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	1.12	require Exporter;
22 :			@ISA = ('Exporter');
23 :	parrello	1.97	@EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency);
24 :			@EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25 :	parrello	1.12	use strict;
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 :	olson	1.1
40 :			=head1 Tracing and Debugging Helpers
41 :
42 :	parrello	1.72	=head2 Tracing
43 :	olson	1.1
44 :			This package provides simple tracing for debugging and reporting purposes. To use it simply call the
45 :	parrello	1.72	L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
46 :			L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
47 :			each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
48 :			level is less than or equal to the setup trace level and whose category is activated will
49 :	parrello	1.2	be written. Thus, a higher trace level on a message indicates that the message
50 :	parrello	1.72	is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
51 :			appear.
52 :	olson	1.1
53 :	parrello	1.72	=head3 Putting Trace Messages in Your Code
54 :
55 :			To generate a trace message, use the following syntax.
56 :
57 :			Trace($message) if T(errors => 4);
58 :	olson	1.1
59 :	parrello	1.2	This statement will produce a trace message if the trace level is 4 or more and the C<errors>
60 :	parrello	1.72	category is active. There is a special category C<main> that is always active, so
61 :	olson	1.1
62 :	parrello	1.72	Trace($message) if T(main => 4);
63 :	olson	1.1
64 :			will trace if the trace level is 4 or more.
65 :
66 :			If the category name is the same as the package name, all you need is the number. So, if the
67 :			following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
68 :			active and the trace level is 2 or more.
69 :
70 :	parrello	1.72	Trace($message) if T(2);
71 :
72 :			In scripts, where no package name is available, the category defaults to C<main>.
73 :
74 :			=head3 Custom Tracing
75 :
76 :			Many programs have customized tracing configured using the L</TSetup> method. This is no longer
77 :			the preferred method, but a knowledge of how custom tracing works can make the more modern
78 :			L</Emergency Tracing> easier to understand.
79 :	olson	1.1
80 :	parrello	1.72	To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
81 :			a list of category names, and a destination. The trace level and list of category names are
82 :	olson	1.1	specified as a space-delimited string. Thus
83 :
84 :	parrello	1.72	TSetup('3 errors Sprout ERDB', 'TEXT');
85 :	olson	1.1
86 :	parrello	1.7	sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
87 :	parrello	1.72	specifies that messages should be sent to the standard output.
88 :	parrello	1.12
89 :			To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
90 :			level 3 and writes the output to the standard error output. This sort of thing might be
91 :			useful in a CGI environment.
92 :
93 :	parrello	1.72	TSetup('3 *', 'WARN');
94 :	olson	1.1
95 :	parrello	1.72	In addition standard error and file output for trace messages, you can specify that the trace messages
96 :	olson	1.1	be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
97 :			is useful if you are building a web page. Instead of having the trace messages interspersed with
98 :			the page output, they can be gathered together and displayed at the end of the page. This makes
99 :			it easier to debug page formatting problems.
100 :
101 :	parrello	1.72	Finally, you can specify that all trace messages be emitted to a file, or the standard output and
102 :			a file at the same time. To trace to a file, specify the filename with an output character in front
103 :			of it.
104 :
105 :			TSetup('4 SQL', ">$fileName");
106 :
107 :			To trace to the standard output and a file at the same time, put a C<+> in front of the angle
108 :			bracket.
109 :
110 :			TSetup('3 *', "+>$fileName");
111 :	parrello	1.4
112 :	olson	1.1	The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
113 :			Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
114 :			Thus, debugging information is available and easily retrieved even when the application is
115 :			being used out in the field.
116 :
117 :	parrello	1.72	=head3 Trace Levels
118 :
119 :	parrello	1.10	There is no hard and fast rule on how to use trace levels. The following is therefore only
120 :			a suggestion.
121 :
122 :			=over 4
123 :
124 :	parrello	1.32	=item Error 0
125 :	parrello	1.10
126 :			Message indicates an error that may lead to incorrect results or that has stopped the
127 :			application entirely.
128 :
129 :	parrello	1.32	=item Warning 1
130 :	parrello	1.10
131 :			Message indicates something that is unexpected but that probably did not interfere
132 :			with program execution.
133 :
134 :	parrello	1.32	=item Notice 2
135 :	parrello	1.10
136 :			Message indicates the beginning or end of a major task.
137 :
138 :	parrello	1.32	=item Information 3
139 :	parrello	1.10
140 :			Message indicates a subtask. In the FIG system, a subtask generally relates to a single
141 :			genome. This would be a big loop that is not expected to execute more than 500 times or so.
142 :
143 :	parrello	1.32	=item Detail 4
144 :	parrello	1.10
145 :			Message indicates a low-level loop iteration.
146 :
147 :			=back
148 :
149 :	parrello	1.69	The format of trace messages is important because some utilities analyze trace files.
150 :	parrello	1.72	There are three fields-- the time stamp, the category name, and the text.
151 :			The time stamp is between square brackets and the category name between angle brackets.
152 :			After the category name there is a colon (C<:>) followed by the message text.
153 :			If the square brackets or angle brackets are missing, then the trace management
154 :			utilities assume that they are encountering a set of pre-formatted lines.
155 :
156 :			Note, however, that this formatting is done automatically by the tracing functions. You
157 :			only need to know about it if you want to parse a trace file.
158 :
159 :			=head3 Emergency Tracing
160 :
161 :			Sometimes, you need a way for tracing to happen automatically without putting parameters
162 :			in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
163 :	parrello	1.97	from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
164 :			that you specify a tracing key. For command-line tools, the key is
165 :	parrello	1.72	taken from the C<TRACING> environment variable. For web services, the key is taken from
166 :			a cookie. Either way, the key tells the tracing facility who you are, so that you control
167 :			the tracing in your environment without stepping on other users.
168 :
169 :			The key can be anything you want. If you don't have a key, the C<SetPassword> page will
170 :			generate one for you.
171 :
172 :			You can activate and de-activate emergency tracing from the debugging control panel, as
173 :			well as display the trace file itself.
174 :
175 :			To enable emergency tracing in your code, call
176 :
177 :			ETracing($cgi)
178 :
179 :			from a web script and
180 :
181 :			ETracing()
182 :
183 :			from a command-line script.
184 :
185 :			The web script will look for the tracing key in the cookies, and the command-line
186 :			script will look for it in the C<TRACING> environment variable. If you are
187 :	parrello	1.97	using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
188 :	parrello	1.72	will be configured automatically.
189 :
190 :	olson	1.1	=cut
191 :	parrello	1.2
192 :	olson	1.1	# Declare the configuration variables.
193 :
194 :	parrello	1.94	my $Destination = "WARN"; # Description of where to send the trace output.
195 :	parrello	1.12	my $TeeFlag = 0; # TRUE if output is going to a file and to the
196 :			# standard output
197 :	parrello	1.3	my %Categories = ( main => 1 );
198 :	parrello	1.12	# hash of active category names
199 :	parrello	1.97	my @LevelNames = qw(error warn notice info detail);
200 :	parrello	1.12	my $TraceLevel = 0; # trace level; a higher trace level produces more
201 :			# messages
202 :			my @Queue = (); # queued list of trace messages.
203 :	parrello	1.7	my $LastCategory = "main"; # name of the last category interrogated
204 :	parrello	1.97	my $LastLevel = 0; # level of the last test call
205 :	parrello	1.11	my $SetupCount = 0; # number of times TSetup called
206 :	parrello	1.12	my $AllTrace = 0; # TRUE if we are tracing all categories.
207 :	olson	1.1
208 :	parrello	1.93	=head2 Tracing Methods
209 :
210 :			=head3 Setups
211 :
212 :			my $count = Tracer::Setups();
213 :
214 :			Return the number of times L</TSetup> has been called.
215 :
216 :			This method allows for the creation of conditional tracing setups where, for example, we
217 :			may want to set up tracing if nobody else has done it before us.
218 :
219 :			=cut
220 :
221 :			sub Setups {
222 :			return $SetupCount;
223 :			}
224 :	olson	1.1
225 :			=head3 TSetup
226 :
227 :	parrello	1.92	TSetup($categoryList, $target);
228 :	olson	1.1
229 :			This method is used to specify the trace options. The options are stored as package data
230 :			and interrogated by the L</Trace> and L</T> methods.
231 :
232 :			=over 4
233 :
234 :			=item categoryList
235 :
236 :			A string specifying the trace level and the categories to be traced, separated by spaces.
237 :			The trace level must come first.
238 :
239 :			=item target
240 :
241 :			The destination for the trace output. To send the trace output to a file, specify the file
242 :			name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
243 :	parrello	1.10	to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
244 :			symbol with a C<+> to echo output to a file AND to the standard output. In addition to
245 :			sending the trace messages to a file, you can specify a special destination. C<HTML> will
246 :			cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
247 :	parrello	1.5	will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
248 :	parrello	1.9	messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
249 :	parrello	1.6	messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
250 :	parrello	1.9	cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
251 :	parrello	1.6	cause tracing to be suppressed.
252 :	olson	1.1
253 :			=back
254 :
255 :			=cut
256 :
257 :			sub TSetup {
258 :	parrello	1.12	# Get the parameters.
259 :			my ($categoryList, $target) = @_;
260 :			# Parse the category list.
261 :			my @categoryData = split /\s+/, $categoryList;
262 :			# Extract the trace level.
263 :			$TraceLevel = shift @categoryData;
264 :			# Presume category-based tracing until we learn otherwise.
265 :			$AllTrace = 0;
266 :			# Build the category hash. Note that if we find a "*", we turn on non-category
267 :	parrello	1.33	# tracing. We must also clear away any pre-existing data.
268 :	parrello	1.34	%Categories = ( main => 1 );
269 :	parrello	1.12	for my $category (@categoryData) {
270 :			if ($category eq '*') {
271 :			$AllTrace = 1;
272 :			} else {
273 :	parrello	1.13	$Categories{lc $category} = 1;
274 :	parrello	1.12	}
275 :			}
276 :			# Now we need to process the destination information. The most important special
277 :	parrello	1.98	# case is when we're writing to a file. This is indicated by ">" (overwrite) and
278 :			# ">>" (append). A leading "+" for either indicates that we are also writing to
279 :			# the standard output (tee mode).
280 :	parrello	1.12	if ($target =~ m/^\+?>>?/) {
281 :			if ($target =~ m/^\+/) {
282 :			$TeeFlag = 1;
283 :			$target = substr($target, 1);
284 :			}
285 :			if ($target =~ m/^>[^>]/) {
286 :	parrello	1.98	# We need to initialize the file (which clears it).
287 :	parrello	1.12	open TRACEFILE, $target;
288 :	parrello	1.98	print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
289 :	parrello	1.12	close TRACEFILE;
290 :	parrello	1.98	# Set to append mode now that the file has been cleared.
291 :	parrello	1.12	$Destination = ">$target";
292 :			} else {
293 :			$Destination = $target;
294 :			}
295 :			} else {
296 :			$Destination = uc($target);
297 :			}
298 :			# Increment the setup counter.
299 :			$SetupCount++;
300 :	parrello	1.11	}
301 :
302 :	parrello	1.93	=head3 SetLevel
303 :	parrello	1.31
304 :	parrello	1.93	Tracer::SetLevel($newLevel);
305 :	parrello	1.31
306 :	parrello	1.93	Modify the trace level. A higher trace level will cause more messages to appear.
307 :	parrello	1.31
308 :	parrello	1.93	=over 4
309 :	parrello	1.31
310 :	parrello	1.93	=item newLevel
311 :	parrello	1.31
312 :	parrello	1.93	Proposed new trace level.
313 :	parrello	1.31
314 :	parrello	1.93	=back
315 :	parrello	1.31
316 :	parrello	1.93	=cut
317 :	parrello	1.31
318 :	parrello	1.93	sub SetLevel {
319 :			$TraceLevel = $_[0];
320 :			}
321 :	parrello	1.31
322 :	parrello	1.97	=head3 ParseDate
323 :
324 :			my $time = Tracer::ParseDate($dateString);
325 :
326 :			Convert a date into a PERL time number. This method expects a date-like string
327 :			and parses it into a number. The string must be vaguely date-like or it will
328 :			return an undefined value. Our requirement is that a month and day be
329 :			present and that three pieces of the date string (time of day, month and day,
330 :			year) be separated by likely delimiters, such as spaces, commas, and such-like.
331 :
332 :			If a time of day is present, it must be in military time with two digits for
333 :			everything but the hour.
334 :	parrello	1.31
335 :	parrello	1.97	The year must be exactly four digits.
336 :	parrello	1.31
337 :	parrello	1.97	Additional stuff can be in the string. We presume it's time zones or weekdays or something
338 :			equally innocuous. This means, however, that a sufficiently long sentence with date-like
339 :			parts in it may be interpreted as a date. Hopefully this will not be a problem.
340 :
341 :			It should be guaranteed that this method will parse the output of the L</Now> function.
342 :
343 :			The parameters are as follows.
344 :	parrello	1.31
345 :	parrello	1.93	=over 4
346 :	parrello	1.31
347 :	parrello	1.93	=item dateString
348 :	parrello	1.31
349 :	parrello	1.97	The date string to convert.
350 :	parrello	1.31
351 :	parrello	1.93	=item RETURN
352 :	parrello	1.31
353 :	parrello	1.93	Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
354 :	parrello	1.97	the date string is invalid. A valid date string must contain a month and day.
355 :	parrello	1.31
356 :	parrello	1.93	=back
357 :	parrello	1.38
358 :	parrello	1.93	=cut
359 :	parrello	1.38
360 :	parrello	1.97	# Universal month conversion table.
361 :			use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
362 :			Feb => 1, February => 1, '02' => 1, '2' => 1,
363 :			Mar => 2, March => 2, '03' => 2, '3' => 2,
364 :			Apr => 3, April => 3, '04' => 3, '4' => 3,
365 :			May => 4, May => 4, '05' => 4, '5' => 4,
366 :			Jun => 5, June => 5, '06' => 5, '6' => 5,
367 :			Jul => 6, July => 6, '07' => 6, '7' => 6,
368 :			Aug => 7, August => 7, '08' => 7, '8' => 7,
369 :			Sep => 8, September => 8, '09' => 8, '9' => 8,
370 :			Oct => 9, October => 9, '10' => 9,
371 :			Nov => 10, November => 10, '11' => 10,
372 :			Dec => 11, December => 11, '12' => 11
373 :			};
374 :
375 :			sub ParseDate {
376 :	parrello	1.93	# Get the parameters.
377 :			my ($dateString) = @_;
378 :			# Declare the return variable.
379 :			my $retVal;
380 :	parrello	1.97	# Find the month and day of month. There are two ways that can happen. We check for the
381 :			# numeric style first. That way, if the user's done something like "Sun 12/22", then we
382 :			# won't be fooled into thinking the month is Sunday.
383 :			if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# \|\| $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
384 :			my ($mon, $mday) = (MONTHS->{$1}, $2);
385 :			# Insist that the month and day are valid.
386 :			if (defined($mon) && $2 >= 1 && $2 <= 31) {
387 :			# Find the time.
388 :			my ($hour, $min, $sec) = (0, 0, 0);
389 :			if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
390 :			($hour, $min, $sec) = ($1, $2, $3);
391 :			}
392 :			# Find the year.
393 :			my $year;
394 :			if ($dateString =~ /\b(\d{4})\b/) {
395 :			$year = $1;
396 :			} else {
397 :			# Get the default year, which is this one. Note we must convert it to
398 :			# the four-digit value expected by "timelocal".
399 :			(undef, undef, undef, undef, undef, $year) = localtime();
400 :			$year += 1900;
401 :			}
402 :			$retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
403 :			}
404 :	parrello	1.93	}
405 :			# Return the result.
406 :			return $retVal;
407 :			}
408 :	parrello	1.31
409 :	parrello	1.93	=head3 LogErrors
410 :	parrello	1.42
411 :	parrello	1.93	Tracer::LogErrors($fileName);
412 :	parrello	1.31
413 :	parrello	1.93	Route the standard error output to a log file.
414 :	parrello	1.31
415 :	parrello	1.93	=over 4
416 :	parrello	1.31
417 :	parrello	1.93	=item fileName
418 :	parrello	1.31
419 :	parrello	1.93	Name of the file to receive the error output.
420 :	parrello	1.31
421 :	parrello	1.93	=back
422 :	parrello	1.31
423 :	parrello	1.93	=cut
424 :	parrello	1.84
425 :	parrello	1.93	sub LogErrors {
426 :			# Get the file name.
427 :			my ($fileName) = @_;
428 :			# Open the file as the standard error output.
429 :			open STDERR, '>', $fileName;
430 :			}
431 :	parrello	1.84
432 :	parrello	1.93	=head3 Trace
433 :	parrello	1.31
434 :	parrello	1.93	Trace($message);
435 :	parrello	1.31
436 :	parrello	1.93	Write a trace message to the target location specified in L</TSetup>. If there has not been
437 :			any prior call to B<TSetup>.
438 :	parrello	1.31
439 :	parrello	1.93	=over 4
440 :	parrello	1.42
441 :	parrello	1.93	=item message
442 :	parrello	1.42
443 :	parrello	1.93	Message to write.
444 :	parrello	1.42
445 :	parrello	1.93	=back
446 :	parrello	1.72
447 :	parrello	1.93	=cut
448 :	parrello	1.36
449 :	parrello	1.93	sub Trace {
450 :			# Get the parameters.
451 :			my ($message) = @_;
452 :	parrello	1.97	# Strip off any line terminators at the end of the message. We will add
453 :			# new-line stuff ourselves.
454 :			my $stripped = Strip($message);
455 :			# Compute the caller information.
456 :			my ($callPackage, $callFile, $callLine) = caller();
457 :			my $callFileTitle = basename($callFile);
458 :			# Check the caller.
459 :	parrello	1.98	my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
460 :	parrello	1.93	# Get the timestamp.
461 :			my $timeStamp = Now();
462 :	parrello	1.97	# Build the prefix.
463 :			my $level = $LevelNames[$LastLevel] \|\| "($LastLevel)";
464 :	parrello	1.98	my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
465 :	parrello	1.97	# Format the message.
466 :			my $formatted = "$prefix $stripped";
467 :	parrello	1.93	# Process according to the destination.
468 :			if ($Destination eq "TEXT") {
469 :			# Write the message to the standard output.
470 :			print "$formatted\n";
471 :			} elsif ($Destination eq "ERROR") {
472 :	parrello	1.97	# Write the message to the error output. Here, we want our prefix fields.
473 :	parrello	1.93	print STDERR "$formatted\n";
474 :	parrello	1.97	} elsif ($Destination eq "WARN") {
475 :			# Emit the message to the standard error output. It is presumed that the
476 :	parrello	1.98	# error logger will add its own prefix fields, the notable exception being
477 :			# the caller info.
478 :			print STDERR "$callerInfo$stripped\n";
479 :	parrello	1.93	} elsif ($Destination eq "QUEUE") {
480 :			# Push the message into the queue.
481 :			push @Queue, "$formatted";
482 :			} elsif ($Destination eq "HTML") {
483 :			# Convert the message to HTML and write it to the standard output.
484 :	parrello	1.97	my $escapedMessage = CGI::escapeHTML($stripped);
485 :			print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
486 :	parrello	1.93	} elsif ($Destination =~ m/^>>/) {
487 :			# Write the trace message to an output file.
488 :	parrello	1.97	open(TRACING, $Destination) \|\| die "Tracing open for \"$Destination\" failed: $!";
489 :	parrello	1.93	print TRACING "$formatted\n";
490 :			close TRACING;
491 :			# If the Tee flag is on, echo it to the standard output.
492 :			if ($TeeFlag) {
493 :			print "$formatted\n";
494 :			}
495 :			}
496 :			}
497 :	parrello	1.36
498 :	parrello	1.93	=head3 T
499 :	parrello	1.36
500 :	parrello	1.93	my $switch = T($category, $traceLevel);
501 :	parrello	1.36
502 :	parrello	1.93	or
503 :	parrello	1.44
504 :	parrello	1.93	my $switch = T($traceLevel);
505 :	parrello	1.44
506 :	parrello	1.93	Return TRUE if the trace level is at or above a specified value and the specified category
507 :			is active, else FALSE. If no category is specified, the caller's package name is used.
508 :	parrello	1.44
509 :	parrello	1.93	=over 4
510 :	parrello	1.44
511 :	parrello	1.93	=item category
512 :	parrello	1.44
513 :	parrello	1.93	Category to which the message belongs. If not specified, the caller's package name is
514 :			used.
515 :	parrello	1.31
516 :	parrello	1.93	=item traceLevel
517 :	parrello	1.31
518 :	parrello	1.93	Relevant tracing level.
519 :	parrello	1.31
520 :	parrello	1.93	=item RETURN
521 :	parrello	1.31
522 :	parrello	1.93	TRUE if a message at the specified trace level would appear in the trace, else FALSE.
523 :	parrello	1.31
524 :	parrello	1.93	=back
525 :	parrello	1.36
526 :	parrello	1.93	=cut
527 :
528 :			sub T {
529 :			# Declare the return variable.
530 :			my $retVal = 0;
531 :			# Only proceed if tracing is turned on.
532 :			if ($Destination ne "NONE") {
533 :			# Get the parameters.
534 :			my ($category, $traceLevel) = @_;
535 :			if (!defined $traceLevel) {
536 :			# Here we have no category, so we need to get the calling package.
537 :			# The calling package is normally the first parameter. If it is
538 :			# omitted, the first parameter will be the tracelevel. So, the
539 :			# first thing we do is shift the so-called category into the
540 :			# $traceLevel variable where it belongs.
541 :			$traceLevel = $category;
542 :			my ($package, $fileName, $line) = caller;
543 :			# If there is no calling package, we default to "main".
544 :			if (!$package) {
545 :			$category = "main";
546 :			} else {
547 :			my @cats = split /::/, $package;
548 :			$category = $cats[$#cats];
549 :			}
550 :			}
551 :	parrello	1.97	# Save the category name and level.
552 :	parrello	1.93	$LastCategory = $category;
553 :	parrello	1.97	$LastLevel = $traceLevel;
554 :	parrello	1.93	# Convert it to lower case before we hash it.
555 :			$category = lc $category;
556 :			# Use the category and tracelevel to compute the result.
557 :			if (ref $traceLevel) {
558 :			Confess("Bad trace level.");
559 :			} elsif (ref $TraceLevel) {
560 :			Confess("Bad trace config.");
561 :			}
562 :			$retVal = ($traceLevel <= $TraceLevel && ($AllTrace \|\| exists $Categories{$category}));
563 :			}
564 :			# Return the computed result.
565 :			return $retVal;
566 :			}
567 :
568 :			=head3 QTrace
569 :
570 :			my $data = QTrace($format);
571 :
572 :			Return the queued trace data in the specified format.
573 :
574 :			=over 4
575 :
576 :			=item format
577 :
578 :			C<html> to format the data as an HTML list, C<text> to format it as straight text.
579 :
580 :			=back
581 :
582 :			=cut
583 :
584 :			sub QTrace {
585 :			# Get the parameter.
586 :			my ($format) = @_;
587 :			# Create the return variable.
588 :			my $retVal = "";
589 :			# Only proceed if there is an actual queue.
590 :			if (@Queue) {
591 :			# Process according to the format.
592 :			if ($format =~ m/^HTML$/i) {
593 :			# Convert the queue into an HTML list.
594 :			$retVal = "<ul>\n";
595 :			for my $line (@Queue) {
596 :			my $escapedLine = CGI::escapeHTML($line);
597 :			$retVal .= "<li>$escapedLine</li>\n";
598 :			}
599 :			$retVal .= "</ul>\n";
600 :			} elsif ($format =~ m/^TEXT$/i) {
601 :			# Convert the queue into a list of text lines.
602 :			$retVal = join("\n", @Queue) . "\n";
603 :			}
604 :			# Clear the queue.
605 :			@Queue = ();
606 :			}
607 :			# Return the formatted list.
608 :			return $retVal;
609 :			}
610 :
611 :			=head3 Confess
612 :
613 :			Confess($message);
614 :
615 :			Trace the call stack and abort the program with the specified message. When used with
616 :			the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
617 :			So, for example
618 :
619 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
620 :
621 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
622 :
623 :			=over 4
624 :
625 :			=item message
626 :
627 :			Message to include in the trace.
628 :
629 :			=back
630 :
631 :			=cut
632 :
633 :			sub Confess {
634 :			# Get the parameters.
635 :			my ($message) = @_;
636 :	parrello	1.97	# Set up the category and level.
637 :			$LastCategory = "(confess)";
638 :			$LastLevel = 0;
639 :	parrello	1.93	if (! defined($FIG_Config::no_tool_hdr)) {
640 :			# Here we have a tool header. Display its length so that the user can adjust the line numbers.
641 :			my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
642 :			# Only proceed if the tool header file is actually present.
643 :			if (-f $toolHeaderFile) {
644 :	parrello	1.97	my $fh;
645 :			if (open $fh, "<$toolHeaderFile") {
646 :			my @lines = <$fh>;
647 :			Trace("Tool header has " . scalar(@lines) . " lines.");
648 :			}
649 :	parrello	1.93	}
650 :			}
651 :			# Trace the call stack.
652 :			Cluck($message);
653 :			# Abort the program.
654 :			croak(">>> $message");
655 :			}
656 :
657 :			=head3 Assert
658 :
659 :			Assert($condition1, $condition2, ... $conditionN);
660 :
661 :			Return TRUE if all the conditions are true. This method can be used in conjunction with
662 :			the OR operator and the L</Confess> method as a debugging assert.
663 :			So, for example
664 :
665 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
666 :
667 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
668 :
669 :			=cut
670 :			sub Assert {
671 :			my $retVal = 1;
672 :			LOOP: for my $condition (@_) {
673 :			if (! $condition) {
674 :			$retVal = 0;
675 :			last LOOP;
676 :			}
677 :			}
678 :			return $retVal;
679 :			}
680 :
681 :			=head3 Cluck
682 :
683 :			Cluck($message);
684 :
685 :			Trace the call stack. Note that for best results, you should qualify the call with a
686 :			trace condition. For example,
687 :
688 :			Cluck("Starting record parse.") if T(3);
689 :
690 :			will only trace the stack if the trace level for the package is 3 or more.
691 :
692 :			=over 4
693 :
694 :			=item message
695 :
696 :			Message to include in the trace.
697 :
698 :			=back
699 :
700 :			=cut
701 :
702 :			sub Cluck {
703 :			# Get the parameters.
704 :			my ($message) = @_;
705 :			# Trace what's happening.
706 :			Trace("Stack trace for event: $message");
707 :			my $confession = longmess($message);
708 :	parrello	1.97	# Convert the confession to a series of trace messages.
709 :	parrello	1.93	for my $line (split /\s*\n/, $confession) {
710 :	parrello	1.97	# Only proceed if this call trace is for a method outside Tracer itself.
711 :			if ($line !~ /Tracer\.pm/) {
712 :			# Replace the leading tab with a series of spaces.
713 :			$line =~ s/\t/ /;
714 :			# Trace the line.
715 :			Trace($line);
716 :			}
717 :	parrello	1.93	}
718 :			}
719 :
720 :	parrello	1.97	=head3 ScriptSetup (deprecated)
721 :	parrello	1.93
722 :			my ($cgi, $varHash) = ScriptSetup($noTrace);
723 :
724 :			Perform standard tracing and debugging setup for scripts. The value returned is
725 :			the CGI object followed by a pre-built variable hash. At the end of the script,
726 :			the client should call L</ScriptFinish> to output the web page.
727 :
728 :			This method calls L</ETracing> to configure tracing, which allows the tracing
729 :			to be configured via the emergency tracing form on the debugging control panel.
730 :			Tracing will then be turned on automatically for all programs that use the L</ETracing>
731 :			method, which includes every program that uses this method or L</StandardSetup>.
732 :	parrello	1.36
733 :	parrello	1.93	=over 4
734 :	parrello	1.31
735 :	parrello	1.93	=item noTrace (optional)
736 :	parrello	1.31
737 :	parrello	1.93	If specified, tracing will be suppressed. This is useful if the script wants to set up
738 :			tracing manually.
739 :	parrello	1.31
740 :			=item RETURN
741 :
742 :	parrello	1.93	Returns a two-element list consisting of a CGI query object and a variable hash for
743 :			the output page.
744 :	parrello	1.31
745 :			=back
746 :
747 :			=cut
748 :
749 :	parrello	1.93	sub ScriptSetup {
750 :	parrello	1.31	# Get the parameters.
751 :	parrello	1.93	my ($noTrace) = @_;
752 :			# Get the CGI query object.
753 :			my $cgi = CGI->new();
754 :			# Set up tracing if it's not suppressed.
755 :			ETracing($cgi) unless $noTrace;
756 :			# Create the variable hash.
757 :			my $varHash = { results => '' };
758 :			# Return the query object and variable hash.
759 :			return ($cgi, $varHash);
760 :			}
761 :
762 :			=head3 ETracing
763 :
764 :			ETracing($parameter);
765 :
766 :			Set up emergency tracing. Emergency tracing is tracing that is turned
767 :			on automatically for any program that calls this method. The emergency
768 :			tracing parameters are stored in a a file identified by a tracing key.
769 :			If this method is called with a CGI object, then the tracing key is
770 :			taken from a cookie. If it is called with no parameters, then the tracing
771 :			key is taken from an environment variable. If it is called with a string,
772 :			the tracing key is that string.
773 :
774 :			=over 4
775 :
776 :			=item parameter
777 :
778 :			A parameter from which the tracing key is computed. If it is a scalar,
779 :			that scalar is used as the tracing key. If it is a CGI object, the
780 :			tracing key is taken from the C<IP> cookie. If it is omitted, the
781 :			tracing key is taken from the C<TRACING> environment variable. If it
782 :			is a CGI object and emergency tracing is not on, the C<Trace> and
783 :			C<TF> parameters will be used to determine the type of tracing.
784 :
785 :			=back
786 :
787 :			=cut
788 :
789 :			sub ETracing {
790 :			# Get the parameter.
791 :			my ($parameter) = @_;
792 :			# Check for CGI mode.
793 :			my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
794 :			# Default to no tracing except errors.
795 :			my ($tracing, $dest) = ("0", "WARN");
796 :			# Check for emergency tracing.
797 :			my $tkey = EmergencyKey($parameter);
798 :			my $emergencyFile = EmergencyFileName($tkey);
799 :			if (-e $emergencyFile) {
800 :			# We have the file. Read in the data.
801 :			my @tracing = GetFile($emergencyFile);
802 :			# Pull off the time limit.
803 :			my $expire = shift @tracing;
804 :			# Convert it to seconds.
805 :			$expire *= 3600;
806 :			# Check the file data.
807 :			my $stat = stat($emergencyFile);
808 :			my ($now) = gettimeofday;
809 :			if ($now - $stat->mtime > $expire) {
810 :			# Delete the expired file.
811 :			unlink $emergencyFile;
812 :	parrello	1.44	} else {
813 :	parrello	1.93	# Emergency tracing is on. Pull off the destination and
814 :			# the trace level;
815 :			$dest = shift @tracing;
816 :			my $level = shift @tracing;
817 :			# Convert the destination to a real tracing destination.
818 :			# temp directory.
819 :			$dest = EmergencyTracingDest($tkey, $dest);
820 :			# Insure Tracer is specified.
821 :			my %moduleHash = map { $_ => 1 } @tracing;
822 :			$moduleHash{Tracer} = 1;
823 :			# Set the trace parameter.
824 :			$tracing = join(" ", $level, sort keys %moduleHash);
825 :	parrello	1.44	}
826 :	parrello	1.93	} elsif (defined $cgi) {
827 :			# There's no emergency tracing, but we have a CGI object, so check
828 :			# for tracing from the form parameters.
829 :			if ($cgi->param('Trace')) {
830 :			# Here the user has requested tracing via a form.
831 :			$dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
832 :			$tracing = $cgi->param('Trace') . " Tracer";
833 :	parrello	1.36	}
834 :			}
835 :	parrello	1.93	# Setup the tracing we've determined from all the stuff above.
836 :			TSetup($tracing, $dest);
837 :	parrello	1.94	# Check to see if we're a web script.
838 :	parrello	1.93	if (defined $cgi) {
839 :	parrello	1.94	# Yes we are. Trace the form and environment data.
840 :	parrello	1.93	TraceParms($cgi);
841 :	parrello	1.94	# Check for RAW mode. In raw mode, we print a fake header so that we see everything
842 :			# emitted by the script in its raw form.
843 :			if (T(Raw => 3)) {
844 :			print CGI::header(-type => 'text/plain', -tracing => 'Raw');
845 :			}
846 :	parrello	1.83	}
847 :	parrello	1.31	}
848 :
849 :	parrello	1.93	=head3 EmergencyFileName
850 :
851 :			my $fileName = Tracer::EmergencyFileName($tkey);
852 :
853 :			Return the emergency tracing file name. This is the file that specifies
854 :			the tracing information.
855 :
856 :			=over 4
857 :
858 :			=item tkey
859 :
860 :			Tracing key for the current program.
861 :	parrello	1.11
862 :	parrello	1.93	=item RETURN
863 :	parrello	1.11
864 :	parrello	1.93	Returns the name of the file to contain the emergency tracing information.
865 :	parrello	1.11
866 :	parrello	1.93	=back
867 :	parrello	1.11
868 :			=cut
869 :
870 :	parrello	1.93	sub EmergencyFileName {
871 :			# Get the parameters.
872 :			my ($tkey) = @_;
873 :			# Compute the emergency tracing file name.
874 :			return "$FIG_Config::temp/Emergency$tkey.txt";
875 :	olson	1.1	}
876 :
877 :	parrello	1.93	=head3 EmergencyFileTarget
878 :	parrello	1.10
879 :	parrello	1.93	my $fileName = Tracer::EmergencyFileTarget($tkey);
880 :	parrello	1.10
881 :	parrello	1.93	Return the emergency tracing target file name. This is the file that receives
882 :			the tracing output for file-based tracing.
883 :	parrello	1.10
884 :	parrello	1.93	=over 4
885 :	parrello	1.10
886 :	parrello	1.93	=item tkey
887 :	parrello	1.10
888 :	parrello	1.93	Tracing key for the current program.
889 :	parrello	1.10
890 :	parrello	1.93	=item RETURN
891 :	parrello	1.10
892 :	parrello	1.93	Returns the name of the file to contain the trace output.
893 :	parrello	1.10
894 :	parrello	1.93	=back
895 :	parrello	1.10
896 :	parrello	1.93	=cut
897 :	parrello	1.10
898 :	parrello	1.93	sub EmergencyFileTarget {
899 :			# Get the parameters.
900 :			my ($tkey) = @_;
901 :			# Compute the emergency tracing file name.
902 :			return "$FIG_Config::temp/trace$tkey.log";
903 :			}
904 :	parrello	1.10
905 :	parrello	1.93	=head3 EmergencyTracingDest
906 :	parrello	1.10
907 :	parrello	1.93	my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
908 :	parrello	1.10
909 :	parrello	1.93	This method converts an emergency tracing destination to a real
910 :			tracing destination. The main difference is that if the
911 :			destination is C<FILE> or C<APPEND>, we convert it to file
912 :			output. If the destination is C<DUAL>, we convert it to file
913 :			and standard output.
914 :	parrello	1.10
915 :			=over 4
916 :
917 :	parrello	1.93	=item tkey
918 :	parrello	1.10
919 :	parrello	1.93	Tracing key for this environment.
920 :	parrello	1.10
921 :	parrello	1.93	=item myDest
922 :	parrello	1.10
923 :	parrello	1.93	Destination from the emergency tracing file.
924 :	parrello	1.10
925 :			=item RETURN
926 :
927 :	parrello	1.93	Returns a destination that can be passed into L</TSetup>.
928 :	parrello	1.10
929 :			=back
930 :
931 :			=cut
932 :
933 :	parrello	1.93	sub EmergencyTracingDest {
934 :	parrello	1.12	# Get the parameters.
935 :	parrello	1.93	my ($tkey, $myDest) = @_;
936 :			# Declare the return variable.
937 :			my $retVal = $myDest;
938 :			# Process according to the destination value.
939 :			if ($myDest eq 'FILE') {
940 :			$retVal = ">" . EmergencyFileTarget($tkey);
941 :			} elsif ($myDest eq 'APPEND') {
942 :			$retVal = ">>" . EmergencyFileTarget($tkey);
943 :			} elsif ($myDest eq 'DUAL') {
944 :			$retVal = "+>" . EmergencyFileTarget($tkey);
945 :	parrello	1.97	} elsif ($myDest eq 'WARN') {
946 :			$retVal = "WARN";
947 :	parrello	1.12	}
948 :	parrello	1.93	# Return the result.
949 :			return $retVal;
950 :	parrello	1.10	}
951 :
952 :	parrello	1.93	=head3 Emergency
953 :
954 :			Emergency($key, $hours, $dest, $level, @modules);
955 :
956 :			Turn on emergency tracing. This method is normally invoked over the web from
957 :			a debugging console, but it can also be called by the C<trace.pl> script.
958 :			The caller specifies the duration of the emergency in hours, the desired tracing
959 :			destination, the trace level, and a list of the trace modules to activate.
960 :			For the length of the duration, when a program in an environment with the
961 :			specified tracing key active invokes a Sprout CGI script, tracing will be
962 :			turned on automatically. See L</TSetup> for more about tracing setup and
963 :			L</ETracing> for more about emergency tracing.
964 :
965 :			=over 4
966 :	parrello	1.11
967 :	parrello	1.93	=item tkey
968 :	parrello	1.11
969 :	parrello	1.93	The tracing key. This is used to identify the control file and the trace file.
970 :	parrello	1.11
971 :	parrello	1.93	=item hours
972 :	parrello	1.11
973 :	parrello	1.93	Number of hours to keep emergency tracing alive.
974 :	parrello	1.11
975 :	parrello	1.93	=item dest
976 :	parrello	1.11
977 :	parrello	1.93	Tracing destination. If no path information is specified for a file
978 :			destination, it is put in the FIG temporary directory.
979 :	parrello	1.11
980 :	parrello	1.93	=item level
981 :	parrello	1.11
982 :	parrello	1.93	Tracing level. A higher level means more trace messages.
983 :	parrello	1.11
984 :	parrello	1.93	=item modules
985 :	parrello	1.11
986 :	parrello	1.93	A list of the tracing modules to activate.
987 :	parrello	1.11
988 :			=back
989 :
990 :			=cut
991 :	parrello	1.93
992 :			sub Emergency {
993 :	parrello	1.11	# Get the parameters.
994 :	parrello	1.93	my ($tkey, $hours, $dest, $level, @modules) = @_;
995 :			# Create the emergency file.
996 :			my $specFile = EmergencyFileName($tkey);
997 :			my $outHandle = Open(undef, ">$specFile");
998 :			print $outHandle join("\n", $hours, $dest, $level, @modules, "");
999 :	parrello	1.11	}
1000 :
1001 :	parrello	1.93	=head3 EmergencyKey
1002 :
1003 :			my $tkey = EmergencyKey($parameter);
1004 :
1005 :			Return the Key to be used for emergency tracing. This could be an IP address,
1006 :			a session ID, or a user name, depending on the environment.
1007 :	parrello	1.11
1008 :	parrello	1.93	=over 4
1009 :	parrello	1.11
1010 :	parrello	1.93	=item parameter
1011 :	parrello	1.11
1012 :	parrello	1.93	Parameter defining the method for finding the tracing key. If it is a scalar,
1013 :			then it is presumed to be the tracing key itself. If it is a CGI object, then
1014 :			the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1015 :			taken from the C<TRACING> environment variable.
1016 :	parrello	1.29
1017 :	parrello	1.93	=item RETURN
1018 :	parrello	1.11
1019 :	parrello	1.93	Returns the key to be used for labels in emergency tracing.
1020 :	parrello	1.11
1021 :	parrello	1.93	=back
1022 :	parrello	1.11
1023 :	parrello	1.93	=cut
1024 :	parrello	1.29
1025 :	parrello	1.93	sub EmergencyKey {
1026 :			# Get the parameters.
1027 :			my ($parameter) = @_;
1028 :			# Declare the return variable.
1029 :			my $retVal;
1030 :			# Determine the parameter type.
1031 :			if (! defined $parameter) {
1032 :			# Here we're supposed to check the environment.
1033 :			$retVal = $ENV{TRACING};
1034 :			} else {
1035 :			my $ptype = ref $parameter;
1036 :			if ($ptype eq 'CGI') {
1037 :			# Here we were invoked from a web page. Look for a cookie.
1038 :			$retVal = $parameter->cookie('IP');
1039 :			} elsif (! $ptype) {
1040 :			# Here the key was passed in.
1041 :			$retVal = $parameter;
1042 :			}
1043 :			}
1044 :			# If no luck finding a key, use the PID.
1045 :			if (! defined $retVal) {
1046 :			$retVal = $$;
1047 :			}
1048 :			# Return the result.
1049 :			return $retVal;
1050 :			}
1051 :	parrello	1.11
1052 :
1053 :	parrello	1.93	=head3 TraceParms
1054 :	parrello	1.11
1055 :	parrello	1.93	Tracer::TraceParms($cgi);
1056 :	parrello	1.11
1057 :	parrello	1.93	Trace the CGI parameters at trace level CGI => 3 and the environment variables
1058 :	parrello	1.94	at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1059 :	parrello	1.11
1060 :	parrello	1.93	=over 4
1061 :	parrello	1.11
1062 :	parrello	1.93	=item cgi
1063 :	parrello	1.31
1064 :	parrello	1.93	CGI query object containing the parameters to trace.
1065 :	parrello	1.31
1066 :	parrello	1.11	=back
1067 :
1068 :			=cut
1069 :	parrello	1.93
1070 :			sub TraceParms {
1071 :	parrello	1.11	# Get the parameters.
1072 :	parrello	1.93	my ($cgi) = @_;
1073 :	parrello	1.94	if (T(CGI => 2)) {
1074 :			# Here we trace the GET-style URL for the script.
1075 :	parrello	1.97	Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1076 :	parrello	1.94	}
1077 :	parrello	1.93	if (T(CGI => 3)) {
1078 :			# Here we want to trace the parameter data.
1079 :			my @names = $cgi->param;
1080 :			for my $parmName (sort @names) {
1081 :			# Note we skip the Trace parameters, which are for our use only.
1082 :			if ($parmName ne 'Trace' && $parmName ne 'TF') {
1083 :			my @values = $cgi->param($parmName);
1084 :	parrello	1.97	Trace("[CGI] $parmName = " . join(", ", @values));
1085 :	parrello	1.93	}
1086 :			}
1087 :			# Display the request method.
1088 :			my $method = $cgi->request_method();
1089 :			Trace("Method: $method");
1090 :			}
1091 :			if (T(CGI => 4)) {
1092 :			# Here we want the environment data too.
1093 :			for my $envName (sort keys %ENV) {
1094 :	parrello	1.97	Trace("[ENV] $envName = $ENV{$envName}");
1095 :	parrello	1.12	}
1096 :			}
1097 :	parrello	1.11	}
1098 :
1099 :	parrello	1.94	=head3 TraceImages
1100 :
1101 :			Tracer::TraceImages($htmlString);
1102 :
1103 :			Trace information about all of an html document's images. The tracing
1104 :			will be for type "IMG" at level 3. The image's source string
1105 :			will be displayed. This is generally either the URL of the image or
1106 :			raw data for the image itself. If the source is too long, only the first 300
1107 :			characters will be shown at trace level 3. The entire source will be shown,
1108 :			however, at trace level 4. This method is not very smart, and might catch
1109 :			Javascript code, but it is still useful when debugging the arcane
1110 :			behavior of images in multiple browser environments.
1111 :
1112 :			=over 4
1113 :
1114 :			=item htmlString
1115 :
1116 :			HTML text for an outgoing web page.
1117 :
1118 :			=back
1119 :
1120 :			=cut
1121 :
1122 :			sub TraceImages {
1123 :			# Only proceed if we're at the proper trace level.
1124 :			if (T(IMG => 3)) {
1125 :			# For performance reasons we're manipulating $_[0] instead of retrieving the string
1126 :			# into a variable called "$htmlString". This is because we expect html strings to be
1127 :			# long, and don't want to copy them any more than we have to.
1128 :			Trace(length($_[0]) . " characters in web page.");
1129 :			# Loop through the HTML, culling image tags.
1130 :			while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1131 :			# Extract the source string and determine whether or not it's too long.
1132 :			my $srcString = $1;
1133 :			my $pos = pos($_[0]) - length($srcString);
1134 :			my $excess = length($srcString) - 300;
1135 :			# We'll put the display string in here.
1136 :			my $srcDisplay = $srcString;
1137 :			# If it's a data string, split it at the comma.
1138 :			$srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1139 :			# If there's no excess or we're at trace level 4, we're done. At level 3 with
1140 :			# a long string, however, we only show the first 300 characters.
1141 :			if ($excess > 0 && ! T(IMG => 4)) {
1142 :			$srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1143 :			}
1144 :			# Output the trace message.
1145 :			Trace("Image tag at position $pos:\n$srcDisplay");
1146 :			}
1147 :			}
1148 :			}
1149 :
1150 :
1151 :	parrello	1.97	=head3 ScriptFinish (deprecated)
1152 :	parrello	1.93
1153 :			ScriptFinish($webData, $varHash);
1154 :
1155 :			Output a web page at the end of a script. Either the string to be output or the
1156 :			name of a template file can be specified. If the second parameter is omitted,
1157 :			it is assumed we have a string to be output; otherwise, it is assumed we have the
1158 :			name of a template file. The template should have the variable C<DebugData>
1159 :			specified in any form that invokes a standard script. If debugging mode is turned
1160 :			on, a form field will be put in that allows the user to enter tracing data.
1161 :			Trace messages will be placed immediately before the terminal C<BODY> tag in
1162 :			the output, formatted as a list.
1163 :
1164 :			A typical standard script would loook like the following.
1165 :
1166 :			BEGIN {
1167 :			# Print the HTML header.
1168 :			print "CONTENT-TYPE: text/html\n\n";
1169 :			}
1170 :			use Tracer;
1171 :			use CGI;
1172 :			use FIG;
1173 :			# ... more uses ...
1174 :	parrello	1.6
1175 :	parrello	1.93	my ($cgi, $varHash) = ScriptSetup();
1176 :			eval {
1177 :			# ... get data from $cgi, put it in $varHash ...
1178 :			};
1179 :			if ($@) {
1180 :			Trace("Script Error: $@") if T(0);
1181 :			}
1182 :			ScriptFinish("Html/MyTemplate.html", $varHash);
1183 :	parrello	1.6
1184 :	parrello	1.93	The idea here is that even if the script fails, you'll see trace messages and
1185 :			useful output.
1186 :	parrello	1.6
1187 :			=over 4
1188 :
1189 :	parrello	1.93	=item webData
1190 :
1191 :			A string containing either the full web page to be written to the output or the
1192 :			name of a template file from which the page is to be constructed. If the name
1193 :			of a template file is specified, then the second parameter must be present;
1194 :			otherwise, it must be absent.
1195 :
1196 :			=item varHash (optional)
1197 :	parrello	1.6
1198 :	parrello	1.93	If specified, then a reference to a hash mapping variable names for a template
1199 :			to their values. The template file will be read into memory, and variable markers
1200 :			will be replaced by data in this hash reference.
1201 :	parrello	1.6
1202 :			=back
1203 :
1204 :			=cut
1205 :
1206 :	parrello	1.93	sub ScriptFinish {
1207 :			# Get the parameters.
1208 :			my ($webData, $varHash) = @_;
1209 :			# Check for a template file situation.
1210 :			my $outputString;
1211 :			if (defined $varHash) {
1212 :			# Here we have a template file. We need to determine the template type.
1213 :			my $template;
1214 :			if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1215 :			$template = "$FIG_Config::template_url/$webData";
1216 :			} else {
1217 :			$template = "<<$webData";
1218 :			}
1219 :			$outputString = PageBuilder::Build($template, $varHash, "Html");
1220 :			} else {
1221 :			# Here the user gave us a raw string.
1222 :			$outputString = $webData;
1223 :			}
1224 :			# Check for trace messages.
1225 :			if ($Destination ne "NONE" && $TraceLevel > 0) {
1226 :			# We have trace messages, so we want to put them at the end of the body. This
1227 :			# is either at the end of the whole string or at the beginning of the BODY
1228 :			# end-tag.
1229 :			my $pos = length $outputString;
1230 :			if ($outputString =~ m#</body>#gi) {
1231 :			$pos = (pos $outputString) - 7;
1232 :			}
1233 :			# If the trace messages were queued, we unroll them. Otherwise, we display the
1234 :			# destination.
1235 :			my $traceHtml;
1236 :			if ($Destination eq "QUEUE") {
1237 :			$traceHtml = QTrace('Html');
1238 :			} elsif ($Destination =~ /^>>(.+)$/) {
1239 :			# Here the tracing output it to a file. We code it as a hyperlink so the user
1240 :			# can copy the file name into the clipboard easily.
1241 :			my $actualDest = $1;
1242 :			$traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1243 :			} else {
1244 :			# Here we have one of the special destinations.
1245 :			$traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1246 :			}
1247 :			substr $outputString, $pos, 0, $traceHtml;
1248 :			}
1249 :			# Write the output string.
1250 :			print $outputString;
1251 :	parrello	1.6	}
1252 :
1253 :	parrello	1.93	=head2 Command-Line Utility Methods
1254 :	olson	1.1
1255 :	parrello	1.93	=head3 SendSMS
1256 :	olson	1.1
1257 :	parrello	1.93	my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1258 :	olson	1.1
1259 :	parrello	1.93	Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1260 :			user name, password, and API ID for the relevant account in the hash reference variable
1261 :			I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1262 :			example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1263 :			is C<2561022>, then the FIG_Config file must contain
1264 :	olson	1.1
1265 :	parrello	1.93	$phone = { user => 'BruceTheHumanPet',
1266 :			password => 'silly',
1267 :			api_id => '2561022' };
1268 :	olson	1.1
1269 :	parrello	1.93	The original purpose of this method was to insure Bruce would be notified immediately when the
1270 :			Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1271 :			when you call this method.
1272 :	olson	1.1
1273 :	parrello	1.93	The message ID will be returned if successful, and C<undef> if an error occurs.
1274 :	parrello	1.74
1275 :	parrello	1.93	=over 4
1276 :	parrello	1.74
1277 :	parrello	1.93	=item phoneNumber
1278 :	parrello	1.74
1279 :	parrello	1.93	Phone number to receive the message, in international format. A United States phone number
1280 :			would be prefixed by "1". A British phone number would be prefixed by "44".
1281 :	parrello	1.74
1282 :	parrello	1.93	=item msg
1283 :	parrello	1.74
1284 :	parrello	1.93	Message to send to the specified phone.
1285 :	parrello	1.74
1286 :			=item RETURN
1287 :
1288 :	parrello	1.93	Returns the message ID if successful, and C<undef> if the message could not be sent.
1289 :	parrello	1.74
1290 :	parrello	1.78	=back
1291 :
1292 :	parrello	1.74	=cut
1293 :
1294 :	parrello	1.93	sub SendSMS {
1295 :	parrello	1.74	# Get the parameters.
1296 :	parrello	1.93	my ($phoneNumber, $msg) = @_;
1297 :			# Declare the return variable. If we do not change it, C<undef> will be returned.
1298 :	parrello	1.74	my $retVal;
1299 :	parrello	1.93	# Only proceed if we have phone support.
1300 :			if (! defined $FIG_Config::phone) {
1301 :			Trace("Phone support not present in FIG_Config.") if T(1);
1302 :			} else {
1303 :			# Get the phone data.
1304 :			my $parms = $FIG_Config::phone;
1305 :			# Get the Clickatell URL.
1306 :			my $url = "http://api.clickatell.com/http/";
1307 :			# Create the user agent.
1308 :			my $ua = LWP::UserAgent->new;
1309 :			# Request a Clickatell session.
1310 :			my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1311 :			password => $parms->{password},
1312 :			api_id => $parms->{api_id},
1313 :			to => $phoneNumber,
1314 :			text => $msg});
1315 :			# Check for an error.
1316 :			if (! $resp->is_success) {
1317 :			Trace("Alert failed.") if T(1);
1318 :			} else {
1319 :			# Get the message ID.
1320 :			my $rstring = $resp->content;
1321 :			if ($rstring =~ /^ID:\s+(.*)$/) {
1322 :			$retVal = $1;
1323 :			} else {
1324 :			Trace("Phone attempt failed with $rstring") if T(1);
1325 :			}
1326 :			}
1327 :	parrello	1.74	}
1328 :			# Return the result.
1329 :			return $retVal;
1330 :			}
1331 :
1332 :	parrello	1.93	=head3 StandardSetup
1333 :	olson	1.1
1334 :	parrello	1.93	my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1335 :	olson	1.1
1336 :	parrello	1.93	This method performs standard command-line parsing and tracing setup. The return
1337 :			values are a hash of the command-line options and a list of the positional
1338 :			parameters. Tracing is automatically set up and the command-line options are
1339 :			validated.
1340 :	olson	1.1
1341 :	parrello	1.93	This is a complex method that does a lot of grunt work. The parameters can
1342 :			be more easily understood, however, once they are examined individually.
1343 :	olson	1.1
1344 :	parrello	1.93	The I<categories> parameter is the most obtuse. It is a reference to a list of
1345 :			special-purpose tracing categories. Most tracing categories are PERL package
1346 :			names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1347 :			B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1348 :	olson	1.1
1349 :	parrello	1.93	["Sprout", "SproutLoad", "ERDB"]
1350 :	olson	1.1
1351 :	parrello	1.93	This would cause trace messages in the specified three packages to appear in
1352 :			the output. There are two special tracing categories that are automatically
1353 :			handled by this method. In other words, if you used L</TSetup> you would need
1354 :			to include these categories manually, but if you use this method they are turned
1355 :			on automatically.
1356 :	parrello	1.5
1357 :			=over 4
1358 :
1359 :	parrello	1.93	=item SQL
1360 :	parrello	1.5
1361 :	parrello	1.93	Traces SQL commands and activity.
1362 :	parrello	1.5
1363 :	parrello	1.93	=item Tracer
1364 :	parrello	1.5
1365 :	parrello	1.93	Traces error messages and call stacks.
1366 :	parrello	1.5
1367 :			=back
1368 :
1369 :	parrello	1.93	C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1370 :			The trace level is specified using the C<-trace> command-line option. For example,
1371 :			the following command line for C<TransactFeatures> turns on SQL tracing and runs
1372 :			all tracing at level 3.
1373 :	parrello	1.5
1374 :	parrello	1.93	TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1375 :	parrello	1.5
1376 :	parrello	1.93	Standard tracing is output to the standard output and echoed to the file
1377 :			C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1378 :			process ID. You can also specify the C<user> parameter to put a user ID
1379 :			instead of a process ID in the trace file name. So, for example
1380 :	olson	1.1
1381 :	parrello	1.93	The default trace level is 2. To get all messages, specify a trace level of 4.
1382 :			For a genome-by-genome update, use 3.
1383 :	olson	1.1
1384 :	parrello	1.93	TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1385 :	olson	1.1
1386 :	parrello	1.93	would send the trace output to C<traceBruce.log> in the temporary directory.
1387 :	olson	1.1
1388 :	parrello	1.93	The I<options> parameter is a reference to a hash containing the command-line
1389 :			options, their default values, and an explanation of what they mean. Command-line
1390 :			options may be in the form of switches or keywords. In the case of a switch, the
1391 :			option value is 1 if it is specified and 0 if it is not specified. In the case
1392 :			of a keyword, the value is separated from the option name by an equal sign. You
1393 :			can see this last in the command-line example above.
1394 :	olson	1.1
1395 :	parrello	1.93	You can specify a different default trace level by setting C<$options->{trace}>
1396 :			prior to calling this method.
1397 :	olson	1.1
1398 :	parrello	1.93	An example at this point would help. Consider, for example, the command-line utility
1399 :			C<TransactFeatures>. It accepts a list of positional parameters plus the options
1400 :			C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1401 :			the following code.
1402 :	olson	1.1
1403 :	parrello	1.93	my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1404 :			{ safe => [0, "use database transactions"],
1405 :			noAlias => [0, "do not expect aliases in CHANGE transactions"],
1406 :			start => [' ', "start with this genome"],
1407 :			tblFiles => [0, "output TBL files containing the corrected IDs"] },
1408 :			"<command> <transactionDirectory> <IDfile>",
1409 :			@ARGV);
1410 :	olson	1.1
1411 :
1412 :	parrello	1.93	The call to C<ParseCommand> specifies the default values for the options and
1413 :			stores the actual options in a hash that is returned as C<$options>. The
1414 :			positional parameters are returned in C<@parameters>.
1415 :	olson	1.1
1416 :	parrello	1.93	The following is a sample command line for C<TransactFeatures>.
1417 :	olson	1.1
1418 :	parrello	1.93	TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1419 :	olson	1.1
1420 :	parrello	1.93	Single and double hyphens are equivalent. So, you could also code the
1421 :			above command as
1422 :	olson	1.1
1423 :	parrello	1.93	TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1424 :	olson	1.1
1425 :	parrello	1.93	In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1426 :			parameters, and would find themselves in I<@parameters> after executing the
1427 :			above code fragment. The tracing would be set to level 2, and the categories
1428 :			would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1429 :			and C<DocUtils> was included because it came in within the first parameter
1430 :			to this method. The I<$options> hash would be
1431 :	olson	1.1
1432 :	parrello	1.93	{ trace => 2, sql => 0, safe => 0,
1433 :			noAlias => 1, start => ' ', tblFiles => 0 }
1434 :	olson	1.1
1435 :	parrello	1.93	Use of C<StandardSetup> in this way provides a simple way of performing
1436 :			standard tracing setup and command-line parsing. Note that the caller is
1437 :			not even aware of the command-line switches C<-trace> and C<-sql>, which
1438 :			are used by this method to control the tracing. If additional tracing features
1439 :			need to be added in the future, they can be processed by this method without
1440 :			upsetting the command-line utilities.
1441 :	olson	1.1
1442 :	parrello	1.93	If the C<background> option is specified on the command line, then the
1443 :			standard and error outputs will be directed to files in the temporary
1444 :			directory, using the same suffix as the trace file. So, if the command
1445 :			line specified
1446 :	olson	1.1
1447 :	parrello	1.93	-user=Bruce -background
1448 :	olson	1.1
1449 :	parrello	1.93	then the trace output would go to C<traceBruce.log>, the standard output to
1450 :			C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1451 :			simplify starting a command in the background.
1452 :	olson	1.1
1453 :	parrello	1.93	The user name is also used as the tracing key for L</Emergency Tracing>.
1454 :			Specifying a value of C<E> for the trace level causes emergency tracing to
1455 :			be used instead of custom tracing. If the user name is not specified,
1456 :			the tracing key is taken from the C<Tracing> environment variable. If there
1457 :			is no value for that variable, the tracing key will be computed from the PID.
1458 :	olson	1.1
1459 :	parrello	1.93	Finally, if the special option C<-help> is specified, the option
1460 :			names will be traced at level 0 and the program will exit without processing.
1461 :			This provides a limited help capability. For example, if the user enters
1462 :	olson	1.1
1463 :	parrello	1.93	TransactFeatures -help
1464 :	olson	1.1
1465 :	parrello	1.93	he would see the following output.
1466 :	olson	1.1
1467 :	parrello	1.93	TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1468 :			-trace tracing level (default E)
1469 :			-sql trace SQL commands
1470 :			-safe use database transactions
1471 :			-noAlias do not expect aliases in CHANGE transactions
1472 :			-start start with this genome
1473 :			-tblFiles output TBL files containing the corrected IDs
1474 :	olson	1.1
1475 :	parrello	1.93	The caller has the option of modifying the tracing scheme by placing a value
1476 :			for C<trace> in the incoming options hash. The default value can be overridden,
1477 :			or the tracing to the standard output can be turned off by suffixing a minus
1478 :			sign to the trace level. So, for example,
1479 :	olson	1.1
1480 :	parrello	1.93	{ trace => [0, "tracing level (default 0)"],
1481 :			...
1482 :	olson	1.1
1483 :	parrello	1.93	would set the default trace level to 0 instead of E, while
1484 :	olson	1.1
1485 :	parrello	1.93	{ trace => ["2-", "tracing level (default 2)"],
1486 :			...
1487 :	olson	1.1
1488 :	parrello	1.93	would set the default to 2, but trace only to the log file, not to the
1489 :			standard output.
1490 :	olson	1.1
1491 :	parrello	1.93	The parameters to this method are as follows.
1492 :	olson	1.1
1493 :	parrello	1.93	=over 4
1494 :	olson	1.1
1495 :	parrello	1.93	=item categories
1496 :	parrello	1.2
1497 :	parrello	1.93	Reference to a list of tracing category names. These should be names of
1498 :			packages whose internal workings will need to be debugged to get the
1499 :			command working.
1500 :	olson	1.1
1501 :	parrello	1.93	=item options
1502 :	olson	1.1
1503 :	parrello	1.93	Reference to a hash containing the legal options for the current command mapped
1504 :			to their default values and descriptions. The user can override the defaults
1505 :			by specifying the options as command-line switches prefixed by a hyphen.
1506 :			Tracing-related options may be added to this hash. If the C<-h> option is
1507 :			specified on the command line, the option descriptions will be used to
1508 :			explain the options. To turn off tracing to the standard output, add a
1509 :			minus sign to the value for C<trace> (see above).
1510 :	olson	1.1
1511 :	parrello	1.93	=item parmHelp
1512 :	olson	1.1
1513 :	parrello	1.93	A string that vaguely describes the positional parameters. This is used
1514 :			if the user specifies the C<-h> option.
1515 :	olson	1.1
1516 :	parrello	1.93	=item argv
1517 :	olson	1.1
1518 :	parrello	1.93	List of command line parameters, including the option switches, which must
1519 :			precede the positional parameters and be prefixed by a hyphen.
1520 :	olson	1.1
1521 :			=item RETURN
1522 :
1523 :	parrello	1.93	Returns a list. The first element of the list is the reference to a hash that
1524 :			maps the command-line option switches to their values. These will either be the
1525 :			default values or overrides specified on the command line. The remaining
1526 :			elements of the list are the position parameters, in order.
1527 :	olson	1.1
1528 :			=back
1529 :
1530 :			=cut
1531 :
1532 :	parrello	1.93	sub StandardSetup {
1533 :			# Get the parameters.
1534 :			my ($categories, $options, $parmHelp, @argv) = @_;
1535 :			# Get the default tracing key.
1536 :			my $tkey = EmergencyKey();
1537 :			# Add the tracing options.
1538 :			if (! exists $options->{trace}) {
1539 :			$options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1540 :			}
1541 :			$options->{sql} = [0, "turn on SQL tracing"];
1542 :			$options->{help} = [0, "display command-line options"];
1543 :			$options->{user} = [$tkey, "tracing key"];
1544 :			$options->{background} = [0, "spool standard and error output"];
1545 :			# Create a parsing hash from the options hash. The parsing hash
1546 :			# contains the default values rather than the default value
1547 :			# and the description. While we're at it, we'll memorize the
1548 :			# length of the longest option name.
1549 :			my $longestName = 0;
1550 :			my %parseOptions = ();
1551 :			for my $key (keys %{$options}) {
1552 :			if (length $key > $longestName) {
1553 :			$longestName = length $key;
1554 :			}
1555 :			$parseOptions{$key} = $options->{$key}->[0];
1556 :			}
1557 :			# Parse the command line.
1558 :			my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1559 :			# Get the logfile suffix.
1560 :			my $suffix = $retOptions->{user};
1561 :			# Check for background mode.
1562 :			if ($retOptions->{background}) {
1563 :			my $outFileName = "$FIG_Config::temp/out$suffix.log";
1564 :			my $errFileName = "$FIG_Config::temp/err$suffix.log";
1565 :			open STDOUT, ">$outFileName";
1566 :			open STDERR, ">$errFileName";
1567 :			# Check for phone support. If we have phone support and a phone number,
1568 :			# we want to turn it on.
1569 :			if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1570 :			$retOptions->{phone} = $ENV{PHONE};
1571 :			}
1572 :			}
1573 :			# Now we want to set up tracing. First, we need to know if the user
1574 :			# wants emergency tracing.
1575 :			if ($retOptions->{trace} eq 'E') {
1576 :			ETracing($retOptions->{user});
1577 :			} else {
1578 :			# Here the tracing is controlled from the command line.
1579 :			my @cats = @{$categories};
1580 :			if ($retOptions->{sql}) {
1581 :			push @cats, "SQL";
1582 :			}
1583 :			# Add the default categories.
1584 :			push @cats, "Tracer";
1585 :			# Next, we create the category string by joining the categories.
1586 :			my $cats = join(" ", @cats);
1587 :			# Check to determine whether or not the caller wants to turn off tracing
1588 :			# to the standard output.
1589 :			my $traceLevel = $retOptions->{trace};
1590 :			my $textOKFlag = 1;
1591 :			if ($traceLevel =~ /^(.)-/) {
1592 :			$traceLevel = $1;
1593 :			$textOKFlag = 0;
1594 :			}
1595 :			# Now we set up the trace mode.
1596 :			my $traceMode;
1597 :			# Verify that we can open a file in the FIG temporary directory.
1598 :			my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1599 :			if (open TESTTRACE, ">$traceFileName") {
1600 :			# Here we can trace to a file.
1601 :			$traceMode = ">$traceFileName";
1602 :			if ($textOKFlag) {
1603 :			# Echo to standard output if the text-OK flag is set.
1604 :			$traceMode = "+$traceMode";
1605 :			}
1606 :			# Close the test file.
1607 :			close TESTTRACE;
1608 :			} else {
1609 :	parrello	1.98	# Here we can't trace to a file. Complain about this.
1610 :			warn "Could not open trace file $traceFileName: $!\n";
1611 :			# We trace to the standard output if it's
1612 :			# okay, and the error log otherwise.
1613 :	parrello	1.93	if ($textOKFlag) {
1614 :			$traceMode = "TEXT";
1615 :	parrello	1.12	} else {
1616 :	parrello	1.93	$traceMode = "WARN";
1617 :	parrello	1.12	}
1618 :			}
1619 :	parrello	1.93	# Now set up the tracing.
1620 :			TSetup("$traceLevel $cats", $traceMode);
1621 :			}
1622 :			# Check for the "help" option. If it is specified, dump the command-line
1623 :			# options and exit the program.
1624 :			if ($retOptions->{help}) {
1625 :			$0 =~ m#[/\\](\w+)(\.pl)?$#i;
1626 :			print "$1 [options] $parmHelp\n";
1627 :			for my $key (sort keys %{$options}) {
1628 :			my $name = Pad($key, $longestName, 0, ' ');
1629 :			my $desc = $options->{$key}->[1];
1630 :			if ($options->{$key}->[0]) {
1631 :			$desc .= " (default " . $options->{$key}->[0] . ")";
1632 :			}
1633 :			print " $name $desc\n";
1634 :	parrello	1.36	}
1635 :	parrello	1.93	exit(0);
1636 :			}
1637 :			# Trace the options, if applicable.
1638 :			if (T(3)) {
1639 :			my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1640 :			Trace("Selected options: " . join(", ", sort @parms) . ".");
1641 :	parrello	1.3	}
1642 :	parrello	1.93	# Return the parsed parameters.
1643 :			return ($retOptions, @retParameters);
1644 :	olson	1.1	}
1645 :
1646 :	parrello	1.93	=head3 ReadOptions
1647 :	olson	1.1
1648 :	parrello	1.93	my %options = Tracer::ReadOptions($fileName);
1649 :	olson	1.1
1650 :	parrello	1.93	Read a set of options from a file. Each option is encoded in a line of text that has the
1651 :			format
1652 :	olson	1.1
1653 :	parrello	1.93	I<optionName>C<=>I<optionValue>C<; >I<comment>
1654 :	olson	1.1
1655 :	parrello	1.93	The option name must consist entirely of letters, digits, and the punctuation characters
1656 :			C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1657 :			character is a semi-colon will be ignored. The return hash will map each option name to
1658 :			the corresponding option value.
1659 :	olson	1.1
1660 :			=over 4
1661 :
1662 :	parrello	1.93	=item fileName
1663 :	olson	1.1
1664 :	parrello	1.93	Name of the file containing the option data.
1665 :	olson	1.1
1666 :			=item RETURN
1667 :
1668 :	parrello	1.93	Returns a hash mapping the option names specified in the file to their corresponding option
1669 :			value.
1670 :	olson	1.1
1671 :			=back
1672 :
1673 :			=cut
1674 :
1675 :	parrello	1.93	sub ReadOptions {
1676 :	parrello	1.12	# Get the parameters.
1677 :	parrello	1.93	my ($fileName) = @_;
1678 :			# Open the file.
1679 :			(open CONFIGFILE, "<$fileName") \|\| Confess("Could not open option file $fileName.");
1680 :			# Count the number of records read.
1681 :			my ($records, $comments) = 0;
1682 :			# Create the return hash.
1683 :			my %retVal = ();
1684 :			# Loop through the file, accumulating key-value pairs.
1685 :			while (my $line = <CONFIGFILE>) {
1686 :			# Denote we've read a line.
1687 :			$records++;
1688 :			# Determine the line type.
1689 :			if ($line =~ /^\s*[\n\r]/) {
1690 :			# A blank line is a comment.
1691 :			$comments++;
1692 :			} elsif ($line =~ /^\s([A-Za-z0-9_\.]+)=([^;]);/) {
1693 :			# Here we have an option assignment.
1694 :			retVal{$1} = $2;
1695 :			} elsif ($line =~ /^\s*;/) {
1696 :			# Here we have a text comment.
1697 :			$comments++;
1698 :	parrello	1.12	} else {
1699 :	parrello	1.93	# Here we have an invalid line.
1700 :			Trace("Invalid option statement in record $records.") if T(0);
1701 :	parrello	1.12	}
1702 :			}
1703 :	parrello	1.93	# Return the hash created.
1704 :			return %retVal;
1705 :	olson	1.1	}
1706 :
1707 :	parrello	1.93	=head3 GetOptions
1708 :	parrello	1.9
1709 :	parrello	1.93	Tracer::GetOptions(\%defaults, \%options);
1710 :	parrello	1.9
1711 :	parrello	1.93	Merge a specified set of options into a table of defaults. This method takes two hash references
1712 :			as input and uses the data from the second to update the first. If the second does not exist,
1713 :			there will be no effect. An error will be thrown if one of the entries in the second hash does not
1714 :			exist in the first.
1715 :	parrello	1.9
1716 :	parrello	1.93	Consider the following example.
1717 :	parrello	1.9
1718 :	parrello	1.93	my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1719 :	parrello	1.9
1720 :	parrello	1.93	In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1721 :			B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1722 :			B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1723 :			the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1724 :			will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1725 :	parrello	1.9
1726 :	parrello	1.93	{databaseType => 'Oracle'}
1727 :	parrello	1.9
1728 :	parrello	1.93	an error will occur because the B<databaseType> option does not exist.
1729 :	parrello	1.9
1730 :	parrello	1.93	=over 4
1731 :	parrello	1.9
1732 :	parrello	1.93	=item defaults
1733 :	parrello	1.9
1734 :	parrello	1.93	Table of default option values.
1735 :	parrello	1.9
1736 :	parrello	1.93	=item options
1737 :	olson	1.1
1738 :	parrello	1.93	Table of overrides, if any.
1739 :	olson	1.1
1740 :			=item RETURN
1741 :
1742 :	parrello	1.93	Returns a reference to the default table passed in as the first parameter.
1743 :	olson	1.1
1744 :			=back
1745 :
1746 :			=cut
1747 :
1748 :	parrello	1.93	sub GetOptions {
1749 :			# Get the parameters.
1750 :			my ($defaults, $options) = @_;
1751 :			# Check for overrides.
1752 :			if ($options) {
1753 :			# Loop through the overrides.
1754 :			while (my ($option, $setting) = each %{$options}) {
1755 :			# Insure this override exists.
1756 :			if (!exists $defaults->{$option}) {
1757 :			croak "Unrecognized option $option encountered.";
1758 :	parrello	1.12	} else {
1759 :	parrello	1.93	# Apply the override.
1760 :			$defaults->{$option} = $setting;
1761 :	parrello	1.12	}
1762 :			}
1763 :			}
1764 :	parrello	1.93	# Return the merged table.
1765 :			return $defaults;
1766 :	olson	1.1	}
1767 :
1768 :	parrello	1.93	=head3 MergeOptions
1769 :	olson	1.1
1770 :	parrello	1.93	Tracer::MergeOptions(\%table, \%defaults);
1771 :	olson	1.1
1772 :	parrello	1.93	Merge default values into a hash table. This method looks at the key-value pairs in the
1773 :			second (default) hash, and if a matching key is not found in the first hash, the default
1774 :			pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1775 :			checking and no return value.
1776 :	olson	1.1
1777 :			=over 4
1778 :
1779 :	parrello	1.93	=item table
1780 :	olson	1.1
1781 :	parrello	1.93	Hash table to be updated with the default values.
1782 :	olson	1.1
1783 :	parrello	1.93	=item defaults
1784 :	olson	1.1
1785 :	parrello	1.93	Default values to be merged into the first hash table if they are not already present.
1786 :	olson	1.1
1787 :			=back
1788 :
1789 :			=cut
1790 :
1791 :	parrello	1.93	sub MergeOptions {
1792 :			# Get the parameters.
1793 :			my ($table, $defaults) = @_;
1794 :			# Loop through the defaults.
1795 :			while (my ($key, $value) = each %{$defaults}) {
1796 :			if (!exists $table->{$key}) {
1797 :			$table->{$key} = $value;
1798 :			}
1799 :	parrello	1.12	}
1800 :	olson	1.1	}
1801 :
1802 :	parrello	1.93	=head3 ParseCommand
1803 :	olson	1.1
1804 :	parrello	1.93	my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1805 :	olson	1.1
1806 :	parrello	1.93	Parse a command line consisting of a list of parameters. The initial parameters may be option
1807 :			specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1808 :			off and merged into a table of default options. The remainder of the command line is
1809 :			returned as a list of positional arguments. For example, consider the following invocation.
1810 :	olson	1.1
1811 :	parrello	1.93	my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1812 :	olson	1.1
1813 :	parrello	1.93	In this case, the list @words will be treated as a command line and there are two options available,
1814 :			B<errors> and B<logFile>. If @words has the following format
1815 :	olson	1.1
1816 :	parrello	1.93	-logFile=error.log apple orange rutabaga
1817 :	olson	1.1
1818 :	parrello	1.93	then at the end of the invocation, C<$options> will be
1819 :	olson	1.1
1820 :	parrello	1.93	{ errors => 0, logFile => 'error.log' }
1821 :	olson	1.1
1822 :	parrello	1.93	and C<@arguments> will contain
1823 :	olson	1.1
1824 :	parrello	1.93	apple orange rutabaga
1825 :	olson	1.1
1826 :	parrello	1.93	The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1827 :			support for quote characters. Options can be specified with single or double hyphens.
1828 :	parrello	1.54
1829 :			=over 4
1830 :
1831 :	parrello	1.93	=item optionTable
1832 :	parrello	1.54
1833 :	parrello	1.93	Table of default options.
1834 :	parrello	1.54
1835 :	parrello	1.93	=item inputList
1836 :	parrello	1.54
1837 :	parrello	1.93	List of words on the command line.
1838 :	parrello	1.54
1839 :			=item RETURN
1840 :
1841 :	parrello	1.93	Returns a reference to the option table and a list of the positional arguments.
1842 :	parrello	1.54
1843 :			=back
1844 :
1845 :			=cut
1846 :
1847 :	parrello	1.93	sub ParseCommand {
1848 :	parrello	1.54	# Get the parameters.
1849 :	parrello	1.93	my ($optionTable, @inputList) = @_;
1850 :			# Process any options in the input list.
1851 :			my %overrides = ();
1852 :			while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1853 :			# Get the current option.
1854 :			my $arg = shift @inputList;
1855 :			# Pull out the option name.
1856 :			$arg =~ /^--?([^=]*)/g;
1857 :			my $name = $1;
1858 :			# Check for an option value.
1859 :			if ($arg =~ /\G=(.*)$/g) {
1860 :			# Here we have a value for the option.
1861 :			$overrides{$name} = UnEscape($1);
1862 :			} else {
1863 :			# Here there is no value, so we use 1.
1864 :			$overrides{$name} = 1;
1865 :			}
1866 :			}
1867 :			# Merge the options into the defaults.
1868 :			GetOptions($optionTable, \%overrides);
1869 :			# Translate the remaining parameters.
1870 :			my @retVal = ();
1871 :			for my $inputParm (@inputList) {
1872 :			push @retVal, UnEscape($inputParm);
1873 :	parrello	1.54	}
1874 :	parrello	1.93	# Return the results.
1875 :			return ($optionTable, @retVal);
1876 :	parrello	1.54	}
1877 :
1878 :	parrello	1.93
1879 :			=head2 File Utility Methods
1880 :
1881 :	olson	1.1	=head3 GetFile
1882 :
1883 :	parrello	1.92	my @fileContents = Tracer::GetFile($fileName);
1884 :	olson	1.1
1885 :	parrello	1.35	or
1886 :
1887 :	parrello	1.92	my $fileContents = Tracer::GetFile($fileName);
1888 :	parrello	1.35
1889 :			Return the entire contents of a file. In list context, line-ends are removed and
1890 :			each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1891 :	olson	1.1
1892 :			=over 4
1893 :
1894 :			=item fileName
1895 :
1896 :			Name of the file to read.
1897 :
1898 :			=item RETURN
1899 :
1900 :	parrello	1.6	In a list context, returns the entire file as a list with the line terminators removed.
1901 :	parrello	1.39	In a scalar context, returns the entire file as a string. If an error occurs opening
1902 :			the file, an empty list will be returned.
1903 :	olson	1.1
1904 :			=back
1905 :
1906 :			=cut
1907 :
1908 :			sub GetFile {
1909 :	parrello	1.12	# Get the parameters.
1910 :			my ($fileName) = @_;
1911 :			# Declare the return variable.
1912 :			my @retVal = ();
1913 :			# Open the file for input.
1914 :	parrello	1.60	my $handle = Open(undef, "<$fileName");
1915 :			# Read the whole file into the return variable, stripping off any terminator
1916 :			# characters.
1917 :			my $lineCount = 0;
1918 :			while (my $line = <$handle>) {
1919 :			$lineCount++;
1920 :			$line = Strip($line);
1921 :			push @retVal, $line;
1922 :			}
1923 :			# Close it.
1924 :			close $handle;
1925 :			my $actualLines = @retVal;
1926 :	parrello	1.77	Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1927 :	parrello	1.12	# Return the file's contents in the desired format.
1928 :	parrello	1.9	if (wantarray) {
1929 :	parrello	1.12	return @retVal;
1930 :	parrello	1.6	} else {
1931 :			return join "\n", @retVal;
1932 :			}
1933 :	olson	1.1	}
1934 :
1935 :	parrello	1.60	=head3 PutFile
1936 :
1937 :	parrello	1.92	Tracer::PutFile($fileName, \@lines);
1938 :	parrello	1.60
1939 :			Write out a file from a list of lines of text.
1940 :
1941 :			=over 4
1942 :
1943 :			=item fileName
1944 :
1945 :			Name of the output file.
1946 :
1947 :			=item lines
1948 :
1949 :			Reference to a list of text lines. The lines will be written to the file in order, with trailing
1950 :	parrello	1.66	new-line characters. Alternatively, may be a string, in which case the string will be written without
1951 :			modification.
1952 :	parrello	1.60
1953 :			=back
1954 :
1955 :			=cut
1956 :
1957 :			sub PutFile {
1958 :			# Get the parameters.
1959 :			my ($fileName, $lines) = @_;
1960 :			# Open the output file.
1961 :			my $handle = Open(undef, ">$fileName");
1962 :	parrello	1.77	# Count the lines written.
1963 :	parrello	1.66	if (ref $lines ne 'ARRAY') {
1964 :			# Here we have a scalar, so we write it raw.
1965 :			print $handle $lines;
1966 :	parrello	1.77	Trace("Scalar put to file $fileName.") if T(File => 3);
1967 :	parrello	1.66	} else {
1968 :			# Write the lines one at a time.
1969 :	parrello	1.77	my $count = 0;
1970 :	parrello	1.66	for my $line (@{$lines}) {
1971 :			print $handle "$line\n";
1972 :	parrello	1.77	$count++;
1973 :	parrello	1.66	}
1974 :	parrello	1.77	Trace("$count lines put to file $fileName.") if T(File => 3);
1975 :	parrello	1.60	}
1976 :			# Close the output file.
1977 :			close $handle;
1978 :			}
1979 :
1980 :	parrello	1.93	=head3 ParseRecord
1981 :	olson	1.1
1982 :	parrello	1.93	my @fields = Tracer::ParseRecord($line);
1983 :	olson	1.1
1984 :	parrello	1.93	Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1985 :			and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1986 :			These will automatically be converted.
1987 :	olson	1.1
1988 :			=over 4
1989 :
1990 :	parrello	1.93	=item line
1991 :
1992 :			Line of data containing the tab-delimited fields.
1993 :
1994 :			=item RETURN
1995 :	olson	1.1
1996 :	parrello	1.93	Returns a list of the fields found in the data line.
1997 :	olson	1.1
1998 :			=back
1999 :
2000 :			=cut
2001 :
2002 :	parrello	1.93	sub ParseRecord {
2003 :	parrello	1.12	# Get the parameter.
2004 :	parrello	1.93	my ($line) = @_;
2005 :			# Remove the trailing new-line, if any.
2006 :			chomp $line;
2007 :			# Split the line read into pieces using the tab character.
2008 :			my @retVal = split /\t/, $line;
2009 :			# Trim and fix the escapes in each piece.
2010 :			for my $value (@retVal) {
2011 :			# Trim leading whitespace.
2012 :			$value =~ s/^\s+//;
2013 :			# Trim trailing whitespace.
2014 :			$value =~ s/\s+$//;
2015 :			# Delete the carriage returns.
2016 :			$value =~ s/\r//g;
2017 :			# Convert the escapes into their real values.
2018 :			$value =~ s/\\t/"\t"/ge;
2019 :			$value =~ s/\\n/"\n"/ge;
2020 :			}
2021 :			# Return the result.
2022 :			return @retVal;
2023 :			}
2024 :
2025 :			=head3 Merge
2026 :
2027 :			my @mergedList = Tracer::Merge(@inputList);
2028 :
2029 :			Sort a list of strings and remove duplicates.
2030 :
2031 :			=over 4
2032 :
2033 :			=item inputList
2034 :
2035 :			List of scalars to sort and merge.
2036 :
2037 :			=item RETURN
2038 :
2039 :			Returns a list containing the same elements sorted in ascending order with duplicates
2040 :			removed.
2041 :
2042 :			=back
2043 :
2044 :			=cut
2045 :
2046 :			sub Merge {
2047 :			# Get the input list in sort order.
2048 :			my @inputList = sort @_;
2049 :			# Only proceed if the list has at least two elements.
2050 :			if (@inputList > 1) {
2051 :			# Now we want to move through the list splicing out duplicates.
2052 :			my $i = 0;
2053 :			while ($i < @inputList) {
2054 :			# Get the current entry.
2055 :			my $thisEntry = $inputList[$i];
2056 :			# Find out how many elements duplicate the current entry.
2057 :			my $j = $i + 1;
2058 :			my $dup1 = $i + 1;
2059 :			while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2060 :			# If the number is nonzero, splice out the duplicates found.
2061 :			if ($j > $dup1) {
2062 :			splice @inputList, $dup1, $j - $dup1;
2063 :	parrello	1.14	}
2064 :	parrello	1.93	# Now the element at position $dup1 is different from the element before it
2065 :			# at position $i. We push $i forward one position and start again.
2066 :			$i++;
2067 :	parrello	1.14	}
2068 :	parrello	1.12	}
2069 :	parrello	1.93	# Return the merged list.
2070 :			return @inputList;
2071 :	olson	1.1	}
2072 :
2073 :	parrello	1.93	=head3 Open
2074 :	olson	1.1
2075 :	parrello	1.93	my $handle = Open($fileHandle, $fileSpec, $message);
2076 :	olson	1.1
2077 :	parrello	1.93	Open a file.
2078 :	olson	1.1
2079 :	parrello	1.93	The I<$fileSpec> is essentially the second argument of the PERL C<open>
2080 :			function. The mode is specified using Unix-like shell information. So, for
2081 :			example,
2082 :	olson	1.1
2083 :	parrello	1.93	Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2084 :	olson	1.1
2085 :	parrello	1.93	would open for output appended to the specified file, and
2086 :	olson	1.1
2087 :	parrello	1.93	Open(\*DATASTREAM, "\| sort -u >$outputFile", "Could not open $outputFile.");
2088 :	olson	1.1
2089 :	parrello	1.93	would open a pipe that sorts the records written and removes duplicates. Note
2090 :			the use of file handle syntax in the Open call. To use anonymous file handles,
2091 :			code as follows.
2092 :	olson	1.1
2093 :	parrello	1.93	my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2094 :	olson	1.1
2095 :	parrello	1.93	The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2096 :			the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2097 :			failed open will throw an exception and the third parameter will be used to construct
2098 :			an error message. If the parameter is omitted, a standard message is constructed
2099 :			using the file spec.
2100 :	olson	1.1
2101 :	parrello	1.93	Could not open "/usr/spool/news/twitlog"
2102 :	olson	1.1
2103 :	parrello	1.93	Note that the mode characters are automatically cleaned from the file name.
2104 :			The actual error message from the file system will be captured and appended to the
2105 :			message in any case.
2106 :	parrello	1.6
2107 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": file not found.
2108 :	parrello	1.6
2109 :	parrello	1.93	In some versions of PERL the only error message we get is a number, which
2110 :			corresponds to the C++ C<errno> value.
2111 :	parrello	1.6
2112 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": 6.
2113 :	parrello	1.6
2114 :	parrello	1.93	=over 4
2115 :	parrello	1.6
2116 :	parrello	1.93	=item fileHandle
2117 :	parrello	1.6
2118 :	parrello	1.93	File handle. If this parameter is C<undef>, a file handle will be generated
2119 :			and returned as the value of this method.
2120 :	olson	1.1
2121 :	parrello	1.93	=item fileSpec
2122 :	olson	1.1
2123 :	parrello	1.93	File name and mode, as per the PERL C<open> function.
2124 :	olson	1.1
2125 :	parrello	1.93	=item message (optional)
2126 :	olson	1.1
2127 :	parrello	1.93	Error message to use if the open fails. If omitted, a standard error message
2128 :			will be generated. In either case, the error information from the file system
2129 :			is appended to the message. To specify a conditional open that does not throw
2130 :			an error if it fails, use C<0>.
2131 :	olson	1.1
2132 :	parrello	1.93	=item RETURN
2133 :	olson	1.1
2134 :	parrello	1.93	Returns the name of the file handle assigned to the file, or C<undef> if the
2135 :			open failed.
2136 :	olson	1.1
2137 :			=back
2138 :
2139 :			=cut
2140 :
2141 :	parrello	1.93	sub Open {
2142 :	parrello	1.12	# Get the parameters.
2143 :	parrello	1.93	my ($fileHandle, $fileSpec, $message) = @_;
2144 :			# Attempt to open the file.
2145 :			my $rv = open $fileHandle, $fileSpec;
2146 :			# If the open failed, generate an error message.
2147 :			if (! $rv) {
2148 :			# Save the system error message.
2149 :			my $sysMessage = $!;
2150 :			# See if we need a default message.
2151 :			if (!$message) {
2152 :			# Clean any obvious mode characters and leading spaces from the
2153 :			# filename.
2154 :			my ($fileName) = FindNamePart($fileSpec);
2155 :			$message = "Could not open \"$fileName\"";
2156 :			}
2157 :			# Terminate with an error using the supplied message and the
2158 :			# error message from the file system.
2159 :			Confess("$message: $!");
2160 :	parrello	1.12	}
2161 :	parrello	1.93	# Return the file handle.
2162 :			return $fileHandle;
2163 :	olson	1.1	}
2164 :
2165 :	parrello	1.93	=head3 FindNamePart
2166 :
2167 :			my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2168 :
2169 :			Extract the portion of a file specification that contains the file name.
2170 :
2171 :			A file specification is the string passed to an C<open> call. It specifies the file
2172 :			mode and name. In a truly complex situation, it can specify a pipe sequence. This
2173 :			method assumes that the file name is whatever follows the first angle bracket
2174 :			sequence. So, for example, in the following strings the file name is
2175 :			C</usr/fig/myfile.txt>.
2176 :	parrello	1.5
2177 :	parrello	1.93	>>/usr/fig/myfile.txt
2178 :			</usr/fig/myfile.txt
2179 :			\| sort -u > /usr/fig/myfile.txt
2180 :	parrello	1.5
2181 :	parrello	1.93	If the method cannot find a file name using its normal methods, it will return the
2182 :			whole incoming string.
2183 :	parrello	1.5
2184 :			=over 4
2185 :
2186 :	parrello	1.93	=item fileSpec
2187 :	parrello	1.5
2188 :	parrello	1.93	File specification string from which the file name is to be extracted.
2189 :	parrello	1.5
2190 :			=item RETURN
2191 :
2192 :	parrello	1.93	Returns a three-element list. The first element contains the file name portion of
2193 :			the specified string, or the whole string if a file name cannot be found via normal
2194 :			methods. The second element contains the start position of the file name portion and
2195 :			the third element contains the length.
2196 :	parrello	1.5
2197 :			=back
2198 :
2199 :			=cut
2200 :	parrello	1.93	#: Return Type $;
2201 :			sub FindNamePart {
2202 :			# Get the parameters.
2203 :			my ($fileSpec) = @_;
2204 :			# Default to the whole input string.
2205 :			my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2206 :			# Parse out the file name if we can.
2207 :			if ($fileSpec =~ m/(<\|>>?)(.+?)(\s*)$/) {
2208 :			$retVal = $2;
2209 :			$len = length $retVal;
2210 :			$pos = (length $fileSpec) - (length $3) - $len;
2211 :	parrello	1.12	}
2212 :	parrello	1.93	# Return the result.
2213 :			return ($retVal, $pos, $len);
2214 :	parrello	1.5	}
2215 :
2216 :	parrello	1.93	=head3 OpenDir
2217 :	parrello	1.5
2218 :	parrello	1.93	my @files = OpenDir($dirName, $filtered, $flag);
2219 :	parrello	1.5
2220 :	parrello	1.93	Open a directory and return all the file names. This function essentially performs
2221 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2222 :			set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2223 :			or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2224 :			filtered out of the return list. If the directory does not open and I<$flag> is not
2225 :			set, an exception is thrown. So, for example,
2226 :	parrello	1.5
2227 :	parrello	1.93	my @files = OpenDir("/Volumes/fig/contigs", 1);
2228 :	parrello	1.5
2229 :	parrello	1.93	is effectively the same as
2230 :	parrello	1.5
2231 :	parrello	1.93	opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
2232 :			my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2233 :	parrello	1.5
2234 :	parrello	1.93	Similarly, the following code
2235 :	parrello	1.5
2236 :	parrello	1.93	my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2237 :	parrello	1.5
2238 :	parrello	1.93	Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2239 :			automatically returns an empty list if the directory fails to open.
2240 :	parrello	1.5
2241 :	parrello	1.93	=over 4
2242 :	parrello	1.5
2243 :	parrello	1.93	=item dirName
2244 :	parrello	1.5
2245 :	parrello	1.93	Name of the directory to open.
2246 :	parrello	1.5
2247 :	parrello	1.93	=item filtered
2248 :	parrello	1.5
2249 :	parrello	1.93	TRUE if files whose names begin with a period (C<.>) should be automatically removed
2250 :			from the list, else FALSE.
2251 :	parrello	1.5
2252 :	parrello	1.93	=item flag
2253 :	parrello	1.5
2254 :	parrello	1.93	TRUE if a failure to open is okay, else FALSE
2255 :	parrello	1.5
2256 :	parrello	1.93	=back
2257 :	parrello	1.5
2258 :	parrello	1.93	=cut
2259 :			#: Return Type @;
2260 :			sub OpenDir {
2261 :			# Get the parameters.
2262 :			my ($dirName, $filtered, $flag) = @_;
2263 :			# Declare the return variable.
2264 :			my @retVal = ();
2265 :			# Open the directory.
2266 :			if (opendir(my $dirHandle, $dirName)) {
2267 :			# The directory opened successfully. Get the appropriate list according to the
2268 :			# strictures of the filter parameter.
2269 :			if ($filtered) {
2270 :			@retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2271 :			} else {
2272 :			@retVal = readdir $dirHandle;
2273 :			}
2274 :			} elsif (! $flag) {
2275 :			# Here the directory would not open and it's considered an error.
2276 :			Confess("Could not open directory $dirName.");
2277 :			}
2278 :			# Return the result.
2279 :			return @retVal;
2280 :			}
2281 :	parrello	1.5
2282 :
2283 :	parrello	1.93	=head3 Insure
2284 :	parrello	1.5
2285 :	parrello	1.93	Insure($dirName, $chmod);
2286 :	parrello	1.5
2287 :	parrello	1.93	Insure a directory is present.
2288 :	parrello	1.5
2289 :	parrello	1.93	=over 4
2290 :	parrello	1.5
2291 :	parrello	1.93	=item dirName
2292 :	olson	1.1
2293 :	parrello	1.93	Name of the directory to check. If it does not exist, it will be created.
2294 :	parrello	1.7
2295 :	parrello	1.93	=item chmod (optional)
2296 :	parrello	1.7
2297 :	parrello	1.93	Security privileges to be given to the directory if it is created.
2298 :	parrello	1.7
2299 :	parrello	1.93	=back
2300 :	parrello	1.7
2301 :			=cut
2302 :
2303 :	parrello	1.93	sub Insure {
2304 :			my ($dirName, $chmod) = @_;
2305 :			if (! -d $dirName) {
2306 :			Trace("Creating $dirName directory.") if T(2);
2307 :			eval {
2308 :			mkpath $dirName;
2309 :			# If we have permissions specified, set them here.
2310 :			if (defined($chmod)) {
2311 :			chmod $chmod, $dirName;
2312 :			}
2313 :			};
2314 :			if ($@) {
2315 :			Confess("Error creating $dirName: $@");
2316 :			}
2317 :	parrello	1.12	}
2318 :	parrello	1.9	}
2319 :
2320 :	parrello	1.93	=head3 ChDir
2321 :	parrello	1.9
2322 :	parrello	1.93	ChDir($dirName);
2323 :	parrello	1.9
2324 :	parrello	1.93	Change to the specified directory.
2325 :	parrello	1.9
2326 :			=over 4
2327 :
2328 :	parrello	1.93	=item dirName
2329 :	parrello	1.9
2330 :	parrello	1.93	Name of the directory to which we want to change.
2331 :	parrello	1.9
2332 :			=back
2333 :
2334 :			=cut
2335 :
2336 :	parrello	1.93	sub ChDir {
2337 :			my ($dirName) = @_;
2338 :			if (! -d $dirName) {
2339 :			Confess("Cannot change to directory $dirName: no such directory.");
2340 :			} else {
2341 :			Trace("Changing to directory $dirName.") if T(File => 4);
2342 :			my $okFlag = chdir $dirName;
2343 :			if (! $okFlag) {
2344 :			Confess("Error switching to directory $dirName.");
2345 :			}
2346 :			}
2347 :	parrello	1.9	}
2348 :
2349 :	parrello	1.93	=head3 SetPermissions
2350 :
2351 :			Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2352 :	parrello	1.9
2353 :	parrello	1.93	Set the permissions for a directory and all the files and folders inside it.
2354 :			In addition, the group ownership will be changed to the specified value.
2355 :	parrello	1.9
2356 :	parrello	1.93	This method is more vulnerable than most to permission and compatability
2357 :			problems, so it does internal error recovery.
2358 :	parrello	1.9
2359 :			=over 4
2360 :
2361 :	parrello	1.93	=item dirName
2362 :
2363 :			Name of the directory to process.
2364 :
2365 :			=item group
2366 :	parrello	1.9
2367 :	parrello	1.93	Name of the group to be assigned.
2368 :	parrello	1.9
2369 :	parrello	1.93	=item mask
2370 :	parrello	1.9
2371 :	parrello	1.93	Permission mask. Bits that are C<1> in this mask will be ORed into the
2372 :			permission bits of any file or directory that does not already have them
2373 :			set to 1.
2374 :	parrello	1.9
2375 :	parrello	1.93	=item otherMasks
2376 :	parrello	1.9
2377 :	parrello	1.93	Map of search patterns to permission masks. If a directory name matches
2378 :			one of the patterns, that directory and all its members and subdirectories
2379 :			will be assigned the new pattern. For example, the following would
2380 :			assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2381 :	parrello	1.9
2382 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2383 :	parrello	1.9
2384 :	parrello	1.93	The list is ordered, so the following would use 0777 for C<tmp1> and
2385 :			0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2386 :	parrello	1.22
2387 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2388 :			'^tmp' => 0666);
2389 :	parrello	1.9
2390 :	parrello	1.93	Note that the pattern matches are all case-insensitive, and only directory
2391 :			names are matched, not file names.
2392 :	parrello	1.9
2393 :			=back
2394 :
2395 :			=cut
2396 :
2397 :	parrello	1.93	sub SetPermissions {
2398 :	parrello	1.12	# Get the parameters.
2399 :	parrello	1.93	my ($dirName, $group, $mask, @otherMasks) = @_;
2400 :			# Set up for error recovery.
2401 :			eval {
2402 :			# Switch to the specified directory.
2403 :			ChDir($dirName);
2404 :			# Get the group ID.
2405 :			my $gid = getgrnam($group);
2406 :			# Get the mask for tracing.
2407 :			my $traceMask = sprintf("%04o", $mask) . "($mask)";
2408 :			Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2409 :			my $fixCount = 0;
2410 :			my $lookCount = 0;
2411 :			# @dirs will be a stack of directories to be processed.
2412 :			my @dirs = (getcwd());
2413 :			while (scalar(@dirs) > 0) {
2414 :			# Get the current directory.
2415 :			my $dir = pop @dirs;
2416 :			# Check for a match to one of the specified directory names. To do
2417 :			# that, we need to pull the individual part of the name off of the
2418 :			# whole path.
2419 :			my $simpleName = $dir;
2420 :			if ($dir =~ m!/([^/]+)$!) {
2421 :			$simpleName = $1;
2422 :			}
2423 :			Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2424 :			# Search for a match.
2425 :			my $match = 0;
2426 :			my $i;
2427 :			for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2428 :			my $pattern = $otherMasks[$i];
2429 :			if ($simpleName =~ /$pattern/i) {
2430 :			$match = 1;
2431 :			}
2432 :			}
2433 :			# Check for a match. Note we use $i-1 because the loop added 2
2434 :			# before terminating due to the match.
2435 :			if ($match && $otherMasks[$i-1] != $mask) {
2436 :			# This directory matches one of the incoming patterns, and it's
2437 :			# a different mask, so we process it recursively with that mask.
2438 :			SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2439 :			} else {
2440 :			# Here we can process normally. Get all of the non-hidden members.
2441 :			my @submems = OpenDir($dir, 1);
2442 :			for my $submem (@submems) {
2443 :			# Get the full name.
2444 :			my $thisMem = "$dir/$submem";
2445 :			Trace("Checking member $thisMem.") if T(4);
2446 :			$lookCount++;
2447 :			if ($lookCount % 1000 == 0) {
2448 :			Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2449 :			}
2450 :			# Fix the group.
2451 :			chown -1, $gid, $thisMem;
2452 :			# Insure this member is not a symlink.
2453 :			if (! -l $thisMem) {
2454 :			# Get its info.
2455 :			my $fileInfo = stat $thisMem;
2456 :			# Only proceed if we got the info. Otherwise, it's a hard link
2457 :			# and we want to skip it anyway.
2458 :			if ($fileInfo) {
2459 :			my $fileMode = $fileInfo->mode;
2460 :			if (($fileMode & $mask) != $mask) {
2461 :			# Fix this member.
2462 :			$fileMode \|= $mask;
2463 :			chmod $fileMode, $thisMem;
2464 :			$fixCount++;
2465 :			}
2466 :			# If it's a subdirectory, stack it.
2467 :			if (-d $thisMem) {
2468 :			push @dirs, $thisMem;
2469 :			}
2470 :			}
2471 :			}
2472 :			}
2473 :			}
2474 :	parrello	1.12	}
2475 :	parrello	1.93	Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2476 :			};
2477 :			# Check for an error.
2478 :			if ($@) {
2479 :			Confess("SetPermissions error: $@");
2480 :	parrello	1.12	}
2481 :	parrello	1.7	}
2482 :
2483 :	parrello	1.93	=head3 GetLine
2484 :	parrello	1.29
2485 :	parrello	1.93	my @data = Tracer::GetLine($handle);
2486 :	parrello	1.15
2487 :	parrello	1.93	Read a line of data from a tab-delimited file.
2488 :	parrello	1.15
2489 :			=over 4
2490 :
2491 :	parrello	1.93	=item handle
2492 :	parrello	1.15
2493 :	parrello	1.93	Open file handle from which to read.
2494 :	parrello	1.15
2495 :			=item RETURN
2496 :
2497 :	parrello	1.93	Returns a list of the fields in the record read. The fields are presumed to be
2498 :			tab-delimited. If we are at the end of the file, then an empty list will be
2499 :			returned. If an empty line is read, a single list item consisting of a null
2500 :			string will be returned.
2501 :	parrello	1.15
2502 :			=back
2503 :
2504 :			=cut
2505 :	parrello	1.93
2506 :			sub GetLine {
2507 :	parrello	1.15	# Get the parameters.
2508 :	parrello	1.93	my ($handle) = @_;
2509 :			# Declare the return variable.
2510 :			my @retVal = ();
2511 :			Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2512 :			# Read from the file.
2513 :			my $line = <$handle>;
2514 :			# Only proceed if we found something.
2515 :			if (defined $line) {
2516 :			# Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2517 :			# upload control and have a nonstandard EOL combination.
2518 :			$line =~ s/(\r\|\n)+$//;
2519 :			# Here we do some fancy tracing to help in debugging complicated EOL marks.
2520 :			if (T(File => 4)) {
2521 :			my $escapedLine = $line;
2522 :			$escapedLine =~ s/\n/\\n/g;
2523 :			$escapedLine =~ s/\r/\\r/g;
2524 :			$escapedLine =~ s/\t/\\t/g;
2525 :			Trace("Line read: -->$escapedLine<--");
2526 :			}
2527 :			# If the line is empty, return a single empty string; otherwise, parse
2528 :			# it into fields.
2529 :			if ($line eq "") {
2530 :			push @retVal, "";
2531 :			} else {
2532 :			push @retVal, split /\t/,$line;
2533 :			}
2534 :			} else {
2535 :			# Trace the reason the read failed.
2536 :			Trace("End of file: $!") if T(File => 3);
2537 :	parrello	1.15	}
2538 :	parrello	1.93	# Return the result.
2539 :			return @retVal;
2540 :	parrello	1.15	}
2541 :
2542 :	parrello	1.93	=head3 PutLine
2543 :
2544 :			Tracer::PutLine($handle, \@fields, $eol);
2545 :	parrello	1.35
2546 :	parrello	1.93	Write a line of data to a tab-delimited file. The specified field values will be
2547 :			output in tab-separated form, with a trailing new-line.
2548 :	parrello	1.35
2549 :	parrello	1.93	=over 4
2550 :	parrello	1.35
2551 :	parrello	1.93	=item handle
2552 :	parrello	1.69
2553 :	parrello	1.93	Output file handle.
2554 :	parrello	1.69
2555 :	parrello	1.93	=item fields
2556 :	parrello	1.69
2557 :	parrello	1.93	List of field values.
2558 :	parrello	1.69
2559 :	parrello	1.93	=item eol (optional)
2560 :	parrello	1.69
2561 :	parrello	1.93	End-of-line character (default is "\n").
2562 :	parrello	1.69
2563 :			=back
2564 :	parrello	1.35
2565 :			=cut
2566 :
2567 :	parrello	1.93	sub PutLine {
2568 :	parrello	1.69	# Get the parameters.
2569 :	parrello	1.93	my ($handle, $fields, $eol) = @_;
2570 :			# Write the data.
2571 :			print $handle join("\t", @{$fields}) . ($eol \|\| "\n");
2572 :	parrello	1.69	}
2573 :
2574 :
2575 :	parrello	1.97	=head3 PrintLine
2576 :
2577 :			Tracer::PrintLine($line);
2578 :
2579 :			Print a line of text with a trailing new-line.
2580 :
2581 :			=over 4
2582 :
2583 :			=item line
2584 :
2585 :			Line of text to print.
2586 :
2587 :			=back
2588 :
2589 :			=cut
2590 :
2591 :			sub PrintLine {
2592 :			# Get the parameters.
2593 :			my ($line) = @_;
2594 :			# Print the line.
2595 :			print "$line\n";
2596 :			}
2597 :
2598 :	parrello	1.69
2599 :	parrello	1.93	=head2 Other Useful Methods
2600 :
2601 :			=head3 ParseParm
2602 :
2603 :			my $listValue = Tracer::ParseParm($string);
2604 :
2605 :			Convert a parameter into a list reference. If the parameter is undefined,
2606 :			an undefined value will be returned. Otherwise, it will be parsed as a
2607 :			comma-separated list of values.
2608 :	parrello	1.69
2609 :			=over 4
2610 :
2611 :	parrello	1.93	=item string
2612 :
2613 :			Incoming string.
2614 :
2615 :			=item RETURN
2616 :	parrello	1.69
2617 :	parrello	1.93	Returns a reference to a list of values, or C<undef> if the incoming value
2618 :			was undefined.
2619 :	parrello	1.69
2620 :			=back
2621 :
2622 :			=cut
2623 :
2624 :	parrello	1.93	sub ParseParm {
2625 :			# Get the parameters.
2626 :			my ($string) = @_;
2627 :			# Declare the return variable.
2628 :			my $retVal;
2629 :			# Check for data.
2630 :			if (defined $string) {
2631 :			# We have some, so split it into a list.
2632 :			$retVal = [ split /\s,\s/, $string];
2633 :	parrello	1.72	}
2634 :	parrello	1.93	# Return the result.
2635 :			return $retVal;
2636 :	parrello	1.69	}
2637 :
2638 :	parrello	1.97	=head3 Now
2639 :
2640 :			my $string = Tracer::Now();
2641 :
2642 :			Return a displayable time stamp containing the local time. Whatever format this
2643 :			method produces must be parseable by L</ParseDate>.
2644 :
2645 :			=cut
2646 :
2647 :			sub Now {
2648 :			return DisplayTime(time);
2649 :			}
2650 :
2651 :			=head3 DisplayTime
2652 :
2653 :			my $string = Tracer::DisplayTime($time);
2654 :	parrello	1.69
2655 :	parrello	1.97	Convert a time value to a displayable time stamp. Whatever format this
2656 :			method produces must be parseable by L</ParseDate>.
2657 :
2658 :			=over 4
2659 :	parrello	1.69
2660 :	parrello	1.97	=item time
2661 :	parrello	1.69
2662 :	parrello	1.97	Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2663 :
2664 :			=item RETURN
2665 :	parrello	1.69
2666 :	parrello	1.97	Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2667 :	parrello	1.69
2668 :	parrello	1.97	=back
2669 :	parrello	1.69
2670 :	parrello	1.93	=cut
2671 :	parrello	1.69
2672 :	parrello	1.97	sub DisplayTime {
2673 :			my ($time) = @_;
2674 :			my $retVal = "(n/a)";
2675 :			if (defined $time) {
2676 :			my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2677 :			$retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2678 :			_p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2679 :			}
2680 :	parrello	1.93	return $retVal;
2681 :			}
2682 :	parrello	1.69
2683 :	parrello	1.93	# Pad a number to 2 digits.
2684 :			sub _p2 {
2685 :			my ($value) = @_;
2686 :			$value = "0$value" if ($value < 10);
2687 :			return $value;
2688 :	parrello	1.69	}
2689 :
2690 :	parrello	1.93	=head3 Escape
2691 :	parrello	1.69
2692 :	parrello	1.93	my $codedString = Tracer::Escape($realString);
2693 :	parrello	1.69
2694 :	parrello	1.93	Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2695 :			replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2696 :			result is to reverse the effect of L</UnEscape>.
2697 :	parrello	1.69
2698 :			=over 4
2699 :
2700 :	parrello	1.93	=item realString
2701 :	parrello	1.69
2702 :	parrello	1.93	String to escape.
2703 :	parrello	1.69
2704 :			=item RETURN
2705 :
2706 :	parrello	1.93	Escaped equivalent of the real string.
2707 :
2708 :			=back
2709 :
2710 :			=cut
2711 :
2712 :			sub Escape {
2713 :			# Get the parameter.
2714 :			my ($realString) = @_;
2715 :			# Initialize the return variable.
2716 :			my $retVal = "";
2717 :			# Loop through the parameter string, looking for sequences to escape.
2718 :			while (length $realString > 0) {
2719 :			# Look for the first sequence to escape.
2720 :			if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2721 :			# Here we found it. The text preceding the sequence is in $1. The sequence
2722 :			# itself is in $2. First, move the clear text to the return variable.
2723 :			$retVal .= $1;
2724 :			# Strip the processed section off the real string.
2725 :			$realString = substr $realString, (length $2) + (length $1);
2726 :			# Get the matched character.
2727 :			my $char = $2;
2728 :			# If we have a CR, we are done.
2729 :			if ($char ne "\r") {
2730 :			# It's not a CR, so encode the escape sequence.
2731 :			$char =~ tr/\t\n/tn/;
2732 :			$retVal .= "\\" . $char;
2733 :			}
2734 :			} else {
2735 :			# Here there are no more escape sequences. The rest of the string is
2736 :			# transferred unmodified.
2737 :			$retVal .= $realString;
2738 :			$realString = "";
2739 :			}
2740 :			}
2741 :			# Return the result.
2742 :			return $retVal;
2743 :	parrello	1.69	}
2744 :
2745 :	parrello	1.93	=head3 UnEscape
2746 :	parrello	1.69
2747 :	parrello	1.93	my $realString = Tracer::UnEscape($codedString);
2748 :	parrello	1.69
2749 :	parrello	1.93	Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2750 :			a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2751 :			be deleted.
2752 :	parrello	1.69
2753 :			=over 4
2754 :
2755 :	parrello	1.93	=item codedString
2756 :	parrello	1.69
2757 :	parrello	1.93	String to un-escape.
2758 :	parrello	1.69
2759 :			=item RETURN
2760 :
2761 :	parrello	1.93	Returns a copy of the original string with the escape sequences converted to their actual
2762 :			values.
2763 :	parrello	1.69
2764 :			=back
2765 :
2766 :			=cut
2767 :
2768 :	parrello	1.93	sub UnEscape {
2769 :			# Get the parameter.
2770 :			my ($codedString) = @_;
2771 :			# Initialize the return variable.
2772 :			my $retVal = "";
2773 :			# Only proceed if the incoming string is nonempty.
2774 :			if (defined $codedString) {
2775 :			# Loop through the parameter string, looking for escape sequences. We can't do
2776 :			# translating because it causes problems with the escaped slash. ("\\t" becomes
2777 :			# "\<tab>" no matter what we do.)
2778 :			while (length $codedString > 0) {
2779 :			# Look for the first escape sequence.
2780 :			if ($codedString =~ /^(.*?)\\(\\\|n\|t\|r)/) {
2781 :			# Here we found it. The text preceding the sequence is in $1. The sequence
2782 :			# itself is in $2. First, move the clear text to the return variable.
2783 :			$retVal .= $1;
2784 :			$codedString = substr $codedString, (2 + length $1);
2785 :			# Get the escape value.
2786 :			my $char = $2;
2787 :			# If we have a "\r", we are done.
2788 :			if ($char ne 'r') {
2789 :			# Here it's not an 'r', so we convert it.
2790 :			$char =~ tr/\\tn/\\\t\n/;
2791 :			$retVal .= $char;
2792 :			}
2793 :			} else {
2794 :			# Here there are no more escape sequences. The rest of the string is
2795 :			# transferred unmodified.
2796 :			$retVal .= $codedString;
2797 :			$codedString = "";
2798 :			}
2799 :			}
2800 :	parrello	1.35	}
2801 :	parrello	1.69	# Return the result.
2802 :			return $retVal;
2803 :			}
2804 :
2805 :	parrello	1.93	=head3 Percent
2806 :	parrello	1.69
2807 :	parrello	1.93	my $percent = Tracer::Percent($number, $base);
2808 :	parrello	1.69
2809 :	parrello	1.93	Returns the percent of the base represented by the given number. If the base
2810 :			is zero, returns zero.
2811 :	parrello	1.69
2812 :			=over 4
2813 :
2814 :	parrello	1.93	=item number
2815 :	parrello	1.69
2816 :	parrello	1.93	Percent numerator.
2817 :	parrello	1.69
2818 :	parrello	1.93	=item base
2819 :	parrello	1.69
2820 :	parrello	1.93	Percent base.
2821 :	parrello	1.69
2822 :	parrello	1.93	=item RETURN
2823 :	parrello	1.69
2824 :	parrello	1.93	Returns the percentage of the base represented by the numerator.
2825 :	parrello	1.69
2826 :			=back
2827 :
2828 :			=cut
2829 :
2830 :	parrello	1.93	sub Percent {
2831 :	parrello	1.69	# Get the parameters.
2832 :	parrello	1.93	my ($number, $base) = @_;
2833 :			# Declare the return variable.
2834 :			my $retVal = 0;
2835 :			# Compute the percent.
2836 :			if ($base != 0) {
2837 :			$retVal = $number * 100 / $base;
2838 :			}
2839 :			# Return the result.
2840 :			return $retVal;
2841 :	parrello	1.69	}
2842 :
2843 :	parrello	1.97	=head3 Constrain
2844 :
2845 :			my $constrained = Constrain($value, $min, $max);
2846 :
2847 :			Modify a numeric value to bring it to a point in between a maximum and a minimum.
2848 :
2849 :			=over 4
2850 :
2851 :			=item value
2852 :
2853 :			Value to constrain.
2854 :
2855 :			=item min (optional)
2856 :
2857 :			Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2858 :
2859 :			=item max (optional)
2860 :
2861 :			Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
2862 :
2863 :			=item RETURN
2864 :
2865 :			Returns the incoming value, constrained according to the other parameters.
2866 :
2867 :			=back
2868 :
2869 :			=cut
2870 :
2871 :			sub Constrain {
2872 :			# Get the parameters.
2873 :			my ($value, $min, $max) = @_;
2874 :			# Declare the return variable.
2875 :			my $retVal = $value;
2876 :			# Apply the minimum constraint.
2877 :			if (defined $min && $retVal < $min) {
2878 :			$retVal = $min;
2879 :			}
2880 :			# Apply the maximum constraint.
2881 :			if (defined $max && $retVal > $max) {
2882 :			$retVal = $max;
2883 :			}
2884 :			# Return the result.
2885 :			return $retVal;
2886 :			}
2887 :
2888 :	parrello	1.93	=head3 Min
2889 :	parrello	1.69
2890 :	parrello	1.93	my $min = Min($value1, $value2, ... $valueN);
2891 :	parrello	1.69
2892 :	parrello	1.93	Return the minimum argument. The arguments are treated as numbers.
2893 :	parrello	1.69
2894 :			=over 4
2895 :
2896 :	parrello	1.93	=item $value1, $value2, ... $valueN
2897 :	parrello	1.69
2898 :	parrello	1.93	List of numbers to compare.
2899 :	parrello	1.69
2900 :			=item RETURN
2901 :
2902 :	parrello	1.93	Returns the lowest number in the list.
2903 :	parrello	1.69
2904 :			=back
2905 :
2906 :			=cut
2907 :
2908 :	parrello	1.93	sub Min {
2909 :			# Get the parameters. Note that we prime the return value with the first parameter.
2910 :			my ($retVal, @values) = @_;
2911 :			# Loop through the remaining parameters, looking for the lowest.
2912 :			for my $value (@values) {
2913 :			if ($value < $retVal) {
2914 :			$retVal = $value;
2915 :	parrello	1.72	}
2916 :			}
2917 :	parrello	1.93	# Return the minimum found.
2918 :	parrello	1.70	return $retVal;
2919 :	parrello	1.35	}
2920 :
2921 :	parrello	1.93	=head3 Max
2922 :
2923 :			my $max = Max($value1, $value2, ... $valueN);
2924 :	parrello	1.69
2925 :	parrello	1.93	Return the maximum argument. The arguments are treated as numbers.
2926 :	parrello	1.65
2927 :	parrello	1.93	=over 4
2928 :	parrello	1.65
2929 :	parrello	1.93	=item $value1, $value2, ... $valueN
2930 :	parrello	1.65
2931 :	parrello	1.93	List of numbers to compare.
2932 :	parrello	1.65
2933 :	parrello	1.93	=item RETURN
2934 :	parrello	1.65
2935 :	parrello	1.93	Returns the highest number in the list.
2936 :	parrello	1.65
2937 :			=back
2938 :
2939 :			=cut
2940 :
2941 :	parrello	1.93	sub Max {
2942 :			# Get the parameters. Note that we prime the return value with the first parameter.
2943 :			my ($retVal, @values) = @_;
2944 :			# Loop through the remaining parameters, looking for the highest.
2945 :			for my $value (@values) {
2946 :			if ($value > $retVal) {
2947 :			$retVal = $value;
2948 :	parrello	1.65	}
2949 :			}
2950 :	parrello	1.93	# Return the maximum found.
2951 :			return $retVal;
2952 :	parrello	1.65	}
2953 :
2954 :	parrello	1.35
2955 :	parrello	1.93	=head3 Strip
2956 :	parrello	1.37
2957 :	parrello	1.93	my $string = Tracer::Strip($line);
2958 :	parrello	1.37
2959 :	parrello	1.93	Strip all line terminators off a string. This is necessary when dealing with files
2960 :			that may have been transferred back and forth several times among different
2961 :			operating environments.
2962 :	parrello	1.37
2963 :			=over 4
2964 :
2965 :	parrello	1.93	=item line
2966 :	parrello	1.37
2967 :	parrello	1.93	Line of text to be stripped.
2968 :	parrello	1.37
2969 :	parrello	1.93	=item RETURN
2970 :	parrello	1.91
2971 :	parrello	1.93	The same line of text with all the line-ending characters chopped from the end.
2972 :	parrello	1.91
2973 :	parrello	1.37	=back
2974 :
2975 :			=cut
2976 :
2977 :	parrello	1.93	sub Strip {
2978 :			# Get a copy of the parameter string.
2979 :			my ($string) = @_;
2980 :			my $retVal = (defined $string ? $string : "");
2981 :			# Strip the line terminator characters.
2982 :			$retVal =~ s/(\r\|\n)+$//g;
2983 :			# Return the result.
2984 :			return $retVal;
2985 :	parrello	1.43	}
2986 :
2987 :	parrello	1.93	=head3 Pad
2988 :	parrello	1.43
2989 :	parrello	1.93	my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
2990 :	parrello	1.43
2991 :	parrello	1.93	Pad a string to a specified length. The pad character will be a
2992 :			space, and the padding will be on the right side unless specified
2993 :			in the third parameter.
2994 :	parrello	1.43
2995 :			=over 4
2996 :
2997 :	parrello	1.93	=item string
2998 :
2999 :			String to be padded.
3000 :
3001 :			=item len
3002 :
3003 :			Desired length of the padded string.
3004 :
3005 :			=item left (optional)
3006 :
3007 :			TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3008 :
3009 :			=item padChar (optional)
3010 :
3011 :			Character to use for padding. The default is a space.
3012 :
3013 :			=item RETURN
3014 :	parrello	1.43
3015 :	parrello	1.93	Returns a copy of the original string with the pad character added to the
3016 :			specified end so that it achieves the desired length.
3017 :	parrello	1.43
3018 :			=back
3019 :
3020 :			=cut
3021 :
3022 :	parrello	1.93	sub Pad {
3023 :			# Get the parameters.
3024 :			my ($string, $len, $left, $padChar) = @_;
3025 :			# Compute the padding character.
3026 :			if (! defined $padChar) {
3027 :			$padChar = " ";
3028 :			}
3029 :			# Compute the number of spaces needed.
3030 :			my $needed = $len - length $string;
3031 :			# Copy the string into the return variable.
3032 :			my $retVal = $string;
3033 :			# Only proceed if padding is needed.
3034 :			if ($needed > 0) {
3035 :			# Create the pad string.
3036 :			my $pad = $padChar x $needed;
3037 :			# Affix it to the return value.
3038 :			if ($left) {
3039 :			$retVal = $pad . $retVal;
3040 :			} else {
3041 :			$retVal .= $pad;
3042 :	parrello	1.43	}
3043 :	parrello	1.37	}
3044 :	parrello	1.93	# Return the result.
3045 :			return $retVal;
3046 :	parrello	1.37	}
3047 :
3048 :	parrello	1.93	=head3 EOF
3049 :
3050 :			This is a constant that is lexically greater than any useful string.
3051 :
3052 :			=cut
3053 :
3054 :			sub EOF {
3055 :			return "\xFF\xFF\xFF\xFF\xFF";
3056 :			}
3057 :	parrello	1.59
3058 :	parrello	1.93	=head3 TICK
3059 :	parrello	1.59
3060 :	parrello	1.93	my @results = TICK($commandString);
3061 :	parrello	1.59
3062 :	parrello	1.93	Perform a back-tick operation on a command. If this is a Windows environment, any leading
3063 :			dot-slash (C<./> will be removed. So, for example, if you were doing
3064 :	parrello	1.59
3065 :	parrello	1.93	`./protein.cgi`
3066 :	parrello	1.59
3067 :	parrello	1.93	from inside a CGI script, it would work fine in Unix, but would issue an error message
3068 :			in Windows complaining that C<'.'> is not a valid command. If instead you code
3069 :	parrello	1.59
3070 :	parrello	1.93	TICK("./protein.cgi")
3071 :	parrello	1.59
3072 :	parrello	1.93	it will work correctly in both environments.
3073 :	parrello	1.59
3074 :	parrello	1.93	=over 4
3075 :	parrello	1.59
3076 :	parrello	1.93	=item commandString
3077 :	parrello	1.59
3078 :	parrello	1.93	The command string to pass to the system.
3079 :	parrello	1.59
3080 :			=item RETURN
3081 :
3082 :	parrello	1.93	Returns the standard output from the specified command, as a list.
3083 :	parrello	1.59
3084 :			=back
3085 :
3086 :			=cut
3087 :	parrello	1.93	#: Return Type @;
3088 :			sub TICK {
3089 :	parrello	1.59	# Get the parameters.
3090 :	parrello	1.93	my ($commandString) = @_;
3091 :			# Chop off the dot-slash if this is Windows.
3092 :			if ($FIG_Config::win_mode) {
3093 :			$commandString =~ s!^\./!!;
3094 :	parrello	1.59	}
3095 :	parrello	1.93	# Activate the command and return the result.
3096 :			return `$commandString`;
3097 :	parrello	1.59	}
3098 :
3099 :	parrello	1.93
3100 :	parrello	1.55	=head3 CommaFormat
3101 :
3102 :	parrello	1.92	my $formatted = Tracer::CommaFormat($number);
3103 :	parrello	1.55
3104 :			Insert commas into a number.
3105 :
3106 :			=over 4
3107 :
3108 :			=item number
3109 :
3110 :			A sequence of digits.
3111 :
3112 :			=item RETURN
3113 :
3114 :			Returns the same digits with commas strategically inserted.
3115 :
3116 :			=back
3117 :
3118 :			=cut
3119 :
3120 :			sub CommaFormat {
3121 :			# Get the parameters.
3122 :			my ($number) = @_;
3123 :			# Pad the length up to a multiple of three.
3124 :			my $padded = "$number";
3125 :			$padded = " " . $padded while length($padded) % 3 != 0;
3126 :			# This is a fancy PERL trick. The parentheses in the SPLIT pattern
3127 :			# cause the delimiters to be included in the output stream. The
3128 :			# GREP removes the empty strings in between the delimiters.
3129 :			my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3130 :			# Clean out the spaces.
3131 :			$retVal =~ s/ //g;
3132 :			# Return the result.
3133 :			return $retVal;
3134 :			}
3135 :	parrello	1.46
3136 :
3137 :	parrello	1.62	=head3 CompareLists
3138 :
3139 :	parrello	1.92	my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3140 :	parrello	1.62
3141 :			Compare two lists of tuples, and return a hash analyzing the differences. The lists
3142 :			are presumed to be sorted alphabetically by the value in the $keyIndex column.
3143 :			The return value contains a list of items that are only in the new list
3144 :			(inserted) and only in the old list (deleted).
3145 :
3146 :			=over 4
3147 :
3148 :			=item newList
3149 :
3150 :			Reference to a list of new tuples.
3151 :
3152 :			=item oldList
3153 :
3154 :			Reference to a list of old tuples.
3155 :
3156 :			=item keyIndex (optional)
3157 :
3158 :			Index into each tuple of its key field. The default is 0.
3159 :
3160 :			=item RETURN
3161 :
3162 :			Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3163 :			list (inserted) followed by a reference to the list of items that are only in the old
3164 :			list (deleted).
3165 :
3166 :			=back
3167 :
3168 :			=cut
3169 :
3170 :			sub CompareLists {
3171 :			# Get the parameters.
3172 :			my ($newList, $oldList, $keyIndex) = @_;
3173 :			if (! defined $keyIndex) {
3174 :			$keyIndex = 0;
3175 :			}
3176 :			# Declare the return variables.
3177 :			my ($inserted, $deleted) = ([], []);
3178 :			# Loop through the two lists simultaneously.
3179 :			my ($newI, $oldI) = (0, 0);
3180 :			my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3181 :			while ($newI < $newN \|\| $oldI < $oldN) {
3182 :			# Get the current object in each list. Note that if one
3183 :			# of the lists is past the end, we'll get undef.
3184 :			my $newItem = $newList->[$newI];
3185 :			my $oldItem = $oldList->[$oldI];
3186 :	parrello	1.63	if (! defined($newItem) \|\| defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3187 :	parrello	1.62	# The old item is not in the new list, so mark it deleted.
3188 :			push @{$deleted}, $oldItem;
3189 :			$oldI++;
3190 :			} elsif (! defined($oldItem) \|\| $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3191 :			# The new item is not in the old list, so mark it inserted.
3192 :			push @{$inserted}, $newItem;
3193 :			$newI++;
3194 :			} else {
3195 :			# The item is in both lists, so push forward.
3196 :			$oldI++;
3197 :			$newI++;
3198 :			}
3199 :			}
3200 :			# Return the result.
3201 :			return ($inserted, $deleted);
3202 :			}
3203 :
3204 :	parrello	1.65	=head3 GenerateURL
3205 :
3206 :	parrello	1.92	my $queryUrl = Tracer::GenerateURL($page, %parameters);
3207 :	parrello	1.65
3208 :			Generate a GET-style URL for the specified page with the specified parameter
3209 :			names and values. The values will be URL-escaped automatically. So, for
3210 :			example
3211 :
3212 :			Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3213 :
3214 :			would return
3215 :
3216 :	parrello	1.79	form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3217 :	parrello	1.65
3218 :			=over 4
3219 :
3220 :			=item page
3221 :
3222 :			Page URL.
3223 :
3224 :			=item parameters
3225 :
3226 :			Hash mapping parameter names to parameter values.
3227 :
3228 :			=item RETURN
3229 :
3230 :			Returns a GET-style URL that goes to the specified page and passes in the
3231 :			specified parameters and values.
3232 :
3233 :			=back
3234 :
3235 :			=cut
3236 :
3237 :			sub GenerateURL {
3238 :			# Get the parameters.
3239 :			my ($page, %parameters) = @_;
3240 :			# Prime the return variable with the page URL.
3241 :			my $retVal = $page;
3242 :			# Loop through the parameters, creating parameter elements in a list.
3243 :			my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3244 :			# If the list is nonempty, tack it on.
3245 :			if (@parmList) {
3246 :	parrello	1.79	$retVal .= "?" . join(";", @parmList);
3247 :	parrello	1.65	}
3248 :			# Return the result.
3249 :			return $retVal;
3250 :			}
3251 :
3252 :	parrello	1.78	=head3 ApplyURL
3253 :
3254 :	parrello	1.92	Tracer::ApplyURL($table, $target, $url);
3255 :	parrello	1.78
3256 :			Run through a two-dimensional table (or more accurately, a list of lists), converting the
3257 :			I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3258 :			URL column will be deleted by this process and the target column will be HTML-escaped.
3259 :
3260 :			This provides a simple way to process the results of a database query into something
3261 :			displayable by combining a URL with text.
3262 :
3263 :			=over 4
3264 :
3265 :			=item table
3266 :
3267 :			Reference to a list of lists. The elements in the containing list will be updated by
3268 :			this method.
3269 :
3270 :			=item target
3271 :
3272 :			The index of the column to be converted into HTML.
3273 :
3274 :			=item url
3275 :
3276 :			The index of the column containing the URL. Note that the URL must have a recognizable
3277 :			C<http:> at the beginning.
3278 :
3279 :			=back
3280 :
3281 :			=cut
3282 :
3283 :			sub ApplyURL {
3284 :			# Get the parameters.
3285 :			my ($table, $target, $url) = @_;
3286 :			# Loop through the table.
3287 :			for my $row (@{$table}) {
3288 :			# Apply the URL to the target cell.
3289 :			$row->[$target] = CombineURL($row->[$target], $row->[$url]);
3290 :			# Delete the URL from the row.
3291 :			delete $row->[$url];
3292 :			}
3293 :			}
3294 :
3295 :			=head3 CombineURL
3296 :
3297 :	parrello	1.92	my $combinedHtml = Tracer::CombineURL($text, $url);
3298 :	parrello	1.78
3299 :			This method will convert the specified text into HTML hyperlinked to the specified
3300 :			URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3301 :			is defined and begins with an C<http:> header.
3302 :
3303 :			=over 4
3304 :
3305 :			=item text
3306 :
3307 :			Text to return. This will be HTML-escaped automatically.
3308 :
3309 :			=item url
3310 :
3311 :			A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3312 :			will be returned without any hyperlinking.
3313 :
3314 :			=item RETURN
3315 :
3316 :			Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3317 :			doesn't look right, the HTML-escaped text will be returned without any further
3318 :			modification.
3319 :
3320 :			=back
3321 :
3322 :			=cut
3323 :
3324 :			sub CombineURL {
3325 :			# Get the parameters.
3326 :			my ($text, $url) = @_;
3327 :			# Declare the return variable.
3328 :			my $retVal = CGI::escapeHTML($text);
3329 :			# Verify the URL.
3330 :			if (defined($url) && $url =~ m!http://!i) {
3331 :			# It's good, so we apply it to the text.
3332 :			$retVal = "<a href=\"$url\">$retVal</a>";
3333 :			}
3334 :			# Return the result.
3335 :			return $retVal;
3336 :			}
3337 :
3338 :	parrello	1.93	=head3 Cmp
3339 :
3340 :			my $cmp = Tracer::Cmp($a, $b);
3341 :
3342 :			This method performs a universal sort comparison. Each value coming in is
3343 :			separated into a leading text part and a trailing number part. The text
3344 :			part is string compared, and if both parts are equal, then the number
3345 :			parts are compared numerically. A stream of just numbers or a stream of
3346 :			just strings will sort correctly, and a mixed stream will sort with the
3347 :			numbers first. Strings with a label and a number will sort in the
3348 :			expected manner instead of lexically.
3349 :
3350 :			=over 4
3351 :
3352 :			=item a
3353 :
3354 :			First item to compare.
3355 :
3356 :			=item b
3357 :
3358 :			Second item to compare.
3359 :
3360 :			=item RETURN
3361 :
3362 :			Returns a negative number if the first item should sort first (is less), a positive
3363 :			number if the first item should sort second (is greater), and a zero if the items are
3364 :			equal.
3365 :
3366 :			=back
3367 :
3368 :			=cut
3369 :
3370 :			sub Cmp {
3371 :			# Get the parameters.
3372 :			my ($a, $b) = @_;
3373 :			# Declare the return value.
3374 :			my $retVal;
3375 :			# Check for nulls.
3376 :			if (! defined($a)) {
3377 :			$retVal = (! defined($b) ? 0 : -1);
3378 :			} elsif (! defined($b)) {
3379 :			$retVal = 1;
3380 :			} else {
3381 :			# Here we have two real values. Parse the two strings.
3382 :			$a =~ /^(\D)(\d)$/;
3383 :			my $aParsed = [$1, $2];
3384 :			$b =~ /^(\D)(\d)$/;
3385 :			my $bParsed = [$1, $2];
3386 :			# Compare the string parts.
3387 :			$retVal = $aParsed->[0] cmp $bParsed->[0];
3388 :			if (! $retVal) {
3389 :			$retVal = $aParsed->[1] <=> $bParsed->[1];
3390 :			}
3391 :			}
3392 :			# Return the result.
3393 :			return $retVal;
3394 :			}
3395 :
3396 :	parrello	1.87
3397 :	parrello	1.97	=head3 TrackingCode
3398 :
3399 :			my $html = Tracer::TrackingCode();
3400 :
3401 :			Returns the HTML code for doing web page traffic monitoring. If the
3402 :			current environment is a test system, then it returns a null string;
3403 :			otherwise, it returns a bunch of javascript containing code for turning
3404 :			on SiteMeter and Google Analytics.
3405 :
3406 :			=cut
3407 :
3408 :			sub TrackingCode {
3409 :			# Declare the return variable.
3410 :			my $retVal = "<!-- tracking off -->";
3411 :			# Determine if we're in production.
3412 :			if ($FIG_Config::site_meter) {
3413 :			$retVal = <<END_HTML
3414 :			<!-- Site Meter -->
3415 :			<script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3416 :			</script>
3417 :			<noscript>
3418 :			<a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3419 :			<img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3420 :			</noscript>
3421 :			<!-- Copyright (c)2006 Site Meter -->
3422 :			END_HTML
3423 :			}
3424 :			return $retVal;
3425 :			}
3426 :
3427 :
3428 :	olson	1.88	1;

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