to pull the individual part of the name off of the
2695 :     # whole path.
2696 :     my $simpleName = $dir;
2697 :     if ($dir =~ m!/([^/]+)$!) {
2698 :     $simpleName = $1;
2699 :     }
2700 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2701 :     # Search for a match.
2702 :     my $match = 0;
2703 :     my $i;
2704 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2705 :     my $pattern = $otherMasks[$i];
2706 :     if ($simpleName =~ /$pattern/i) {
2707 :     $match = 1;
2708 :     }
2709 :     }
2710 : parrello 1.110 # Find out if we have a match. Note we use $i-1 because the loop added 2
2711 : parrello 1.93 # before terminating due to the match.
2712 :     if ($match && $otherMasks[$i-1] != $mask) {
2713 :     # This directory matches one of the incoming patterns, and it's
2714 :     # a different mask, so we process it recursively with that mask.
2715 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2716 :     } else {
2717 :     # Here we can process normally. Get all of the non-hidden members.
2718 :     my @submems = OpenDir($dir, 1);
2719 :     for my $submem (@submems) {
2720 :     # Get the full name.
2721 :     my $thisMem = "$dir/$submem";
2722 :     Trace("Checking member $thisMem.") if T(4);
2723 :     $lookCount++;
2724 :     if ($lookCount % 1000 == 0) {
2725 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2726 :     }
2727 :     # Fix the group.
2728 :     chown -1, $gid, $thisMem;
2729 :     # Insure this member is not a symlink.
2730 :     if (! -l $thisMem) {
2731 :     # Get its info.
2732 :     my $fileInfo = stat $thisMem;
2733 :     # Only proceed if we got the info. Otherwise, it's a hard link
2734 :     # and we want to skip it anyway.
2735 :     if ($fileInfo) {
2736 :     my $fileMode = $fileInfo->mode;
2737 :     if (($fileMode & $mask) != $mask) {
2738 :     # Fix this member.
2739 :     $fileMode |= $mask;
2740 :     chmod $fileMode, $thisMem;
2741 :     $fixCount++;
2742 :     }
2743 :     # If it's a subdirectory, stack it.
2744 :     if (-d $thisMem) {
2745 :     push @dirs, $thisMem;
2746 :     }
2747 :     }
2748 :     }
2749 :     }
2750 :     }
2751 : parrello 1.12 }
2752 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2753 :     };
2754 :     # Check for an error.
2755 :     if ($@) {
2756 :     Confess("SetPermissions error: $@");
2757 : parrello 1.12 }
2758 : parrello 1.7 }
2759 :    
2760 : parrello 1.93 =head3 GetLine
2761 : parrello 1.29
2762 : parrello 1.93 my @data = Tracer::GetLine($handle);
2763 : parrello 1.15
2764 : parrello 1.93 Read a line of data from a tab-delimited file.
2765 : parrello 1.15
2766 :     =over 4
2767 :    
2768 : parrello 1.93 =item handle
2769 : parrello 1.15
2770 : parrello 1.93 Open file handle from which to read.
2771 : parrello 1.15
2772 :     =item RETURN
2773 :    
2774 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2775 :     tab-delimited. If we are at the end of the file, then an empty list will be
2776 :     returned. If an empty line is read, a single list item consisting of a null
2777 :     string will be returned.
2778 : parrello 1.15
2779 :     =back
2780 :    
2781 :     =cut
2782 : parrello 1.93
2783 :     sub GetLine {
2784 : parrello 1.15 # Get the parameters.
2785 : parrello 1.93 my ($handle) = @_;
2786 :     # Declare the return variable.
2787 :     my @retVal = ();
2788 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2789 :     # Read from the file.
2790 :     my $line = <$handle>;
2791 :     # Only proceed if we found something.
2792 :     if (defined $line) {
2793 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2794 :     # upload control and have a nonstandard EOL combination.
2795 :     $line =~ s/(\r|\n)+$//;
2796 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2797 :     if (T(File => 4)) {
2798 :     my $escapedLine = $line;
2799 :     $escapedLine =~ s/\n/\\n/g;
2800 :     $escapedLine =~ s/\r/\\r/g;
2801 :     $escapedLine =~ s/\t/\\t/g;
2802 :     Trace("Line read: -->$escapedLine<--");
2803 :     }
2804 :     # If the line is empty, return a single empty string; otherwise, parse
2805 :     # it into fields.
2806 :     if ($line eq "") {
2807 :     push @retVal, "";
2808 :     } else {
2809 :     push @retVal, split /\t/,$line;
2810 :     }
2811 :     } else {
2812 :     # Trace the reason the read failed.
2813 :     Trace("End of file: $!") if T(File => 3);
2814 : parrello 1.15 }
2815 : parrello 1.93 # Return the result.
2816 :     return @retVal;
2817 : parrello 1.15 }
2818 :    
2819 : parrello 1.93 =head3 PutLine
2820 :    
2821 :     Tracer::PutLine($handle, \@fields, $eol);
2822 : parrello 1.35
2823 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2824 :     output in tab-separated form, with a trailing new-line.
2825 : parrello 1.35
2826 : parrello 1.93 =over 4
2827 : parrello 1.35
2828 : parrello 1.93 =item handle
2829 : parrello 1.69
2830 : parrello 1.93 Output file handle.
2831 : parrello 1.69
2832 : parrello 1.93 =item fields
2833 : parrello 1.69
2834 : parrello 1.93 List of field values.
2835 : parrello 1.69
2836 : parrello 1.93 =item eol (optional)
2837 : parrello 1.69
2838 : parrello 1.93 End-of-line character (default is "\n").
2839 : parrello 1.69
2840 :     =back
2841 : parrello 1.35
2842 :     =cut
2843 :    
2844 : parrello 1.93 sub PutLine {
2845 : parrello 1.69 # Get the parameters.
2846 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2847 :     # Write the data.
2848 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2849 : parrello 1.69 }
2850 :    
2851 :    
2852 : parrello 1.97 =head3 PrintLine
2853 :    
2854 :     Tracer::PrintLine($line);
2855 :    
2856 :     Print a line of text with a trailing new-line.
2857 :    
2858 :     =over 4
2859 :    
2860 :     =item line
2861 :    
2862 :     Line of text to print.
2863 :    
2864 :     =back
2865 :    
2866 :     =cut
2867 :    
2868 :     sub PrintLine {
2869 :     # Get the parameters.
2870 :     my ($line) = @_;
2871 :     # Print the line.
2872 :     print "$line\n";
2873 :     }
2874 :    
2875 : parrello 1.69
2876 : parrello 1.93 =head2 Other Useful Methods
2877 :    
2878 : parrello 1.115 =head3 IDHASH
2879 :    
2880 :     my $hash = SHTargetSearch::IDHASH(@keys);
2881 :    
2882 :     This is a dinky little method that converts a list of values to a reference
2883 :     to hash of values to labels. The values and labels are the same.
2884 :    
2885 :     =cut
2886 :    
2887 :     sub IDHASH {
2888 :     my %retVal = map { $_ => $_ } @_;
2889 :     return \%retVal;
2890 :     }
2891 :    
2892 :     =head3 Pluralize
2893 :    
2894 :     my $plural = Tracer::Pluralize($word);
2895 :    
2896 :     This is a very simple pluralization utility. It adds an C<s> at the end
2897 :     of the input word unless it already ends in an C<s>, in which case it
2898 :     adds C<es>.
2899 :    
2900 :     =over 4
2901 :    
2902 :     =item word
2903 :    
2904 :     Singular word to pluralize.
2905 :    
2906 :     =item RETURN
2907 :    
2908 :     Returns the probable plural form of the word.
2909 :    
2910 :     =back
2911 :    
2912 :     =cut
2913 :    
2914 :     sub Pluralize {
2915 :     # Get the parameters.
2916 :     my ($word) = @_;
2917 :     # Declare the return variable.
2918 :     my $retVal;
2919 :     if ($word =~ /s$/) {
2920 :     $retVal = $word . 'es';
2921 :     } else {
2922 :     $retVal = $word . 's';
2923 :     }
2924 :     # Return the result.
2925 :     return $retVal;
2926 :     }
2927 :    
2928 :     =head3 Numeric
2929 :    
2930 :     my $okFlag = Tracer::Numeric($string);
2931 :    
2932 :     Return the value of the specified string if it is numeric, or an undefined value
2933 :     if it is not numeric.
2934 :    
2935 :     =over 4
2936 :    
2937 :     =item string
2938 :    
2939 :     String to check.
2940 :    
2941 :     =item RETURN
2942 :    
2943 :     Returns the numeric value of the string if successful, or C<undef> if the string
2944 :     is not numeric.
2945 :    
2946 :     =back
2947 :    
2948 :     =cut
2949 :    
2950 :     sub Numeric {
2951 :     # Get the parameters.
2952 :     my ($string) = @_;
2953 :     # We'll put the value in here if we succeed.
2954 :     my $retVal;
2955 :     # Get a working copy of the string.
2956 :     my $copy = $string;
2957 :     # Trim leading and trailing spaces.
2958 :     $copy =~ s/^\s+//;
2959 :     $copy =~ s/\s+$//;
2960 :     # Check the result.
2961 :     if ($copy =~ /^[+-]?\d+$/) {
2962 :     $retVal = $copy;
2963 :     } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2964 :     $retVal = $copy;
2965 :     } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2966 :     $retVal = $copy;
2967 :     }
2968 :     # Return the result.
2969 :     return $retVal;
2970 :     }
2971 :    
2972 :    
2973 : parrello 1.93 =head3 ParseParm
2974 :    
2975 :     my $listValue = Tracer::ParseParm($string);
2976 :    
2977 :     Convert a parameter into a list reference. If the parameter is undefined,
2978 :     an undefined value will be returned. Otherwise, it will be parsed as a
2979 :     comma-separated list of values.
2980 : parrello 1.69
2981 :     =over 4
2982 :    
2983 : parrello 1.93 =item string
2984 :    
2985 :     Incoming string.
2986 :    
2987 :     =item RETURN
2988 : parrello 1.69
2989 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2990 :     was undefined.
2991 : parrello 1.69
2992 :     =back
2993 :    
2994 :     =cut
2995 :    
2996 : parrello 1.93 sub ParseParm {
2997 :     # Get the parameters.
2998 :     my ($string) = @_;
2999 :     # Declare the return variable.
3000 :     my $retVal;
3001 :     # Check for data.
3002 :     if (defined $string) {
3003 :     # We have some, so split it into a list.
3004 :     $retVal = [ split /\s*,\s*/, $string];
3005 : parrello 1.72 }
3006 : parrello 1.93 # Return the result.
3007 :     return $retVal;
3008 : parrello 1.69 }
3009 :    
3010 : parrello 1.97 =head3 Now
3011 :    
3012 :     my $string = Tracer::Now();
3013 :    
3014 :     Return a displayable time stamp containing the local time. Whatever format this
3015 :     method produces must be parseable by L</ParseDate>.
3016 :    
3017 :     =cut
3018 :    
3019 :     sub Now {
3020 :     return DisplayTime(time);
3021 :     }
3022 :    
3023 :     =head3 DisplayTime
3024 :    
3025 :     my $string = Tracer::DisplayTime($time);
3026 : parrello 1.69
3027 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
3028 :     method produces must be parseable by L</ParseDate>.
3029 :    
3030 :     =over 4
3031 : parrello 1.69
3032 : parrello 1.97 =item time
3033 : parrello 1.69
3034 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3035 :    
3036 :     =item RETURN
3037 : parrello 1.69
3038 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3039 : parrello 1.69
3040 : parrello 1.97 =back
3041 : parrello 1.69
3042 : parrello 1.93 =cut
3043 : parrello 1.69
3044 : parrello 1.97 sub DisplayTime {
3045 :     my ($time) = @_;
3046 :     my $retVal = "(n/a)";
3047 :     if (defined $time) {
3048 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3049 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3050 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3051 :     }
3052 : parrello 1.93 return $retVal;
3053 :     }
3054 : parrello 1.69
3055 : parrello 1.93 # Pad a number to 2 digits.
3056 :     sub _p2 {
3057 :     my ($value) = @_;
3058 :     $value = "0$value" if ($value < 10);
3059 :     return $value;
3060 : parrello 1.69 }
3061 :    
3062 : parrello 1.93 =head3 Escape
3063 : parrello 1.69
3064 : parrello 1.93 my $codedString = Tracer::Escape($realString);
3065 : parrello 1.69
3066 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3067 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3068 :     result is to reverse the effect of L</UnEscape>.
3069 : parrello 1.69
3070 :     =over 4
3071 :    
3072 : parrello 1.93 =item realString
3073 : parrello 1.69
3074 : parrello 1.93 String to escape.
3075 : parrello 1.69
3076 :     =item RETURN
3077 :    
3078 : parrello 1.93 Escaped equivalent of the real string.
3079 :    
3080 :     =back
3081 :    
3082 :     =cut
3083 :    
3084 :     sub Escape {
3085 :     # Get the parameter.
3086 :     my ($realString) = @_;
3087 :     # Initialize the return variable.
3088 :     my $retVal = "";
3089 :     # Loop through the parameter string, looking for sequences to escape.
3090 :     while (length $realString > 0) {
3091 :     # Look for the first sequence to escape.
3092 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3093 :     # Here we found it. The text preceding the sequence is in $1. The sequence
3094 :     # itself is in $2. First, move the clear text to the return variable.
3095 :     $retVal .= $1;
3096 :     # Strip the processed section off the real string.
3097 :     $realString = substr $realString, (length $2) + (length $1);
3098 :     # Get the matched character.
3099 :     my $char = $2;
3100 :     # If we have a CR, we are done.
3101 :     if ($char ne "\r") {
3102 :     # It's not a CR, so encode the escape sequence.
3103 :     $char =~ tr/\t\n/tn/;
3104 :     $retVal .= "\\" . $char;
3105 :     }
3106 :     } else {
3107 :     # Here there are no more escape sequences. The rest of the string is
3108 :     # transferred unmodified.
3109 :     $retVal .= $realString;
3110 :     $realString = "";
3111 :     }
3112 :     }
3113 :     # Return the result.
3114 :     return $retVal;
3115 : parrello 1.69 }
3116 :    
3117 : parrello 1.93 =head3 UnEscape
3118 : parrello 1.69
3119 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
3120 : parrello 1.69
3121 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3122 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3123 :     be deleted.
3124 : parrello 1.69
3125 :     =over 4
3126 :    
3127 : parrello 1.93 =item codedString
3128 : parrello 1.69
3129 : parrello 1.93 String to un-escape.
3130 : parrello 1.69
3131 :     =item RETURN
3132 :    
3133 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
3134 :     values.
3135 : parrello 1.69
3136 :     =back
3137 :    
3138 :     =cut
3139 :    
3140 : parrello 1.93 sub UnEscape {
3141 :     # Get the parameter.
3142 :     my ($codedString) = @_;
3143 :     # Initialize the return variable.
3144 :     my $retVal = "";
3145 :     # Only proceed if the incoming string is nonempty.
3146 :     if (defined $codedString) {
3147 :     # Loop through the parameter string, looking for escape sequences. We can't do
3148 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
3149 :     # "\<tab>" no matter what we do.)
3150 :     while (length $codedString > 0) {
3151 :     # Look for the first escape sequence.
3152 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3153 :     # Here we found it. The text preceding the sequence is in $1. The sequence
3154 :     # itself is in $2. First, move the clear text to the return variable.
3155 :     $retVal .= $1;
3156 :     $codedString = substr $codedString, (2 + length $1);
3157 :     # Get the escape value.
3158 :     my $char = $2;
3159 :     # If we have a "\r", we are done.
3160 :     if ($char ne 'r') {
3161 :     # Here it's not an 'r', so we convert it.
3162 :     $char =~ tr/\\tn/\\\t\n/;
3163 :     $retVal .= $char;
3164 :     }
3165 :     } else {
3166 :     # Here there are no more escape sequences. The rest of the string is
3167 :     # transferred unmodified.
3168 :     $retVal .= $codedString;
3169 :     $codedString = "";
3170 :     }
3171 :     }
3172 : parrello 1.35 }
3173 : parrello 1.69 # Return the result.
3174 :     return $retVal;
3175 :     }
3176 :    
3177 : parrello 1.93 =head3 Percent
3178 : parrello 1.69
3179 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
3180 : parrello 1.69
3181 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
3182 :     is zero, returns zero.
3183 : parrello 1.69
3184 :     =over 4
3185 :    
3186 : parrello 1.93 =item number
3187 : parrello 1.69
3188 : parrello 1.93 Percent numerator.
3189 : parrello 1.69
3190 : parrello 1.93 =item base
3191 : parrello 1.69
3192 : parrello 1.93 Percent base.
3193 : parrello 1.69
3194 : parrello 1.93 =item RETURN
3195 : parrello 1.69
3196 : parrello 1.93 Returns the percentage of the base represented by the numerator.
3197 : parrello 1.69
3198 :     =back
3199 :    
3200 :     =cut
3201 :    
3202 : parrello 1.93 sub Percent {
3203 : parrello 1.69 # Get the parameters.
3204 : parrello 1.93 my ($number, $base) = @_;
3205 :     # Declare the return variable.
3206 :     my $retVal = 0;
3207 :     # Compute the percent.
3208 :     if ($base != 0) {
3209 :     $retVal = $number * 100 / $base;
3210 :     }
3211 :     # Return the result.
3212 :     return $retVal;
3213 : parrello 1.69 }
3214 :    
3215 : parrello 1.115 =head3 In
3216 :    
3217 :     my $flag = Tracer::In($value, $min, $max);
3218 :    
3219 :     Return TRUE if the value is between the minimum and the maximum, else FALSE.
3220 :    
3221 :     =cut
3222 :    
3223 :     sub In {
3224 :     return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3225 :     }
3226 :    
3227 :    
3228 : parrello 1.97 =head3 Constrain
3229 :    
3230 :     my $constrained = Constrain($value, $min, $max);
3231 :    
3232 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3233 :    
3234 :     =over 4
3235 :    
3236 :     =item value
3237 :    
3238 :     Value to constrain.
3239 :    
3240 :     =item min (optional)
3241 :    
3242 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3243 :    
3244 :     =item max (optional)
3245 :    
3246 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3247 :    
3248 :     =item RETURN
3249 :    
3250 :     Returns the incoming value, constrained according to the other parameters.
3251 :    
3252 :     =back
3253 :    
3254 :     =cut
3255 :    
3256 :     sub Constrain {
3257 :     # Get the parameters.
3258 :     my ($value, $min, $max) = @_;
3259 :     # Declare the return variable.
3260 :     my $retVal = $value;
3261 :     # Apply the minimum constraint.
3262 :     if (defined $min && $retVal < $min) {
3263 :     $retVal = $min;
3264 :     }
3265 :     # Apply the maximum constraint.
3266 :     if (defined $max && $retVal > $max) {
3267 :     $retVal = $max;
3268 :     }
3269 :     # Return the result.
3270 :     return $retVal;
3271 :     }
3272 :    
3273 : parrello 1.93 =head3 Min
3274 : parrello 1.69
3275 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3276 : parrello 1.69
3277 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3278 : parrello 1.69
3279 :     =over 4
3280 :    
3281 : parrello 1.93 =item $value1, $value2, ... $valueN
3282 : parrello 1.69
3283 : parrello 1.93 List of numbers to compare.
3284 : parrello 1.69
3285 :     =item RETURN
3286 :    
3287 : parrello 1.93 Returns the lowest number in the list.
3288 : parrello 1.69
3289 :     =back
3290 :    
3291 :     =cut
3292 :    
3293 : parrello 1.93 sub Min {
3294 :     # Get the parameters. Note that we prime the return value with the first parameter.
3295 :     my ($retVal, @values) = @_;
3296 :     # Loop through the remaining parameters, looking for the lowest.
3297 :     for my $value (@values) {
3298 :     if ($value < $retVal) {
3299 :     $retVal = $value;
3300 : parrello 1.72 }
3301 :     }
3302 : parrello 1.93 # Return the minimum found.
3303 : parrello 1.70 return $retVal;
3304 : parrello 1.35 }
3305 :    
3306 : parrello 1.93 =head3 Max
3307 :    
3308 :     my $max = Max($value1, $value2, ... $valueN);
3309 : parrello 1.69
3310 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3311 : parrello 1.65
3312 : parrello 1.93 =over 4
3313 : parrello 1.65
3314 : parrello 1.93 =item $value1, $value2, ... $valueN
3315 : parrello 1.65
3316 : parrello 1.93 List of numbers to compare.
3317 : parrello 1.65
3318 : parrello 1.93 =item RETURN
3319 : parrello 1.65
3320 : parrello 1.93 Returns the highest number in the list.
3321 : parrello 1.65
3322 :     =back
3323 :    
3324 :     =cut
3325 :    
3326 : parrello 1.93 sub Max {
3327 :     # Get the parameters. Note that we prime the return value with the first parameter.
3328 :     my ($retVal, @values) = @_;
3329 :     # Loop through the remaining parameters, looking for the highest.
3330 :     for my $value (@values) {
3331 :     if ($value > $retVal) {
3332 :     $retVal = $value;
3333 : parrello 1.65 }
3334 :     }
3335 : parrello 1.93 # Return the maximum found.
3336 :     return $retVal;
3337 : parrello 1.65 }
3338 :    
3339 : parrello 1.93 =head3 Strip
3340 : parrello 1.37
3341 : parrello 1.93 my $string = Tracer::Strip($line);
3342 : parrello 1.37
3343 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3344 :     that may have been transferred back and forth several times among different
3345 :     operating environments.
3346 : parrello 1.37
3347 :     =over 4
3348 :    
3349 : parrello 1.93 =item line
3350 : parrello 1.37
3351 : parrello 1.93 Line of text to be stripped.
3352 : parrello 1.37
3353 : parrello 1.93 =item RETURN
3354 : parrello 1.91
3355 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3356 : parrello 1.91
3357 : parrello 1.37 =back
3358 :    
3359 :     =cut
3360 :    
3361 : parrello 1.93 sub Strip {
3362 :     # Get a copy of the parameter string.
3363 :     my ($string) = @_;
3364 :     my $retVal = (defined $string ? $string : "");
3365 :     # Strip the line terminator characters.
3366 :     $retVal =~ s/(\r|\n)+$//g;
3367 :     # Return the result.
3368 :     return $retVal;
3369 : parrello 1.43 }
3370 :    
3371 : parrello 1.115 =head3 Trim
3372 :    
3373 :     my $string = Tracer::Trim($line);
3374 :    
3375 :     Trim all spaces from the beginning and ending of a string.
3376 :    
3377 :     =over 4
3378 :    
3379 :     =item line
3380 :    
3381 :     Line of text to be trimmed.
3382 :    
3383 :     =item RETURN
3384 :    
3385 :     The same line of text with all whitespace chopped off either end.
3386 :    
3387 :     =back
3388 :    
3389 :     =cut
3390 :    
3391 :     sub Trim {
3392 :     # Get a copy of the parameter string.
3393 :     my ($string) = @_;
3394 :     my $retVal = (defined $string ? $string : "");
3395 :     # Strip the front spaces.
3396 :     $retVal =~ s/^\s+//;
3397 :     # Strip the back spaces.
3398 :     $retVal =~ s/\s+$//;
3399 :     # Return the result.
3400 :     return $retVal;
3401 :     }
3402 :    
3403 : parrello 1.93 =head3 Pad
3404 : parrello 1.43
3405 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3406 : parrello 1.43
3407 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3408 :     space, and the padding will be on the right side unless specified
3409 :     in the third parameter.
3410 : parrello 1.43
3411 :     =over 4
3412 :    
3413 : parrello 1.93 =item string
3414 :    
3415 :     String to be padded.
3416 :    
3417 :     =item len
3418 :    
3419 :     Desired length of the padded string.
3420 :    
3421 :     =item left (optional)
3422 :    
3423 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3424 :    
3425 :     =item padChar (optional)
3426 :    
3427 :     Character to use for padding. The default is a space.
3428 :    
3429 :     =item RETURN
3430 : parrello 1.43
3431 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3432 :     specified end so that it achieves the desired length.
3433 : parrello 1.43
3434 :     =back
3435 :    
3436 :     =cut
3437 :    
3438 : parrello 1.93 sub Pad {
3439 :     # Get the parameters.
3440 :     my ($string, $len, $left, $padChar) = @_;
3441 :     # Compute the padding character.
3442 :     if (! defined $padChar) {
3443 :     $padChar = " ";
3444 :     }
3445 :     # Compute the number of spaces needed.
3446 :     my $needed = $len - length $string;
3447 :     # Copy the string into the return variable.
3448 :     my $retVal = $string;
3449 :     # Only proceed if padding is needed.
3450 :     if ($needed > 0) {
3451 :     # Create the pad string.
3452 :     my $pad = $padChar x $needed;
3453 :     # Affix it to the return value.
3454 :     if ($left) {
3455 :     $retVal = $pad . $retVal;
3456 :     } else {
3457 :     $retVal .= $pad;
3458 : parrello 1.43 }
3459 : parrello 1.37 }
3460 : parrello 1.93 # Return the result.
3461 :     return $retVal;
3462 : parrello 1.37 }
3463 :    
3464 : parrello 1.118 =head3 Quoted
3465 :    
3466 :     my $string = Tracer::Quoted($var);
3467 :    
3468 :     Convert the specified value to a string and enclose it in single quotes.
3469 :     If it's undefined, the string C<undef> in angle brackets will be used
3470 :     instead.
3471 :    
3472 :     =over 4
3473 :    
3474 :     =item var
3475 :    
3476 :     Value to quote.
3477 :    
3478 :     =item RETURN
3479 :    
3480 :     Returns a string enclosed in quotes, or an indication the value is undefined.
3481 :    
3482 :     =back
3483 :    
3484 :     =cut
3485 :    
3486 :     sub Quoted {
3487 :     # Get the parameters.
3488 :     my ($var) = @_;
3489 :     # Declare the return variable.
3490 :     my $retVal;
3491 :     # Are we undefined?
3492 :     if (! defined $var) {
3493 :     $retVal = "<undef>";
3494 :     } else {
3495 :     # No, so convert to a string and enclose in quotes.
3496 :     $retVal = $var;
3497 :     $retVal =~ s/'/\\'/;
3498 :     $retVal = "'$retVal'";
3499 :     }
3500 :     # Return the result.
3501 :     return $retVal;
3502 :     }
3503 :    
3504 : parrello 1.93 =head3 EOF
3505 :    
3506 :     This is a constant that is lexically greater than any useful string.
3507 :    
3508 :     =cut
3509 :    
3510 :     sub EOF {
3511 :     return "\xFF\xFF\xFF\xFF\xFF";
3512 :     }
3513 : parrello 1.59
3514 : parrello 1.93 =head3 TICK
3515 : parrello 1.59
3516 : parrello 1.93 my @results = TICK($commandString);
3517 : parrello 1.59
3518 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3519 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3520 : parrello 1.59
3521 : parrello 1.93 `./protein.cgi`
3522 : parrello 1.59
3523 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3524 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3525 : parrello 1.59
3526 : parrello 1.93 TICK("./protein.cgi")
3527 : parrello 1.59
3528 : parrello 1.93 it will work correctly in both environments.
3529 : parrello 1.59
3530 : parrello 1.93 =over 4
3531 : parrello 1.59
3532 : parrello 1.93 =item commandString
3533 : parrello 1.59
3534 : parrello 1.93 The command string to pass to the system.
3535 : parrello 1.59
3536 :     =item RETURN
3537 :    
3538 : parrello 1.93 Returns the standard output from the specified command, as a list.
3539 : parrello 1.59
3540 :     =back
3541 :    
3542 :     =cut
3543 : parrello 1.93 #: Return Type @;
3544 :     sub TICK {
3545 : parrello 1.59 # Get the parameters.
3546 : parrello 1.93 my ($commandString) = @_;
3547 :     # Chop off the dot-slash if this is Windows.
3548 :     if ($FIG_Config::win_mode) {
3549 :     $commandString =~ s!^\./!!;
3550 : parrello 1.59 }
3551 : parrello 1.93 # Activate the command and return the result.
3552 :     return `$commandString`;
3553 : parrello 1.59 }
3554 :    
3555 : parrello 1.93
3556 : parrello 1.55 =head3 CommaFormat
3557 :    
3558 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3559 : parrello 1.55
3560 :     Insert commas into a number.
3561 :    
3562 :     =over 4
3563 :    
3564 :     =item number
3565 :    
3566 :     A sequence of digits.
3567 :    
3568 :     =item RETURN
3569 :    
3570 :     Returns the same digits with commas strategically inserted.
3571 :    
3572 :     =back
3573 :    
3574 :     =cut
3575 :    
3576 :     sub CommaFormat {
3577 :     # Get the parameters.
3578 :     my ($number) = @_;
3579 :     # Pad the length up to a multiple of three.
3580 :     my $padded = "$number";
3581 :     $padded = " " . $padded while length($padded) % 3 != 0;
3582 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3583 :     # cause the delimiters to be included in the output stream. The
3584 :     # GREP removes the empty strings in between the delimiters.
3585 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3586 :     # Clean out the spaces.
3587 :     $retVal =~ s/ //g;
3588 :     # Return the result.
3589 :     return $retVal;
3590 :     }
3591 : parrello 1.46
3592 :    
3593 : parrello 1.117 =head3 GetMemorySize
3594 :    
3595 :     my $string = Tracer::GetMemorySize();
3596 :    
3597 :     Return a memory size string for the current process. The string will be
3598 :     in comma format, with a size indicator (K, M, G) at the end.
3599 :    
3600 :     =cut
3601 :    
3602 :     sub GetMemorySize {
3603 :     # Get the memory size from Unix.
3604 :     my ($retVal) = `ps h -o vsz $$`;
3605 :     # Remove the ending new-line.
3606 :     chomp $retVal;
3607 :     # Format and return the result.
3608 :     return CommaFormat($retVal) . "K";
3609 :     }
3610 :    
3611 : parrello 1.62 =head3 CompareLists
3612 :    
3613 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3614 : parrello 1.62
3615 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3616 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3617 :     The return value contains a list of items that are only in the new list
3618 :     (inserted) and only in the old list (deleted).
3619 :    
3620 :     =over 4
3621 :    
3622 :     =item newList
3623 :    
3624 :     Reference to a list of new tuples.
3625 :    
3626 :     =item oldList
3627 :    
3628 :     Reference to a list of old tuples.
3629 :    
3630 :     =item keyIndex (optional)
3631 :    
3632 :     Index into each tuple of its key field. The default is 0.
3633 :    
3634 :     =item RETURN
3635 :    
3636 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3637 :     list (inserted) followed by a reference to the list of items that are only in the old
3638 :     list (deleted).
3639 :    
3640 :     =back
3641 :    
3642 :     =cut
3643 :    
3644 :     sub CompareLists {
3645 :     # Get the parameters.
3646 :     my ($newList, $oldList, $keyIndex) = @_;
3647 :     if (! defined $keyIndex) {
3648 :     $keyIndex = 0;
3649 :     }
3650 :     # Declare the return variables.
3651 :     my ($inserted, $deleted) = ([], []);
3652 :     # Loop through the two lists simultaneously.
3653 :     my ($newI, $oldI) = (0, 0);
3654 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3655 :     while ($newI < $newN || $oldI < $oldN) {
3656 :     # Get the current object in each list. Note that if one
3657 :     # of the lists is past the end, we'll get undef.
3658 :     my $newItem = $newList->[$newI];
3659 :     my $oldItem = $oldList->[$oldI];
3660 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3661 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3662 :     push @{$deleted}, $oldItem;
3663 :     $oldI++;
3664 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3665 :     # The new item is not in the old list, so mark it inserted.
3666 :     push @{$inserted}, $newItem;
3667 :     $newI++;
3668 :     } else {
3669 :     # The item is in both lists, so push forward.
3670 :     $oldI++;
3671 :     $newI++;
3672 :     }
3673 :     }
3674 :     # Return the result.
3675 :     return ($inserted, $deleted);
3676 :     }
3677 :    
3678 : parrello 1.105 =head3 Cmp
3679 :    
3680 :     my $cmp = Tracer::Cmp($a, $b);
3681 :    
3682 :     This method performs a universal sort comparison. Each value coming in is
3683 :     separated into a leading text part and a trailing number part. The text
3684 :     part is string compared, and if both parts are equal, then the number
3685 :     parts are compared numerically. A stream of just numbers or a stream of
3686 :     just strings will sort correctly, and a mixed stream will sort with the
3687 :     numbers first. Strings with a label and a number will sort in the
3688 :     expected manner instead of lexically.
3689 :    
3690 :     =over 4
3691 :    
3692 :     =item a
3693 :    
3694 :     First item to compare.
3695 :    
3696 :     =item b
3697 :    
3698 :     Second item to compare.
3699 :    
3700 :     =item RETURN
3701 :    
3702 :     Returns a negative number if the first item should sort first (is less), a positive
3703 :     number if the first item should sort second (is greater), and a zero if the items are
3704 :     equal.
3705 :    
3706 :     =back
3707 :    
3708 :     =cut
3709 :    
3710 :     sub Cmp {
3711 :     # Get the parameters.
3712 :     my ($a, $b) = @_;
3713 :     # Declare the return value.
3714 :     my $retVal;
3715 :     # Check for nulls.
3716 :     if (! defined($a)) {
3717 :     $retVal = (! defined($b) ? 0 : -1);
3718 :     } elsif (! defined($b)) {
3719 :     $retVal = 1;
3720 :     } else {
3721 :     # Here we have two real values. Parse the two strings.
3722 : parrello 1.115 my $aParsed = _Parse($a);
3723 :     my $bParsed = _Parse($b);
3724 :     # Compare the string parts insensitively.
3725 :     $retVal = (lc $aParsed->[0] cmp lc $bParsed->[0]);
3726 :     # If they're equal, compare them sensitively.
3727 :     if (! $retVal) {
3728 :     $retVal = ($aParsed->[0] cmp $bParsed->[0]);
3729 :     }
3730 :     # If they're STILL equal, compare the number parts.
3731 : parrello 1.105 if (! $retVal) {
3732 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3733 :     }
3734 :     }
3735 :     # Return the result.
3736 :     return $retVal;
3737 :     }
3738 :    
3739 : parrello 1.115 # This method parses an input string into a string part and a number part.
3740 :     sub _Parse {
3741 :     my ($string) = @_;
3742 :     my ($alpha, $num);
3743 :     if ($string =~ /^(.*?)(\d+(?:\.\d+)?)$/) {
3744 :     $alpha = $1;
3745 :     $num = $2;
3746 :     } else {
3747 :     $alpha = $string;
3748 :     $num = 0;
3749 :     }
3750 :     return [$alpha, $num];
3751 :     }
3752 :    
3753 : parrello 1.108 =head3 ListEQ
3754 :    
3755 :     my $flag = Tracer::ListEQ(\@a, \@b);
3756 :    
3757 :     Return TRUE if the specified lists contain the same strings in the same
3758 :     order, else FALSE.
3759 :    
3760 :     =over 4
3761 :    
3762 :     =item a
3763 :    
3764 :     Reference to the first list.
3765 :    
3766 :     =item b
3767 :    
3768 :     Reference to the second list.
3769 :    
3770 :     =item RETURN
3771 :    
3772 :     Returns TRUE if the two parameters are identical string lists, else FALSE.
3773 :    
3774 :     =back
3775 :    
3776 :     =cut
3777 :    
3778 :     sub ListEQ {
3779 :     # Get the parameters.
3780 :     my ($a, $b) = @_;
3781 :     # Declare the return variable. Start by checking the lengths.
3782 :     my $n = scalar(@$a);
3783 :     my $retVal = ($n == scalar(@$b));
3784 :     # Now compare the list elements.
3785 :     for (my $i = 0; $retVal && $i < $n; $i++) {
3786 :     $retVal = ($a->[$i] eq $b->[$i]);
3787 :     }
3788 :     # Return the result.
3789 :     return $retVal;
3790 :     }
3791 :    
3792 : parrello 1.105 =head2 CGI Script Utilities
3793 :    
3794 :     =head3 ScriptSetup (deprecated)
3795 :    
3796 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
3797 :    
3798 :     Perform standard tracing and debugging setup for scripts. The value returned is
3799 :     the CGI object followed by a pre-built variable hash. At the end of the script,
3800 :     the client should call L</ScriptFinish> to output the web page.
3801 :    
3802 :     This method calls L</ETracing> to configure tracing, which allows the tracing
3803 :     to be configured via the emergency tracing form on the debugging control panel.
3804 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
3805 :     method, which includes every program that uses this method or L</StandardSetup>.
3806 :    
3807 :     =over 4
3808 :    
3809 :     =item noTrace (optional)
3810 :    
3811 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
3812 :     tracing manually.
3813 :    
3814 :     =item RETURN
3815 :    
3816 :     Returns a two-element list consisting of a CGI query object and a variable hash for
3817 :     the output page.
3818 :    
3819 :     =back
3820 :    
3821 :     =cut
3822 :    
3823 :     sub ScriptSetup {
3824 :     # Get the parameters.
3825 :     my ($noTrace) = @_;
3826 :     # Get the CGI query object.
3827 :     my $cgi = CGI->new();
3828 :     # Set up tracing if it's not suppressed.
3829 :     ETracing($cgi) unless $noTrace;
3830 :     # Create the variable hash.
3831 :     my $varHash = { results => '' };
3832 :     # Return the query object and variable hash.
3833 :     return ($cgi, $varHash);
3834 :     }
3835 :    
3836 :     =head3 ScriptFinish (deprecated)
3837 :    
3838 :     ScriptFinish($webData, $varHash);
3839 :    
3840 :     Output a web page at the end of a script. Either the string to be output or the
3841 :     name of a template file can be specified. If the second parameter is omitted,
3842 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
3843 :     name of a template file. The template should have the variable C<DebugData>
3844 :     specified in any form that invokes a standard script. If debugging mode is turned
3845 :     on, a form field will be put in that allows the user to enter tracing data.
3846 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
3847 :     the output, formatted as a list.
3848 :    
3849 :     A typical standard script would loook like the following.
3850 :    
3851 :     BEGIN {
3852 :     # Print the HTML header.
3853 :     print "CONTENT-TYPE: text/html\n\n";
3854 :     }
3855 :     use Tracer;
3856 :     use CGI;
3857 :     use FIG;
3858 :     # ... more uses ...
3859 :    
3860 :     my ($cgi, $varHash) = ScriptSetup();
3861 :     eval {
3862 :     # ... get data from $cgi, put it in $varHash ...
3863 :     };
3864 :     if ($@) {
3865 :     Trace("Script Error: $@") if T(0);
3866 :     }
3867 :     ScriptFinish("Html/MyTemplate.html", $varHash);
3868 :    
3869 :     The idea here is that even if the script fails, you'll see trace messages and
3870 :     useful output.
3871 :    
3872 :     =over 4
3873 :    
3874 :     =item webData
3875 :    
3876 :     A string containing either the full web page to be written to the output or the
3877 :     name of a template file from which the page is to be constructed. If the name
3878 :     of a template file is specified, then the second parameter must be present;
3879 :     otherwise, it must be absent.
3880 :    
3881 :     =item varHash (optional)
3882 :    
3883 :     If specified, then a reference to a hash mapping variable names for a template
3884 :     to their values. The template file will be read into memory, and variable markers
3885 :     will be replaced by data in this hash reference.
3886 :    
3887 :     =back
3888 :    
3889 :     =cut
3890 :    
3891 :     sub ScriptFinish {
3892 :     # Get the parameters.
3893 :     my ($webData, $varHash) = @_;
3894 :     # Check for a template file situation.
3895 :     my $outputString;
3896 :     if (defined $varHash) {
3897 :     # Here we have a template file. We need to determine the template type.
3898 :     my $template;
3899 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3900 :     $template = "$FIG_Config::template_url/$webData";
3901 :     } else {
3902 :     $template = "<<$webData";
3903 :     }
3904 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
3905 :     } else {
3906 :     # Here the user gave us a raw string.
3907 :     $outputString = $webData;
3908 :     }
3909 :     # Check for trace messages.
3910 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
3911 :     # We have trace messages, so we want to put them at the end of the body. This
3912 :     # is either at the end of the whole string or at the beginning of the BODY
3913 :     # end-tag.
3914 :     my $pos = length $outputString;
3915 :     if ($outputString =~ m#</body>#gi) {
3916 :     $pos = (pos $outputString) - 7;
3917 :     }
3918 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
3919 :     # destination.
3920 :     my $traceHtml;
3921 :     if ($Destination eq "QUEUE") {
3922 :     $traceHtml = QTrace('Html');
3923 :     } elsif ($Destination =~ /^>>(.+)$/) {
3924 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
3925 :     # can copy the file name into the clipboard easily.
3926 :     my $actualDest = $1;
3927 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3928 :     } else {
3929 :     # Here we have one of the special destinations.
3930 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3931 :     }
3932 :     substr $outputString, $pos, 0, $traceHtml;
3933 :     }
3934 :     # Write the output string.
3935 :     print $outputString;
3936 :     }
3937 :    
3938 : parrello 1.65 =head3 GenerateURL
3939 :    
3940 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3941 : parrello 1.65
3942 :     Generate a GET-style URL for the specified page with the specified parameter
3943 :     names and values. The values will be URL-escaped automatically. So, for
3944 :     example
3945 :    
3946 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3947 :    
3948 :     would return
3949 :    
3950 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3951 : parrello 1.65
3952 :     =over 4
3953 :    
3954 :     =item page
3955 :    
3956 :     Page URL.
3957 :    
3958 :     =item parameters
3959 :    
3960 :     Hash mapping parameter names to parameter values.
3961 :    
3962 :     =item RETURN
3963 :    
3964 :     Returns a GET-style URL that goes to the specified page and passes in the
3965 :     specified parameters and values.
3966 :    
3967 :     =back
3968 :    
3969 :     =cut
3970 :    
3971 :     sub GenerateURL {
3972 :     # Get the parameters.
3973 :     my ($page, %parameters) = @_;
3974 :     # Prime the return variable with the page URL.
3975 :     my $retVal = $page;
3976 :     # Loop through the parameters, creating parameter elements in a list.
3977 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3978 :     # If the list is nonempty, tack it on.
3979 :     if (@parmList) {
3980 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3981 : parrello 1.65 }
3982 :     # Return the result.
3983 :     return $retVal;
3984 :     }
3985 :    
3986 : parrello 1.78 =head3 ApplyURL
3987 :    
3988 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3989 : parrello 1.78
3990 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3991 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3992 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3993 :    
3994 :     This provides a simple way to process the results of a database query into something
3995 :     displayable by combining a URL with text.
3996 :    
3997 :     =over 4
3998 :    
3999 :     =item table
4000 :    
4001 :     Reference to a list of lists. The elements in the containing list will be updated by
4002 :     this method.
4003 :    
4004 :     =item target
4005 :    
4006 :     The index of the column to be converted into HTML.
4007 :    
4008 :     =item url
4009 :    
4010 :     The index of the column containing the URL. Note that the URL must have a recognizable
4011 :     C<http:> at the beginning.
4012 :    
4013 :     =back
4014 :    
4015 :     =cut
4016 :    
4017 :     sub ApplyURL {
4018 :     # Get the parameters.
4019 :     my ($table, $target, $url) = @_;
4020 :     # Loop through the table.
4021 :     for my $row (@{$table}) {
4022 :     # Apply the URL to the target cell.
4023 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
4024 :     # Delete the URL from the row.
4025 :     delete $row->[$url];
4026 :     }
4027 :     }
4028 :    
4029 :     =head3 CombineURL
4030 :    
4031 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
4032 : parrello 1.78
4033 :     This method will convert the specified text into HTML hyperlinked to the specified
4034 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
4035 :     is defined and begins with an C<http:> header.
4036 :    
4037 :     =over 4
4038 :    
4039 :     =item text
4040 :    
4041 :     Text to return. This will be HTML-escaped automatically.
4042 :    
4043 :     =item url
4044 :    
4045 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
4046 :     will be returned without any hyperlinking.
4047 :    
4048 :     =item RETURN
4049 :    
4050 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
4051 :     doesn't look right, the HTML-escaped text will be returned without any further
4052 :     modification.
4053 :    
4054 :     =back
4055 :    
4056 :     =cut
4057 :    
4058 :     sub CombineURL {
4059 :     # Get the parameters.
4060 :     my ($text, $url) = @_;
4061 :     # Declare the return variable.
4062 :     my $retVal = CGI::escapeHTML($text);
4063 :     # Verify the URL.
4064 :     if (defined($url) && $url =~ m!http://!i) {
4065 :     # It's good, so we apply it to the text.
4066 :     $retVal = "<a href=\"$url\">$retVal</a>";
4067 :     }
4068 :     # Return the result.
4069 :     return $retVal;
4070 :     }
4071 :    
4072 : parrello 1.97 =head3 TrackingCode
4073 :    
4074 :     my $html = Tracer::TrackingCode();
4075 :    
4076 :     Returns the HTML code for doing web page traffic monitoring. If the
4077 :     current environment is a test system, then it returns a null string;
4078 :     otherwise, it returns a bunch of javascript containing code for turning
4079 :     on SiteMeter and Google Analytics.
4080 :    
4081 :     =cut
4082 :    
4083 :     sub TrackingCode {
4084 :     # Declare the return variable.
4085 :     my $retVal = "<!-- tracking off -->";
4086 :     # Determine if we're in production.
4087 :     if ($FIG_Config::site_meter) {
4088 :     $retVal = <<END_HTML
4089 :     <!-- Site Meter -->
4090 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
4091 :     </script>
4092 :     <noscript>
4093 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
4094 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
4095 :     </noscript>
4096 :     <!-- Copyright (c)2006 Site Meter -->
4097 :     END_HTML
4098 :     }
4099 :     return $retVal;
4100 :     }
4101 :    
4102 : parrello 1.105 =head3 Clean
4103 :    
4104 :     my $cleaned = Tracer::Clean($string);
4105 :    
4106 :     Clean up a string for HTML display. This not only converts special
4107 :     characters to HTML entity names, it also removes control characters.
4108 :    
4109 :     =over 4
4110 :    
4111 :     =item string
4112 :    
4113 :     String to convert.
4114 :    
4115 :     =item RETURN
4116 :    
4117 :     Returns the input string with anything that might disrupt an HTML literal removed. An
4118 :     undefined value will be converted to an empty string.
4119 :