Annotation of /FigKernelPackages/Tracer.pm

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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	1.119	my $Confessions = 0; # confession count
215 :	parrello	1.99	umask 2; # Fix the damn umask so everything is group-writable.
216 :	olson	1.1
217 :	parrello	1.93	=head2 Tracing Methods
218 :
219 :			=head3 Setups
220 :
221 :			my $count = Tracer::Setups();
222 :
223 :			Return the number of times L</TSetup> has been called.
224 :
225 :			This method allows for the creation of conditional tracing setups where, for example, we
226 :			may want to set up tracing if nobody else has done it before us.
227 :
228 :			=cut
229 :
230 :			sub Setups {
231 :			return $SetupCount;
232 :			}
233 :	olson	1.1
234 :			=head3 TSetup
235 :
236 :	parrello	1.92	TSetup($categoryList, $target);
237 :	olson	1.1
238 :			This method is used to specify the trace options. The options are stored as package data
239 :			and interrogated by the L</Trace> and L</T> methods.
240 :
241 :			=over 4
242 :
243 :			=item categoryList
244 :
245 :			A string specifying the trace level and the categories to be traced, separated by spaces.
246 :			The trace level must come first.
247 :
248 :			=item target
249 :
250 :			The destination for the trace output. To send the trace output to a file, specify the file
251 :			name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
252 :	parrello	1.10	to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
253 :			symbol with a C<+> to echo output to a file AND to the standard output. In addition to
254 :			sending the trace messages to a file, you can specify a special destination. C<HTML> will
255 :			cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
256 :	parrello	1.5	will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
257 :	parrello	1.9	messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
258 :	parrello	1.6	messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
259 :	parrello	1.9	cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
260 :	parrello	1.6	cause tracing to be suppressed.
261 :	olson	1.1
262 :			=back
263 :
264 :			=cut
265 :
266 :			sub TSetup {
267 :	parrello	1.12	# Get the parameters.
268 :			my ($categoryList, $target) = @_;
269 :			# Parse the category list.
270 :			my @categoryData = split /\s+/, $categoryList;
271 :			# Extract the trace level.
272 :			$TraceLevel = shift @categoryData;
273 :			# Presume category-based tracing until we learn otherwise.
274 :			$AllTrace = 0;
275 :			# Build the category hash. Note that if we find a "*", we turn on non-category
276 :	parrello	1.33	# tracing. We must also clear away any pre-existing data.
277 :	parrello	1.34	%Categories = ( main => 1 );
278 :	parrello	1.12	for my $category (@categoryData) {
279 :			if ($category eq '*') {
280 :			$AllTrace = 1;
281 :			} else {
282 :	parrello	1.13	$Categories{lc $category} = 1;
283 :	parrello	1.12	}
284 :			}
285 :			# Now we need to process the destination information. The most important special
286 :	parrello	1.98	# case is when we're writing to a file. This is indicated by ">" (overwrite) and
287 :			# ">>" (append). A leading "+" for either indicates that we are also writing to
288 :			# the standard output (tee mode).
289 :	parrello	1.12	if ($target =~ m/^\+?>>?/) {
290 :			if ($target =~ m/^\+/) {
291 :			$TeeFlag = 1;
292 :			$target = substr($target, 1);
293 :			}
294 :			if ($target =~ m/^>[^>]/) {
295 :	parrello	1.98	# We need to initialize the file (which clears it).
296 :	parrello	1.12	open TRACEFILE, $target;
297 :	parrello	1.98	print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
298 :	parrello	1.12	close TRACEFILE;
299 :	parrello	1.98	# Set to append mode now that the file has been cleared.
300 :	parrello	1.12	$Destination = ">$target";
301 :			} else {
302 :			$Destination = $target;
303 :			}
304 :			} else {
305 :			$Destination = uc($target);
306 :			}
307 :			# Increment the setup counter.
308 :			$SetupCount++;
309 :	parrello	1.11	}
310 :
311 :	parrello	1.93	=head3 SetLevel
312 :	parrello	1.31
313 :	parrello	1.93	Tracer::SetLevel($newLevel);
314 :	parrello	1.31
315 :	parrello	1.93	Modify the trace level. A higher trace level will cause more messages to appear.
316 :	parrello	1.31
317 :	parrello	1.93	=over 4
318 :	parrello	1.31
319 :	parrello	1.93	=item newLevel
320 :	parrello	1.31
321 :	parrello	1.93	Proposed new trace level.
322 :	parrello	1.31
323 :	parrello	1.93	=back
324 :	parrello	1.31
325 :	parrello	1.93	=cut
326 :	parrello	1.31
327 :	parrello	1.93	sub SetLevel {
328 :			$TraceLevel = $_[0];
329 :			}
330 :	parrello	1.31
331 :	parrello	1.97	=head3 ParseDate
332 :
333 :			my $time = Tracer::ParseDate($dateString);
334 :
335 :			Convert a date into a PERL time number. This method expects a date-like string
336 :			and parses it into a number. The string must be vaguely date-like or it will
337 :			return an undefined value. Our requirement is that a month and day be
338 :			present and that three pieces of the date string (time of day, month and day,
339 :			year) be separated by likely delimiters, such as spaces, commas, and such-like.
340 :
341 :			If a time of day is present, it must be in military time with two digits for
342 :			everything but the hour.
343 :	parrello	1.31
344 :	parrello	1.97	The year must be exactly four digits.
345 :	parrello	1.31
346 :	parrello	1.97	Additional stuff can be in the string. We presume it's time zones or weekdays or something
347 :			equally innocuous. This means, however, that a sufficiently long sentence with date-like
348 :			parts in it may be interpreted as a date. Hopefully this will not be a problem.
349 :
350 :			It should be guaranteed that this method will parse the output of the L</Now> function.
351 :
352 :			The parameters are as follows.
353 :	parrello	1.31
354 :	parrello	1.93	=over 4
355 :	parrello	1.31
356 :	parrello	1.93	=item dateString
357 :	parrello	1.31
358 :	parrello	1.97	The date string to convert.
359 :	parrello	1.31
360 :	parrello	1.93	=item RETURN
361 :	parrello	1.31
362 :	parrello	1.93	Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
363 :	parrello	1.97	the date string is invalid. A valid date string must contain a month and day.
364 :	parrello	1.31
365 :	parrello	1.93	=back
366 :	parrello	1.38
367 :	parrello	1.93	=cut
368 :	parrello	1.38
369 :	parrello	1.97	# Universal month conversion table.
370 :			use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
371 :			Feb => 1, February => 1, '02' => 1, '2' => 1,
372 :			Mar => 2, March => 2, '03' => 2, '3' => 2,
373 :			Apr => 3, April => 3, '04' => 3, '4' => 3,
374 :			May => 4, May => 4, '05' => 4, '5' => 4,
375 :			Jun => 5, June => 5, '06' => 5, '6' => 5,
376 :			Jul => 6, July => 6, '07' => 6, '7' => 6,
377 :			Aug => 7, August => 7, '08' => 7, '8' => 7,
378 :			Sep => 8, September => 8, '09' => 8, '9' => 8,
379 :			Oct => 9, October => 9, '10' => 9,
380 :			Nov => 10, November => 10, '11' => 10,
381 :			Dec => 11, December => 11, '12' => 11
382 :			};
383 :
384 :			sub ParseDate {
385 :	parrello	1.93	# Get the parameters.
386 :			my ($dateString) = @_;
387 :			# Declare the return variable.
388 :			my $retVal;
389 :	parrello	1.97	# Find the month and day of month. There are two ways that can happen. We check for the
390 :			# numeric style first. That way, if the user's done something like "Sun 12/22", then we
391 :			# won't be fooled into thinking the month is Sunday.
392 :			if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# \|\| $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
393 :			my ($mon, $mday) = (MONTHS->{$1}, $2);
394 :			# Insist that the month and day are valid.
395 :			if (defined($mon) && $2 >= 1 && $2 <= 31) {
396 :			# Find the time.
397 :			my ($hour, $min, $sec) = (0, 0, 0);
398 :			if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
399 :			($hour, $min, $sec) = ($1, $2, $3);
400 :			}
401 :			# Find the year.
402 :			my $year;
403 :			if ($dateString =~ /\b(\d{4})\b/) {
404 :			$year = $1;
405 :			} else {
406 :			# Get the default year, which is this one. Note we must convert it to
407 :			# the four-digit value expected by "timelocal".
408 :			(undef, undef, undef, undef, undef, $year) = localtime();
409 :			$year += 1900;
410 :			}
411 :			$retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
412 :			}
413 :	parrello	1.93	}
414 :			# Return the result.
415 :			return $retVal;
416 :			}
417 :	parrello	1.31
418 :	parrello	1.93	=head3 LogErrors
419 :	parrello	1.42
420 :	parrello	1.93	Tracer::LogErrors($fileName);
421 :	parrello	1.31
422 :	parrello	1.93	Route the standard error output to a log file.
423 :	parrello	1.31
424 :	parrello	1.93	=over 4
425 :	parrello	1.31
426 :	parrello	1.93	=item fileName
427 :	parrello	1.31
428 :	parrello	1.93	Name of the file to receive the error output.
429 :	parrello	1.31
430 :	parrello	1.93	=back
431 :	parrello	1.31
432 :	parrello	1.93	=cut
433 :	parrello	1.84
434 :	parrello	1.93	sub LogErrors {
435 :			# Get the file name.
436 :			my ($fileName) = @_;
437 :			# Open the file as the standard error output.
438 :			open STDERR, '>', $fileName;
439 :			}
440 :	parrello	1.84
441 :	parrello	1.93	=head3 Trace
442 :	parrello	1.31
443 :	parrello	1.93	Trace($message);
444 :	parrello	1.31
445 :	parrello	1.93	Write a trace message to the target location specified in L</TSetup>. If there has not been
446 :			any prior call to B<TSetup>.
447 :	parrello	1.31
448 :	parrello	1.93	=over 4
449 :	parrello	1.42
450 :	parrello	1.93	=item message
451 :	parrello	1.42
452 :	parrello	1.93	Message to write.
453 :	parrello	1.42
454 :	parrello	1.93	=back
455 :	parrello	1.72
456 :	parrello	1.93	=cut
457 :	parrello	1.36
458 :	parrello	1.93	sub Trace {
459 :			# Get the parameters.
460 :			my ($message) = @_;
461 :	parrello	1.97	# Strip off any line terminators at the end of the message. We will add
462 :			# new-line stuff ourselves.
463 :			my $stripped = Strip($message);
464 :			# Compute the caller information.
465 :			my ($callPackage, $callFile, $callLine) = caller();
466 :			my $callFileTitle = basename($callFile);
467 :			# Check the caller.
468 :	parrello	1.98	my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
469 :	parrello	1.93	# Get the timestamp.
470 :			my $timeStamp = Now();
471 :	parrello	1.97	# Build the prefix.
472 :			my $level = $LevelNames[$LastLevel] \|\| "($LastLevel)";
473 :	parrello	1.98	my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
474 :	parrello	1.97	# Format the message.
475 :			my $formatted = "$prefix $stripped";
476 :	parrello	1.93	# Process according to the destination.
477 :			if ($Destination eq "TEXT") {
478 :			# Write the message to the standard output.
479 :			print "$formatted\n";
480 :			} elsif ($Destination eq "ERROR") {
481 :	parrello	1.97	# Write the message to the error output. Here, we want our prefix fields.
482 :	parrello	1.93	print STDERR "$formatted\n";
483 :	parrello	1.97	} elsif ($Destination eq "WARN") {
484 :			# Emit the message to the standard error output. It is presumed that the
485 :	parrello	1.98	# error logger will add its own prefix fields, the notable exception being
486 :			# the caller info.
487 :			print STDERR "$callerInfo$stripped\n";
488 :	parrello	1.93	} elsif ($Destination eq "QUEUE") {
489 :			# Push the message into the queue.
490 :			push @Queue, "$formatted";
491 :			} elsif ($Destination eq "HTML") {
492 :	parrello	1.116	# Convert the message to HTML.
493 :	parrello	1.97	my $escapedMessage = CGI::escapeHTML($stripped);
494 :	parrello	1.116	# The stuff after the first line feed should be pre-formatted.
495 :			my @lines = split /\s*\n/, $escapedMessage;
496 :			# Get the normal portion.
497 :			my $line1 = shift @lines;
498 :			print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
499 :			if (@lines) {
500 :	parrello	1.120	print "<pre>" . join("\n", @lines, "</pre>");
501 :	parrello	1.116	}
502 :	parrello	1.93	} elsif ($Destination =~ m/^>>/) {
503 :			# Write the trace message to an output file.
504 :	parrello	1.97	open(TRACING, $Destination) \|\| die "Tracing open for \"$Destination\" failed: $!";
505 :	parrello	1.111	# Lock the file.
506 :			flock TRACING, LOCK_EX;
507 :	parrello	1.93	print TRACING "$formatted\n";
508 :			close TRACING;
509 :			# If the Tee flag is on, echo it to the standard output.
510 :			if ($TeeFlag) {
511 :			print "$formatted\n";
512 :			}
513 :			}
514 :			}
515 :	parrello	1.36
516 :	parrello	1.117	=head3 MemTrace
517 :
518 :			MemTrace($message);
519 :
520 :			Output a trace message that includes memory size information.
521 :
522 :			=over 4
523 :
524 :			=item message
525 :
526 :			Message to display. The message will be followed by a sentence about the memory size.
527 :
528 :			=back
529 :
530 :			=cut
531 :
532 :			sub MemTrace {
533 :			# Get the parameters.
534 :			my ($message) = @_;
535 :			my $memory = GetMemorySize();
536 :			Trace("$message $memory in use.");
537 :			}
538 :
539 :
540 :	parrello	1.115	=head3 TraceDump
541 :
542 :			TraceDump($title, $object);
543 :
544 :			Dump an object to the trace log. This method simply calls the C<Dumper>
545 :			function, but routes the output to the trace log instead of returning it
546 :			as a string. The output is arranged so that it comes out monospaced when
547 :			it appears in an HTML trace dump.
548 :
549 :			=over 4
550 :
551 :			=item title
552 :
553 :			Title to give to the object being dumped.
554 :
555 :			=item object
556 :
557 :			Reference to a list, hash, or object to dump.
558 :
559 :			=back
560 :
561 :			=cut
562 :
563 :			sub TraceDump {
564 :			# Get the parameters.
565 :			my ($title, $object) = @_;
566 :			# Trace the object.
567 :			Trace("Object dump for $title:\n" . Dumper($object));
568 :			}
569 :
570 :	parrello	1.93	=head3 T
571 :	parrello	1.36
572 :	parrello	1.93	my $switch = T($category, $traceLevel);
573 :	parrello	1.36
574 :	parrello	1.93	or
575 :	parrello	1.44
576 :	parrello	1.93	my $switch = T($traceLevel);
577 :	parrello	1.44
578 :	parrello	1.93	Return TRUE if the trace level is at or above a specified value and the specified category
579 :			is active, else FALSE. If no category is specified, the caller's package name is used.
580 :	parrello	1.44
581 :	parrello	1.93	=over 4
582 :	parrello	1.44
583 :	parrello	1.93	=item category
584 :	parrello	1.44
585 :	parrello	1.93	Category to which the message belongs. If not specified, the caller's package name is
586 :			used.
587 :	parrello	1.31
588 :	parrello	1.93	=item traceLevel
589 :	parrello	1.31
590 :	parrello	1.93	Relevant tracing level.
591 :	parrello	1.31
592 :	parrello	1.93	=item RETURN
593 :	parrello	1.31
594 :	parrello	1.93	TRUE if a message at the specified trace level would appear in the trace, else FALSE.
595 :	parrello	1.31
596 :	parrello	1.93	=back
597 :	parrello	1.36
598 :	parrello	1.93	=cut
599 :
600 :			sub T {
601 :			# Declare the return variable.
602 :			my $retVal = 0;
603 :			# Only proceed if tracing is turned on.
604 :			if ($Destination ne "NONE") {
605 :			# Get the parameters.
606 :			my ($category, $traceLevel) = @_;
607 :			if (!defined $traceLevel) {
608 :			# Here we have no category, so we need to get the calling package.
609 :			# The calling package is normally the first parameter. If it is
610 :			# omitted, the first parameter will be the tracelevel. So, the
611 :			# first thing we do is shift the so-called category into the
612 :			# $traceLevel variable where it belongs.
613 :			$traceLevel = $category;
614 :			my ($package, $fileName, $line) = caller;
615 :			# If there is no calling package, we default to "main".
616 :			if (!$package) {
617 :			$category = "main";
618 :			} else {
619 :			my @cats = split /::/, $package;
620 :			$category = $cats[$#cats];
621 :			}
622 :			}
623 :	parrello	1.97	# Save the category name and level.
624 :	parrello	1.93	$LastCategory = $category;
625 :	parrello	1.97	$LastLevel = $traceLevel;
626 :	parrello	1.93	# Convert it to lower case before we hash it.
627 :			$category = lc $category;
628 :	parrello	1.100	# Validate the trace level.
629 :	parrello	1.93	if (ref $traceLevel) {
630 :			Confess("Bad trace level.");
631 :			} elsif (ref $TraceLevel) {
632 :			Confess("Bad trace config.");
633 :			}
634 :	parrello	1.100	# Make the check. Note that level 0 shows even if the category is turned off.
635 :			$retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 \|\| $AllTrace \|\| exists $Categories{$category}));
636 :	parrello	1.93	}
637 :			# Return the computed result.
638 :			return $retVal;
639 :			}
640 :
641 :			=head3 QTrace
642 :
643 :			my $data = QTrace($format);
644 :
645 :			Return the queued trace data in the specified format.
646 :
647 :			=over 4
648 :
649 :			=item format
650 :
651 :			C<html> to format the data as an HTML list, C<text> to format it as straight text.
652 :
653 :			=back
654 :
655 :			=cut
656 :
657 :			sub QTrace {
658 :			# Get the parameter.
659 :			my ($format) = @_;
660 :			# Create the return variable.
661 :			my $retVal = "";
662 :			# Only proceed if there is an actual queue.
663 :			if (@Queue) {
664 :			# Process according to the format.
665 :			if ($format =~ m/^HTML$/i) {
666 :			# Convert the queue into an HTML list.
667 :			$retVal = "<ul>\n";
668 :			for my $line (@Queue) {
669 :			my $escapedLine = CGI::escapeHTML($line);
670 :			$retVal .= "<li>$escapedLine</li>\n";
671 :			}
672 :			$retVal .= "</ul>\n";
673 :			} elsif ($format =~ m/^TEXT$/i) {
674 :			# Convert the queue into a list of text lines.
675 :			$retVal = join("\n", @Queue) . "\n";
676 :			}
677 :			# Clear the queue.
678 :			@Queue = ();
679 :			}
680 :			# Return the formatted list.
681 :			return $retVal;
682 :			}
683 :
684 :			=head3 Confess
685 :
686 :			Confess($message);
687 :
688 :			Trace the call stack and abort the program with the specified message. When used with
689 :			the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
690 :			So, for example
691 :
692 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
693 :
694 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
695 :
696 :			=over 4
697 :
698 :			=item message
699 :
700 :			Message to include in the trace.
701 :
702 :			=back
703 :
704 :			=cut
705 :
706 :			sub Confess {
707 :			# Get the parameters.
708 :			my ($message) = @_;
709 :	parrello	1.97	# Set up the category and level.
710 :			$LastCategory = "(confess)";
711 :			$LastLevel = 0;
712 :	parrello	1.93	# Trace the call stack.
713 :			Cluck($message);
714 :	parrello	1.119	# Increment the confession count.
715 :			$Confessions++;
716 :	parrello	1.93	# Abort the program.
717 :			croak(">>> $message");
718 :			}
719 :
720 :	parrello	1.119	=head3 Confessions
721 :
722 :			my $count = Tracer::Confessions();
723 :
724 :			Return the number of calls to L</Confess> by the current task.
725 :
726 :			=cut
727 :
728 :			sub Confessions {
729 :			return $Confessions;
730 :			}
731 :
732 :
733 :	parrello	1.106	=head3 SaveCGI
734 :
735 :			Tracer::SaveCGI($cgi);
736 :
737 :			This method saves the CGI object but does not activate emergency tracing.
738 :			It is used to allow L</Warn> to work in situations where emergency
739 :			tracing is contra-indicated (e.g. the wiki).
740 :
741 :			=over 4
742 :
743 :			=item cgi
744 :
745 :			Active CGI query object.
746 :
747 :			=back
748 :
749 :			=cut
750 :
751 :			sub SaveCGI {
752 :			$SavedCGI = $_[0];
753 :			}
754 :
755 :	parrello	1.99	=head3 Warn
756 :
757 :	parrello	1.106	Warn($message, @options);
758 :	parrello	1.99
759 :			This method traces an important message. If an RSS feed is configured
760 :			(via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
761 :			then the message will be echoed to the feed. In general, a tracing
762 :			destination of C<WARN> indicates that the caller is running as a web
763 :			service in a production environment; however, this is not a requirement.
764 :
765 :	parrello	1.103	To force warnings into the RSS feed even when the tracing destination
766 :			is not C<WARN>, simply specify the C<Feed> tracing module. This can be
767 :			configured automatically when L</StandardSetup> is used.
768 :
769 :	parrello	1.99	The L</Cluck> method calls this one for its final message. Since
770 :			L</Confess> calls L</Cluck>, this means that any error which is caught
771 :			and confessed will put something in the feed. This insures that someone
772 :			will be alerted relatively quickly when a failure occurs.
773 :
774 :			=over 4
775 :
776 :			=item message
777 :
778 :			Message to be traced.
779 :
780 :	parrello	1.106	=item options
781 :
782 :			A list containing zero or more options.
783 :
784 :			=back
785 :
786 :			The permissible options are as follows.
787 :
788 :			=over 4
789 :
790 :			=item noStack
791 :
792 :			If specified, then the stack trace is not included in the output.
793 :
794 :	parrello	1.99	=back
795 :
796 :			=cut
797 :
798 :			sub Warn {
799 :			# Get the parameters.
800 :	parrello	1.106	my $message = shift @_;
801 :			my %options = map { $_ => 1 } @_;
802 :	parrello	1.107	# Save $@;
803 :			my $savedError = $@;
804 :	parrello	1.99	# Trace the message.
805 :			Trace($message);
806 :	parrello	1.106	# This will contain the lock handle. If it's defined, it means we need to unlock.
807 :			my $lock;
808 :	parrello	1.103	# Check for feed forcing.
809 :			my $forceFeed = exists $Categories{feed};
810 :	parrello	1.106	# An error here would be disastrous. Note that if debug mode is specified,
811 :			# we do this stuff even in a test environment.
812 :	parrello	1.99	eval {
813 :			# Do we need to put this in the RSS feed?
814 :	parrello	1.103	if ($FIG_Config::error_feed && ($Destination eq 'WARN' \|\| $forceFeed)) {
815 :	parrello	1.109	# Probably. We need to check first, however, to see if it's from an
816 :			# ignored IP. For non-CGI situations, we default the IP to the self-referent.
817 :			my $key = "127.0.0.1";
818 :			if (defined $SavedCGI) {
819 :			# Get the IP address.
820 :			$key = $ENV{HTTP_X_FORWARDED_FOR} \|\| $ENV{REMOTE_ADDR};
821 :	parrello	1.101	}
822 :	parrello	1.109	# Is the IP address in the ignore list?
823 :			my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
824 :			if (! $found) {
825 :			# No. We're good. We now need to compute the date, the link, and the title.
826 :			# First, the date, in a very specific format.
827 :			my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
828 :			(tz_local_offset() / 30);
829 :			# Environment data goes in here. We start with the date.
830 :			my $environment = "$date. ";
831 :			# If we need to recap the message (because it's too long to be a title), we'll
832 :			# put it in here.
833 :			my $recap;
834 :			# Copy the message and remove excess space.
835 :			my $title = $message;
836 :			$title =~ s/\s+/ /gs;
837 :			# If it's too long, we have to split it up.
838 :			if (length $title > 60) {
839 :			# Put the full message in the environment string.
840 :			$recap = $title;
841 :			# Excerpt it as the title.
842 :			$title = substr($title, 0, 50) . "...";
843 :			}
844 :			# If we have a CGI object, then this is a web error. Otherwise, it's
845 :			# command-line.
846 :			if (defined $SavedCGI) {
847 :			# We're in a web service. The environment is the user's IP, and the link
848 :			# is the URL that got us here.
849 :			$environment .= "Event Reported at IP address $key process $$.";
850 :			my $url = $SavedCGI->self_url();
851 :			# We need the user agent string and (if available) the referrer.
852 :			# The referrer will be the link.
853 :			$environment .= " User Agent $ENV{HTTP_USER_AGENT}";
854 :			if ($ENV{HTTP_REFERER}) {
855 :			my $link = $ENV{HTTP_REFERER};
856 :			$environment .= " referred from <a href=\"$link\">$link</a>.";
857 :			} else {
858 :			$environment .= " referrer unknown.";
859 :			}
860 :			# Close off the sentence with the original link.
861 :			$environment .= " URL of event is <a href=\"$url\">$url</a>.";
862 :			} else {
863 :			# No CGI object, so we're a command-line tool. Use the tracing
864 :			# key and the PID as the user identifier, and add the command.
865 :			my $key = EmergencyKey();
866 :			$environment .= "Event Reported by $key process $$.";
867 :			if ($CommandLine) {
868 :			# We're in a StandardSetup script, so we have the real command line.
869 :			$environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
870 :			} elsif ($ENV{_}) {
871 :			# We're in a BASH script, so the command has been stored in the _ variable.
872 :			$environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
873 :			}
874 :			}
875 :			# Build a GUID. We use the current time, the title, and the process ID,
876 :			# then digest the result.
877 :			my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
878 :			# Finally, the description. This is a stack trace plus various environmental stuff.
879 :			# The trace is optional.
880 :			my $stackTrace;
881 :			if ($options{noStack}) {
882 :			$stackTrace = "";
883 :			} else {
884 :			my @trace = LongMess();
885 :			# Only proceed if we got something back.
886 :			if (scalar(@trace) > 0) {
887 :			$trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
888 :			$stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
889 :			}
890 :			}
891 :			# We got the stack trace. Now it's time to put it all together.
892 :			# We have a goofy thing here in that we need to HTML-escape some sections of the description
893 :			# twice. They will be escaped once here, and then once when written by XML::Simple. They are
894 :			# unescaped once when processed by the RSS reader, and stuff in the description is treated as
895 :			# HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
896 :			# our <br>s and <pre>s are used to format the description.
897 :			$recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
898 :			my $description = "$recap$environment $stackTrace";
899 :			# Okay, we have all the pieces. Create a hash of the new event.
900 :			my $newItem = { title => $title,
901 :			description => $description,
902 :			category => $LastCategory,
903 :			pubDate => $date,
904 :			guid => $guid,
905 :			};
906 :			# We need XML capability for this.
907 :			require XML::Simple;
908 :			# The RSS document goes in here.
909 :			my $rss;
910 :			# Get the name of the RSS file. It's in the FIG temporary directory.
911 :			my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
912 :			# Open the config file and lock it.
913 :			$lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
914 :			flock $lock, LOCK_EX;
915 :			# Does it exist?
916 :			if (-s $fileName) {
917 :			# Slurp it in.
918 :			$rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
919 :	parrello	1.102	} else {
920 :	parrello	1.109	my $size = -s $fileName;
921 :			# Create an empty channel.
922 :			$rss = {
923 :			channel => {
924 :			title => 'NMPDR Warning Feed',
925 :			link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
926 :			description => "Important messages regarding the status of the NMPDR.",
927 :			generator => "NMPDR Trace Facility",
928 :			docs => "http://blogs.law.harvard.edu/tech/rss",
929 :			item => []
930 :			},
931 :			};
932 :	parrello	1.100	}
933 :	parrello	1.109	# Get the channel object.
934 :			my $channel = $rss->{channel};
935 :			# Update the last-build date.
936 :			$channel->{lastBuildDate} = $date;
937 :			# Get the item array.
938 :			my $items = $channel->{item};
939 :			# Insure it has only 100 entries.
940 :			while (scalar @{$items} > 100) {
941 :			pop @{$items};
942 :	parrello	1.104	}
943 :	parrello	1.109	# Add our new item at the front.
944 :			unshift @{$items}, $newItem;
945 :			# Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
946 :			# the requirements for those.
947 :			my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
948 :			# Here we put in the root and declaration. The problem is that the root has to have the version attribute
949 :			# in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
950 :			$xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
951 :			# We don't use Open here because we can't afford an error.
952 :			if (open XMLOUT, ">$fileName") {
953 :			print XMLOUT $xml;
954 :			close XMLOUT;
955 :	parrello	1.106	}
956 :	parrello	1.101	}
957 :	parrello	1.99	}
958 :			};
959 :	parrello	1.103	if ($@) {
960 :			# If the feed failed, we need to know why. The error will be traced, but this method will not be involved
961 :			# (which is a good thing).
962 :	parrello	1.102	my $error = $@;
963 :	parrello	1.103	Trace("Feed Error: $error") if T(Feed => 0);
964 :	parrello	1.102	}
965 :	parrello	1.106	# Be sure to unlock.
966 :			if ($lock) {
967 :			flock $lock, LOCK_UN;
968 :			undef $lock;
969 :			}
970 :	parrello	1.107	# Restore the error message.
971 :			$@ = $savedError;
972 :	parrello	1.99	}
973 :
974 :	parrello	1.106
975 :
976 :
977 :	parrello	1.93	=head3 Assert
978 :
979 :			Assert($condition1, $condition2, ... $conditionN);
980 :
981 :			Return TRUE if all the conditions are true. This method can be used in conjunction with
982 :			the OR operator and the L</Confess> method as a debugging assert.
983 :			So, for example
984 :
985 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
986 :
987 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
988 :
989 :			=cut
990 :			sub Assert {
991 :			my $retVal = 1;
992 :			LOOP: for my $condition (@_) {
993 :			if (! $condition) {
994 :			$retVal = 0;
995 :			last LOOP;
996 :			}
997 :			}
998 :			return $retVal;
999 :			}
1000 :
1001 :			=head3 Cluck
1002 :
1003 :			Cluck($message);
1004 :
1005 :			Trace the call stack. Note that for best results, you should qualify the call with a
1006 :			trace condition. For example,
1007 :
1008 :			Cluck("Starting record parse.") if T(3);
1009 :
1010 :			will only trace the stack if the trace level for the package is 3 or more.
1011 :
1012 :			=over 4
1013 :
1014 :			=item message
1015 :
1016 :			Message to include in the trace.
1017 :
1018 :			=back
1019 :
1020 :			=cut
1021 :
1022 :			sub Cluck {
1023 :			# Get the parameters.
1024 :			my ($message) = @_;
1025 :			# Trace what's happening.
1026 :			Trace("Stack trace for event: $message");
1027 :	parrello	1.99	# Get the stack trace.
1028 :			my @trace = LongMess();
1029 :			# Convert the trace to a series of messages.
1030 :			for my $line (@trace) {
1031 :			# Replace the tab at the beginning with spaces.
1032 :			$line =~ s/^\t/ /;
1033 :			# Trace the line.
1034 :			Trace($line);
1035 :			}
1036 :			# Issue a warning. This displays the event message and inserts it into the RSS error feed.
1037 :			Warn($message);
1038 :			}
1039 :
1040 :			=head3 LongMess
1041 :
1042 :			my @lines = Tracer::LongMess();
1043 :
1044 :			Return a stack trace with all tracing methods removed. The return will be in the form of a list
1045 :			of message strings.
1046 :
1047 :			=cut
1048 :
1049 :			sub LongMess {
1050 :			# Declare the return variable.
1051 :			my @retVal = ();
1052 :			my $confession = longmess("");
1053 :	parrello	1.93	for my $line (split /\s*\n/, $confession) {
1054 :	parrello	1.99	unless ($line =~ /Tracer\.pm/) {
1055 :			# Here we have a line worth keeping. Push it onto the result list.
1056 :			push @retVal, $line;
1057 :	parrello	1.97	}
1058 :	parrello	1.93	}
1059 :	parrello	1.99	# Return the result.
1060 :			return @retVal;
1061 :	parrello	1.93	}
1062 :
1063 :			=head3 ETracing
1064 :
1065 :	parrello	1.125	ETracing($parameter, %options);
1066 :	parrello	1.93
1067 :			Set up emergency tracing. Emergency tracing is tracing that is turned
1068 :			on automatically for any program that calls this method. The emergency
1069 :			tracing parameters are stored in a a file identified by a tracing key.
1070 :			If this method is called with a CGI object, then the tracing key is
1071 :			taken from a cookie. If it is called with no parameters, then the tracing
1072 :			key is taken from an environment variable. If it is called with a string,
1073 :			the tracing key is that string.
1074 :
1075 :			=over 4
1076 :
1077 :			=item parameter
1078 :
1079 :			A parameter from which the tracing key is computed. If it is a scalar,
1080 :			that scalar is used as the tracing key. If it is a CGI object, the
1081 :			tracing key is taken from the C<IP> cookie. If it is omitted, the
1082 :			tracing key is taken from the C<TRACING> environment variable. If it
1083 :			is a CGI object and emergency tracing is not on, the C<Trace> and
1084 :			C<TF> parameters will be used to determine the type of tracing.
1085 :
1086 :	parrello	1.125	=item options
1087 :
1088 :			Hash of options. The permissible options are given below.
1089 :
1090 :			=over 8
1091 :
1092 :			=item destType
1093 :
1094 :			Emergency tracing destination type to use if no tracing file is found. The
1095 :			default is C<WARN>.
1096 :
1097 :	parrello	1.124	=item noParms
1098 :
1099 :	parrello	1.125	If TRUE, then display of the saved CGI parms is suppressed. The default is FALSE.
1100 :
1101 :			=item level
1102 :
1103 :			The trace level to use if no tracing file is found. The default is C<0>.
1104 :	parrello	1.124
1105 :	parrello	1.93	=back
1106 :
1107 :			=cut
1108 :
1109 :			sub ETracing {
1110 :			# Get the parameter.
1111 :	parrello	1.125	my ($parameter, %options) = @_;
1112 :	parrello	1.93	# Check for CGI mode.
1113 :	parrello	1.99	if (defined $parameter && ref $parameter eq 'CGI') {
1114 :			$SavedCGI = $parameter;
1115 :			} else {
1116 :			$SavedCGI = undef;
1117 :			}
1118 :	parrello	1.125	# Check for the noParms option.
1119 :			my $noParms = $options{noParms} \|\| 0;
1120 :			# Get the default tracing information.
1121 :			my $tracing = $options{level} \|\| 0;
1122 :			my $dest = $options{destType} \|\| "WARN";
1123 :	parrello	1.93	# Check for emergency tracing.
1124 :			my $tkey = EmergencyKey($parameter);
1125 :			my $emergencyFile = EmergencyFileName($tkey);
1126 :	parrello	1.129	if (-e $emergencyFile && (my $stat = stat($emergencyFile))) {
1127 :	parrello	1.93	# We have the file. Read in the data.
1128 :			my @tracing = GetFile($emergencyFile);
1129 :			# Pull off the time limit.
1130 :			my $expire = shift @tracing;
1131 :			# Convert it to seconds.
1132 :			$expire *= 3600;
1133 :			# Check the file data.
1134 :			my ($now) = gettimeofday;
1135 :	parrello	1.129	if ($now - $stat->mtime <= $expire) {
1136 :	parrello	1.93	# Emergency tracing is on. Pull off the destination and
1137 :			# the trace level;
1138 :			$dest = shift @tracing;
1139 :			my $level = shift @tracing;
1140 :			# Insure Tracer is specified.
1141 :			my %moduleHash = map { $_ => 1 } @tracing;
1142 :			$moduleHash{Tracer} = 1;
1143 :			# Set the trace parameter.
1144 :			$tracing = join(" ", $level, sort keys %moduleHash);
1145 :	parrello	1.44	}
1146 :	parrello	1.36	}
1147 :	parrello	1.125	# Convert the destination to a real tracing destination.
1148 :			$dest = EmergencyTracingDest($tkey, $dest);
1149 :	parrello	1.93	# Setup the tracing we've determined from all the stuff above.
1150 :			TSetup($tracing, $dest);
1151 :	parrello	1.94	# Check to see if we're a web script.
1152 :	parrello	1.125	if (defined $SavedCGI) {
1153 :			# Yes we are. Trace the form and environment data if it's not suppressed.
1154 :			if (! $noParms) {
1155 :			TraceParms($SavedCGI);
1156 :			}
1157 :	parrello	1.94	# Check for RAW mode. In raw mode, we print a fake header so that we see everything
1158 :			# emitted by the script in its raw form.
1159 :			if (T(Raw => 3)) {
1160 :			print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1161 :			}
1162 :	parrello	1.83	}
1163 :	parrello	1.31	}
1164 :
1165 :	parrello	1.93	=head3 EmergencyFileName
1166 :
1167 :			my $fileName = Tracer::EmergencyFileName($tkey);
1168 :
1169 :			Return the emergency tracing file name. This is the file that specifies
1170 :			the tracing information.
1171 :
1172 :			=over 4
1173 :
1174 :			=item tkey
1175 :
1176 :			Tracing key for the current program.
1177 :	parrello	1.11
1178 :	parrello	1.93	=item RETURN
1179 :	parrello	1.11
1180 :	parrello	1.93	Returns the name of the file to contain the emergency tracing information.
1181 :	parrello	1.11
1182 :	parrello	1.93	=back
1183 :	parrello	1.11
1184 :			=cut
1185 :
1186 :	parrello	1.93	sub EmergencyFileName {
1187 :			# Get the parameters.
1188 :			my ($tkey) = @_;
1189 :			# Compute the emergency tracing file name.
1190 :			return "$FIG_Config::temp/Emergency$tkey.txt";
1191 :	olson	1.1	}
1192 :
1193 :	parrello	1.93	=head3 EmergencyFileTarget
1194 :	parrello	1.10
1195 :	parrello	1.93	my $fileName = Tracer::EmergencyFileTarget($tkey);
1196 :	parrello	1.10
1197 :	parrello	1.93	Return the emergency tracing target file name. This is the file that receives
1198 :			the tracing output for file-based tracing.
1199 :	parrello	1.10
1200 :	parrello	1.93	=over 4
1201 :	parrello	1.10
1202 :	parrello	1.93	=item tkey
1203 :	parrello	1.10
1204 :	parrello	1.93	Tracing key for the current program.
1205 :	parrello	1.10
1206 :	parrello	1.93	=item RETURN
1207 :	parrello	1.10
1208 :	parrello	1.93	Returns the name of the file to contain the trace output.
1209 :	parrello	1.10
1210 :	parrello	1.93	=back
1211 :	parrello	1.10
1212 :	parrello	1.93	=cut
1213 :	parrello	1.10
1214 :	parrello	1.93	sub EmergencyFileTarget {
1215 :			# Get the parameters.
1216 :			my ($tkey) = @_;
1217 :			# Compute the emergency tracing file name.
1218 :			return "$FIG_Config::temp/trace$tkey.log";
1219 :			}
1220 :	parrello	1.10
1221 :	parrello	1.93	=head3 EmergencyTracingDest
1222 :	parrello	1.10
1223 :	parrello	1.93	my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1224 :	parrello	1.10
1225 :	parrello	1.93	This method converts an emergency tracing destination to a real
1226 :			tracing destination. The main difference is that if the
1227 :			destination is C<FILE> or C<APPEND>, we convert it to file
1228 :			output. If the destination is C<DUAL>, we convert it to file
1229 :			and standard output.
1230 :	parrello	1.10
1231 :			=over 4
1232 :
1233 :	parrello	1.93	=item tkey
1234 :	parrello	1.10
1235 :	parrello	1.93	Tracing key for this environment.
1236 :	parrello	1.10
1237 :	parrello	1.93	=item myDest
1238 :	parrello	1.10
1239 :	parrello	1.93	Destination from the emergency tracing file.
1240 :	parrello	1.10
1241 :			=item RETURN
1242 :
1243 :	parrello	1.93	Returns a destination that can be passed into L</TSetup>.
1244 :	parrello	1.10
1245 :			=back
1246 :
1247 :			=cut
1248 :
1249 :	parrello	1.93	sub EmergencyTracingDest {
1250 :	parrello	1.12	# Get the parameters.
1251 :	parrello	1.93	my ($tkey, $myDest) = @_;
1252 :			# Declare the return variable.
1253 :			my $retVal = $myDest;
1254 :			# Process according to the destination value.
1255 :			if ($myDest eq 'FILE') {
1256 :			$retVal = ">" . EmergencyFileTarget($tkey);
1257 :			} elsif ($myDest eq 'APPEND') {
1258 :			$retVal = ">>" . EmergencyFileTarget($tkey);
1259 :			} elsif ($myDest eq 'DUAL') {
1260 :			$retVal = "+>" . EmergencyFileTarget($tkey);
1261 :	parrello	1.97	} elsif ($myDest eq 'WARN') {
1262 :			$retVal = "WARN";
1263 :	parrello	1.12	}
1264 :	parrello	1.93	# Return the result.
1265 :			return $retVal;
1266 :	parrello	1.10	}
1267 :
1268 :	parrello	1.93	=head3 Emergency
1269 :
1270 :			Emergency($key, $hours, $dest, $level, @modules);
1271 :
1272 :			Turn on emergency tracing. This method is normally invoked over the web from
1273 :			a debugging console, but it can also be called by the C<trace.pl> script.
1274 :			The caller specifies the duration of the emergency in hours, the desired tracing
1275 :			destination, the trace level, and a list of the trace modules to activate.
1276 :			For the length of the duration, when a program in an environment with the
1277 :			specified tracing key active invokes a Sprout CGI script, tracing will be
1278 :			turned on automatically. See L</TSetup> for more about tracing setup and
1279 :			L</ETracing> for more about emergency tracing.
1280 :
1281 :			=over 4
1282 :	parrello	1.11
1283 :	parrello	1.93	=item tkey
1284 :	parrello	1.11
1285 :	parrello	1.93	The tracing key. This is used to identify the control file and the trace file.
1286 :	parrello	1.11
1287 :	parrello	1.93	=item hours
1288 :	parrello	1.11
1289 :	parrello	1.93	Number of hours to keep emergency tracing alive.
1290 :	parrello	1.11
1291 :	parrello	1.93	=item dest
1292 :	parrello	1.11
1293 :	parrello	1.93	Tracing destination. If no path information is specified for a file
1294 :			destination, it is put in the FIG temporary directory.
1295 :	parrello	1.11
1296 :	parrello	1.93	=item level
1297 :	parrello	1.11
1298 :	parrello	1.93	Tracing level. A higher level means more trace messages.
1299 :	parrello	1.11
1300 :	parrello	1.93	=item modules
1301 :	parrello	1.11
1302 :	parrello	1.93	A list of the tracing modules to activate.
1303 :	parrello	1.11
1304 :			=back
1305 :
1306 :			=cut
1307 :	parrello	1.93
1308 :			sub Emergency {
1309 :	parrello	1.11	# Get the parameters.
1310 :	parrello	1.93	my ($tkey, $hours, $dest, $level, @modules) = @_;
1311 :			# Create the emergency file.
1312 :			my $specFile = EmergencyFileName($tkey);
1313 :			my $outHandle = Open(undef, ">$specFile");
1314 :			print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1315 :	parrello	1.11	}
1316 :
1317 :	parrello	1.93	=head3 EmergencyKey
1318 :
1319 :			my $tkey = EmergencyKey($parameter);
1320 :
1321 :			Return the Key to be used for emergency tracing. This could be an IP address,
1322 :			a session ID, or a user name, depending on the environment.
1323 :	parrello	1.11
1324 :	parrello	1.93	=over 4
1325 :	parrello	1.11
1326 :	parrello	1.93	=item parameter
1327 :	parrello	1.11
1328 :	parrello	1.93	Parameter defining the method for finding the tracing key. If it is a scalar,
1329 :			then it is presumed to be the tracing key itself. If it is a CGI object, then
1330 :			the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1331 :			taken from the C<TRACING> environment variable.
1332 :	parrello	1.29
1333 :	parrello	1.93	=item RETURN
1334 :	parrello	1.11
1335 :	parrello	1.93	Returns the key to be used for labels in emergency tracing.
1336 :	parrello	1.11
1337 :	parrello	1.93	=back
1338 :	parrello	1.11
1339 :	parrello	1.93	=cut
1340 :	parrello	1.29
1341 :	parrello	1.93	sub EmergencyKey {
1342 :			# Get the parameters.
1343 :			my ($parameter) = @_;
1344 :			# Declare the return variable.
1345 :			my $retVal;
1346 :			# Determine the parameter type.
1347 :	parrello	1.128	if (! defined $parameter) {
1348 :	parrello	1.99	# Here we're supposed to check the environment. If that fails, we
1349 :			# get the effective login ID.
1350 :			$retVal = $ENV{TRACING} \|\| scalar getpwuid($<);
1351 :	parrello	1.93	} else {
1352 :			my $ptype = ref $parameter;
1353 :			if ($ptype eq 'CGI') {
1354 :			# Here we were invoked from a web page. Look for a cookie.
1355 :			$retVal = $parameter->cookie('IP');
1356 :			} elsif (! $ptype) {
1357 :			# Here the key was passed in.
1358 :			$retVal = $parameter;
1359 :			}
1360 :			}
1361 :			# If no luck finding a key, use the PID.
1362 :			if (! defined $retVal) {
1363 :			$retVal = $$;
1364 :			}
1365 :			# Return the result.
1366 :			return $retVal;
1367 :			}
1368 :	parrello	1.11
1369 :
1370 :	parrello	1.93	=head3 TraceParms
1371 :	parrello	1.11
1372 :	parrello	1.93	Tracer::TraceParms($cgi);
1373 :	parrello	1.11
1374 :	parrello	1.93	Trace the CGI parameters at trace level CGI => 3 and the environment variables
1375 :	parrello	1.94	at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1376 :	parrello	1.11
1377 :	parrello	1.93	=over 4
1378 :	parrello	1.11
1379 :	parrello	1.93	=item cgi
1380 :	parrello	1.31
1381 :	parrello	1.93	CGI query object containing the parameters to trace.
1382 :	parrello	1.31
1383 :	parrello	1.11	=back
1384 :
1385 :			=cut
1386 :	parrello	1.93
1387 :			sub TraceParms {
1388 :	parrello	1.11	# Get the parameters.
1389 :	parrello	1.93	my ($cgi) = @_;
1390 :	parrello	1.94	if (T(CGI => 2)) {
1391 :	parrello	1.115	# Here we trace the GET-style URL for the script, but only if it's
1392 :			# relatively small.
1393 :			my $url = $cgi->url(-relative => 1, -query => 1);
1394 :			my $len = length($url);
1395 :			if ($len < 500) {
1396 :			Trace("[URL] $url");
1397 :			} elsif ($len > 2048) {
1398 :			Trace("[URL] URL is too long to use with GET ($len characters).");
1399 :			} else {
1400 :			Trace("[URL] URL length is $len characters.");
1401 :			}
1402 :	parrello	1.94	}
1403 :	parrello	1.93	if (T(CGI => 3)) {
1404 :			# Here we want to trace the parameter data.
1405 :			my @names = $cgi->param;
1406 :			for my $parmName (sort @names) {
1407 :			# Note we skip the Trace parameters, which are for our use only.
1408 :			if ($parmName ne 'Trace' && $parmName ne 'TF') {
1409 :			my @values = $cgi->param($parmName);
1410 :	parrello	1.97	Trace("[CGI] $parmName = " . join(", ", @values));
1411 :	parrello	1.93	}
1412 :			}
1413 :			# Display the request method.
1414 :			my $method = $cgi->request_method();
1415 :			Trace("Method: $method");
1416 :			}
1417 :			if (T(CGI => 4)) {
1418 :			# Here we want the environment data too.
1419 :			for my $envName (sort keys %ENV) {
1420 :	parrello	1.97	Trace("[ENV] $envName = $ENV{$envName}");
1421 :	parrello	1.12	}
1422 :			}
1423 :	parrello	1.11	}
1424 :
1425 :	parrello	1.94	=head3 TraceImages
1426 :
1427 :			Tracer::TraceImages($htmlString);
1428 :
1429 :			Trace information about all of an html document's images. The tracing
1430 :			will be for type "IMG" at level 3. The image's source string
1431 :			will be displayed. This is generally either the URL of the image or
1432 :			raw data for the image itself. If the source is too long, only the first 300
1433 :			characters will be shown at trace level 3. The entire source will be shown,
1434 :			however, at trace level 4. This method is not very smart, and might catch
1435 :			Javascript code, but it is still useful when debugging the arcane
1436 :			behavior of images in multiple browser environments.
1437 :
1438 :			=over 4
1439 :
1440 :			=item htmlString
1441 :
1442 :			HTML text for an outgoing web page.
1443 :
1444 :			=back
1445 :
1446 :			=cut
1447 :
1448 :			sub TraceImages {
1449 :			# Only proceed if we're at the proper trace level.
1450 :			if (T(IMG => 3)) {
1451 :			# For performance reasons we're manipulating $_[0] instead of retrieving the string
1452 :			# into a variable called "$htmlString". This is because we expect html strings to be
1453 :			# long, and don't want to copy them any more than we have to.
1454 :			Trace(length($_[0]) . " characters in web page.");
1455 :			# Loop through the HTML, culling image tags.
1456 :			while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1457 :			# Extract the source string and determine whether or not it's too long.
1458 :			my $srcString = $1;
1459 :			my $pos = pos($_[0]) - length($srcString);
1460 :			my $excess = length($srcString) - 300;
1461 :			# We'll put the display string in here.
1462 :			my $srcDisplay = $srcString;
1463 :			# If it's a data string, split it at the comma.
1464 :			$srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1465 :			# If there's no excess or we're at trace level 4, we're done. At level 3 with
1466 :			# a long string, however, we only show the first 300 characters.
1467 :			if ($excess > 0 && ! T(IMG => 4)) {
1468 :			$srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1469 :			}
1470 :			# Output the trace message.
1471 :			Trace("Image tag at position $pos:\n$srcDisplay");
1472 :			}
1473 :			}
1474 :			}
1475 :
1476 :	parrello	1.93	=head2 Command-Line Utility Methods
1477 :	olson	1.1
1478 :	parrello	1.93	=head3 SendSMS
1479 :	olson	1.1
1480 :	parrello	1.93	my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1481 :	olson	1.1
1482 :	parrello	1.93	Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1483 :			user name, password, and API ID for the relevant account in the hash reference variable
1484 :			I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1485 :			example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1486 :			is C<2561022>, then the FIG_Config file must contain
1487 :	olson	1.1
1488 :	parrello	1.93	$phone = { user => 'BruceTheHumanPet',
1489 :			password => 'silly',
1490 :			api_id => '2561022' };
1491 :	olson	1.1
1492 :	parrello	1.93	The original purpose of this method was to insure Bruce would be notified immediately when the
1493 :			Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1494 :			when you call this method.
1495 :	olson	1.1
1496 :	parrello	1.93	The message ID will be returned if successful, and C<undef> if an error occurs.
1497 :	parrello	1.74
1498 :	parrello	1.93	=over 4
1499 :	parrello	1.74
1500 :	parrello	1.93	=item phoneNumber
1501 :	parrello	1.74
1502 :	parrello	1.93	Phone number to receive the message, in international format. A United States phone number
1503 :			would be prefixed by "1". A British phone number would be prefixed by "44".
1504 :	parrello	1.74
1505 :	parrello	1.93	=item msg
1506 :	parrello	1.74
1507 :	parrello	1.93	Message to send to the specified phone.
1508 :	parrello	1.74
1509 :			=item RETURN
1510 :
1511 :	parrello	1.93	Returns the message ID if successful, and C<undef> if the message could not be sent.
1512 :	parrello	1.74
1513 :	parrello	1.78	=back
1514 :
1515 :	parrello	1.74	=cut
1516 :
1517 :	parrello	1.93	sub SendSMS {
1518 :	parrello	1.74	# Get the parameters.
1519 :	parrello	1.93	my ($phoneNumber, $msg) = @_;
1520 :			# Declare the return variable. If we do not change it, C<undef> will be returned.
1521 :	parrello	1.74	my $retVal;
1522 :	parrello	1.93	# Only proceed if we have phone support.
1523 :			if (! defined $FIG_Config::phone) {
1524 :			Trace("Phone support not present in FIG_Config.") if T(1);
1525 :			} else {
1526 :			# Get the phone data.
1527 :			my $parms = $FIG_Config::phone;
1528 :			# Get the Clickatell URL.
1529 :			my $url = "http://api.clickatell.com/http/";
1530 :			# Create the user agent.
1531 :			my $ua = LWP::UserAgent->new;
1532 :			# Request a Clickatell session.
1533 :			my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1534 :			password => $parms->{password},
1535 :			api_id => $parms->{api_id},
1536 :			to => $phoneNumber,
1537 :			text => $msg});
1538 :			# Check for an error.
1539 :			if (! $resp->is_success) {
1540 :			Trace("Alert failed.") if T(1);
1541 :			} else {
1542 :			# Get the message ID.
1543 :			my $rstring = $resp->content;
1544 :			if ($rstring =~ /^ID:\s+(.*)$/) {
1545 :			$retVal = $1;
1546 :			} else {
1547 :			Trace("Phone attempt failed with $rstring") if T(1);
1548 :			}
1549 :			}
1550 :	parrello	1.74	}
1551 :			# Return the result.
1552 :			return $retVal;
1553 :			}
1554 :
1555 :	parrello	1.93	=head3 StandardSetup
1556 :	olson	1.1
1557 :	parrello	1.93	my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1558 :	olson	1.1
1559 :	parrello	1.93	This method performs standard command-line parsing and tracing setup. The return
1560 :			values are a hash of the command-line options and a list of the positional
1561 :			parameters. Tracing is automatically set up and the command-line options are
1562 :			validated.
1563 :	olson	1.1
1564 :	parrello	1.93	This is a complex method that does a lot of grunt work. The parameters can
1565 :			be more easily understood, however, once they are examined individually.
1566 :	olson	1.1
1567 :	parrello	1.93	The I<categories> parameter is the most obtuse. It is a reference to a list of
1568 :			special-purpose tracing categories. Most tracing categories are PERL package
1569 :			names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1570 :			B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1571 :	olson	1.1
1572 :	parrello	1.93	["Sprout", "SproutLoad", "ERDB"]
1573 :	olson	1.1
1574 :	parrello	1.93	This would cause trace messages in the specified three packages to appear in
1575 :			the output. There are two special tracing categories that are automatically
1576 :			handled by this method. In other words, if you used L</TSetup> you would need
1577 :			to include these categories manually, but if you use this method they are turned
1578 :			on automatically.
1579 :	parrello	1.5
1580 :			=over 4
1581 :
1582 :	parrello	1.93	=item SQL
1583 :	parrello	1.5
1584 :	parrello	1.93	Traces SQL commands and activity.
1585 :	parrello	1.5
1586 :	parrello	1.93	=item Tracer
1587 :	parrello	1.5
1588 :	parrello	1.93	Traces error messages and call stacks.
1589 :	parrello	1.5
1590 :			=back
1591 :
1592 :	parrello	1.93	C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1593 :			The trace level is specified using the C<-trace> command-line option. For example,
1594 :			the following command line for C<TransactFeatures> turns on SQL tracing and runs
1595 :			all tracing at level 3.
1596 :	parrello	1.5
1597 :	parrello	1.93	TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1598 :	parrello	1.5
1599 :	parrello	1.93	Standard tracing is output to the standard output and echoed to the file
1600 :			C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1601 :			process ID. You can also specify the C<user> parameter to put a user ID
1602 :			instead of a process ID in the trace file name. So, for example
1603 :	olson	1.1
1604 :	parrello	1.93	The default trace level is 2. To get all messages, specify a trace level of 4.
1605 :			For a genome-by-genome update, use 3.
1606 :	olson	1.1
1607 :	parrello	1.93	TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1608 :	olson	1.1
1609 :	parrello	1.93	would send the trace output to C<traceBruce.log> in the temporary directory.
1610 :	olson	1.1
1611 :	parrello	1.93	The I<options> parameter is a reference to a hash containing the command-line
1612 :			options, their default values, and an explanation of what they mean. Command-line
1613 :			options may be in the form of switches or keywords. In the case of a switch, the
1614 :			option value is 1 if it is specified and 0 if it is not specified. In the case
1615 :			of a keyword, the value is separated from the option name by an equal sign. You
1616 :			can see this last in the command-line example above.
1617 :	olson	1.1
1618 :	parrello	1.93	You can specify a different default trace level by setting C<$options->{trace}>
1619 :			prior to calling this method.
1620 :	olson	1.1
1621 :	parrello	1.93	An example at this point would help. Consider, for example, the command-line utility
1622 :			C<TransactFeatures>. It accepts a list of positional parameters plus the options
1623 :			C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1624 :			the following code.
1625 :	olson	1.1
1626 :	parrello	1.93	my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1627 :			{ safe => [0, "use database transactions"],
1628 :			noAlias => [0, "do not expect aliases in CHANGE transactions"],
1629 :			start => [' ', "start with this genome"],
1630 :			tblFiles => [0, "output TBL files containing the corrected IDs"] },
1631 :			"<command> <transactionDirectory> <IDfile>",
1632 :			@ARGV);
1633 :	olson	1.1
1634 :
1635 :	parrello	1.93	The call to C<ParseCommand> specifies the default values for the options and
1636 :			stores the actual options in a hash that is returned as C<$options>. The
1637 :			positional parameters are returned in C<@parameters>.
1638 :	olson	1.1
1639 :	parrello	1.93	The following is a sample command line for C<TransactFeatures>.
1640 :	olson	1.1
1641 :	parrello	1.93	TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1642 :	olson	1.1
1643 :	parrello	1.93	Single and double hyphens are equivalent. So, you could also code the
1644 :			above command as
1645 :	olson	1.1
1646 :	parrello	1.93	TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1647 :	olson	1.1
1648 :	parrello	1.93	In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1649 :			parameters, and would find themselves in I<@parameters> after executing the
1650 :			above code fragment. The tracing would be set to level 2, and the categories
1651 :			would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1652 :			and C<DocUtils> was included because it came in within the first parameter
1653 :			to this method. The I<$options> hash would be
1654 :	olson	1.1
1655 :	parrello	1.93	{ trace => 2, sql => 0, safe => 0,
1656 :			noAlias => 1, start => ' ', tblFiles => 0 }
1657 :	olson	1.1
1658 :	parrello	1.93	Use of C<StandardSetup> in this way provides a simple way of performing
1659 :			standard tracing setup and command-line parsing. Note that the caller is
1660 :			not even aware of the command-line switches C<-trace> and C<-sql>, which
1661 :			are used by this method to control the tracing. If additional tracing features
1662 :			need to be added in the future, they can be processed by this method without
1663 :			upsetting the command-line utilities.
1664 :	olson	1.1
1665 :	parrello	1.93	If the C<background> option is specified on the command line, then the
1666 :			standard and error outputs will be directed to files in the temporary
1667 :			directory, using the same suffix as the trace file. So, if the command
1668 :			line specified
1669 :	olson	1.1
1670 :	parrello	1.93	-user=Bruce -background
1671 :	olson	1.1
1672 :	parrello	1.93	then the trace output would go to C<traceBruce.log>, the standard output to
1673 :			C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1674 :			simplify starting a command in the background.
1675 :	olson	1.1
1676 :	parrello	1.93	The user name is also used as the tracing key for L</Emergency Tracing>.
1677 :			Specifying a value of C<E> for the trace level causes emergency tracing to
1678 :			be used instead of custom tracing. If the user name is not specified,
1679 :			the tracing key is taken from the C<Tracing> environment variable. If there
1680 :	parrello	1.103	is no value for that variable, the tracing key will be computed from the active
1681 :			login ID.
1682 :
1683 :			Since the default situation in StandardSetup is to trace to the standard
1684 :			output, errors that occur in command-line scripts will not generate
1685 :			RSS events. To force the events, use the C<warn> option.
1686 :
1687 :			TransactFeatures -background -warn register ../xacts IDs.tbl
1688 :	olson	1.1
1689 :	parrello	1.93	Finally, if the special option C<-help> is specified, the option
1690 :			names will be traced at level 0 and the program will exit without processing.
1691 :			This provides a limited help capability. For example, if the user enters
1692 :	olson	1.1
1693 :	parrello	1.93	TransactFeatures -help
1694 :	olson	1.1
1695 :	parrello	1.93	he would see the following output.
1696 :	olson	1.1
1697 :	parrello	1.93	TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1698 :			-trace tracing level (default E)
1699 :			-sql trace SQL commands
1700 :			-safe use database transactions
1701 :			-noAlias do not expect aliases in CHANGE transactions
1702 :			-start start with this genome
1703 :			-tblFiles output TBL files containing the corrected IDs
1704 :	parrello	1.111	-forked do not erase the trace file before tracing
1705 :	olson	1.1
1706 :	parrello	1.93	The caller has the option of modifying the tracing scheme by placing a value
1707 :			for C<trace> in the incoming options hash. The default value can be overridden,
1708 :			or the tracing to the standard output can be turned off by suffixing a minus
1709 :			sign to the trace level. So, for example,
1710 :	olson	1.1
1711 :	parrello	1.93	{ trace => [0, "tracing level (default 0)"],
1712 :			...
1713 :	olson	1.1
1714 :	parrello	1.93	would set the default trace level to 0 instead of E, while
1715 :	olson	1.1
1716 :	parrello	1.93	{ trace => ["2-", "tracing level (default 2)"],
1717 :			...
1718 :	olson	1.1
1719 :	parrello	1.93	would set the default to 2, but trace only to the log file, not to the
1720 :			standard output.
1721 :	olson	1.1
1722 :	parrello	1.93	The parameters to this method are as follows.
1723 :	olson	1.1
1724 :	parrello	1.93	=over 4
1725 :	olson	1.1
1726 :	parrello	1.93	=item categories
1727 :	parrello	1.2
1728 :	parrello	1.93	Reference to a list of tracing category names. These should be names of
1729 :			packages whose internal workings will need to be debugged to get the
1730 :			command working.
1731 :	olson	1.1
1732 :	parrello	1.93	=item options
1733 :	olson	1.1
1734 :	parrello	1.93	Reference to a hash containing the legal options for the current command mapped
1735 :			to their default values and descriptions. The user can override the defaults
1736 :			by specifying the options as command-line switches prefixed by a hyphen.
1737 :			Tracing-related options may be added to this hash. If the C<-h> option is
1738 :			specified on the command line, the option descriptions will be used to
1739 :			explain the options. To turn off tracing to the standard output, add a
1740 :			minus sign to the value for C<trace> (see above).
1741 :	olson	1.1
1742 :	parrello	1.93	=item parmHelp
1743 :	olson	1.1
1744 :	parrello	1.93	A string that vaguely describes the positional parameters. This is used
1745 :			if the user specifies the C<-h> option.
1746 :	olson	1.1
1747 :	parrello	1.93	=item argv
1748 :	olson	1.1
1749 :	parrello	1.93	List of command line parameters, including the option switches, which must
1750 :			precede the positional parameters and be prefixed by a hyphen.
1751 :	olson	1.1
1752 :			=item RETURN
1753 :
1754 :	parrello	1.93	Returns a list. The first element of the list is the reference to a hash that
1755 :			maps the command-line option switches to their values. These will either be the
1756 :			default values or overrides specified on the command line. The remaining
1757 :			elements of the list are the position parameters, in order.
1758 :	olson	1.1
1759 :			=back
1760 :
1761 :			=cut
1762 :
1763 :	parrello	1.93	sub StandardSetup {
1764 :			# Get the parameters.
1765 :			my ($categories, $options, $parmHelp, @argv) = @_;
1766 :			# Get the default tracing key.
1767 :			my $tkey = EmergencyKey();
1768 :	parrello	1.104	# Save the command line.
1769 :			$CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1770 :	parrello	1.93	# Add the tracing options.
1771 :			if (! exists $options->{trace}) {
1772 :			$options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1773 :			}
1774 :	parrello	1.112	if (! exists $options->{forked}) {
1775 :			$options->{forked} = [0, "keep old trace file"];
1776 :			}
1777 :	parrello	1.93	$options->{sql} = [0, "turn on SQL tracing"];
1778 :			$options->{help} = [0, "display command-line options"];
1779 :			$options->{user} = [$tkey, "tracing key"];
1780 :			$options->{background} = [0, "spool standard and error output"];
1781 :	parrello	1.103	$options->{warn} = [0, "send errors to RSS feed"];
1782 :	parrello	1.113	$options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1783 :	parrello	1.93	# Create a parsing hash from the options hash. The parsing hash
1784 :			# contains the default values rather than the default value
1785 :			# and the description. While we're at it, we'll memorize the
1786 :			# length of the longest option name.
1787 :			my $longestName = 0;
1788 :			my %parseOptions = ();
1789 :			for my $key (keys %{$options}) {
1790 :			if (length $key > $longestName) {
1791 :			$longestName = length $key;
1792 :			}
1793 :			$parseOptions{$key} = $options->{$key}->[0];
1794 :			}
1795 :			# Parse the command line.
1796 :			my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1797 :			# Get the logfile suffix.
1798 :			my $suffix = $retOptions->{user};
1799 :	parrello	1.113	# We'll put the trace file name in here. We need it later if background
1800 :			# mode is on.
1801 :			my $traceFileName;
1802 :	parrello	1.93	# Now we want to set up tracing. First, we need to know if the user
1803 :			# wants emergency tracing.
1804 :			if ($retOptions->{trace} eq 'E') {
1805 :			ETracing($retOptions->{user});
1806 :			} else {
1807 :			# Here the tracing is controlled from the command line.
1808 :			my @cats = @{$categories};
1809 :			if ($retOptions->{sql}) {
1810 :			push @cats, "SQL";
1811 :			}
1812 :	parrello	1.103	if ($retOptions->{warn}) {
1813 :			push @cats, "Feed";
1814 :			}
1815 :	parrello	1.93	# Add the default categories.
1816 :			push @cats, "Tracer";
1817 :	parrello	1.113	# Check for more tracing groups.
1818 :			if ($retOptions->{moreTracing}) {
1819 :			push @cats, split /,/, $retOptions->{moreTracing};
1820 :			}
1821 :	parrello	1.93	# Next, we create the category string by joining the categories.
1822 :			my $cats = join(" ", @cats);
1823 :			# Check to determine whether or not the caller wants to turn off tracing
1824 :			# to the standard output.
1825 :			my $traceLevel = $retOptions->{trace};
1826 :			my $textOKFlag = 1;
1827 :			if ($traceLevel =~ /^(.)-/) {
1828 :			$traceLevel = $1;
1829 :			$textOKFlag = 0;
1830 :			}
1831 :			# Now we set up the trace mode.
1832 :			my $traceMode;
1833 :			# Verify that we can open a file in the FIG temporary directory.
1834 :			my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1835 :	parrello	1.111	my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1836 :			if (open TESTTRACE, "$traceFileSpec") {
1837 :	parrello	1.93	# Here we can trace to a file.
1838 :	parrello	1.111	$traceMode = ">>$traceFileName";
1839 :	parrello	1.93	if ($textOKFlag) {
1840 :			# Echo to standard output if the text-OK flag is set.
1841 :			$traceMode = "+$traceMode";
1842 :			}
1843 :			# Close the test file.
1844 :			close TESTTRACE;
1845 :			} else {
1846 :	parrello	1.98	# Here we can't trace to a file. Complain about this.
1847 :			warn "Could not open trace file $traceFileName: $!\n";
1848 :			# We trace to the standard output if it's
1849 :			# okay, and the error log otherwise.
1850 :	parrello	1.93	if ($textOKFlag) {
1851 :			$traceMode = "TEXT";
1852 :	parrello	1.12	} else {
1853 :	parrello	1.93	$traceMode = "WARN";
1854 :	parrello	1.12	}
1855 :			}
1856 :	parrello	1.93	# Now set up the tracing.
1857 :			TSetup("$traceLevel $cats", $traceMode);
1858 :			}
1859 :	parrello	1.113	# Check for background mode.
1860 :			if ($retOptions->{background}) {
1861 :			my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1862 :			my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1863 :			# Spool the output.
1864 :			open STDOUT, ">$outFileName";
1865 :			# If we have a trace file, trace the errors to the log. Otherwise,
1866 :			# spool the errors.
1867 :			if (defined $traceFileName) {
1868 :			open STDERR, "\| Tracer $traceFileName";
1869 :			} else {
1870 :			open STDERR, ">$errFileName";
1871 :			}
1872 :			# Check for phone support. If we have phone support and a phone number,
1873 :			# we want to turn it on.
1874 :			if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1875 :			$retOptions->{phone} = $ENV{PHONE};
1876 :			}
1877 :			}
1878 :	parrello	1.93	# Check for the "help" option. If it is specified, dump the command-line
1879 :			# options and exit the program.
1880 :			if ($retOptions->{help}) {
1881 :			$0 =~ m#[/\\](\w+)(\.pl)?$#i;
1882 :			print "$1 [options] $parmHelp\n";
1883 :			for my $key (sort keys %{$options}) {
1884 :			my $name = Pad($key, $longestName, 0, ' ');
1885 :			my $desc = $options->{$key}->[1];
1886 :			if ($options->{$key}->[0]) {
1887 :			$desc .= " (default " . $options->{$key}->[0] . ")";
1888 :			}
1889 :			print " $name $desc\n";
1890 :	parrello	1.36	}
1891 :	parrello	1.93	exit(0);
1892 :			}
1893 :			# Trace the options, if applicable.
1894 :			if (T(3)) {
1895 :			my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1896 :			Trace("Selected options: " . join(", ", sort @parms) . ".");
1897 :	parrello	1.3	}
1898 :	parrello	1.93	# Return the parsed parameters.
1899 :			return ($retOptions, @retParameters);
1900 :	olson	1.1	}
1901 :
1902 :	parrello	1.93	=head3 ReadOptions
1903 :	olson	1.1
1904 :	parrello	1.93	my %options = Tracer::ReadOptions($fileName);
1905 :	olson	1.1
1906 :	parrello	1.93	Read a set of options from a file. Each option is encoded in a line of text that has the
1907 :			format
1908 :	olson	1.1
1909 :	parrello	1.93	I<optionName>C<=>I<optionValue>C<; >I<comment>
1910 :	olson	1.1
1911 :	parrello	1.93	The option name must consist entirely of letters, digits, and the punctuation characters
1912 :			C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1913 :			character is a semi-colon will be ignored. The return hash will map each option name to
1914 :			the corresponding option value.
1915 :	olson	1.1
1916 :			=over 4
1917 :
1918 :	parrello	1.93	=item fileName
1919 :	olson	1.1
1920 :	parrello	1.93	Name of the file containing the option data.
1921 :	olson	1.1
1922 :			=item RETURN
1923 :
1924 :	parrello	1.93	Returns a hash mapping the option names specified in the file to their corresponding option
1925 :			value.
1926 :	olson	1.1
1927 :			=back
1928 :
1929 :			=cut
1930 :
1931 :	parrello	1.93	sub ReadOptions {
1932 :	parrello	1.12	# Get the parameters.
1933 :	parrello	1.93	my ($fileName) = @_;
1934 :			# Open the file.
1935 :			(open CONFIGFILE, "<$fileName") \|\| Confess("Could not open option file $fileName.");
1936 :			# Count the number of records read.
1937 :			my ($records, $comments) = 0;
1938 :			# Create the return hash.
1939 :			my %retVal = ();
1940 :			# Loop through the file, accumulating key-value pairs.
1941 :			while (my $line = <CONFIGFILE>) {
1942 :			# Denote we've read a line.
1943 :			$records++;
1944 :			# Determine the line type.
1945 :			if ($line =~ /^\s*[\n\r]/) {
1946 :			# A blank line is a comment.
1947 :			$comments++;
1948 :			} elsif ($line =~ /^\s([A-Za-z0-9_\.]+)=([^;]);/) {
1949 :			# Here we have an option assignment.
1950 :			retVal{$1} = $2;
1951 :			} elsif ($line =~ /^\s*;/) {
1952 :			# Here we have a text comment.
1953 :			$comments++;
1954 :	parrello	1.12	} else {
1955 :	parrello	1.93	# Here we have an invalid line.
1956 :			Trace("Invalid option statement in record $records.") if T(0);
1957 :	parrello	1.12	}
1958 :			}
1959 :	parrello	1.93	# Return the hash created.
1960 :			return %retVal;
1961 :	olson	1.1	}
1962 :
1963 :	parrello	1.93	=head3 GetOptions
1964 :	parrello	1.9
1965 :	parrello	1.93	Tracer::GetOptions(\%defaults, \%options);
1966 :	parrello	1.9
1967 :	parrello	1.93	Merge a specified set of options into a table of defaults. This method takes two hash references
1968 :			as input and uses the data from the second to update the first. If the second does not exist,
1969 :			there will be no effect. An error will be thrown if one of the entries in the second hash does not
1970 :			exist in the first.
1971 :	parrello	1.9
1972 :	parrello	1.93	Consider the following example.
1973 :	parrello	1.9
1974 :	parrello	1.93	my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1975 :	parrello	1.9
1976 :	parrello	1.93	In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1977 :			B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1978 :			B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1979 :			the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1980 :			will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1981 :	parrello	1.9
1982 :	parrello	1.93	{databaseType => 'Oracle'}
1983 :	parrello	1.9
1984 :	parrello	1.93	an error will occur because the B<databaseType> option does not exist.
1985 :	parrello	1.9
1986 :	parrello	1.93	=over 4
1987 :	parrello	1.9
1988 :	parrello	1.93	=item defaults
1989 :	parrello	1.9
1990 :	parrello	1.93	Table of default option values.
1991 :	parrello	1.9
1992 :	parrello	1.93	=item options
1993 :	olson	1.1
1994 :	parrello	1.93	Table of overrides, if any.
1995 :	olson	1.1
1996 :			=item RETURN
1997 :
1998 :	parrello	1.93	Returns a reference to the default table passed in as the first parameter.
1999 :	olson	1.1
2000 :			=back
2001 :
2002 :			=cut
2003 :
2004 :	parrello	1.93	sub GetOptions {
2005 :			# Get the parameters.
2006 :			my ($defaults, $options) = @_;
2007 :			# Check for overrides.
2008 :			if ($options) {
2009 :			# Loop through the overrides.
2010 :			while (my ($option, $setting) = each %{$options}) {
2011 :			# Insure this override exists.
2012 :			if (!exists $defaults->{$option}) {
2013 :			croak "Unrecognized option $option encountered.";
2014 :	parrello	1.12	} else {
2015 :	parrello	1.93	# Apply the override.
2016 :			$defaults->{$option} = $setting;
2017 :	parrello	1.12	}
2018 :			}
2019 :			}
2020 :	parrello	1.93	# Return the merged table.
2021 :			return $defaults;
2022 :	olson	1.1	}
2023 :
2024 :	parrello	1.93	=head3 MergeOptions
2025 :	olson	1.1
2026 :	parrello	1.93	Tracer::MergeOptions(\%table, \%defaults);
2027 :	olson	1.1
2028 :	parrello	1.93	Merge default values into a hash table. This method looks at the key-value pairs in the
2029 :			second (default) hash, and if a matching key is not found in the first hash, the default
2030 :			pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2031 :			checking and no return value.
2032 :	olson	1.1
2033 :			=over 4
2034 :
2035 :	parrello	1.93	=item table
2036 :	olson	1.1
2037 :	parrello	1.93	Hash table to be updated with the default values.
2038 :	olson	1.1
2039 :	parrello	1.93	=item defaults
2040 :	olson	1.1
2041 :	parrello	1.93	Default values to be merged into the first hash table if they are not already present.
2042 :	olson	1.1
2043 :			=back
2044 :
2045 :			=cut
2046 :
2047 :	parrello	1.93	sub MergeOptions {
2048 :			# Get the parameters.
2049 :			my ($table, $defaults) = @_;
2050 :			# Loop through the defaults.
2051 :			while (my ($key, $value) = each %{$defaults}) {
2052 :			if (!exists $table->{$key}) {
2053 :			$table->{$key} = $value;
2054 :			}
2055 :	parrello	1.12	}
2056 :	olson	1.1	}
2057 :
2058 :	parrello	1.111	=head3 UnparseOptions
2059 :
2060 :			my $optionString = Tracer::UnparseOptions(\%options);
2061 :
2062 :			Convert an option hash into a command-line string. This will not
2063 :			necessarily be the same text that came in, but it will nonetheless
2064 :			produce the same ultimate result when parsed by L</StandardSetup>.
2065 :
2066 :			=over 4
2067 :
2068 :			=item options
2069 :
2070 :			Reference to a hash of options to convert into an option string.
2071 :
2072 :			=item RETURN
2073 :
2074 :			Returns a string that will parse to the same set of options when
2075 :			parsed by L</StandardSetup>.
2076 :
2077 :			=back
2078 :
2079 :			=cut
2080 :
2081 :			sub UnparseOptions {
2082 :			# Get the parameters.
2083 :			my ($options) = @_;
2084 :			# The option segments will be put in here.
2085 :			my @retVal = ();
2086 :			# Loop through the options.
2087 :			for my $key (keys %$options) {
2088 :			# Get the option value.
2089 :			my $value = $options->{$key};
2090 :			# Only use it if it's nonempty.
2091 :			if (defined $value && $value ne "") {
2092 :			my $segment = "--$key=$value";
2093 :			# Quote it if necessary.
2094 :			if ($segment =~ /[ \|<>*]/) {
2095 :			$segment = '"' . $segment . '"';
2096 :			}
2097 :			# Add it to the return list.
2098 :			push @retVal, $segment;
2099 :			}
2100 :			}
2101 :			# Return the result.
2102 :			return join(" ", @retVal);
2103 :			}
2104 :
2105 :	parrello	1.93	=head3 ParseCommand
2106 :	olson	1.1
2107 :	parrello	1.93	my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2108 :	olson	1.1
2109 :	parrello	1.93	Parse a command line consisting of a list of parameters. The initial parameters may be option
2110 :			specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2111 :			off and merged into a table of default options. The remainder of the command line is
2112 :			returned as a list of positional arguments. For example, consider the following invocation.
2113 :	olson	1.1
2114 :	parrello	1.93	my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2115 :	olson	1.1
2116 :	parrello	1.93	In this case, the list @words will be treated as a command line and there are two options available,
2117 :			B<errors> and B<logFile>. If @words has the following format
2118 :	olson	1.1
2119 :	parrello	1.93	-logFile=error.log apple orange rutabaga
2120 :	olson	1.1
2121 :	parrello	1.93	then at the end of the invocation, C<$options> will be
2122 :	olson	1.1
2123 :	parrello	1.93	{ errors => 0, logFile => 'error.log' }
2124 :	olson	1.1
2125 :	parrello	1.93	and C<@arguments> will contain
2126 :	olson	1.1
2127 :	parrello	1.93	apple orange rutabaga
2128 :	olson	1.1
2129 :	parrello	1.93	The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2130 :			support for quote characters. Options can be specified with single or double hyphens.
2131 :	parrello	1.54
2132 :			=over 4
2133 :
2134 :	parrello	1.93	=item optionTable
2135 :	parrello	1.54
2136 :	parrello	1.93	Table of default options.
2137 :	parrello	1.54
2138 :	parrello	1.93	=item inputList
2139 :	parrello	1.54
2140 :	parrello	1.93	List of words on the command line.
2141 :	parrello	1.54
2142 :			=item RETURN
2143 :
2144 :	parrello	1.93	Returns a reference to the option table and a list of the positional arguments.
2145 :	parrello	1.54
2146 :			=back
2147 :
2148 :			=cut
2149 :
2150 :	parrello	1.93	sub ParseCommand {
2151 :	parrello	1.54	# Get the parameters.
2152 :	parrello	1.93	my ($optionTable, @inputList) = @_;
2153 :			# Process any options in the input list.
2154 :			my %overrides = ();
2155 :			while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2156 :			# Get the current option.
2157 :			my $arg = shift @inputList;
2158 :			# Pull out the option name.
2159 :			$arg =~ /^--?([^=]*)/g;
2160 :			my $name = $1;
2161 :			# Check for an option value.
2162 :			if ($arg =~ /\G=(.*)$/g) {
2163 :			# Here we have a value for the option.
2164 :			$overrides{$name} = UnEscape($1);
2165 :			} else {
2166 :			# Here there is no value, so we use 1.
2167 :			$overrides{$name} = 1;
2168 :			}
2169 :			}
2170 :			# Merge the options into the defaults.
2171 :			GetOptions($optionTable, \%overrides);
2172 :			# Translate the remaining parameters.
2173 :			my @retVal = ();
2174 :			for my $inputParm (@inputList) {
2175 :			push @retVal, UnEscape($inputParm);
2176 :	parrello	1.54	}
2177 :	parrello	1.93	# Return the results.
2178 :			return ($optionTable, @retVal);
2179 :	parrello	1.54	}
2180 :
2181 :	parrello	1.93
2182 :			=head2 File Utility Methods
2183 :
2184 :	olson	1.1	=head3 GetFile
2185 :
2186 :	parrello	1.92	my @fileContents = Tracer::GetFile($fileName);
2187 :	olson	1.1
2188 :	parrello	1.35	or
2189 :
2190 :	parrello	1.92	my $fileContents = Tracer::GetFile($fileName);
2191 :	parrello	1.35
2192 :			Return the entire contents of a file. In list context, line-ends are removed and
2193 :			each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2194 :	olson	1.1
2195 :			=over 4
2196 :
2197 :			=item fileName
2198 :
2199 :			Name of the file to read.
2200 :
2201 :			=item RETURN
2202 :
2203 :	parrello	1.6	In a list context, returns the entire file as a list with the line terminators removed.
2204 :	parrello	1.39	In a scalar context, returns the entire file as a string. If an error occurs opening
2205 :			the file, an empty list will be returned.
2206 :	olson	1.1
2207 :			=back
2208 :
2209 :			=cut
2210 :
2211 :			sub GetFile {
2212 :	parrello	1.12	# Get the parameters.
2213 :			my ($fileName) = @_;
2214 :			# Declare the return variable.
2215 :			my @retVal = ();
2216 :			# Open the file for input.
2217 :	parrello	1.60	my $handle = Open(undef, "<$fileName");
2218 :			# Read the whole file into the return variable, stripping off any terminator
2219 :			# characters.
2220 :			my $lineCount = 0;
2221 :			while (my $line = <$handle>) {
2222 :			$lineCount++;
2223 :			$line = Strip($line);
2224 :			push @retVal, $line;
2225 :			}
2226 :			# Close it.
2227 :			close $handle;
2228 :			my $actualLines = @retVal;
2229 :	parrello	1.77	Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2230 :	parrello	1.12	# Return the file's contents in the desired format.
2231 :	parrello	1.9	if (wantarray) {
2232 :	parrello	1.12	return @retVal;
2233 :	parrello	1.6	} else {
2234 :			return join "\n", @retVal;
2235 :			}
2236 :	olson	1.1	}
2237 :
2238 :	parrello	1.60	=head3 PutFile
2239 :
2240 :	parrello	1.92	Tracer::PutFile($fileName, \@lines);
2241 :	parrello	1.60
2242 :			Write out a file from a list of lines of text.
2243 :
2244 :			=over 4
2245 :
2246 :			=item fileName
2247 :
2248 :			Name of the output file.
2249 :
2250 :			=item lines
2251 :
2252 :			Reference to a list of text lines. The lines will be written to the file in order, with trailing
2253 :	parrello	1.66	new-line characters. Alternatively, may be a string, in which case the string will be written without
2254 :			modification.
2255 :	parrello	1.60
2256 :			=back
2257 :
2258 :			=cut
2259 :
2260 :			sub PutFile {
2261 :			# Get the parameters.
2262 :			my ($fileName, $lines) = @_;
2263 :			# Open the output file.
2264 :			my $handle = Open(undef, ">$fileName");
2265 :	parrello	1.77	# Count the lines written.
2266 :	parrello	1.66	if (ref $lines ne 'ARRAY') {
2267 :			# Here we have a scalar, so we write it raw.
2268 :			print $handle $lines;
2269 :	parrello	1.77	Trace("Scalar put to file $fileName.") if T(File => 3);
2270 :	parrello	1.66	} else {
2271 :			# Write the lines one at a time.
2272 :	parrello	1.77	my $count = 0;
2273 :	parrello	1.66	for my $line (@{$lines}) {
2274 :			print $handle "$line\n";
2275 :	parrello	1.77	$count++;
2276 :	parrello	1.66	}
2277 :	parrello	1.77	Trace("$count lines put to file $fileName.") if T(File => 3);
2278 :	parrello	1.60	}
2279 :			# Close the output file.
2280 :			close $handle;
2281 :			}
2282 :
2283 :	parrello	1.93	=head3 ParseRecord
2284 :	olson	1.1
2285 :	parrello	1.93	my @fields = Tracer::ParseRecord($line);
2286 :	olson	1.1
2287 :	parrello	1.93	Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2288 :			and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2289 :			These will automatically be converted.
2290 :	olson	1.1
2291 :			=over 4
2292 :
2293 :	parrello	1.93	=item line
2294 :
2295 :			Line of data containing the tab-delimited fields.
2296 :
2297 :			=item RETURN
2298 :	olson	1.1
2299 :	parrello	1.93	Returns a list of the fields found in the data line.
2300 :	olson	1.1
2301 :			=back
2302 :
2303 :			=cut
2304 :
2305 :	parrello	1.93	sub ParseRecord {
2306 :	parrello	1.12	# Get the parameter.
2307 :	parrello	1.93	my ($line) = @_;
2308 :			# Remove the trailing new-line, if any.
2309 :			chomp $line;
2310 :			# Split the line read into pieces using the tab character.
2311 :			my @retVal = split /\t/, $line;
2312 :			# Trim and fix the escapes in each piece.
2313 :			for my $value (@retVal) {
2314 :			# Trim leading whitespace.
2315 :			$value =~ s/^\s+//;
2316 :			# Trim trailing whitespace.
2317 :			$value =~ s/\s+$//;
2318 :			# Delete the carriage returns.
2319 :			$value =~ s/\r//g;
2320 :			# Convert the escapes into their real values.
2321 :			$value =~ s/\\t/"\t"/ge;
2322 :			$value =~ s/\\n/"\n"/ge;
2323 :			}
2324 :			# Return the result.
2325 :			return @retVal;
2326 :			}
2327 :
2328 :			=head3 Merge
2329 :
2330 :			my @mergedList = Tracer::Merge(@inputList);
2331 :
2332 :			Sort a list of strings and remove duplicates.
2333 :
2334 :			=over 4
2335 :
2336 :			=item inputList
2337 :
2338 :			List of scalars to sort and merge.
2339 :
2340 :			=item RETURN
2341 :
2342 :			Returns a list containing the same elements sorted in ascending order with duplicates
2343 :			removed.
2344 :
2345 :			=back
2346 :
2347 :			=cut
2348 :
2349 :			sub Merge {
2350 :			# Get the input list in sort order.
2351 :			my @inputList = sort @_;
2352 :			# Only proceed if the list has at least two elements.
2353 :			if (@inputList > 1) {
2354 :			# Now we want to move through the list splicing out duplicates.
2355 :			my $i = 0;
2356 :			while ($i < @inputList) {
2357 :			# Get the current entry.
2358 :			my $thisEntry = $inputList[$i];
2359 :			# Find out how many elements duplicate the current entry.
2360 :			my $j = $i + 1;
2361 :			my $dup1 = $i + 1;
2362 :			while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2363 :			# If the number is nonzero, splice out the duplicates found.
2364 :			if ($j > $dup1) {
2365 :			splice @inputList, $dup1, $j - $dup1;
2366 :	parrello	1.14	}
2367 :	parrello	1.93	# Now the element at position $dup1 is different from the element before it
2368 :			# at position $i. We push $i forward one position and start again.
2369 :			$i++;
2370 :	parrello	1.14	}
2371 :	parrello	1.12	}
2372 :	parrello	1.93	# Return the merged list.
2373 :			return @inputList;
2374 :	olson	1.1	}
2375 :
2376 :	parrello	1.93	=head3 Open
2377 :	olson	1.1
2378 :	parrello	1.93	my $handle = Open($fileHandle, $fileSpec, $message);
2379 :	olson	1.1
2380 :	parrello	1.93	Open a file.
2381 :	olson	1.1
2382 :	parrello	1.93	The I<$fileSpec> is essentially the second argument of the PERL C<open>
2383 :			function. The mode is specified using Unix-like shell information. So, for
2384 :			example,
2385 :	olson	1.1
2386 :	parrello	1.93	Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2387 :	olson	1.1
2388 :	parrello	1.93	would open for output appended to the specified file, and
2389 :	olson	1.1
2390 :	parrello	1.93	Open(\*DATASTREAM, "\| sort -u >$outputFile", "Could not open $outputFile.");
2391 :	olson	1.1
2392 :	parrello	1.93	would open a pipe that sorts the records written and removes duplicates. Note
2393 :			the use of file handle syntax in the Open call. To use anonymous file handles,
2394 :			code as follows.
2395 :	olson	1.1
2396 :	parrello	1.93	my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2397 :	olson	1.1
2398 :	parrello	1.93	The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2399 :			the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2400 :			failed open will throw an exception and the third parameter will be used to construct
2401 :			an error message. If the parameter is omitted, a standard message is constructed
2402 :			using the file spec.
2403 :	olson	1.1
2404 :	parrello	1.93	Could not open "/usr/spool/news/twitlog"
2405 :	olson	1.1
2406 :	parrello	1.93	Note that the mode characters are automatically cleaned from the file name.
2407 :			The actual error message from the file system will be captured and appended to the
2408 :			message in any case.
2409 :	parrello	1.6
2410 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": file not found.
2411 :	parrello	1.6
2412 :	parrello	1.93	In some versions of PERL the only error message we get is a number, which
2413 :			corresponds to the C++ C<errno> value.
2414 :	parrello	1.6
2415 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": 6.
2416 :	parrello	1.6
2417 :	parrello	1.93	=over 4
2418 :	parrello	1.6
2419 :	parrello	1.93	=item fileHandle
2420 :	parrello	1.6
2421 :	parrello	1.93	File handle. If this parameter is C<undef>, a file handle will be generated
2422 :			and returned as the value of this method.
2423 :	olson	1.1
2424 :	parrello	1.93	=item fileSpec
2425 :	olson	1.1
2426 :	parrello	1.93	File name and mode, as per the PERL C<open> function.
2427 :	olson	1.1
2428 :	parrello	1.93	=item message (optional)
2429 :	olson	1.1
2430 :	parrello	1.93	Error message to use if the open fails. If omitted, a standard error message
2431 :			will be generated. In either case, the error information from the file system
2432 :			is appended to the message. To specify a conditional open that does not throw
2433 :			an error if it fails, use C<0>.
2434 :	olson	1.1
2435 :	parrello	1.93	=item RETURN
2436 :	olson	1.1
2437 :	parrello	1.93	Returns the name of the file handle assigned to the file, or C<undef> if the
2438 :			open failed.
2439 :	olson	1.1
2440 :			=back
2441 :
2442 :			=cut
2443 :
2444 :	parrello	1.93	sub Open {
2445 :	parrello	1.12	# Get the parameters.
2446 :	parrello	1.93	my ($fileHandle, $fileSpec, $message) = @_;
2447 :			# Attempt to open the file.
2448 :			my $rv = open $fileHandle, $fileSpec;
2449 :			# If the open failed, generate an error message.
2450 :			if (! $rv) {
2451 :			# Save the system error message.
2452 :			my $sysMessage = $!;
2453 :			# See if we need a default message.
2454 :			if (!$message) {
2455 :			# Clean any obvious mode characters and leading spaces from the
2456 :			# filename.
2457 :			my ($fileName) = FindNamePart($fileSpec);
2458 :			$message = "Could not open \"$fileName\"";
2459 :			}
2460 :			# Terminate with an error using the supplied message and the
2461 :			# error message from the file system.
2462 :			Confess("$message: $!");
2463 :	parrello	1.12	}
2464 :	parrello	1.93	# Return the file handle.
2465 :			return $fileHandle;
2466 :	olson	1.1	}
2467 :
2468 :	parrello	1.93	=head3 FindNamePart
2469 :
2470 :			my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2471 :
2472 :			Extract the portion of a file specification that contains the file name.
2473 :
2474 :			A file specification is the string passed to an C<open> call. It specifies the file
2475 :			mode and name. In a truly complex situation, it can specify a pipe sequence. This
2476 :			method assumes that the file name is whatever follows the first angle bracket
2477 :			sequence. So, for example, in the following strings the file name is
2478 :			C</usr/fig/myfile.txt>.
2479 :	parrello	1.5
2480 :	parrello	1.93	>>/usr/fig/myfile.txt
2481 :			</usr/fig/myfile.txt
2482 :			\| sort -u > /usr/fig/myfile.txt
2483 :	parrello	1.5
2484 :	parrello	1.93	If the method cannot find a file name using its normal methods, it will return the
2485 :			whole incoming string.
2486 :	parrello	1.5
2487 :			=over 4
2488 :
2489 :	parrello	1.93	=item fileSpec
2490 :	parrello	1.5
2491 :	parrello	1.93	File specification string from which the file name is to be extracted.
2492 :	parrello	1.5
2493 :			=item RETURN
2494 :
2495 :	parrello	1.93	Returns a three-element list. The first element contains the file name portion of
2496 :			the specified string, or the whole string if a file name cannot be found via normal
2497 :			methods. The second element contains the start position of the file name portion and
2498 :			the third element contains the length.
2499 :	parrello	1.5
2500 :			=back
2501 :
2502 :			=cut
2503 :	parrello	1.93	#: Return Type $;
2504 :			sub FindNamePart {
2505 :			# Get the parameters.
2506 :			my ($fileSpec) = @_;
2507 :			# Default to the whole input string.
2508 :			my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2509 :			# Parse out the file name if we can.
2510 :			if ($fileSpec =~ m/(<\|>>?)(.+?)(\s*)$/) {
2511 :			$retVal = $2;
2512 :			$len = length $retVal;
2513 :			$pos = (length $fileSpec) - (length $3) - $len;
2514 :	parrello	1.12	}
2515 :	parrello	1.93	# Return the result.
2516 :			return ($retVal, $pos, $len);
2517 :	parrello	1.5	}
2518 :
2519 :	parrello	1.93	=head3 OpenDir
2520 :	parrello	1.5
2521 :	parrello	1.93	my @files = OpenDir($dirName, $filtered, $flag);
2522 :	parrello	1.5
2523 :	parrello	1.93	Open a directory and return all the file names. This function essentially performs
2524 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2525 :			set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2526 :			or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2527 :			filtered out of the return list. If the directory does not open and I<$flag> is not
2528 :			set, an exception is thrown. So, for example,
2529 :	parrello	1.5
2530 :	parrello	1.93	my @files = OpenDir("/Volumes/fig/contigs", 1);
2531 :	parrello	1.5
2532 :	parrello	1.93	is effectively the same as
2533 :	parrello	1.5
2534 :	parrello	1.93	opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
2535 :			my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2536 :	parrello	1.5
2537 :	parrello	1.93	Similarly, the following code
2538 :	parrello	1.5
2539 :	parrello	1.93	my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2540 :	parrello	1.5
2541 :	parrello	1.93	Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2542 :			automatically returns an empty list if the directory fails to open.
2543 :	parrello	1.5
2544 :	parrello	1.93	=over 4
2545 :	parrello	1.5
2546 :	parrello	1.93	=item dirName
2547 :	parrello	1.5
2548 :	parrello	1.93	Name of the directory to open.
2549 :	parrello	1.5
2550 :	parrello	1.93	=item filtered
2551 :	parrello	1.5
2552 :	parrello	1.93	TRUE if files whose names begin with a period (C<.>) should be automatically removed
2553 :			from the list, else FALSE.
2554 :	parrello	1.5
2555 :	parrello	1.93	=item flag
2556 :	parrello	1.5
2557 :	parrello	1.93	TRUE if a failure to open is okay, else FALSE
2558 :	parrello	1.5
2559 :	parrello	1.93	=back
2560 :	parrello	1.5
2561 :	parrello	1.93	=cut
2562 :			#: Return Type @;
2563 :			sub OpenDir {
2564 :			# Get the parameters.
2565 :			my ($dirName, $filtered, $flag) = @_;
2566 :			# Declare the return variable.
2567 :			my @retVal = ();
2568 :			# Open the directory.
2569 :			if (opendir(my $dirHandle, $dirName)) {
2570 :			# The directory opened successfully. Get the appropriate list according to the
2571 :			# strictures of the filter parameter.
2572 :			if ($filtered) {
2573 :			@retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2574 :			} else {
2575 :			@retVal = readdir $dirHandle;
2576 :			}
2577 :	parrello	1.117	closedir $dirHandle;
2578 :	parrello	1.93	} elsif (! $flag) {
2579 :			# Here the directory would not open and it's considered an error.
2580 :			Confess("Could not open directory $dirName.");
2581 :			}
2582 :			# Return the result.
2583 :			return @retVal;
2584 :			}
2585 :	parrello	1.5
2586 :
2587 :	parrello	1.93	=head3 Insure
2588 :	parrello	1.5
2589 :	parrello	1.93	Insure($dirName, $chmod);
2590 :	parrello	1.5
2591 :	parrello	1.93	Insure a directory is present.
2592 :	parrello	1.5
2593 :	parrello	1.93	=over 4
2594 :	parrello	1.5
2595 :	parrello	1.93	=item dirName
2596 :	olson	1.1
2597 :	parrello	1.93	Name of the directory to check. If it does not exist, it will be created.
2598 :	parrello	1.7
2599 :	parrello	1.93	=item chmod (optional)
2600 :	parrello	1.7
2601 :	parrello	1.93	Security privileges to be given to the directory if it is created.
2602 :	parrello	1.7
2603 :	parrello	1.93	=back
2604 :	parrello	1.7
2605 :			=cut
2606 :
2607 :	parrello	1.93	sub Insure {
2608 :			my ($dirName, $chmod) = @_;
2609 :			if (! -d $dirName) {
2610 :			Trace("Creating $dirName directory.") if T(2);
2611 :			eval {
2612 :			mkpath $dirName;
2613 :			# If we have permissions specified, set them here.
2614 :			if (defined($chmod)) {
2615 :			chmod $chmod, $dirName;
2616 :			}
2617 :			};
2618 :			if ($@) {
2619 :			Confess("Error creating $dirName: $@");
2620 :			}
2621 :	parrello	1.12	}
2622 :	parrello	1.9	}
2623 :
2624 :	parrello	1.93	=head3 ChDir
2625 :	parrello	1.9
2626 :	parrello	1.93	ChDir($dirName);
2627 :	parrello	1.9
2628 :	parrello	1.93	Change to the specified directory.
2629 :	parrello	1.9
2630 :			=over 4
2631 :
2632 :	parrello	1.93	=item dirName
2633 :	parrello	1.9
2634 :	parrello	1.93	Name of the directory to which we want to change.
2635 :	parrello	1.9
2636 :			=back
2637 :
2638 :			=cut
2639 :
2640 :	parrello	1.93	sub ChDir {
2641 :			my ($dirName) = @_;
2642 :			if (! -d $dirName) {
2643 :			Confess("Cannot change to directory $dirName: no such directory.");
2644 :			} else {
2645 :			Trace("Changing to directory $dirName.") if T(File => 4);
2646 :			my $okFlag = chdir $dirName;
2647 :			if (! $okFlag) {
2648 :			Confess("Error switching to directory $dirName.");
2649 :			}
2650 :			}
2651 :	parrello	1.9	}
2652 :
2653 :	parrello	1.93	=head3 SetPermissions
2654 :
2655 :			Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2656 :	parrello	1.9
2657 :	parrello	1.93	Set the permissions for a directory and all the files and folders inside it.
2658 :			In addition, the group ownership will be changed to the specified value.
2659 :	parrello	1.9
2660 :	parrello	1.93	This method is more vulnerable than most to permission and compatability
2661 :			problems, so it does internal error recovery.
2662 :	parrello	1.9
2663 :			=over 4
2664 :
2665 :	parrello	1.93	=item dirName
2666 :
2667 :			Name of the directory to process.
2668 :
2669 :			=item group
2670 :	parrello	1.9
2671 :	parrello	1.93	Name of the group to be assigned.
2672 :	parrello	1.9
2673 :	parrello	1.93	=item mask
2674 :	parrello	1.9
2675 :	parrello	1.93	Permission mask. Bits that are C<1> in this mask will be ORed into the
2676 :			permission bits of any file or directory that does not already have them
2677 :			set to 1.
2678 :	parrello	1.9
2679 :	parrello	1.93	=item otherMasks
2680 :	parrello	1.9
2681 :	parrello	1.93	Map of search patterns to permission masks. If a directory name matches
2682 :			one of the patterns, that directory and all its members and subdirectories
2683 :			will be assigned the new pattern. For example, the following would
2684 :	parrello	1.110	assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2685 :	parrello	1.9
2686 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2687 :	parrello	1.9
2688 :	parrello	1.93	The list is ordered, so the following would use 0777 for C<tmp1> and
2689 :			0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2690 :	parrello	1.22
2691 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2692 :			'^tmp' => 0666);
2693 :	parrello	1.9
2694 :	parrello	1.93	Note that the pattern matches are all case-insensitive, and only directory
2695 :			names are matched, not file names.
2696 :	parrello	1.9
2697 :			=back
2698 :
2699 :			=cut
2700 :
2701 :	parrello	1.93	sub SetPermissions {
2702 :	parrello	1.12	# Get the parameters.
2703 :	parrello	1.93	my ($dirName, $group, $mask, @otherMasks) = @_;
2704 :			# Set up for error recovery.
2705 :			eval {
2706 :			# Switch to the specified directory.
2707 :			ChDir($dirName);
2708 :			# Get the group ID.
2709 :			my $gid = getgrnam($group);
2710 :			# Get the mask for tracing.
2711 :			my $traceMask = sprintf("%04o", $mask) . "($mask)";
2712 :			Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2713 :			my $fixCount = 0;
2714 :			my $lookCount = 0;
2715 :			# @dirs will be a stack of directories to be processed.
2716 :			my @dirs = (getcwd());
2717 :			while (scalar(@dirs) > 0) {
2718 :			# Get the current directory.
2719 :			my $dir = pop @dirs;
2720 :			# Check for a match to one of the specified directory names. To do
2721 :			# that, we need to pull the individual part of the name off of the
2722 :			# whole path.
2723 :			my $simpleName = $dir;
2724 :			if ($dir =~ m!/([^/]+)$!) {
2725 :			$simpleName = $1;
2726 :			}
2727 :			Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2728 :			# Search for a match.
2729 :			my $match = 0;
2730 :			my $i;
2731 :			for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2732 :			my $pattern = $otherMasks[$i];
2733 :			if ($simpleName =~ /$pattern/i) {
2734 :			$match = 1;
2735 :			}
2736 :			}
2737 :	parrello	1.110	# Find out if we have a match. Note we use $i-1 because the loop added 2
2738 :	parrello	1.93	# before terminating due to the match.
2739 :			if ($match && $otherMasks[$i-1] != $mask) {
2740 :			# This directory matches one of the incoming patterns, and it's
2741 :			# a different mask, so we process it recursively with that mask.
2742 :			SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2743 :			} else {
2744 :			# Here we can process normally. Get all of the non-hidden members.
2745 :			my @submems = OpenDir($dir, 1);
2746 :			for my $submem (@submems) {
2747 :			# Get the full name.
2748 :			my $thisMem = "$dir/$submem";
2749 :			Trace("Checking member $thisMem.") if T(4);
2750 :			$lookCount++;
2751 :			if ($lookCount % 1000 == 0) {
2752 :			Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2753 :			}
2754 :			# Fix the group.
2755 :			chown -1, $gid, $thisMem;
2756 :			# Insure this member is not a symlink.
2757 :			if (! -l $thisMem) {
2758 :			# Get its info.
2759 :			my $fileInfo = stat $thisMem;
2760 :			# Only proceed if we got the info. Otherwise, it's a hard link
2761 :			# and we want to skip it anyway.
2762 :			if ($fileInfo) {
2763 :			my $fileMode = $fileInfo->mode;
2764 :			if (($fileMode & $mask) != $mask) {
2765 :			# Fix this member.
2766 :			$fileMode \|= $mask;
2767 :			chmod $fileMode, $thisMem;
2768 :			$fixCount++;
2769 :			}
2770 :			# If it's a subdirectory, stack it.
2771 :			if (-d $thisMem) {
2772 :			push @dirs, $thisMem;
2773 :			}
2774 :			}
2775 :			}
2776 :			}
2777 :			}
2778 :	parrello	1.12	}
2779 :	parrello	1.93	Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2780 :			};
2781 :			# Check for an error.
2782 :			if ($@) {
2783 :			Confess("SetPermissions error: $@");
2784 :	parrello	1.12	}
2785 :	parrello	1.7	}
2786 :
2787 :	parrello	1.93	=head3 GetLine
2788 :	parrello	1.29
2789 :	parrello	1.93	my @data = Tracer::GetLine($handle);
2790 :	parrello	1.15
2791 :	parrello	1.93	Read a line of data from a tab-delimited file.
2792 :	parrello	1.15
2793 :			=over 4
2794 :
2795 :	parrello	1.93	=item handle
2796 :	parrello	1.15
2797 :	parrello	1.93	Open file handle from which to read.
2798 :	parrello	1.15
2799 :			=item RETURN
2800 :
2801 :	parrello	1.93	Returns a list of the fields in the record read. The fields are presumed to be
2802 :			tab-delimited. If we are at the end of the file, then an empty list will be
2803 :			returned. If an empty line is read, a single list item consisting of a null
2804 :			string will be returned.
2805 :	parrello	1.15
2806 :			=back
2807 :
2808 :			=cut
2809 :	parrello	1.93
2810 :			sub GetLine {
2811 :	parrello	1.15	# Get the parameters.
2812 :	parrello	1.93	my ($handle) = @_;
2813 :			# Declare the return variable.
2814 :			my @retVal = ();
2815 :			Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2816 :			# Read from the file.
2817 :			my $line = <$handle>;
2818 :			# Only proceed if we found something.
2819 :			if (defined $line) {
2820 :			# Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2821 :			# upload control and have a nonstandard EOL combination.
2822 :			$line =~ s/(\r\|\n)+$//;
2823 :			# Here we do some fancy tracing to help in debugging complicated EOL marks.
2824 :			if (T(File => 4)) {
2825 :			my $escapedLine = $line;
2826 :			$escapedLine =~ s/\n/\\n/g;
2827 :			$escapedLine =~ s/\r/\\r/g;
2828 :			$escapedLine =~ s/\t/\\t/g;
2829 :			Trace("Line read: -->$escapedLine<--");
2830 :			}
2831 :			# If the line is empty, return a single empty string; otherwise, parse
2832 :			# it into fields.
2833 :			if ($line eq "") {
2834 :			push @retVal, "";
2835 :			} else {
2836 :			push @retVal, split /\t/,$line;
2837 :			}
2838 :			} else {
2839 :			# Trace the reason the read failed.
2840 :			Trace("End of file: $!") if T(File => 3);
2841 :	parrello	1.15	}
2842 :	parrello	1.93	# Return the result.
2843 :			return @retVal;
2844 :	parrello	1.15	}
2845 :
2846 :	parrello	1.93	=head3 PutLine
2847 :
2848 :			Tracer::PutLine($handle, \@fields, $eol);
2849 :	parrello	1.35
2850 :	parrello	1.93	Write a line of data to a tab-delimited file. The specified field values will be
2851 :			output in tab-separated form, with a trailing new-line.
2852 :	parrello	1.35
2853 :	parrello	1.93	=over 4
2854 :	parrello	1.35
2855 :	parrello	1.93	=item handle
2856 :	parrello	1.69
2857 :	parrello	1.93	Output file handle.
2858 :	parrello	1.69
2859 :	parrello	1.93	=item fields
2860 :	parrello	1.69
2861 :	parrello	1.93	List of field values.
2862 :	parrello	1.69
2863 :	parrello	1.93	=item eol (optional)
2864 :	parrello	1.69
2865 :	parrello	1.93	End-of-line character (default is "\n").
2866 :	parrello	1.69
2867 :			=back
2868 :	parrello	1.35
2869 :			=cut
2870 :
2871 :	parrello	1.93	sub PutLine {
2872 :	parrello	1.69	# Get the parameters.
2873 :	parrello	1.93	my ($handle, $fields, $eol) = @_;
2874 :			# Write the data.
2875 :			print $handle join("\t", @{$fields}) . ($eol \|\| "\n");
2876 :	parrello	1.69	}
2877 :
2878 :
2879 :	parrello	1.97	=head3 PrintLine
2880 :
2881 :			Tracer::PrintLine($line);
2882 :
2883 :			Print a line of text with a trailing new-line.
2884 :
2885 :			=over 4
2886 :
2887 :			=item line
2888 :
2889 :			Line of text to print.
2890 :
2891 :			=back
2892 :
2893 :			=cut
2894 :
2895 :			sub PrintLine {
2896 :			# Get the parameters.
2897 :			my ($line) = @_;
2898 :			# Print the line.
2899 :			print "$line\n";
2900 :			}
2901 :
2902 :	parrello	1.69
2903 :	parrello	1.93	=head2 Other Useful Methods
2904 :
2905 :	parrello	1.115	=head3 IDHASH
2906 :
2907 :			my $hash = SHTargetSearch::IDHASH(@keys);
2908 :
2909 :			This is a dinky little method that converts a list of values to a reference
2910 :			to hash of values to labels. The values and labels are the same.
2911 :
2912 :			=cut
2913 :
2914 :			sub IDHASH {
2915 :			my %retVal = map { $_ => $_ } @_;
2916 :			return \%retVal;
2917 :			}
2918 :
2919 :			=head3 Pluralize
2920 :
2921 :			my $plural = Tracer::Pluralize($word);
2922 :
2923 :			This is a very simple pluralization utility. It adds an C<s> at the end
2924 :			of the input word unless it already ends in an C<s>, in which case it
2925 :			adds C<es>.
2926 :
2927 :			=over 4
2928 :
2929 :			=item word
2930 :
2931 :			Singular word to pluralize.
2932 :
2933 :			=item RETURN
2934 :
2935 :			Returns the probable plural form of the word.
2936 :
2937 :			=back
2938 :
2939 :			=cut
2940 :
2941 :			sub Pluralize {
2942 :			# Get the parameters.
2943 :			my ($word) = @_;
2944 :			# Declare the return variable.
2945 :			my $retVal;
2946 :			if ($word =~ /s$/) {
2947 :			$retVal = $word . 'es';
2948 :			} else {
2949 :			$retVal = $word . 's';
2950 :			}
2951 :			# Return the result.
2952 :			return $retVal;
2953 :			}
2954 :
2955 :			=head3 Numeric
2956 :
2957 :			my $okFlag = Tracer::Numeric($string);
2958 :
2959 :			Return the value of the specified string if it is numeric, or an undefined value
2960 :			if it is not numeric.
2961 :
2962 :			=over 4
2963 :
2964 :			=item string
2965 :
2966 :			String to check.
2967 :
2968 :			=item RETURN
2969 :
2970 :			Returns the numeric value of the string if successful, or C<undef> if the string
2971 :			is not numeric.
2972 :
2973 :			=back
2974 :
2975 :			=cut
2976 :
2977 :			sub Numeric {
2978 :			# Get the parameters.
2979 :			my ($string) = @_;
2980 :			# We'll put the value in here if we succeed.
2981 :			my $retVal;
2982 :			# Get a working copy of the string.
2983 :			my $copy = $string;
2984 :			# Trim leading and trailing spaces.
2985 :			$copy =~ s/^\s+//;
2986 :			$copy =~ s/\s+$//;
2987 :			# Check the result.
2988 :			if ($copy =~ /^[+-]?\d+$/) {
2989 :			$retVal = $copy;
2990 :			} elsif ($copy =~ /^([+-]\d+\|\d*)[eE][+-]?\d+$/) {
2991 :			$retVal = $copy;
2992 :			} elsif ($copy =~ /^([+-]\d+\|\d)\.\d([eE][+-]?\d+)?$/) {
2993 :			$retVal = $copy;
2994 :			}
2995 :			# Return the result.
2996 :			return $retVal;
2997 :			}
2998 :
2999 :
3000 :	parrello	1.93	=head3 ParseParm
3001 :
3002 :			my $listValue = Tracer::ParseParm($string);
3003 :
3004 :			Convert a parameter into a list reference. If the parameter is undefined,
3005 :			an undefined value will be returned. Otherwise, it will be parsed as a
3006 :			comma-separated list of values.
3007 :	parrello	1.69
3008 :			=over 4
3009 :
3010 :	parrello	1.93	=item string
3011 :
3012 :			Incoming string.
3013 :
3014 :			=item RETURN
3015 :	parrello	1.69
3016 :	parrello	1.93	Returns a reference to a list of values, or C<undef> if the incoming value
3017 :			was undefined.
3018 :	parrello	1.69
3019 :			=back
3020 :
3021 :			=cut
3022 :
3023 :	parrello	1.93	sub ParseParm {
3024 :			# Get the parameters.
3025 :			my ($string) = @_;
3026 :			# Declare the return variable.
3027 :			my $retVal;
3028 :			# Check for data.
3029 :			if (defined $string) {
3030 :			# We have some, so split it into a list.
3031 :			$retVal = [ split /\s,\s/, $string];
3032 :	parrello	1.72	}
3033 :	parrello	1.93	# Return the result.
3034 :			return $retVal;
3035 :	parrello	1.69	}
3036 :
3037 :	parrello	1.97	=head3 Now
3038 :
3039 :			my $string = Tracer::Now();
3040 :
3041 :			Return a displayable time stamp containing the local time. Whatever format this
3042 :			method produces must be parseable by L</ParseDate>.
3043 :
3044 :			=cut
3045 :
3046 :			sub Now {
3047 :			return DisplayTime(time);
3048 :			}
3049 :
3050 :			=head3 DisplayTime
3051 :
3052 :			my $string = Tracer::DisplayTime($time);
3053 :	parrello	1.69
3054 :	parrello	1.97	Convert a time value to a displayable time stamp. Whatever format this
3055 :			method produces must be parseable by L</ParseDate>.
3056 :
3057 :			=over 4
3058 :	parrello	1.69
3059 :	parrello	1.97	=item time
3060 :	parrello	1.69
3061 :	parrello	1.97	Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3062 :
3063 :			=item RETURN
3064 :	parrello	1.69
3065 :	parrello	1.97	Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3066 :	parrello	1.69
3067 :	parrello	1.97	=back
3068 :	parrello	1.69
3069 :	parrello	1.93	=cut
3070 :	parrello	1.69
3071 :	parrello	1.97	sub DisplayTime {
3072 :			my ($time) = @_;
3073 :			my $retVal = "(n/a)";
3074 :			if (defined $time) {
3075 :			my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3076 :			$retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3077 :			_p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3078 :			}
3079 :	parrello	1.93	return $retVal;
3080 :			}
3081 :	parrello	1.69
3082 :	parrello	1.93	# Pad a number to 2 digits.
3083 :			sub _p2 {
3084 :			my ($value) = @_;
3085 :			$value = "0$value" if ($value < 10);
3086 :			return $value;
3087 :	parrello	1.69	}
3088 :
3089 :	parrello	1.93	=head3 Escape
3090 :	parrello	1.69
3091 :	parrello	1.93	my $codedString = Tracer::Escape($realString);
3092 :	parrello	1.69
3093 :	parrello	1.93	Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3094 :			replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3095 :			result is to reverse the effect of L</UnEscape>.
3096 :	parrello	1.69
3097 :			=over 4
3098 :
3099 :	parrello	1.93	=item realString
3100 :	parrello	1.69
3101 :	parrello	1.93	String to escape.
3102 :	parrello	1.69
3103 :			=item RETURN
3104 :
3105 :	parrello	1.93	Escaped equivalent of the real string.
3106 :
3107 :			=back
3108 :
3109 :			=cut
3110 :
3111 :			sub Escape {
3112 :			# Get the parameter.
3113 :			my ($realString) = @_;
3114 :			# Initialize the return variable.
3115 :			my $retVal = "";
3116 :			# Loop through the parameter string, looking for sequences to escape.
3117 :			while (length $realString > 0) {
3118 :			# Look for the first sequence to escape.
3119 :			if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3120 :			# Here we found it. The text preceding the sequence is in $1. The sequence
3121 :			# itself is in $2. First, move the clear text to the return variable.
3122 :			$retVal .= $1;
3123 :			# Strip the processed section off the real string.
3124 :			$realString = substr $realString, (length $2) + (length $1);
3125 :			# Get the matched character.
3126 :			my $char = $2;
3127 :			# If we have a CR, we are done.
3128 :			if ($char ne "\r") {
3129 :			# It's not a CR, so encode the escape sequence.
3130 :			$char =~ tr/\t\n/tn/;
3131 :			$retVal .= "\\" . $char;
3132 :			}
3133 :			} else {
3134 :			# Here there are no more escape sequences. The rest of the string is
3135 :			# transferred unmodified.
3136 :			$retVal .= $realString;
3137 :			$realString = "";
3138 :			}
3139 :			}
3140 :			# Return the result.
3141 :			return $retVal;
3142 :	parrello	1.69	}
3143 :
3144 :	parrello	1.93	=head3 UnEscape
3145 :	parrello	1.69
3146 :	parrello	1.93	my $realString = Tracer::UnEscape($codedString);
3147 :	parrello	1.69
3148 :	parrello	1.93	Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3149 :			a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3150 :			be deleted.
3151 :	parrello	1.69
3152 :			=over 4
3153 :
3154 :	parrello	1.93	=item codedString
3155 :	parrello	1.69
3156 :	parrello	1.93	String to un-escape.
3157 :	parrello	1.69
3158 :			=item RETURN
3159 :
3160 :	parrello	1.93	Returns a copy of the original string with the escape sequences converted to their actual
3161 :			values.
3162 :	parrello	1.69
3163 :			=back
3164 :
3165 :			=cut
3166 :
3167 :	parrello	1.93	sub UnEscape {
3168 :			# Get the parameter.
3169 :			my ($codedString) = @_;
3170 :			# Initialize the return variable.
3171 :			my $retVal = "";
3172 :			# Only proceed if the incoming string is nonempty.
3173 :			if (defined $codedString) {
3174 :			# Loop through the parameter string, looking for escape sequences. We can't do
3175 :			# translating because it causes problems with the escaped slash. ("\\t" becomes
3176 :			# "\<tab>" no matter what we do.)
3177 :			while (length $codedString > 0) {
3178 :			# Look for the first escape sequence.
3179 :			if ($codedString =~ /^(.*?)\\(\\\|n\|t\|r)/) {
3180 :			# Here we found it. The text preceding the sequence is in $1. The sequence
3181 :			# itself is in $2. First, move the clear text to the return variable.
3182 :			$retVal .= $1;
3183 :			$codedString = substr $codedString, (2 + length $1);
3184 :			# Get the escape value.
3185 :			my $char = $2;
3186 :			# If we have a "\r", we are done.
3187 :			if ($char ne 'r') {
3188 :			# Here it's not an 'r', so we convert it.
3189 :			$char =~ tr/\\tn/\\\t\n/;
3190 :			$retVal .= $char;
3191 :			}
3192 :			} else {
3193 :			# Here there are no more escape sequences. The rest of the string is
3194 :			# transferred unmodified.
3195 :			$retVal .= $codedString;
3196 :			$codedString = "";
3197 :			}
3198 :			}
3199 :	parrello	1.35	}
3200 :	parrello	1.69	# Return the result.
3201 :			return $retVal;
3202 :			}
3203 :
3204 :	parrello	1.93	=head3 Percent
3205 :	parrello	1.69
3206 :	parrello	1.93	my $percent = Tracer::Percent($number, $base);
3207 :	parrello	1.69
3208 :	parrello	1.93	Returns the percent of the base represented by the given number. If the base
3209 :			is zero, returns zero.
3210 :	parrello	1.69
3211 :			=over 4
3212 :
3213 :	parrello	1.93	=item number
3214 :	parrello	1.69
3215 :	parrello	1.93	Percent numerator.
3216 :	parrello	1.69
3217 :	parrello	1.93	=item base
3218 :	parrello	1.69
3219 :	parrello	1.93	Percent base.
3220 :	parrello	1.69
3221 :	parrello	1.93	=item RETURN
3222 :	parrello	1.69
3223 :	parrello	1.93	Returns the percentage of the base represented by the numerator.
3224 :	parrello	1.69
3225 :			=back
3226 :
3227 :			=cut
3228 :
3229 :	parrello	1.93	sub Percent {
3230 :	parrello	1.69	# Get the parameters.
3231 :	parrello	1.93	my ($number, $base) = @_;
3232 :			# Declare the return variable.
3233 :			my $retVal = 0;
3234 :			# Compute the percent.
3235 :			if ($base != 0) {
3236 :			$retVal = $number * 100 / $base;
3237 :			}
3238 :			# Return the result.
3239 :			return $retVal;
3240 :	parrello	1.69	}
3241 :
3242 :	parrello	1.115	=head3 In
3243 :
3244 :			my $flag = Tracer::In($value, $min, $max);
3245 :
3246 :			Return TRUE if the value is between the minimum and the maximum, else FALSE.
3247 :
3248 :			=cut
3249 :
3250 :			sub In {
3251 :			return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3252 :			}
3253 :
3254 :
3255 :	parrello	1.97	=head3 Constrain
3256 :
3257 :			my $constrained = Constrain($value, $min, $max);
3258 :
3259 :			Modify a numeric value to bring it to a point in between a maximum and a minimum.
3260 :
3261 :			=over 4
3262 :
3263 :			=item value
3264 :
3265 :			Value to constrain.
3266 :
3267 :			=item min (optional)
3268 :
3269 :			Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3270 :
3271 :			=item max (optional)
3272 :
3273 :			Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3274 :
3275 :			=item RETURN
3276 :
3277 :			Returns the incoming value, constrained according to the other parameters.
3278 :
3279 :			=back
3280 :
3281 :			=cut
3282 :
3283 :			sub Constrain {
3284 :			# Get the parameters.
3285 :			my ($value, $min, $max) = @_;
3286 :			# Declare the return variable.
3287 :			my $retVal = $value;
3288 :			# Apply the minimum constraint.
3289 :			if (defined $min && $retVal < $min) {
3290 :			$retVal = $min;
3291 :			}
3292 :			# Apply the maximum constraint.
3293 :			if (defined $max && $retVal > $max) {
3294 :			$retVal = $max;
3295 :			}
3296 :			# Return the result.
3297 :			return $retVal;
3298 :			}
3299 :
3300 :	parrello	1.93	=head3 Min
3301 :	parrello	1.69
3302 :	parrello	1.93	my $min = Min($value1, $value2, ... $valueN);
3303 :	parrello	1.69
3304 :	parrello	1.93	Return the minimum argument. The arguments are treated as numbers.
3305 :	parrello	1.69
3306 :			=over 4
3307 :
3308 :	parrello	1.93	=item $value1, $value2, ... $valueN
3309 :	parrello	1.69
3310 :	parrello	1.93	List of numbers to compare.
3311 :	parrello	1.69
3312 :			=item RETURN
3313 :
3314 :	parrello	1.93	Returns the lowest number in the list.
3315 :	parrello	1.69
3316 :			=back
3317 :
3318 :			=cut
3319 :
3320 :	parrello	1.93	sub Min {
3321 :			# Get the parameters. Note that we prime the return value with the first parameter.
3322 :			my ($retVal, @values) = @_;
3323 :			# Loop through the remaining parameters, looking for the lowest.
3324 :			for my $value (@values) {
3325 :			if ($value < $retVal) {
3326 :			$retVal = $value;
3327 :	parrello	1.72	}
3328 :			}
3329 :	parrello	1.93	# Return the minimum found.
3330 :	parrello	1.70	return $retVal;
3331 :	parrello	1.35	}
3332 :
3333 :	parrello	1.93	=head3 Max
3334 :
3335 :			my $max = Max($value1, $value2, ... $valueN);
3336 :	parrello	1.69
3337 :	parrello	1.93	Return the maximum argument. The arguments are treated as numbers.
3338 :	parrello	1.65
3339 :	parrello	1.93	=over 4
3340 :	parrello	1.65
3341 :	parrello	1.93	=item $value1, $value2, ... $valueN
3342 :	parrello	1.65
3343 :	parrello	1.93	List of numbers to compare.
3344 :	parrello	1.65
3345 :	parrello	1.93	=item RETURN
3346 :	parrello	1.65
3347 :	parrello	1.93	Returns the highest number in the list.
3348 :	parrello	1.65
3349 :			=back
3350 :
3351 :			=cut
3352 :
3353 :	parrello	1.93	sub Max {
3354 :			# Get the parameters. Note that we prime the return value with the first parameter.
3355 :			my ($retVal, @values) = @_;
3356 :			# Loop through the remaining parameters, looking for the highest.
3357 :			for my $value (@values) {
3358 :			if ($value > $retVal) {
3359 :			$retVal = $value;
3360 :	parrello	1.65	}
3361 :			}
3362 :	parrello	1.93	# Return the maximum found.
3363 :			return $retVal;
3364 :	parrello	1.65	}
3365 :
3366 :	parrello	1.93	=head3 Strip
3367 :	parrello	1.37
3368 :	parrello	1.93	my $string = Tracer::Strip($line);
3369 :	parrello	1.37
3370 :	parrello	1.93	Strip all line terminators off a string. This is necessary when dealing with files
3371 :			that may have been transferred back and forth several times among different
3372 :			operating environments.
3373 :	parrello	1.37
3374 :			=over 4
3375 :
3376 :	parrello	1.93	=item line
3377 :	parrello	1.37
3378 :	parrello	1.93	Line of text to be stripped.
3379 :	parrello	1.37
3380 :	parrello	1.93	=item RETURN
3381 :	parrello	1.91
3382 :	parrello	1.93	The same line of text with all the line-ending characters chopped from the end.
3383 :	parrello	1.91
3384 :	parrello	1.37	=back
3385 :
3386 :			=cut
3387 :
3388 :	parrello	1.93	sub Strip {
3389 :			# Get a copy of the parameter string.
3390 :			my ($string) = @_;
3391 :			my $retVal = (defined $string ? $string : "");
3392 :			# Strip the line terminator characters.
3393 :			$retVal =~ s/(\r\|\n)+$//g;
3394 :			# Return the result.
3395 :			return $retVal;
3396 :	parrello	1.43	}
3397 :
3398 :	parrello	1.115	=head3 Trim
3399 :
3400 :			my $string = Tracer::Trim($line);
3401 :
3402 :			Trim all spaces from the beginning and ending of a string.
3403 :
3404 :			=over 4
3405 :
3406 :			=item line
3407 :
3408 :			Line of text to be trimmed.
3409 :
3410 :			=item RETURN
3411 :
3412 :			The same line of text with all whitespace chopped off either end.
3413 :
3414 :			=back
3415 :
3416 :			=cut
3417 :
3418 :			sub Trim {
3419 :			# Get a copy of the parameter string.
3420 :			my ($string) = @_;
3421 :			my $retVal = (defined $string ? $string : "");
3422 :			# Strip the front spaces.
3423 :			$retVal =~ s/^\s+//;
3424 :			# Strip the back spaces.
3425 :			$retVal =~ s/\s+$//;
3426 :			# Return the result.
3427 :			return $retVal;
3428 :			}
3429 :
3430 :	parrello	1.93	=head3 Pad
3431 :	parrello	1.43
3432 :	parrello	1.93	my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3433 :	parrello	1.43
3434 :	parrello	1.93	Pad a string to a specified length. The pad character will be a
3435 :			space, and the padding will be on the right side unless specified
3436 :			in the third parameter.
3437 :	parrello	1.43
3438 :			=over 4
3439 :
3440 :	parrello	1.93	=item string
3441 :
3442 :			String to be padded.
3443 :
3444 :			=item len
3445 :
3446 :			Desired length of the padded string.
3447 :
3448 :			=item left (optional)
3449 :
3450 :			TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3451 :
3452 :			=item padChar (optional)
3453 :
3454 :			Character to use for padding. The default is a space.
3455 :
3456 :			=item RETURN
3457 :	parrello	1.43
3458 :	parrello	1.93	Returns a copy of the original string with the pad character added to the
3459 :			specified end so that it achieves the desired length.
3460 :	parrello	1.43
3461 :			=back
3462 :
3463 :			=cut
3464 :
3465 :	parrello	1.93	sub Pad {
3466 :			# Get the parameters.
3467 :			my ($string, $len, $left, $padChar) = @_;
3468 :			# Compute the padding character.
3469 :			if (! defined $padChar) {
3470 :			$padChar = " ";
3471 :			}
3472 :			# Compute the number of spaces needed.
3473 :			my $needed = $len - length $string;
3474 :			# Copy the string into the return variable.
3475 :			my $retVal = $string;
3476 :			# Only proceed if padding is needed.
3477 :			if ($needed > 0) {
3478 :			# Create the pad string.
3479 :			my $pad = $padChar x $needed;
3480 :			# Affix it to the return value.
3481 :			if ($left) {
3482 :			$retVal = $pad . $retVal;
3483 :			} else {
3484 :			$retVal .= $pad;
3485 :	parrello	1.43	}
3486 :	parrello	1.37	}
3487 :	parrello	1.93	# Return the result.
3488 :			return $retVal;
3489 :	parrello	1.37	}
3490 :
3491 :	parrello	1.118	=head3 Quoted
3492 :
3493 :			my $string = Tracer::Quoted($var);
3494 :
3495 :			Convert the specified value to a string and enclose it in single quotes.
3496 :			If it's undefined, the string C<undef> in angle brackets will be used
3497 :			instead.
3498 :
3499 :			=over 4
3500 :
3501 :			=item var
3502 :
3503 :			Value to quote.
3504 :
3505 :			=item RETURN
3506 :
3507 :			Returns a string enclosed in quotes, or an indication the value is undefined.
3508 :
3509 :			=back
3510 :
3511 :			=cut
3512 :
3513 :			sub Quoted {
3514 :			# Get the parameters.
3515 :			my ($var) = @_;
3516 :			# Declare the return variable.
3517 :			my $retVal;
3518 :			# Are we undefined?
3519 :			if (! defined $var) {
3520 :			$retVal = "<undef>";
3521 :			} else {
3522 :			# No, so convert to a string and enclose in quotes.
3523 :			$retVal = $var;
3524 :			$retVal =~ s/'/\\'/;
3525 :			$retVal = "'$retVal'";
3526 :			}
3527 :			# Return the result.
3528 :			return $retVal;
3529 :			}
3530 :
3531 :	parrello	1.93	=head3 EOF
3532 :
3533 :			This is a constant that is lexically greater than any useful string.
3534 :
3535 :			=cut
3536 :
3537 :			sub EOF {
3538 :			return "\xFF\xFF\xFF\xFF\xFF";
3539 :			}
3540 :	parrello	1.59
3541 :	parrello	1.93	=head3 TICK
3542 :	parrello	1.59
3543 :	parrello	1.93	my @results = TICK($commandString);
3544 :	parrello	1.59
3545 :	parrello	1.93	Perform a back-tick operation on a command. If this is a Windows environment, any leading
3546 :			dot-slash (C<./> will be removed. So, for example, if you were doing
3547 :	parrello	1.59
3548 :	parrello	1.93	`./protein.cgi`
3549 :	parrello	1.59
3550 :	parrello	1.93	from inside a CGI script, it would work fine in Unix, but would issue an error message
3551 :			in Windows complaining that C<'.'> is not a valid command. If instead you code
3552 :	parrello	1.59
3553 :	parrello	1.93	TICK("./protein.cgi")
3554 :	parrello	1.59
3555 :	parrello	1.93	it will work correctly in both environments.
3556 :	parrello	1.59
3557 :	parrello	1.93	=over 4
3558 :	parrello	1.59
3559 :	parrello	1.93	=item commandString
3560 :	parrello	1.59
3561 :	parrello	1.93	The command string to pass to the system.
3562 :	parrello	1.59
3563 :			=item RETURN
3564 :
3565 :	parrello	1.93	Returns the standard output from the specified command, as a list.
3566 :	parrello	1.59
3567 :			=back
3568 :
3569 :			=cut
3570 :	parrello	1.93	#: Return Type @;
3571 :			sub TICK {
3572 :	parrello	1.59	# Get the parameters.
3573 :	parrello	1.93	my ($commandString) = @_;
3574 :			# Chop off the dot-slash if this is Windows.
3575 :			if ($FIG_Config::win_mode) {
3576 :			$commandString =~ s!^\./!!;
3577 :	parrello	1.59	}
3578 :	parrello	1.93	# Activate the command and return the result.
3579 :			return `$commandString`;
3580 :	parrello	1.59	}
3581 :
3582 :	parrello	1.93
3583 :	parrello	1.55	=head3 CommaFormat
3584 :
3585 :	parrello	1.92	my $formatted = Tracer::CommaFormat($number);
3586 :	parrello	1.55
3587 :			Insert commas into a number.
3588 :
3589 :			=over 4
3590 :
3591 :			=item number
3592 :
3593 :			A sequence of digits.
3594 :
3595 :			=item RETURN
3596 :
3597 :			Returns the same digits with commas strategically inserted.
3598 :
3599 :			=back
3600 :
3601 :			=cut
3602 :
3603 :			sub CommaFormat {
3604 :			# Get the parameters.
3605 :			my ($number) = @_;
3606 :			# Pad the length up to a multiple of three.
3607 :			my $padded = "$number";
3608 :			$padded = " " . $padded while length($padded) % 3 != 0;
3609 :			# This is a fancy PERL trick. The parentheses in the SPLIT pattern
3610 :			# cause the delimiters to be included in the output stream. The
3611 :			# GREP removes the empty strings in between the delimiters.
3612 :			my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3613 :			# Clean out the spaces.
3614 :			$retVal =~ s/ //g;
3615 :			# Return the result.
3616 :			return $retVal;
3617 :			}
3618 :	parrello	1.46
3619 :
3620 :	parrello	1.117	=head3 GetMemorySize
3621 :
3622 :			my $string = Tracer::GetMemorySize();
3623 :
3624 :			Return a memory size string for the current process. The string will be
3625 :			in comma format, with a size indicator (K, M, G) at the end.
3626 :
3627 :			=cut
3628 :
3629 :			sub GetMemorySize {
3630 :			# Get the memory size from Unix.
3631 :			my ($retVal) = `ps h -o vsz $$`;
3632 :			# Remove the ending new-line.
3633 :			chomp $retVal;
3634 :			# Format and return the result.
3635 :			return CommaFormat($retVal) . "K";
3636 :			}
3637 :
3638 :	parrello	1.62	=head3 CompareLists
3639 :
3640 :	parrello	1.92	my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3641 :	parrello	1.62
3642 :			Compare two lists of tuples, and return a hash analyzing the differences. The lists
3643 :			are presumed to be sorted alphabetically by the value in the $keyIndex column.
3644 :			The return value contains a list of items that are only in the new list
3645 :			(inserted) and only in the old list (deleted).
3646 :
3647 :			=over 4
3648 :
3649 :			=item newList
3650 :
3651 :			Reference to a list of new tuples.
3652 :
3653 :			=item oldList
3654 :
3655 :			Reference to a list of old tuples.
3656 :
3657 :			=item keyIndex (optional)
3658 :
3659 :			Index into each tuple of its key field. The default is 0.
3660 :
3661 :			=item RETURN
3662 :
3663 :			Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3664 :			list (inserted) followed by a reference to the list of items that are only in the old
3665 :			list (deleted).
3666 :
3667 :			=back
3668 :
3669 :			=cut
3670 :
3671 :			sub CompareLists {
3672 :			# Get the parameters.
3673 :			my ($newList, $oldList, $keyIndex) = @_;
3674 :			if (! defined $keyIndex) {
3675 :			$keyIndex = 0;
3676 :			}
3677 :			# Declare the return variables.
3678 :			my ($inserted, $deleted) = ([], []);
3679 :			# Loop through the two lists simultaneously.
3680 :			my ($newI, $oldI) = (0, 0);
3681 :			my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3682 :			while ($newI < $newN \|\| $oldI < $oldN) {
3683 :			# Get the current object in each list. Note that if one
3684 :			# of the lists is past the end, we'll get undef.
3685 :			my $newItem = $newList->[$newI];
3686 :			my $oldItem = $oldList->[$oldI];
3687 :	parrello	1.63	if (! defined($newItem) \|\| defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3688 :	parrello	1.62	# The old item is not in the new list, so mark it deleted.
3689 :			push @{$deleted}, $oldItem;
3690 :			$oldI++;
3691 :			} elsif (! defined($oldItem) \|\| $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3692 :			# The new item is not in the old list, so mark it inserted.
3693 :			push @{$inserted}, $newItem;
3694 :			$newI++;
3695 :			} else {
3696 :			# The item is in both lists, so push forward.
3697 :			$oldI++;
3698 :			$newI++;
3699 :			}
3700 :			}
3701 :			# Return the result.
3702 :			return ($inserted, $deleted);
3703 :			}
3704 :
3705 :	parrello	1.105	=head3 Cmp
3706 :
3707 :			my $cmp = Tracer::Cmp($a, $b);
3708 :
3709 :			This method performs a universal sort comparison. Each value coming in is
3710 :	parrello	1.121	separated into a text parts and number parts. The text
3711 :	parrello	1.105	part is string compared, and if both parts are equal, then the number
3712 :			parts are compared numerically. A stream of just numbers or a stream of
3713 :			just strings will sort correctly, and a mixed stream will sort with the
3714 :			numbers first. Strings with a label and a number will sort in the
3715 :	parrello	1.121	expected manner instead of lexically. Undefined values sort last.
3716 :	parrello	1.105
3717 :			=over 4
3718 :
3719 :			=item a
3720 :
3721 :			First item to compare.
3722 :
3723 :			=item b
3724 :
3725 :			Second item to compare.
3726 :
3727 :			=item RETURN
3728 :
3729 :			Returns a negative number if the first item should sort first (is less), a positive
3730 :			number if the first item should sort second (is greater), and a zero if the items are
3731 :			equal.
3732 :
3733 :			=back
3734 :
3735 :			=cut
3736 :
3737 :			sub Cmp {
3738 :			# Get the parameters.
3739 :			my ($a, $b) = @_;
3740 :			# Declare the return value.
3741 :			my $retVal;
3742 :			# Check for nulls.
3743 :			if (! defined($a)) {
3744 :			$retVal = (! defined($b) ? 0 : -1);
3745 :			} elsif (! defined($b)) {
3746 :			$retVal = 1;
3747 :			} else {
3748 :			# Here we have two real values. Parse the two strings.
3749 :	parrello	1.121	my @aParsed = _Parse($a);
3750 :			my @bParsed = _Parse($b);
3751 :			# Loop through the first string.
3752 :			while (! $retVal && @aParsed) {
3753 :			# Extract the string parts.
3754 :			my $aPiece = shift(@aParsed);
3755 :			my $bPiece = shift(@bParsed) \|\| '';
3756 :			# Extract the number parts.
3757 :			my $aNum = shift(@aParsed);
3758 :			my $bNum = shift(@bParsed) \|\| 0;
3759 :			# Compare the string parts insensitively.
3760 :			$retVal = (lc($aPiece) cmp lc($bPiece));
3761 :			# If they're equal, compare them sensitively.
3762 :			if (! $retVal) {
3763 :			$retVal = ($aPiece cmp $bPiece);
3764 :			# If they're STILL equal, compare the number parts.
3765 :			if (! $retVal) {
3766 :			$retVal = $aNum <=> $bNum;
3767 :			}
3768 :			}
3769 :	parrello	1.105	}
3770 :			}
3771 :			# Return the result.
3772 :			return $retVal;
3773 :			}
3774 :
3775 :	parrello	1.121	# This method parses an input string into a string parts alternating with
3776 :			# number parts.
3777 :	parrello	1.115	sub _Parse {
3778 :	parrello	1.121	# Get the incoming string.
3779 :	parrello	1.115	my ($string) = @_;
3780 :	parrello	1.121	# The pieces will be put in here.
3781 :			my @retVal;
3782 :			# Loop through as many alpha/num sets as we can.
3783 :			while ($string =~ /^(\D)(\d+)(.)/) {
3784 :			# Push the alpha and number parts into the return string.
3785 :			push @retVal, $1, $2;
3786 :			# Save the residual.
3787 :			$string = $3;
3788 :			}
3789 :			# If there's still stuff left, add it to the end with a trailing
3790 :			# zero.
3791 :			if ($string) {
3792 :			push @retVal, $string, 0;
3793 :	parrello	1.115	}
3794 :	parrello	1.121	# Return the list.
3795 :			return @retVal;
3796 :	parrello	1.115	}
3797 :
3798 :	parrello	1.108	=head3 ListEQ
3799 :
3800 :			my $flag = Tracer::ListEQ(\@a, \@b);
3801 :
3802 :			Return TRUE if the specified lists contain the same strings in the same
3803 :			order, else FALSE.
3804 :
3805 :			=over 4
3806 :
3807 :			=item a
3808 :
3809 :			Reference to the first list.
3810 :
3811 :			=item b
3812 :
3813 :			Reference to the second list.
3814 :
3815 :			=item RETURN
3816 :
3817 :			Returns TRUE if the two parameters are identical string lists, else FALSE.
3818 :
3819 :			=back
3820 :
3821 :			=cut
3822 :
3823 :			sub ListEQ {
3824 :			# Get the parameters.
3825 :			my ($a, $b) = @_;
3826 :			# Declare the return variable. Start by checking the lengths.
3827 :			my $n = scalar(@$a);
3828 :			my $retVal = ($n == scalar(@$b));
3829 :			# Now compare the list elements.
3830 :			for (my $i = 0; $retVal && $i < $n; $i++) {
3831 :			$retVal = ($a->[$i] eq $b->[$i]);
3832 :			}
3833 :			# Return the result.
3834 :			return $retVal;
3835 :			}
3836 :
3837 :	parrello	1.105	=head2 CGI Script Utilities
3838 :
3839 :			=head3 ScriptSetup (deprecated)
3840 :
3841 :			my ($cgi, $varHash) = ScriptSetup($noTrace);
3842 :
3843 :			Perform standard tracing and debugging setup for scripts. The value returned is
3844 :			the CGI object followed by a pre-built variable hash. At the end of the script,
3845 :			the client should call L</ScriptFinish> to output the web page.
3846 :
3847 :			This method calls L</ETracing> to configure tracing, which allows the tracing
3848 :			to be configured via the emergency tracing form on the debugging control panel.
3849 :			Tracing will then be turned on automatically for all programs that use the L</ETracing>
3850 :			method, which includes every program that uses this method or L</StandardSetup>.
3851 :
3852 :			=over 4
3853 :
3854 :			=item noTrace (optional)
3855 :
3856 :			If specified, tracing will be suppressed. This is useful if the script wants to set up
3857 :			tracing manually.
3858 :
3859 :			=item RETURN
3860 :
3861 :			Returns a two-element list consisting of a CGI query object and a variable hash for
3862 :			the output page.
3863 :
3864 :			=back
3865 :
3866 :			=cut
3867 :
3868 :			sub ScriptSetup {
3869 :			# Get the parameters.
3870 :			my ($noTrace) = @_;
3871 :			# Get the CGI query object.
3872 :			my $cgi = CGI->new();
3873 :			# Set up tracing if it's not suppressed.
3874 :			ETracing($cgi) unless $noTrace;
3875 :			# Create the variable hash.
3876 :			my $varHash = { results => '' };
3877 :			# Return the query object and variable hash.
3878 :			return ($cgi, $varHash);
3879 :			}
3880 :
3881 :			=head3 ScriptFinish (deprecated)
3882 :
3883 :			ScriptFinish($webData, $varHash);
3884 :
3885 :			Output a web page at the end of a script. Either the string to be output or the
3886 :			name of a template file can be specified. If the second parameter is omitted,
3887 :			it is assumed we have a string to be output; otherwise, it is assumed we have the
3888 :			name of a template file. The template should have the variable C<DebugData>
3889 :			specified in any form that invokes a standard script. If debugging mode is turned
3890 :			on, a form field will be put in that allows the user to enter tracing data.
3891 :			Trace messages will be placed immediately before the terminal C<BODY> tag in
3892 :			the output, formatted as a list.
3893 :
3894 :			A typical standard script would loook like the following.
3895 :
3896 :			BEGIN {
3897 :			# Print the HTML header.
3898 :			print "CONTENT-TYPE: text/html\n\n";
3899 :			}
3900 :			use Tracer;
3901 :			use CGI;
3902 :			use FIG;
3903 :			# ... more uses ...
3904 :
3905 :			my ($cgi, $varHash) = ScriptSetup();
3906 :			eval {
3907 :			# ... get data from $cgi, put it in $varHash ...
3908 :			};
3909 :			if ($@) {
3910 :			Trace("Script Error: $@") if T(0);
3911 :			}
3912 :			ScriptFinish("Html/MyTemplate.html", $varHash);
3913 :
3914 :			The idea here is that even if the script fails, you'll see trace messages and
3915 :			useful output.
3916 :
3917 :			=over 4
3918 :
3919 :			=item webData
3920 :
3921 :			A string containing either the full web page to be written to the output or the
3922 :			name of a template file from which the page is to be constructed. If the name
3923 :			of a template file is specified, then the second parameter must be present;
3924 :			otherwise, it must be absent.
3925 :
3926 :			=item varHash (optional)
3927 :
3928 :			If specified, then a reference to a hash mapping variable names for a template
3929 :			to their values. The template file will be read into memory, and variable markers
3930 :			will be replaced by data in this hash reference.
3931 :
3932 :			=back
3933 :
3934 :			=cut
3935 :
3936 :			sub ScriptFinish {
3937 :			# Get the parameters.
3938 :			my ($webData, $varHash) = @_;
3939 :			# Check for a template file situation.
3940 :			my $outputString;
3941 :			if (defined $varHash) {
3942 :			# Here we have a template file. We need to determine the template type.
3943 :			my $template;
3944 :			if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3945 :			$template = "$FIG_Config::template_url/$webData";
3946 :			} else {
3947 :			$template = "<<$webData";
3948 :			}
3949 :			$outputString = PageBuilder::Build($template, $varHash, "Html");
3950 :			} else {
3951 :			# Here the user gave us a raw string.
3952 :			$outputString = $webData;
3953 :			}
3954 :			# Check for trace messages.
3955 :			if ($Destination ne "NONE" && $TraceLevel > 0) {
3956 :			# We have trace messages, so we want to put them at the end of the body. This
3957 :			# is either at the end of the whole string or at the beginning of the BODY
3958 :			# end-tag.
3959 :			my $pos = length $outputString;
3960 :			if ($outputString =~ m#</body>#gi) {
3961 :			$pos = (pos $outputString) - 7;
3962 :			}
3963 :			# If the trace messages were queued, we unroll them. Otherwise, we display the
3964 :			# destination.
3965 :			my $traceHtml;
3966 :			if ($Destination eq "QUEUE") {
3967 :			$traceHtml = QTrace('Html');
3968 :			} elsif ($Destination =~ /^>>(.+)$/) {
3969 :			# Here the tracing output it to a file. We code it as a hyperlink so the user
3970 :			# can copy the file name into the clipboard easily.
3971 :			my $actualDest = $1;
3972 :			$traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3973 :			} else {
3974 :			# Here we have one of the special destinations.
3975 :			$traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3976 :			}
3977 :			substr $outputString, $pos, 0, $traceHtml;
3978 :			}
3979 :			# Write the output string.
3980 :			print $outputString;
3981 :			}
3982 :
3983 :	parrello	1.65	=head3 GenerateURL
3984 :
3985 :	parrello	1.92	my $queryUrl = Tracer::GenerateURL($page, %parameters);
3986 :	parrello	1.65
3987 :			Generate a GET-style URL for the specified page with the specified parameter
3988 :			names and values. The values will be URL-escaped automatically. So, for
3989 :			example
3990 :
3991 :			Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3992 :
3993 :			would return
3994 :
3995 :	parrello	1.79	form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3996 :	parrello	1.65
3997 :			=over 4
3998 :
3999 :			=item page
4000 :
4001 :			Page URL.
4002 :
4003 :			=item parameters
4004 :
4005 :			Hash mapping parameter names to parameter values.
4006 :
4007 :			=item RETURN
4008 :
4009 :			Returns a GET-style URL that goes to the specified page and passes in the
4010 :			specified parameters and values.
4011 :
4012 :			=back
4013 :
4014 :			=cut
4015 :
4016 :			sub GenerateURL {
4017 :			# Get the parameters.
4018 :			my ($page, %parameters) = @_;
4019 :			# Prime the return variable with the page URL.
4020 :			my $retVal = $page;
4021 :			# Loop through the parameters, creating parameter elements in a list.
4022 :			my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
4023 :			# If the list is nonempty, tack it on.
4024 :			if (@parmList) {
4025 :	parrello	1.79	$retVal .= "?" . join(";", @parmList);
4026 :	parrello	1.65	}
4027 :			# Return the result.
4028 :			return $retVal;
4029 :			}
4030 :
4031 :	parrello	1.78	=head3 ApplyURL
4032 :
4033 :	parrello	1.92	Tracer::ApplyURL($table, $target, $url);
4034 :	parrello	1.78
4035 :			Run through a two-dimensional table (or more accurately, a list of lists), converting the
4036 :			I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
4037 :			URL column will be deleted by this process and the target column will be HTML-escaped.
4038 :
4039 :			This provides a simple way to process the results of a database query into something
4040 :			displayable by combining a URL with text.
4041 :
4042 :			=over 4
4043 :
4044 :			=item table
4045 :
4046 :			Reference to a list of lists. The elements in the containing list will be updated by
4047 :			this method.
4048 :
4049 :			=item target
4050 :
4051 :			The index of the column to be converted into HTML.
4052 :
4053 :			=item url
4054 :
4055 :			The index of the column containing the URL. Note that the URL must have a recognizable
4056 :			C<http:> at the beginning.
4057 :
4058 :			=back
4059 :
4060 :			=cut
4061 :
4062 :			sub ApplyURL {
4063 :			# Get the parameters.
4064 :			my ($table, $target, $url) = @_;
4065 :			# Loop through the table.
4066 :			for my $row (@{$table}) {
4067 :			# Apply the URL to the target cell.
4068 :			$row->[$target] = CombineURL($row->[$target], $row->[$url]);
4069 :			# Delete the URL from the row.
4070 :			delete $row->[$url];
4071 :			}
4072 :			}
4073 :
4074 :			=head3 CombineURL
4075 :
4076 :	parrello	1.92	my $combinedHtml = Tracer::CombineURL($text, $url);
4077 :	parrello	1.78
4078 :			This method will convert the specified text into HTML hyperlinked to the specified
4079 :			URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
4080 :			is defined and begins with an C<http:> header.
4081 :
4082 :			=over 4
4083 :
4084 :			=item text
4085 :
4086 :			Text to return. This will be HTML-escaped automatically.
4087 :
4088 :			=item url
4089 :
4090 :			A URL to be hyperlinked to the text. If it does not look like a URL, then the text
4091 :			will be returned without any hyperlinking.
4092 :
4093 :			=item RETURN
4094 :
4095 :			Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
4096 :			doesn't look right, the HTML-escaped text will be returned without any further
4097 :			modification.
4098 :
4099 :			=back
4100 :
4101 :			=cut
4102 :
4103 :			sub CombineURL {
4104 :			# Get the parameters.
4105 :			my ($text, $url) = @_;
4106 :			# Declare the return variable.
4107 :			my $retVal =