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	1.99	@EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24 :	parrello	1.97	@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 :	parrello	1.99	use POSIX qw(strftime);
40 :			use Time::Zone;
41 :	parrello	1.106	use Fcntl ':flock';
42 :	parrello	1.99
43 :	olson	1.1
44 :			=head1 Tracing and Debugging Helpers
45 :
46 :	parrello	1.72	=head2 Tracing
47 :	olson	1.1
48 :			This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49 :	parrello	1.72	L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50 :			L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51 :			each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52 :			level is less than or equal to the setup trace level and whose category is activated will
53 :	parrello	1.2	be written. Thus, a higher trace level on a message indicates that the message
54 :	parrello	1.72	is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
55 :			appear.
56 :	olson	1.1
57 :	parrello	1.72	=head3 Putting Trace Messages in Your Code
58 :
59 :			To generate a trace message, use the following syntax.
60 :
61 :			Trace($message) if T(errors => 4);
62 :	olson	1.1
63 :	parrello	1.2	This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64 :	parrello	1.72	category is active. There is a special category C<main> that is always active, so
65 :	olson	1.1
66 :	parrello	1.72	Trace($message) if T(main => 4);
67 :	olson	1.1
68 :			will trace if the trace level is 4 or more.
69 :
70 :			If the category name is the same as the package name, all you need is the number. So, if the
71 :			following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72 :			active and the trace level is 2 or more.
73 :
74 :	parrello	1.72	Trace($message) if T(2);
75 :
76 :			In scripts, where no package name is available, the category defaults to C<main>.
77 :
78 :			=head3 Custom Tracing
79 :
80 :			Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81 :			the preferred method, but a knowledge of how custom tracing works can make the more modern
82 :			L</Emergency Tracing> easier to understand.
83 :	olson	1.1
84 :	parrello	1.72	To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
85 :			a list of category names, and a destination. The trace level and list of category names are
86 :	olson	1.1	specified as a space-delimited string. Thus
87 :
88 :	parrello	1.72	TSetup('3 errors Sprout ERDB', 'TEXT');
89 :	olson	1.1
90 :	parrello	1.7	sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91 :	parrello	1.72	specifies that messages should be sent to the standard output.
92 :	parrello	1.12
93 :			To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
94 :			level 3 and writes the output to the standard error output. This sort of thing might be
95 :			useful in a CGI environment.
96 :
97 :	parrello	1.72	TSetup('3 *', 'WARN');
98 :	olson	1.1
99 :	parrello	1.72	In addition standard error and file output for trace messages, you can specify that the trace messages
100 :	olson	1.1	be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101 :			is useful if you are building a web page. Instead of having the trace messages interspersed with
102 :			the page output, they can be gathered together and displayed at the end of the page. This makes
103 :			it easier to debug page formatting problems.
104 :
105 :	parrello	1.72	Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106 :			a file at the same time. To trace to a file, specify the filename with an output character in front
107 :			of it.
108 :
109 :			TSetup('4 SQL', ">$fileName");
110 :
111 :			To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112 :			bracket.
113 :
114 :			TSetup('3 *', "+>$fileName");
115 :	parrello	1.4
116 :	olson	1.1	The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117 :			Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118 :			Thus, debugging information is available and easily retrieved even when the application is
119 :			being used out in the field.
120 :
121 :	parrello	1.72	=head3 Trace Levels
122 :
123 :	parrello	1.10	There is no hard and fast rule on how to use trace levels. The following is therefore only
124 :			a suggestion.
125 :
126 :			=over 4
127 :
128 :	parrello	1.32	=item Error 0
129 :	parrello	1.10
130 :			Message indicates an error that may lead to incorrect results or that has stopped the
131 :			application entirely.
132 :
133 :	parrello	1.32	=item Warning 1
134 :	parrello	1.10
135 :			Message indicates something that is unexpected but that probably did not interfere
136 :			with program execution.
137 :
138 :	parrello	1.32	=item Notice 2
139 :	parrello	1.10
140 :			Message indicates the beginning or end of a major task.
141 :
142 :	parrello	1.32	=item Information 3
143 :	parrello	1.10
144 :			Message indicates a subtask. In the FIG system, a subtask generally relates to a single
145 :			genome. This would be a big loop that is not expected to execute more than 500 times or so.
146 :
147 :	parrello	1.32	=item Detail 4
148 :	parrello	1.10
149 :			Message indicates a low-level loop iteration.
150 :
151 :			=back
152 :
153 :	parrello	1.69	The format of trace messages is important because some utilities analyze trace files.
154 :	parrello	1.72	There are three fields-- the time stamp, the category name, and the text.
155 :			The time stamp is between square brackets and the category name between angle brackets.
156 :			After the category name there is a colon (C<:>) followed by the message text.
157 :			If the square brackets or angle brackets are missing, then the trace management
158 :			utilities assume that they are encountering a set of pre-formatted lines.
159 :
160 :			Note, however, that this formatting is done automatically by the tracing functions. You
161 :			only need to know about it if you want to parse a trace file.
162 :
163 :			=head3 Emergency Tracing
164 :
165 :			Sometimes, you need a way for tracing to happen automatically without putting parameters
166 :			in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167 :	parrello	1.97	from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168 :			that you specify a tracing key. For command-line tools, the key is
169 :	parrello	1.72	taken from the C<TRACING> environment variable. For web services, the key is taken from
170 :			a cookie. Either way, the key tells the tracing facility who you are, so that you control
171 :			the tracing in your environment without stepping on other users.
172 :
173 :			The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174 :			generate one for you.
175 :
176 :			You can activate and de-activate emergency tracing from the debugging control panel, as
177 :			well as display the trace file itself.
178 :
179 :			To enable emergency tracing in your code, call
180 :
181 :			ETracing($cgi)
182 :
183 :			from a web script and
184 :
185 :			ETracing()
186 :
187 :			from a command-line script.
188 :
189 :			The web script will look for the tracing key in the cookies, and the command-line
190 :			script will look for it in the C<TRACING> environment variable. If you are
191 :	parrello	1.97	using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192 :	parrello	1.72	will be configured automatically.
193 :
194 :	olson	1.1	=cut
195 :	parrello	1.2
196 :	olson	1.1	# Declare the configuration variables.
197 :
198 :	parrello	1.94	my $Destination = "WARN"; # Description of where to send the trace output.
199 :	parrello	1.12	my $TeeFlag = 0; # TRUE if output is going to a file and to the
200 :			# standard output
201 :	parrello	1.3	my %Categories = ( main => 1 );
202 :	parrello	1.12	# hash of active category names
203 :	parrello	1.97	my @LevelNames = qw(error warn notice info detail);
204 :	parrello	1.12	my $TraceLevel = 0; # trace level; a higher trace level produces more
205 :			# messages
206 :			my @Queue = (); # queued list of trace messages.
207 :	parrello	1.7	my $LastCategory = "main"; # name of the last category interrogated
208 :	parrello	1.97	my $LastLevel = 0; # level of the last test call
209 :	parrello	1.11	my $SetupCount = 0; # number of times TSetup called
210 :	parrello	1.12	my $AllTrace = 0; # TRUE if we are tracing all categories.
211 :	parrello	1.99	my $SavedCGI; # CGI object passed to ETracing
212 :	parrello	1.104	my $CommandLine; # Command line passed to StandardSetup
213 :	parrello	1.99	umask 2; # Fix the damn umask so everything is group-writable.
214 :	olson	1.1
215 :	parrello	1.93	=head2 Tracing Methods
216 :
217 :			=head3 Setups
218 :
219 :			my $count = Tracer::Setups();
220 :
221 :			Return the number of times L</TSetup> has been called.
222 :
223 :			This method allows for the creation of conditional tracing setups where, for example, we
224 :			may want to set up tracing if nobody else has done it before us.
225 :
226 :			=cut
227 :
228 :			sub Setups {
229 :			return $SetupCount;
230 :			}
231 :	olson	1.1
232 :			=head3 TSetup
233 :
234 :	parrello	1.92	TSetup($categoryList, $target);
235 :	olson	1.1
236 :			This method is used to specify the trace options. The options are stored as package data
237 :			and interrogated by the L</Trace> and L</T> methods.
238 :
239 :			=over 4
240 :
241 :			=item categoryList
242 :
243 :			A string specifying the trace level and the categories to be traced, separated by spaces.
244 :			The trace level must come first.
245 :
246 :			=item target
247 :
248 :			The destination for the trace output. To send the trace output to a file, specify the file
249 :			name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
250 :	parrello	1.10	to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
251 :			symbol with a C<+> to echo output to a file AND to the standard output. In addition to
252 :			sending the trace messages to a file, you can specify a special destination. C<HTML> will
253 :			cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
254 :	parrello	1.5	will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
255 :	parrello	1.9	messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
256 :	parrello	1.6	messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
257 :	parrello	1.9	cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
258 :	parrello	1.6	cause tracing to be suppressed.
259 :	olson	1.1
260 :			=back
261 :
262 :			=cut
263 :
264 :			sub TSetup {
265 :	parrello	1.12	# Get the parameters.
266 :			my ($categoryList, $target) = @_;
267 :			# Parse the category list.
268 :			my @categoryData = split /\s+/, $categoryList;
269 :			# Extract the trace level.
270 :			$TraceLevel = shift @categoryData;
271 :			# Presume category-based tracing until we learn otherwise.
272 :			$AllTrace = 0;
273 :			# Build the category hash. Note that if we find a "*", we turn on non-category
274 :	parrello	1.33	# tracing. We must also clear away any pre-existing data.
275 :	parrello	1.34	%Categories = ( main => 1 );
276 :	parrello	1.12	for my $category (@categoryData) {
277 :			if ($category eq '*') {
278 :			$AllTrace = 1;
279 :			} else {
280 :	parrello	1.13	$Categories{lc $category} = 1;
281 :	parrello	1.12	}
282 :			}
283 :			# Now we need to process the destination information. The most important special
284 :	parrello	1.98	# case is when we're writing to a file. This is indicated by ">" (overwrite) and
285 :			# ">>" (append). A leading "+" for either indicates that we are also writing to
286 :			# the standard output (tee mode).
287 :	parrello	1.12	if ($target =~ m/^\+?>>?/) {
288 :			if ($target =~ m/^\+/) {
289 :			$TeeFlag = 1;
290 :			$target = substr($target, 1);
291 :			}
292 :			if ($target =~ m/^>[^>]/) {
293 :	parrello	1.98	# We need to initialize the file (which clears it).
294 :	parrello	1.12	open TRACEFILE, $target;
295 :	parrello	1.98	print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296 :	parrello	1.12	close TRACEFILE;
297 :	parrello	1.98	# Set to append mode now that the file has been cleared.
298 :	parrello	1.12	$Destination = ">$target";
299 :			} else {
300 :			$Destination = $target;
301 :			}
302 :			} else {
303 :			$Destination = uc($target);
304 :			}
305 :			# Increment the setup counter.
306 :			$SetupCount++;
307 :	parrello	1.11	}
308 :
309 :	parrello	1.93	=head3 SetLevel
310 :	parrello	1.31
311 :	parrello	1.93	Tracer::SetLevel($newLevel);
312 :	parrello	1.31
313 :	parrello	1.93	Modify the trace level. A higher trace level will cause more messages to appear.
314 :	parrello	1.31
315 :	parrello	1.93	=over 4
316 :	parrello	1.31
317 :	parrello	1.93	=item newLevel
318 :	parrello	1.31
319 :	parrello	1.93	Proposed new trace level.
320 :	parrello	1.31
321 :	parrello	1.93	=back
322 :	parrello	1.31
323 :	parrello	1.93	=cut
324 :	parrello	1.31
325 :	parrello	1.93	sub SetLevel {
326 :			$TraceLevel = $_[0];
327 :			}
328 :	parrello	1.31
329 :	parrello	1.97	=head3 ParseDate
330 :
331 :			my $time = Tracer::ParseDate($dateString);
332 :
333 :			Convert a date into a PERL time number. This method expects a date-like string
334 :			and parses it into a number. The string must be vaguely date-like or it will
335 :			return an undefined value. Our requirement is that a month and day be
336 :			present and that three pieces of the date string (time of day, month and day,
337 :			year) be separated by likely delimiters, such as spaces, commas, and such-like.
338 :
339 :			If a time of day is present, it must be in military time with two digits for
340 :			everything but the hour.
341 :	parrello	1.31
342 :	parrello	1.97	The year must be exactly four digits.
343 :	parrello	1.31
344 :	parrello	1.97	Additional stuff can be in the string. We presume it's time zones or weekdays or something
345 :			equally innocuous. This means, however, that a sufficiently long sentence with date-like
346 :			parts in it may be interpreted as a date. Hopefully this will not be a problem.
347 :
348 :			It should be guaranteed that this method will parse the output of the L</Now> function.
349 :
350 :			The parameters are as follows.
351 :	parrello	1.31
352 :	parrello	1.93	=over 4
353 :	parrello	1.31
354 :	parrello	1.93	=item dateString
355 :	parrello	1.31
356 :	parrello	1.97	The date string to convert.
357 :	parrello	1.31
358 :	parrello	1.93	=item RETURN
359 :	parrello	1.31
360 :	parrello	1.93	Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361 :	parrello	1.97	the date string is invalid. A valid date string must contain a month and day.
362 :	parrello	1.31
363 :	parrello	1.93	=back
364 :	parrello	1.38
365 :	parrello	1.93	=cut
366 :	parrello	1.38
367 :	parrello	1.97	# Universal month conversion table.
368 :			use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
369 :			Feb => 1, February => 1, '02' => 1, '2' => 1,
370 :			Mar => 2, March => 2, '03' => 2, '3' => 2,
371 :			Apr => 3, April => 3, '04' => 3, '4' => 3,
372 :			May => 4, May => 4, '05' => 4, '5' => 4,
373 :			Jun => 5, June => 5, '06' => 5, '6' => 5,
374 :			Jul => 6, July => 6, '07' => 6, '7' => 6,
375 :			Aug => 7, August => 7, '08' => 7, '8' => 7,
376 :			Sep => 8, September => 8, '09' => 8, '9' => 8,
377 :			Oct => 9, October => 9, '10' => 9,
378 :			Nov => 10, November => 10, '11' => 10,
379 :			Dec => 11, December => 11, '12' => 11
380 :			};
381 :
382 :			sub ParseDate {
383 :	parrello	1.93	# Get the parameters.
384 :			my ($dateString) = @_;
385 :			# Declare the return variable.
386 :			my $retVal;
387 :	parrello	1.97	# Find the month and day of month. There are two ways that can happen. We check for the
388 :			# numeric style first. That way, if the user's done something like "Sun 12/22", then we
389 :			# won't be fooled into thinking the month is Sunday.
390 :			if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# \|\| $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391 :			my ($mon, $mday) = (MONTHS->{$1}, $2);
392 :			# Insist that the month and day are valid.
393 :			if (defined($mon) && $2 >= 1 && $2 <= 31) {
394 :			# Find the time.
395 :			my ($hour, $min, $sec) = (0, 0, 0);
396 :			if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397 :			($hour, $min, $sec) = ($1, $2, $3);
398 :			}
399 :			# Find the year.
400 :			my $year;
401 :			if ($dateString =~ /\b(\d{4})\b/) {
402 :			$year = $1;
403 :			} else {
404 :			# Get the default year, which is this one. Note we must convert it to
405 :			# the four-digit value expected by "timelocal".
406 :			(undef, undef, undef, undef, undef, $year) = localtime();
407 :			$year += 1900;
408 :			}
409 :			$retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410 :			}
411 :	parrello	1.93	}
412 :			# Return the result.
413 :			return $retVal;
414 :			}
415 :	parrello	1.31
416 :	parrello	1.93	=head3 LogErrors
417 :	parrello	1.42
418 :	parrello	1.93	Tracer::LogErrors($fileName);
419 :	parrello	1.31
420 :	parrello	1.93	Route the standard error output to a log file.
421 :	parrello	1.31
422 :	parrello	1.93	=over 4
423 :	parrello	1.31
424 :	parrello	1.93	=item fileName
425 :	parrello	1.31
426 :	parrello	1.93	Name of the file to receive the error output.
427 :	parrello	1.31
428 :	parrello	1.93	=back
429 :	parrello	1.31
430 :	parrello	1.93	=cut
431 :	parrello	1.84
432 :	parrello	1.93	sub LogErrors {
433 :			# Get the file name.
434 :			my ($fileName) = @_;
435 :			# Open the file as the standard error output.
436 :			open STDERR, '>', $fileName;
437 :			}
438 :	parrello	1.84
439 :	parrello	1.93	=head3 Trace
440 :	parrello	1.31
441 :	parrello	1.93	Trace($message);
442 :	parrello	1.31
443 :	parrello	1.93	Write a trace message to the target location specified in L</TSetup>. If there has not been
444 :			any prior call to B<TSetup>.
445 :	parrello	1.31
446 :	parrello	1.93	=over 4
447 :	parrello	1.42
448 :	parrello	1.93	=item message
449 :	parrello	1.42
450 :	parrello	1.93	Message to write.
451 :	parrello	1.42
452 :	parrello	1.93	=back
453 :	parrello	1.72
454 :	parrello	1.93	=cut
455 :	parrello	1.36
456 :	parrello	1.93	sub Trace {
457 :			# Get the parameters.
458 :			my ($message) = @_;
459 :	parrello	1.97	# Strip off any line terminators at the end of the message. We will add
460 :			# new-line stuff ourselves.
461 :			my $stripped = Strip($message);
462 :			# Compute the caller information.
463 :			my ($callPackage, $callFile, $callLine) = caller();
464 :			my $callFileTitle = basename($callFile);
465 :			# Check the caller.
466 :	parrello	1.98	my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467 :	parrello	1.93	# Get the timestamp.
468 :			my $timeStamp = Now();
469 :	parrello	1.97	# Build the prefix.
470 :			my $level = $LevelNames[$LastLevel] \|\| "($LastLevel)";
471 :	parrello	1.98	my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472 :	parrello	1.97	# Format the message.
473 :			my $formatted = "$prefix $stripped";
474 :	parrello	1.93	# Process according to the destination.
475 :			if ($Destination eq "TEXT") {
476 :			# Write the message to the standard output.
477 :			print "$formatted\n";
478 :			} elsif ($Destination eq "ERROR") {
479 :	parrello	1.97	# Write the message to the error output. Here, we want our prefix fields.
480 :	parrello	1.93	print STDERR "$formatted\n";
481 :	parrello	1.97	} elsif ($Destination eq "WARN") {
482 :			# Emit the message to the standard error output. It is presumed that the
483 :	parrello	1.98	# error logger will add its own prefix fields, the notable exception being
484 :			# the caller info.
485 :			print STDERR "$callerInfo$stripped\n";
486 :	parrello	1.93	} elsif ($Destination eq "QUEUE") {
487 :			# Push the message into the queue.
488 :			push @Queue, "$formatted";
489 :			} elsif ($Destination eq "HTML") {
490 :			# Convert the message to HTML and write it to the standard output.
491 :	parrello	1.97	my $escapedMessage = CGI::escapeHTML($stripped);
492 :			print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493 :	parrello	1.93	} elsif ($Destination =~ m/^>>/) {
494 :			# Write the trace message to an output file.
495 :	parrello	1.97	open(TRACING, $Destination) \|\| die "Tracing open for \"$Destination\" failed: $!";
496 :	parrello	1.93	print TRACING "$formatted\n";
497 :			close TRACING;
498 :			# If the Tee flag is on, echo it to the standard output.
499 :			if ($TeeFlag) {
500 :			print "$formatted\n";
501 :			}
502 :			}
503 :			}
504 :	parrello	1.36
505 :	parrello	1.93	=head3 T
506 :	parrello	1.36
507 :	parrello	1.93	my $switch = T($category, $traceLevel);
508 :	parrello	1.36
509 :	parrello	1.93	or
510 :	parrello	1.44
511 :	parrello	1.93	my $switch = T($traceLevel);
512 :	parrello	1.44
513 :	parrello	1.93	Return TRUE if the trace level is at or above a specified value and the specified category
514 :			is active, else FALSE. If no category is specified, the caller's package name is used.
515 :	parrello	1.44
516 :	parrello	1.93	=over 4
517 :	parrello	1.44
518 :	parrello	1.93	=item category
519 :	parrello	1.44
520 :	parrello	1.93	Category to which the message belongs. If not specified, the caller's package name is
521 :			used.
522 :	parrello	1.31
523 :	parrello	1.93	=item traceLevel
524 :	parrello	1.31
525 :	parrello	1.93	Relevant tracing level.
526 :	parrello	1.31
527 :	parrello	1.93	=item RETURN
528 :	parrello	1.31
529 :	parrello	1.93	TRUE if a message at the specified trace level would appear in the trace, else FALSE.
530 :	parrello	1.31
531 :	parrello	1.93	=back
532 :	parrello	1.36
533 :	parrello	1.93	=cut
534 :
535 :			sub T {
536 :			# Declare the return variable.
537 :			my $retVal = 0;
538 :			# Only proceed if tracing is turned on.
539 :			if ($Destination ne "NONE") {
540 :			# Get the parameters.
541 :			my ($category, $traceLevel) = @_;
542 :			if (!defined $traceLevel) {
543 :			# Here we have no category, so we need to get the calling package.
544 :			# The calling package is normally the first parameter. If it is
545 :			# omitted, the first parameter will be the tracelevel. So, the
546 :			# first thing we do is shift the so-called category into the
547 :			# $traceLevel variable where it belongs.
548 :			$traceLevel = $category;
549 :			my ($package, $fileName, $line) = caller;
550 :			# If there is no calling package, we default to "main".
551 :			if (!$package) {
552 :			$category = "main";
553 :			} else {
554 :			my @cats = split /::/, $package;
555 :			$category = $cats[$#cats];
556 :			}
557 :			}
558 :	parrello	1.97	# Save the category name and level.
559 :	parrello	1.93	$LastCategory = $category;
560 :	parrello	1.97	$LastLevel = $traceLevel;
561 :	parrello	1.93	# Convert it to lower case before we hash it.
562 :			$category = lc $category;
563 :	parrello	1.100	# Validate the trace level.
564 :	parrello	1.93	if (ref $traceLevel) {
565 :			Confess("Bad trace level.");
566 :			} elsif (ref $TraceLevel) {
567 :			Confess("Bad trace config.");
568 :			}
569 :	parrello	1.100	# Make the check. Note that level 0 shows even if the category is turned off.
570 :			$retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 \|\| $AllTrace \|\| exists $Categories{$category}));
571 :	parrello	1.93	}
572 :			# Return the computed result.
573 :			return $retVal;
574 :			}
575 :
576 :			=head3 QTrace
577 :
578 :			my $data = QTrace($format);
579 :
580 :			Return the queued trace data in the specified format.
581 :
582 :			=over 4
583 :
584 :			=item format
585 :
586 :			C<html> to format the data as an HTML list, C<text> to format it as straight text.
587 :
588 :			=back
589 :
590 :			=cut
591 :
592 :			sub QTrace {
593 :			# Get the parameter.
594 :			my ($format) = @_;
595 :			# Create the return variable.
596 :			my $retVal = "";
597 :			# Only proceed if there is an actual queue.
598 :			if (@Queue) {
599 :			# Process according to the format.
600 :			if ($format =~ m/^HTML$/i) {
601 :			# Convert the queue into an HTML list.
602 :			$retVal = "<ul>\n";
603 :			for my $line (@Queue) {
604 :			my $escapedLine = CGI::escapeHTML($line);
605 :			$retVal .= "<li>$escapedLine</li>\n";
606 :			}
607 :			$retVal .= "</ul>\n";
608 :			} elsif ($format =~ m/^TEXT$/i) {
609 :			# Convert the queue into a list of text lines.
610 :			$retVal = join("\n", @Queue) . "\n";
611 :			}
612 :			# Clear the queue.
613 :			@Queue = ();
614 :			}
615 :			# Return the formatted list.
616 :			return $retVal;
617 :			}
618 :
619 :			=head3 Confess
620 :
621 :			Confess($message);
622 :
623 :			Trace the call stack and abort the program with the specified message. When used with
624 :			the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625 :			So, for example
626 :
627 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
628 :
629 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
630 :
631 :			=over 4
632 :
633 :			=item message
634 :
635 :			Message to include in the trace.
636 :
637 :			=back
638 :
639 :			=cut
640 :
641 :			sub Confess {
642 :			# Get the parameters.
643 :			my ($message) = @_;
644 :	parrello	1.97	# Set up the category and level.
645 :			$LastCategory = "(confess)";
646 :			$LastLevel = 0;
647 :	parrello	1.93	if (! defined($FIG_Config::no_tool_hdr)) {
648 :			# Here we have a tool header. Display its length so that the user can adjust the line numbers.
649 :			my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650 :			# Only proceed if the tool header file is actually present.
651 :			if (-f $toolHeaderFile) {
652 :	parrello	1.97	my $fh;
653 :			if (open $fh, "<$toolHeaderFile") {
654 :			my @lines = <$fh>;
655 :			Trace("Tool header has " . scalar(@lines) . " lines.");
656 :			}
657 :	parrello	1.93	}
658 :			}
659 :			# Trace the call stack.
660 :			Cluck($message);
661 :			# Abort the program.
662 :			croak(">>> $message");
663 :			}
664 :
665 :	parrello	1.106	=head3 SaveCGI
666 :
667 :			Tracer::SaveCGI($cgi);
668 :
669 :			This method saves the CGI object but does not activate emergency tracing.
670 :			It is used to allow L</Warn> to work in situations where emergency
671 :			tracing is contra-indicated (e.g. the wiki).
672 :
673 :			=over 4
674 :
675 :			=item cgi
676 :
677 :			Active CGI query object.
678 :
679 :			=back
680 :
681 :			=cut
682 :
683 :			sub SaveCGI {
684 :			$SavedCGI = $_[0];
685 :			}
686 :
687 :	parrello	1.99	=head3 Warn
688 :
689 :	parrello	1.106	Warn($message, @options);
690 :	parrello	1.99
691 :			This method traces an important message. If an RSS feed is configured
692 :			(via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693 :			then the message will be echoed to the feed. In general, a tracing
694 :			destination of C<WARN> indicates that the caller is running as a web
695 :			service in a production environment; however, this is not a requirement.
696 :
697 :	parrello	1.103	To force warnings into the RSS feed even when the tracing destination
698 :			is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699 :			configured automatically when L</StandardSetup> is used.
700 :
701 :	parrello	1.99	The L</Cluck> method calls this one for its final message. Since
702 :			L</Confess> calls L</Cluck>, this means that any error which is caught
703 :			and confessed will put something in the feed. This insures that someone
704 :			will be alerted relatively quickly when a failure occurs.
705 :
706 :			=over 4
707 :
708 :			=item message
709 :
710 :			Message to be traced.
711 :
712 :	parrello	1.106	=item options
713 :
714 :			A list containing zero or more options.
715 :
716 :			=back
717 :
718 :			The permissible options are as follows.
719 :
720 :			=over 4
721 :
722 :			=item noStack
723 :
724 :			If specified, then the stack trace is not included in the output.
725 :
726 :	parrello	1.99	=back
727 :
728 :			=cut
729 :
730 :			sub Warn {
731 :			# Get the parameters.
732 :	parrello	1.106	my $message = shift @_;
733 :			my %options = map { $_ => 1 } @_;
734 :	parrello	1.107	# Save $@;
735 :			my $savedError = $@;
736 :	parrello	1.99	# Trace the message.
737 :			Trace($message);
738 :	parrello	1.106	# This will contain the lock handle. If it's defined, it means we need to unlock.
739 :			my $lock;
740 :	parrello	1.103	# Check for feed forcing.
741 :			my $forceFeed = exists $Categories{feed};
742 :	parrello	1.106	# An error here would be disastrous. Note that if debug mode is specified,
743 :			# we do this stuff even in a test environment.
744 :	parrello	1.99	eval {
745 :			# Do we need to put this in the RSS feed?
746 :	parrello	1.103	if ($FIG_Config::error_feed && ($Destination eq 'WARN' \|\| $forceFeed)) {
747 :	parrello	1.99	# Yes. We now need to compute the date, the link, and the title.
748 :			# First, the date, in a very specific format.
749 :			my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
750 :			(tz_local_offset() / 30);
751 :	parrello	1.102	# Environment data goes in here. We start with the date.
752 :			my $environment = "$date. ";
753 :			# If we need to recap the message (because it's too long to be a title), we'll
754 :			# put it in here.
755 :			my $recap;
756 :			# Copy the message and remove excess space.
757 :			my $title = $message;
758 :	parrello	1.101	$title =~ s/\s+/ /gs;
759 :	parrello	1.102	# If it's too long, we have to split it up.
760 :	parrello	1.101	if (length $title > 60) {
761 :	parrello	1.102	# Put the full message in the environment string.
762 :			$recap = $title;
763 :			# Excerpt it as the title.
764 :	parrello	1.101	$title = substr($title, 0, 50) . "...";
765 :			}
766 :	parrello	1.99	# If we have a CGI object, then this is a web error. Otherwise, it's
767 :			# command-line.
768 :			if (defined $SavedCGI) {
769 :	parrello	1.101	# We're in a web service. The environment is the user's IP, and the link
770 :	parrello	1.99	# is the URL that got us here.
771 :			my $key = $ENV{HTTP_X_FORWARDED_FOR} \|\| $ENV{REMOTE_ADDR};
772 :	parrello	1.106	$environment .= "Event Reported at IP address $key process $$.";
773 :			my $url = $SavedCGI->self_url();
774 :	parrello	1.100	# We need the user agent string and (if available) the referrer.
775 :	parrello	1.102	# The referrer will be the link.
776 :	parrello	1.106	$environment .= " User Agent $ENV{HTTP_USER_AGENT}";
777 :	parrello	1.100	if ($ENV{HTTP_REFERER}) {
778 :	parrello	1.102	my $link = $ENV{HTTP_REFERER};
779 :			$environment .= " referred from <a href=\"$link\">$link</a>.";
780 :			} else {
781 :			$environment .= " referrer unknown.";
782 :	parrello	1.100	}
783 :	parrello	1.102	# Close off the sentence with the original link.
784 :	parrello	1.106	$environment .= " URL of event is <a href=\"$url\">$url</a>.";
785 :	parrello	1.99	} else {
786 :			# No CGI object, so we're a command-line tool. Use the tracing
787 :	parrello	1.101	# key and the PID as the user identifier, and add the command.
788 :	parrello	1.99	my $key = EmergencyKey();
789 :	parrello	1.106	$environment .= "Event Reported by $key process $$.";
790 :	parrello	1.104	if ($CommandLine) {
791 :			# We're in a StandardSetup script, so we have the real command line.
792 :			$environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
793 :			} elsif ($ENV{_}) {
794 :			# We're in a BASH script, so the command has been stored in the _ variable.
795 :			$environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
796 :			}
797 :	parrello	1.99	}
798 :			# Build a GUID. We use the current time, the title, and the process ID,
799 :			# then digest the result.
800 :			my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
801 :			# Finally, the description. This is a stack trace plus various environmental stuff.
802 :	parrello	1.106	# The trace is optional.
803 :			my $stackTrace;
804 :			if ($options{noStack}) {
805 :			$stackTrace = "";
806 :			} else {
807 :			my @trace = LongMess();
808 :			# Only proceed if we got something back.
809 :			if (scalar(@trace) > 0) {
810 :			$trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
811 :			$stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
812 :			}
813 :	parrello	1.101	}
814 :	parrello	1.102	# We got the stack trace. Now it's time to put it all together.
815 :			# We have a goofy thing here in that we need to HTML-escape some sections of the description
816 :			# twice. They will be escaped once here, and then once when written by XML::Simple. They are
817 :			# unescaped once when processed by the RSS reader, and stuff in the description is treated as
818 :			# HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
819 :			# our <br>s and <pre>s are used to format the description.
820 :			$recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
821 :			my $description = "$recap$environment $stackTrace";
822 :	parrello	1.99	# Okay, we have all the pieces. Create a hash of the new event.
823 :			my $newItem = { title => $title,
824 :	parrello	1.102	description => $description,
825 :	parrello	1.99	category => $LastCategory,
826 :			pubDate => $date,
827 :			guid => $guid,
828 :	parrello	1.106	};
829 :	parrello	1.99	# We need XML capability for this.
830 :			require XML::Simple;
831 :			# The RSS document goes in here.
832 :			my $rss;
833 :			# Get the name of the RSS file. It's in the FIG temporary directory.
834 :			my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
835 :	parrello	1.106	# Open the config file and lock it.
836 :			$lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
837 :			flock $lock, LOCK_EX;
838 :	parrello	1.99	# Does it exist?
839 :			if (-s $fileName) {
840 :			# Slurp it in.
841 :			$rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
842 :			} else {
843 :			my $size = -s $fileName;
844 :			# Create an empty channel.
845 :			$rss = {
846 :			channel => {
847 :			title => 'NMPDR Warning Feed',
848 :			link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
849 :			description => "Important messages regarding the status of the NMPDR.",
850 :			generator => "NMPDR Trace Facility",
851 :			docs => "http://blogs.law.harvard.edu/tech/rss",
852 :			item => []
853 :			},
854 :			};
855 :			}
856 :			# Get the channel object.
857 :			my $channel = $rss->{channel};
858 :			# Update the last-build date.
859 :			$channel->{lastBuildDate} = $date;
860 :			# Get the item array.
861 :			my $items = $channel->{item};
862 :			# Insure it has only 100 entries.
863 :			while (scalar @{$items} > 100) {
864 :			pop @{$items};
865 :			}
866 :			# Add our new item at the front.
867 :			unshift @{$items}, $newItem;
868 :	parrello	1.102	# Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
869 :			# the requirements for those.
870 :	parrello	1.106	my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
871 :	parrello	1.102	# Here we put in the root and declaration. The problem is that the root has to have the version attribute
872 :			# in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
873 :			$xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
874 :	parrello	1.99	# We don't use Open here because we can't afford an error.
875 :			if (open XMLOUT, ">$fileName") {
876 :			print XMLOUT $xml;
877 :			close XMLOUT;
878 :			}
879 :			}
880 :			};
881 :	parrello	1.103	if ($@) {
882 :			# If the feed failed, we need to know why. The error will be traced, but this method will not be involved
883 :			# (which is a good thing).
884 :	parrello	1.102	my $error = $@;
885 :	parrello	1.103	Trace("Feed Error: $error") if T(Feed => 0);
886 :	parrello	1.102	}
887 :	parrello	1.106	# Be sure to unlock.
888 :			if ($lock) {
889 :			flock $lock, LOCK_UN;
890 :			undef $lock;
891 :			}
892 :	parrello	1.107	# Restore the error message.
893 :			$@ = $savedError;
894 :	parrello	1.99	}
895 :
896 :	parrello	1.106
897 :
898 :
899 :	parrello	1.93	=head3 Assert
900 :
901 :			Assert($condition1, $condition2, ... $conditionN);
902 :
903 :			Return TRUE if all the conditions are true. This method can be used in conjunction with
904 :			the OR operator and the L</Confess> method as a debugging assert.
905 :			So, for example
906 :
907 :			Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum.");
908 :
909 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
910 :
911 :			=cut
912 :			sub Assert {
913 :			my $retVal = 1;
914 :			LOOP: for my $condition (@_) {
915 :			if (! $condition) {
916 :			$retVal = 0;
917 :			last LOOP;
918 :			}
919 :			}
920 :			return $retVal;
921 :			}
922 :
923 :			=head3 Cluck
924 :
925 :			Cluck($message);
926 :
927 :			Trace the call stack. Note that for best results, you should qualify the call with a
928 :			trace condition. For example,
929 :
930 :			Cluck("Starting record parse.") if T(3);
931 :
932 :			will only trace the stack if the trace level for the package is 3 or more.
933 :
934 :			=over 4
935 :
936 :			=item message
937 :
938 :			Message to include in the trace.
939 :
940 :			=back
941 :
942 :			=cut
943 :
944 :			sub Cluck {
945 :			# Get the parameters.
946 :			my ($message) = @_;
947 :			# Trace what's happening.
948 :			Trace("Stack trace for event: $message");
949 :	parrello	1.99	# Get the stack trace.
950 :			my @trace = LongMess();
951 :			# Convert the trace to a series of messages.
952 :			for my $line (@trace) {
953 :			# Replace the tab at the beginning with spaces.
954 :			$line =~ s/^\t/ /;
955 :			# Trace the line.
956 :			Trace($line);
957 :			}
958 :			# Issue a warning. This displays the event message and inserts it into the RSS error feed.
959 :			Warn($message);
960 :			}
961 :
962 :			=head3 LongMess
963 :
964 :			my @lines = Tracer::LongMess();
965 :
966 :			Return a stack trace with all tracing methods removed. The return will be in the form of a list
967 :			of message strings.
968 :
969 :			=cut
970 :
971 :			sub LongMess {
972 :			# Declare the return variable.
973 :			my @retVal = ();
974 :			my $confession = longmess("");
975 :	parrello	1.93	for my $line (split /\s*\n/, $confession) {
976 :	parrello	1.99	unless ($line =~ /Tracer\.pm/) {
977 :			# Here we have a line worth keeping. Push it onto the result list.
978 :			push @retVal, $line;
979 :	parrello	1.97	}
980 :	parrello	1.93	}
981 :	parrello	1.99	# Return the result.
982 :			return @retVal;
983 :	parrello	1.93	}
984 :
985 :			=head3 ETracing
986 :
987 :			ETracing($parameter);
988 :
989 :			Set up emergency tracing. Emergency tracing is tracing that is turned
990 :			on automatically for any program that calls this method. The emergency
991 :			tracing parameters are stored in a a file identified by a tracing key.
992 :			If this method is called with a CGI object, then the tracing key is
993 :			taken from a cookie. If it is called with no parameters, then the tracing
994 :			key is taken from an environment variable. If it is called with a string,
995 :			the tracing key is that string.
996 :
997 :			=over 4
998 :
999 :			=item parameter
1000 :
1001 :			A parameter from which the tracing key is computed. If it is a scalar,
1002 :			that scalar is used as the tracing key. If it is a CGI object, the
1003 :			tracing key is taken from the C<IP> cookie. If it is omitted, the
1004 :			tracing key is taken from the C<TRACING> environment variable. If it
1005 :			is a CGI object and emergency tracing is not on, the C<Trace> and
1006 :			C<TF> parameters will be used to determine the type of tracing.
1007 :
1008 :			=back
1009 :
1010 :			=cut
1011 :
1012 :			sub ETracing {
1013 :			# Get the parameter.
1014 :			my ($parameter) = @_;
1015 :			# Check for CGI mode.
1016 :	parrello	1.99	if (defined $parameter && ref $parameter eq 'CGI') {
1017 :			$SavedCGI = $parameter;
1018 :			} else {
1019 :			$SavedCGI = undef;
1020 :			}
1021 :	parrello	1.93	# Default to no tracing except errors.
1022 :			my ($tracing, $dest) = ("0", "WARN");
1023 :			# Check for emergency tracing.
1024 :			my $tkey = EmergencyKey($parameter);
1025 :			my $emergencyFile = EmergencyFileName($tkey);
1026 :			if (-e $emergencyFile) {
1027 :			# We have the file. Read in the data.
1028 :			my @tracing = GetFile($emergencyFile);
1029 :			# Pull off the time limit.
1030 :			my $expire = shift @tracing;
1031 :			# Convert it to seconds.
1032 :			$expire *= 3600;
1033 :			# Check the file data.
1034 :			my $stat = stat($emergencyFile);
1035 :			my ($now) = gettimeofday;
1036 :			if ($now - $stat->mtime > $expire) {
1037 :			# Delete the expired file.
1038 :			unlink $emergencyFile;
1039 :	parrello	1.44	} else {
1040 :	parrello	1.93	# Emergency tracing is on. Pull off the destination and
1041 :			# the trace level;
1042 :			$dest = shift @tracing;
1043 :			my $level = shift @tracing;
1044 :			# Convert the destination to a real tracing destination.
1045 :			# temp directory.
1046 :			$dest = EmergencyTracingDest($tkey, $dest);
1047 :			# Insure Tracer is specified.
1048 :			my %moduleHash = map { $_ => 1 } @tracing;
1049 :			$moduleHash{Tracer} = 1;
1050 :			# Set the trace parameter.
1051 :			$tracing = join(" ", $level, sort keys %moduleHash);
1052 :	parrello	1.44	}
1053 :	parrello	1.99	} elsif (defined $SavedCGI) {
1054 :	parrello	1.93	# There's no emergency tracing, but we have a CGI object, so check
1055 :			# for tracing from the form parameters.
1056 :	parrello	1.99	if ($SavedCGI->param('Trace')) {
1057 :	parrello	1.93	# Here the user has requested tracing via a form.
1058 :	parrello	1.99	$dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1059 :			$tracing = $SavedCGI->param('Trace') . " Tracer";
1060 :	parrello	1.36	}
1061 :			}
1062 :	parrello	1.93	# Setup the tracing we've determined from all the stuff above.
1063 :			TSetup($tracing, $dest);
1064 :	parrello	1.94	# Check to see if we're a web script.
1065 :	parrello	1.99	if (defined $SavedCGI) {
1066 :	parrello	1.94	# Yes we are. Trace the form and environment data.
1067 :	parrello	1.99	TraceParms($SavedCGI);
1068 :	parrello	1.94	# Check for RAW mode. In raw mode, we print a fake header so that we see everything
1069 :			# emitted by the script in its raw form.
1070 :			if (T(Raw => 3)) {
1071 :			print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1072 :			}
1073 :	parrello	1.83	}
1074 :	parrello	1.31	}
1075 :
1076 :	parrello	1.93	=head3 EmergencyFileName
1077 :
1078 :			my $fileName = Tracer::EmergencyFileName($tkey);
1079 :
1080 :			Return the emergency tracing file name. This is the file that specifies
1081 :			the tracing information.
1082 :
1083 :			=over 4
1084 :
1085 :			=item tkey
1086 :
1087 :			Tracing key for the current program.
1088 :	parrello	1.11
1089 :	parrello	1.93	=item RETURN
1090 :	parrello	1.11
1091 :	parrello	1.93	Returns the name of the file to contain the emergency tracing information.
1092 :	parrello	1.11
1093 :	parrello	1.93	=back
1094 :	parrello	1.11
1095 :			=cut
1096 :
1097 :	parrello	1.93	sub EmergencyFileName {
1098 :			# Get the parameters.
1099 :			my ($tkey) = @_;
1100 :			# Compute the emergency tracing file name.
1101 :			return "$FIG_Config::temp/Emergency$tkey.txt";
1102 :	olson	1.1	}
1103 :
1104 :	parrello	1.93	=head3 EmergencyFileTarget
1105 :	parrello	1.10
1106 :	parrello	1.93	my $fileName = Tracer::EmergencyFileTarget($tkey);
1107 :	parrello	1.10
1108 :	parrello	1.93	Return the emergency tracing target file name. This is the file that receives
1109 :			the tracing output for file-based tracing.
1110 :	parrello	1.10
1111 :	parrello	1.93	=over 4
1112 :	parrello	1.10
1113 :	parrello	1.93	=item tkey
1114 :	parrello	1.10
1115 :	parrello	1.93	Tracing key for the current program.
1116 :	parrello	1.10
1117 :	parrello	1.93	=item RETURN
1118 :	parrello	1.10
1119 :	parrello	1.93	Returns the name of the file to contain the trace output.
1120 :	parrello	1.10
1121 :	parrello	1.93	=back
1122 :	parrello	1.10
1123 :	parrello	1.93	=cut
1124 :	parrello	1.10
1125 :	parrello	1.93	sub EmergencyFileTarget {
1126 :			# Get the parameters.
1127 :			my ($tkey) = @_;
1128 :			# Compute the emergency tracing file name.
1129 :			return "$FIG_Config::temp/trace$tkey.log";
1130 :			}
1131 :	parrello	1.10
1132 :	parrello	1.93	=head3 EmergencyTracingDest
1133 :	parrello	1.10
1134 :	parrello	1.93	my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1135 :	parrello	1.10
1136 :	parrello	1.93	This method converts an emergency tracing destination to a real
1137 :			tracing destination. The main difference is that if the
1138 :			destination is C<FILE> or C<APPEND>, we convert it to file
1139 :			output. If the destination is C<DUAL>, we convert it to file
1140 :			and standard output.
1141 :	parrello	1.10
1142 :			=over 4
1143 :
1144 :	parrello	1.93	=item tkey
1145 :	parrello	1.10
1146 :	parrello	1.93	Tracing key for this environment.
1147 :	parrello	1.10
1148 :	parrello	1.93	=item myDest
1149 :	parrello	1.10
1150 :	parrello	1.93	Destination from the emergency tracing file.
1151 :	parrello	1.10
1152 :			=item RETURN
1153 :
1154 :	parrello	1.93	Returns a destination that can be passed into L</TSetup>.
1155 :	parrello	1.10
1156 :			=back
1157 :
1158 :			=cut
1159 :
1160 :	parrello	1.93	sub EmergencyTracingDest {
1161 :	parrello	1.12	# Get the parameters.
1162 :	parrello	1.93	my ($tkey, $myDest) = @_;
1163 :			# Declare the return variable.
1164 :			my $retVal = $myDest;
1165 :			# Process according to the destination value.
1166 :			if ($myDest eq 'FILE') {
1167 :			$retVal = ">" . EmergencyFileTarget($tkey);
1168 :			} elsif ($myDest eq 'APPEND') {
1169 :			$retVal = ">>" . EmergencyFileTarget($tkey);
1170 :			} elsif ($myDest eq 'DUAL') {
1171 :			$retVal = "+>" . EmergencyFileTarget($tkey);
1172 :	parrello	1.97	} elsif ($myDest eq 'WARN') {
1173 :			$retVal = "WARN";
1174 :	parrello	1.12	}
1175 :	parrello	1.93	# Return the result.
1176 :			return $retVal;
1177 :	parrello	1.10	}
1178 :
1179 :	parrello	1.93	=head3 Emergency
1180 :
1181 :			Emergency($key, $hours, $dest, $level, @modules);
1182 :
1183 :			Turn on emergency tracing. This method is normally invoked over the web from
1184 :			a debugging console, but it can also be called by the C<trace.pl> script.
1185 :			The caller specifies the duration of the emergency in hours, the desired tracing
1186 :			destination, the trace level, and a list of the trace modules to activate.
1187 :			For the length of the duration, when a program in an environment with the
1188 :			specified tracing key active invokes a Sprout CGI script, tracing will be
1189 :			turned on automatically. See L</TSetup> for more about tracing setup and
1190 :			L</ETracing> for more about emergency tracing.
1191 :
1192 :			=over 4
1193 :	parrello	1.11
1194 :	parrello	1.93	=item tkey
1195 :	parrello	1.11
1196 :	parrello	1.93	The tracing key. This is used to identify the control file and the trace file.
1197 :	parrello	1.11
1198 :	parrello	1.93	=item hours
1199 :	parrello	1.11
1200 :	parrello	1.93	Number of hours to keep emergency tracing alive.
1201 :	parrello	1.11
1202 :	parrello	1.93	=item dest
1203 :	parrello	1.11
1204 :	parrello	1.93	Tracing destination. If no path information is specified for a file
1205 :			destination, it is put in the FIG temporary directory.
1206 :	parrello	1.11
1207 :	parrello	1.93	=item level
1208 :	parrello	1.11
1209 :	parrello	1.93	Tracing level. A higher level means more trace messages.
1210 :	parrello	1.11
1211 :	parrello	1.93	=item modules
1212 :	parrello	1.11
1213 :	parrello	1.93	A list of the tracing modules to activate.
1214 :	parrello	1.11
1215 :			=back
1216 :
1217 :			=cut
1218 :	parrello	1.93
1219 :			sub Emergency {
1220 :	parrello	1.11	# Get the parameters.
1221 :	parrello	1.93	my ($tkey, $hours, $dest, $level, @modules) = @_;
1222 :			# Create the emergency file.
1223 :			my $specFile = EmergencyFileName($tkey);
1224 :			my $outHandle = Open(undef, ">$specFile");
1225 :			print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1226 :	parrello	1.11	}
1227 :
1228 :	parrello	1.93	=head3 EmergencyKey
1229 :
1230 :			my $tkey = EmergencyKey($parameter);
1231 :
1232 :			Return the Key to be used for emergency tracing. This could be an IP address,
1233 :			a session ID, or a user name, depending on the environment.
1234 :	parrello	1.11
1235 :	parrello	1.93	=over 4
1236 :	parrello	1.11
1237 :	parrello	1.93	=item parameter
1238 :	parrello	1.11
1239 :	parrello	1.93	Parameter defining the method for finding the tracing key. If it is a scalar,
1240 :			then it is presumed to be the tracing key itself. If it is a CGI object, then
1241 :			the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1242 :			taken from the C<TRACING> environment variable.
1243 :	parrello	1.29
1244 :	parrello	1.93	=item RETURN
1245 :	parrello	1.11
1246 :	parrello	1.93	Returns the key to be used for labels in emergency tracing.
1247 :	parrello	1.11
1248 :	parrello	1.93	=back
1249 :	parrello	1.11
1250 :	parrello	1.93	=cut
1251 :	parrello	1.29
1252 :	parrello	1.93	sub EmergencyKey {
1253 :			# Get the parameters.
1254 :			my ($parameter) = @_;
1255 :			# Declare the return variable.
1256 :			my $retVal;
1257 :			# Determine the parameter type.
1258 :			if (! defined $parameter) {
1259 :	parrello	1.99	# Here we're supposed to check the environment. If that fails, we
1260 :			# get the effective login ID.
1261 :			$retVal = $ENV{TRACING} \|\| scalar getpwuid($<);
1262 :	parrello	1.93	} else {
1263 :			my $ptype = ref $parameter;
1264 :			if ($ptype eq 'CGI') {
1265 :			# Here we were invoked from a web page. Look for a cookie.
1266 :			$retVal = $parameter->cookie('IP');
1267 :			} elsif (! $ptype) {
1268 :			# Here the key was passed in.
1269 :			$retVal = $parameter;
1270 :			}
1271 :			}
1272 :			# If no luck finding a key, use the PID.
1273 :			if (! defined $retVal) {
1274 :			$retVal = $$;
1275 :			}
1276 :			# Return the result.
1277 :			return $retVal;
1278 :			}
1279 :	parrello	1.11
1280 :
1281 :	parrello	1.93	=head3 TraceParms
1282 :	parrello	1.11
1283 :	parrello	1.93	Tracer::TraceParms($cgi);
1284 :	parrello	1.11
1285 :	parrello	1.93	Trace the CGI parameters at trace level CGI => 3 and the environment variables
1286 :	parrello	1.94	at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1287 :	parrello	1.11
1288 :	parrello	1.93	=over 4
1289 :	parrello	1.11
1290 :	parrello	1.93	=item cgi
1291 :	parrello	1.31
1292 :	parrello	1.93	CGI query object containing the parameters to trace.
1293 :	parrello	1.31
1294 :	parrello	1.11	=back
1295 :
1296 :			=cut
1297 :	parrello	1.93
1298 :			sub TraceParms {
1299 :	parrello	1.11	# Get the parameters.
1300 :	parrello	1.93	my ($cgi) = @_;
1301 :	parrello	1.94	if (T(CGI => 2)) {
1302 :			# Here we trace the GET-style URL for the script.
1303 :	parrello	1.97	Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1304 :	parrello	1.94	}
1305 :	parrello	1.93	if (T(CGI => 3)) {
1306 :			# Here we want to trace the parameter data.
1307 :			my @names = $cgi->param;
1308 :			for my $parmName (sort @names) {
1309 :			# Note we skip the Trace parameters, which are for our use only.
1310 :			if ($parmName ne 'Trace' && $parmName ne 'TF') {
1311 :			my @values = $cgi->param($parmName);
1312 :	parrello	1.97	Trace("[CGI] $parmName = " . join(", ", @values));
1313 :	parrello	1.93	}
1314 :			}
1315 :			# Display the request method.
1316 :			my $method = $cgi->request_method();
1317 :			Trace("Method: $method");
1318 :			}
1319 :			if (T(CGI => 4)) {
1320 :			# Here we want the environment data too.
1321 :			for my $envName (sort keys %ENV) {
1322 :	parrello	1.97	Trace("[ENV] $envName = $ENV{$envName}");
1323 :	parrello	1.12	}
1324 :			}
1325 :	parrello	1.11	}
1326 :
1327 :	parrello	1.94	=head3 TraceImages
1328 :
1329 :			Tracer::TraceImages($htmlString);
1330 :
1331 :			Trace information about all of an html document's images. The tracing
1332 :			will be for type "IMG" at level 3. The image's source string
1333 :			will be displayed. This is generally either the URL of the image or
1334 :			raw data for the image itself. If the source is too long, only the first 300
1335 :			characters will be shown at trace level 3. The entire source will be shown,
1336 :			however, at trace level 4. This method is not very smart, and might catch
1337 :			Javascript code, but it is still useful when debugging the arcane
1338 :			behavior of images in multiple browser environments.
1339 :
1340 :			=over 4
1341 :
1342 :			=item htmlString
1343 :
1344 :			HTML text for an outgoing web page.
1345 :
1346 :			=back
1347 :
1348 :			=cut
1349 :
1350 :			sub TraceImages {
1351 :			# Only proceed if we're at the proper trace level.
1352 :			if (T(IMG => 3)) {
1353 :			# For performance reasons we're manipulating $_[0] instead of retrieving the string
1354 :			# into a variable called "$htmlString". This is because we expect html strings to be
1355 :			# long, and don't want to copy them any more than we have to.
1356 :			Trace(length($_[0]) . " characters in web page.");
1357 :			# Loop through the HTML, culling image tags.
1358 :			while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1359 :			# Extract the source string and determine whether or not it's too long.
1360 :			my $srcString = $1;
1361 :			my $pos = pos($_[0]) - length($srcString);
1362 :			my $excess = length($srcString) - 300;
1363 :			# We'll put the display string in here.
1364 :			my $srcDisplay = $srcString;
1365 :			# If it's a data string, split it at the comma.
1366 :			$srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1367 :			# If there's no excess or we're at trace level 4, we're done. At level 3 with
1368 :			# a long string, however, we only show the first 300 characters.
1369 :			if ($excess > 0 && ! T(IMG => 4)) {
1370 :			$srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1371 :			}
1372 :			# Output the trace message.
1373 :			Trace("Image tag at position $pos:\n$srcDisplay");
1374 :			}
1375 :			}
1376 :			}
1377 :
1378 :	parrello	1.93	=head2 Command-Line Utility Methods
1379 :	olson	1.1
1380 :	parrello	1.93	=head3 SendSMS
1381 :	olson	1.1
1382 :	parrello	1.93	my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1383 :	olson	1.1
1384 :	parrello	1.93	Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1385 :			user name, password, and API ID for the relevant account in the hash reference variable
1386 :			I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1387 :			example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1388 :			is C<2561022>, then the FIG_Config file must contain
1389 :	olson	1.1
1390 :	parrello	1.93	$phone = { user => 'BruceTheHumanPet',
1391 :			password => 'silly',
1392 :			api_id => '2561022' };
1393 :	olson	1.1
1394 :	parrello	1.93	The original purpose of this method was to insure Bruce would be notified immediately when the
1395 :			Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1396 :			when you call this method.
1397 :	olson	1.1
1398 :	parrello	1.93	The message ID will be returned if successful, and C<undef> if an error occurs.
1399 :	parrello	1.74
1400 :	parrello	1.93	=over 4
1401 :	parrello	1.74
1402 :	parrello	1.93	=item phoneNumber
1403 :	parrello	1.74
1404 :	parrello	1.93	Phone number to receive the message, in international format. A United States phone number
1405 :			would be prefixed by "1". A British phone number would be prefixed by "44".
1406 :	parrello	1.74
1407 :	parrello	1.93	=item msg
1408 :	parrello	1.74
1409 :	parrello	1.93	Message to send to the specified phone.
1410 :	parrello	1.74
1411 :			=item RETURN
1412 :
1413 :	parrello	1.93	Returns the message ID if successful, and C<undef> if the message could not be sent.
1414 :	parrello	1.74
1415 :	parrello	1.78	=back
1416 :
1417 :	parrello	1.74	=cut
1418 :
1419 :	parrello	1.93	sub SendSMS {
1420 :	parrello	1.74	# Get the parameters.
1421 :	parrello	1.93	my ($phoneNumber, $msg) = @_;
1422 :			# Declare the return variable. If we do not change it, C<undef> will be returned.
1423 :	parrello	1.74	my $retVal;
1424 :	parrello	1.93	# Only proceed if we have phone support.
1425 :			if (! defined $FIG_Config::phone) {
1426 :			Trace("Phone support not present in FIG_Config.") if T(1);
1427 :			} else {
1428 :			# Get the phone data.
1429 :			my $parms = $FIG_Config::phone;
1430 :			# Get the Clickatell URL.
1431 :			my $url = "http://api.clickatell.com/http/";
1432 :			# Create the user agent.
1433 :			my $ua = LWP::UserAgent->new;
1434 :			# Request a Clickatell session.
1435 :			my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1436 :			password => $parms->{password},
1437 :			api_id => $parms->{api_id},
1438 :			to => $phoneNumber,
1439 :			text => $msg});
1440 :			# Check for an error.
1441 :			if (! $resp->is_success) {
1442 :			Trace("Alert failed.") if T(1);
1443 :			} else {
1444 :			# Get the message ID.
1445 :			my $rstring = $resp->content;
1446 :			if ($rstring =~ /^ID:\s+(.*)$/) {
1447 :			$retVal = $1;
1448 :			} else {
1449 :			Trace("Phone attempt failed with $rstring") if T(1);
1450 :			}
1451 :			}
1452 :	parrello	1.74	}
1453 :			# Return the result.
1454 :			return $retVal;
1455 :			}
1456 :
1457 :	parrello	1.93	=head3 StandardSetup
1458 :	olson	1.1
1459 :	parrello	1.93	my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1460 :	olson	1.1
1461 :	parrello	1.93	This method performs standard command-line parsing and tracing setup. The return
1462 :			values are a hash of the command-line options and a list of the positional
1463 :			parameters. Tracing is automatically set up and the command-line options are
1464 :			validated.
1465 :	olson	1.1
1466 :	parrello	1.93	This is a complex method that does a lot of grunt work. The parameters can
1467 :			be more easily understood, however, once they are examined individually.
1468 :	olson	1.1
1469 :	parrello	1.93	The I<categories> parameter is the most obtuse. It is a reference to a list of
1470 :			special-purpose tracing categories. Most tracing categories are PERL package
1471 :			names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1472 :			B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1473 :	olson	1.1
1474 :	parrello	1.93	["Sprout", "SproutLoad", "ERDB"]
1475 :	olson	1.1
1476 :	parrello	1.93	This would cause trace messages in the specified three packages to appear in
1477 :			the output. There are two special tracing categories that are automatically
1478 :			handled by this method. In other words, if you used L</TSetup> you would need
1479 :			to include these categories manually, but if you use this method they are turned
1480 :			on automatically.
1481 :	parrello	1.5
1482 :			=over 4
1483 :
1484 :	parrello	1.93	=item SQL
1485 :	parrello	1.5
1486 :	parrello	1.93	Traces SQL commands and activity.
1487 :	parrello	1.5
1488 :	parrello	1.93	=item Tracer
1489 :	parrello	1.5
1490 :	parrello	1.93	Traces error messages and call stacks.
1491 :	parrello	1.5
1492 :			=back
1493 :
1494 :	parrello	1.93	C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1495 :			The trace level is specified using the C<-trace> command-line option. For example,
1496 :			the following command line for C<TransactFeatures> turns on SQL tracing and runs
1497 :			all tracing at level 3.
1498 :	parrello	1.5
1499 :	parrello	1.93	TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1500 :	parrello	1.5
1501 :	parrello	1.93	Standard tracing is output to the standard output and echoed to the file
1502 :			C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1503 :			process ID. You can also specify the C<user> parameter to put a user ID
1504 :			instead of a process ID in the trace file name. So, for example
1505 :	olson	1.1
1506 :	parrello	1.93	The default trace level is 2. To get all messages, specify a trace level of 4.
1507 :			For a genome-by-genome update, use 3.
1508 :	olson	1.1
1509 :	parrello	1.93	TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1510 :	olson	1.1
1511 :	parrello	1.93	would send the trace output to C<traceBruce.log> in the temporary directory.
1512 :	olson	1.1
1513 :	parrello	1.93	The I<options> parameter is a reference to a hash containing the command-line
1514 :			options, their default values, and an explanation of what they mean. Command-line
1515 :			options may be in the form of switches or keywords. In the case of a switch, the
1516 :			option value is 1 if it is specified and 0 if it is not specified. In the case
1517 :			of a keyword, the value is separated from the option name by an equal sign. You
1518 :			can see this last in the command-line example above.
1519 :	olson	1.1
1520 :	parrello	1.93	You can specify a different default trace level by setting C<$options->{trace}>
1521 :			prior to calling this method.
1522 :	olson	1.1
1523 :	parrello	1.93	An example at this point would help. Consider, for example, the command-line utility
1524 :			C<TransactFeatures>. It accepts a list of positional parameters plus the options
1525 :			C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1526 :			the following code.
1527 :	olson	1.1
1528 :	parrello	1.93	my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1529 :			{ safe => [0, "use database transactions"],
1530 :			noAlias => [0, "do not expect aliases in CHANGE transactions"],
1531 :			start => [' ', "start with this genome"],
1532 :			tblFiles => [0, "output TBL files containing the corrected IDs"] },
1533 :			"<command> <transactionDirectory> <IDfile>",
1534 :			@ARGV);
1535 :	olson	1.1
1536 :
1537 :	parrello	1.93	The call to C<ParseCommand> specifies the default values for the options and
1538 :			stores the actual options in a hash that is returned as C<$options>. The
1539 :			positional parameters are returned in C<@parameters>.
1540 :	olson	1.1
1541 :	parrello	1.93	The following is a sample command line for C<TransactFeatures>.
1542 :	olson	1.1
1543 :	parrello	1.93	TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1544 :	olson	1.1
1545 :	parrello	1.93	Single and double hyphens are equivalent. So, you could also code the
1546 :			above command as
1547 :	olson	1.1
1548 :	parrello	1.93	TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1549 :	olson	1.1
1550 :	parrello	1.93	In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1551 :			parameters, and would find themselves in I<@parameters> after executing the
1552 :			above code fragment. The tracing would be set to level 2, and the categories
1553 :			would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1554 :			and C<DocUtils> was included because it came in within the first parameter
1555 :			to this method. The I<$options> hash would be
1556 :	olson	1.1
1557 :	parrello	1.93	{ trace => 2, sql => 0, safe => 0,
1558 :			noAlias => 1, start => ' ', tblFiles => 0 }
1559 :	olson	1.1
1560 :	parrello	1.93	Use of C<StandardSetup> in this way provides a simple way of performing
1561 :			standard tracing setup and command-line parsing. Note that the caller is
1562 :			not even aware of the command-line switches C<-trace> and C<-sql>, which
1563 :			are used by this method to control the tracing. If additional tracing features
1564 :			need to be added in the future, they can be processed by this method without
1565 :			upsetting the command-line utilities.
1566 :	olson	1.1
1567 :	parrello	1.93	If the C<background> option is specified on the command line, then the
1568 :			standard and error outputs will be directed to files in the temporary
1569 :			directory, using the same suffix as the trace file. So, if the command
1570 :			line specified
1571 :	olson	1.1
1572 :	parrello	1.93	-user=Bruce -background
1573 :	olson	1.1
1574 :	parrello	1.93	then the trace output would go to C<traceBruce.log>, the standard output to
1575 :			C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1576 :			simplify starting a command in the background.
1577 :	olson	1.1
1578 :	parrello	1.93	The user name is also used as the tracing key for L</Emergency Tracing>.
1579 :			Specifying a value of C<E> for the trace level causes emergency tracing to
1580 :			be used instead of custom tracing. If the user name is not specified,
1581 :			the tracing key is taken from the C<Tracing> environment variable. If there
1582 :	parrello	1.103	is no value for that variable, the tracing key will be computed from the active
1583 :			login ID.
1584 :
1585 :			Since the default situation in StandardSetup is to trace to the standard
1586 :			output, errors that occur in command-line scripts will not generate
1587 :			RSS events. To force the events, use the C<warn> option.
1588 :
1589 :			TransactFeatures -background -warn register ../xacts IDs.tbl
1590 :	olson	1.1
1591 :	parrello	1.93	Finally, if the special option C<-help> is specified, the option
1592 :			names will be traced at level 0 and the program will exit without processing.
1593 :			This provides a limited help capability. For example, if the user enters
1594 :	olson	1.1
1595 :	parrello	1.93	TransactFeatures -help
1596 :	olson	1.1
1597 :	parrello	1.93	he would see the following output.
1598 :	olson	1.1
1599 :	parrello	1.93	TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1600 :			-trace tracing level (default E)
1601 :			-sql trace SQL commands
1602 :			-safe use database transactions
1603 :			-noAlias do not expect aliases in CHANGE transactions
1604 :			-start start with this genome
1605 :			-tblFiles output TBL files containing the corrected IDs
1606 :	olson	1.1
1607 :	parrello	1.93	The caller has the option of modifying the tracing scheme by placing a value
1608 :			for C<trace> in the incoming options hash. The default value can be overridden,
1609 :			or the tracing to the standard output can be turned off by suffixing a minus
1610 :			sign to the trace level. So, for example,
1611 :	olson	1.1
1612 :	parrello	1.93	{ trace => [0, "tracing level (default 0)"],
1613 :			...
1614 :	olson	1.1
1615 :	parrello	1.93	would set the default trace level to 0 instead of E, while
1616 :	olson	1.1
1617 :	parrello	1.93	{ trace => ["2-", "tracing level (default 2)"],
1618 :			...
1619 :	olson	1.1
1620 :	parrello	1.93	would set the default to 2, but trace only to the log file, not to the
1621 :			standard output.
1622 :	olson	1.1
1623 :	parrello	1.93	The parameters to this method are as follows.
1624 :	olson	1.1
1625 :	parrello	1.93	=over 4
1626 :	olson	1.1
1627 :	parrello	1.93	=item categories
1628 :	parrello	1.2
1629 :	parrello	1.93	Reference to a list of tracing category names. These should be names of
1630 :			packages whose internal workings will need to be debugged to get the
1631 :			command working.
1632 :	olson	1.1
1633 :	parrello	1.93	=item options
1634 :	olson	1.1
1635 :	parrello	1.93	Reference to a hash containing the legal options for the current command mapped
1636 :			to their default values and descriptions. The user can override the defaults
1637 :			by specifying the options as command-line switches prefixed by a hyphen.
1638 :			Tracing-related options may be added to this hash. If the C<-h> option is
1639 :			specified on the command line, the option descriptions will be used to
1640 :			explain the options. To turn off tracing to the standard output, add a
1641 :			minus sign to the value for C<trace> (see above).
1642 :	olson	1.1
1643 :	parrello	1.93	=item parmHelp
1644 :	olson	1.1
1645 :	parrello	1.93	A string that vaguely describes the positional parameters. This is used
1646 :			if the user specifies the C<-h> option.
1647 :	olson	1.1
1648 :	parrello	1.93	=item argv
1649 :	olson	1.1
1650 :	parrello	1.93	List of command line parameters, including the option switches, which must
1651 :			precede the positional parameters and be prefixed by a hyphen.
1652 :	olson	1.1
1653 :			=item RETURN
1654 :
1655 :	parrello	1.93	Returns a list. The first element of the list is the reference to a hash that
1656 :			maps the command-line option switches to their values. These will either be the
1657 :			default values or overrides specified on the command line. The remaining
1658 :			elements of the list are the position parameters, in order.
1659 :	olson	1.1
1660 :			=back
1661 :
1662 :			=cut
1663 :
1664 :	parrello	1.93	sub StandardSetup {
1665 :			# Get the parameters.
1666 :			my ($categories, $options, $parmHelp, @argv) = @_;
1667 :			# Get the default tracing key.
1668 :			my $tkey = EmergencyKey();
1669 :	parrello	1.104	# Save the command line.
1670 :			$CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1671 :	parrello	1.93	# Add the tracing options.
1672 :			if (! exists $options->{trace}) {
1673 :			$options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1674 :			}
1675 :			$options->{sql} = [0, "turn on SQL tracing"];
1676 :			$options->{help} = [0, "display command-line options"];
1677 :			$options->{user} = [$tkey, "tracing key"];
1678 :			$options->{background} = [0, "spool standard and error output"];
1679 :	parrello	1.103	$options->{warn} = [0, "send errors to RSS feed"];
1680 :	parrello	1.93	# Create a parsing hash from the options hash. The parsing hash
1681 :			# contains the default values rather than the default value
1682 :			# and the description. While we're at it, we'll memorize the
1683 :			# length of the longest option name.
1684 :			my $longestName = 0;
1685 :			my %parseOptions = ();
1686 :			for my $key (keys %{$options}) {
1687 :			if (length $key > $longestName) {
1688 :			$longestName = length $key;
1689 :			}
1690 :			$parseOptions{$key} = $options->{$key}->[0];
1691 :			}
1692 :			# Parse the command line.
1693 :			my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1694 :			# Get the logfile suffix.
1695 :			my $suffix = $retOptions->{user};
1696 :			# Check for background mode.
1697 :			if ($retOptions->{background}) {
1698 :			my $outFileName = "$FIG_Config::temp/out$suffix.log";
1699 :			my $errFileName = "$FIG_Config::temp/err$suffix.log";
1700 :			open STDOUT, ">$outFileName";
1701 :			open STDERR, ">$errFileName";
1702 :			# Check for phone support. If we have phone support and a phone number,
1703 :			# we want to turn it on.
1704 :			if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1705 :			$retOptions->{phone} = $ENV{PHONE};
1706 :			}
1707 :			}
1708 :			# Now we want to set up tracing. First, we need to know if the user
1709 :			# wants emergency tracing.
1710 :			if ($retOptions->{trace} eq 'E') {
1711 :			ETracing($retOptions->{user});
1712 :			} else {
1713 :			# Here the tracing is controlled from the command line.
1714 :			my @cats = @{$categories};
1715 :			if ($retOptions->{sql}) {
1716 :			push @cats, "SQL";
1717 :			}
1718 :	parrello	1.103	if ($retOptions->{warn}) {
1719 :			push @cats, "Feed";
1720 :			}
1721 :	parrello	1.93	# Add the default categories.
1722 :			push @cats, "Tracer";
1723 :			# Next, we create the category string by joining the categories.
1724 :			my $cats = join(" ", @cats);
1725 :			# Check to determine whether or not the caller wants to turn off tracing
1726 :			# to the standard output.
1727 :			my $traceLevel = $retOptions->{trace};
1728 :			my $textOKFlag = 1;
1729 :			if ($traceLevel =~ /^(.)-/) {
1730 :			$traceLevel = $1;
1731 :			$textOKFlag = 0;
1732 :			}
1733 :			# Now we set up the trace mode.
1734 :			my $traceMode;
1735 :			# Verify that we can open a file in the FIG temporary directory.
1736 :			my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1737 :			if (open TESTTRACE, ">$traceFileName") {
1738 :			# Here we can trace to a file.
1739 :			$traceMode = ">$traceFileName";
1740 :			if ($textOKFlag) {
1741 :			# Echo to standard output if the text-OK flag is set.
1742 :			$traceMode = "+$traceMode";
1743 :			}
1744 :			# Close the test file.
1745 :			close TESTTRACE;
1746 :			} else {
1747 :	parrello	1.98	# Here we can't trace to a file. Complain about this.
1748 :			warn "Could not open trace file $traceFileName: $!\n";
1749 :			# We trace to the standard output if it's
1750 :			# okay, and the error log otherwise.
1751 :	parrello	1.93	if ($textOKFlag) {
1752 :			$traceMode = "TEXT";
1753 :	parrello	1.12	} else {
1754 :	parrello	1.93	$traceMode = "WARN";
1755 :	parrello	1.12	}
1756 :			}
1757 :	parrello	1.93	# Now set up the tracing.
1758 :			TSetup("$traceLevel $cats", $traceMode);
1759 :			}
1760 :			# Check for the "help" option. If it is specified, dump the command-line
1761 :			# options and exit the program.
1762 :			if ($retOptions->{help}) {
1763 :			$0 =~ m#[/\\](\w+)(\.pl)?$#i;
1764 :			print "$1 [options] $parmHelp\n";
1765 :			for my $key (sort keys %{$options}) {
1766 :			my $name = Pad($key, $longestName, 0, ' ');
1767 :			my $desc = $options->{$key}->[1];
1768 :			if ($options->{$key}->[0]) {
1769 :			$desc .= " (default " . $options->{$key}->[0] . ")";
1770 :			}
1771 :			print " $name $desc\n";
1772 :	parrello	1.36	}
1773 :	parrello	1.93	exit(0);
1774 :			}
1775 :			# Trace the options, if applicable.
1776 :			if (T(3)) {
1777 :			my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1778 :			Trace("Selected options: " . join(", ", sort @parms) . ".");
1779 :	parrello	1.3	}
1780 :	parrello	1.93	# Return the parsed parameters.
1781 :			return ($retOptions, @retParameters);
1782 :	olson	1.1	}
1783 :
1784 :	parrello	1.93	=head3 ReadOptions
1785 :	olson	1.1
1786 :	parrello	1.93	my %options = Tracer::ReadOptions($fileName);
1787 :	olson	1.1
1788 :	parrello	1.93	Read a set of options from a file. Each option is encoded in a line of text that has the
1789 :			format
1790 :	olson	1.1
1791 :	parrello	1.93	I<optionName>C<=>I<optionValue>C<; >I<comment>
1792 :	olson	1.1
1793 :	parrello	1.93	The option name must consist entirely of letters, digits, and the punctuation characters
1794 :			C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1795 :			character is a semi-colon will be ignored. The return hash will map each option name to
1796 :			the corresponding option value.
1797 :	olson	1.1
1798 :			=over 4
1799 :
1800 :	parrello	1.93	=item fileName
1801 :	olson	1.1
1802 :	parrello	1.93	Name of the file containing the option data.
1803 :	olson	1.1
1804 :			=item RETURN
1805 :
1806 :	parrello	1.93	Returns a hash mapping the option names specified in the file to their corresponding option
1807 :			value.
1808 :	olson	1.1
1809 :			=back
1810 :
1811 :			=cut
1812 :
1813 :	parrello	1.93	sub ReadOptions {
1814 :	parrello	1.12	# Get the parameters.
1815 :	parrello	1.93	my ($fileName) = @_;
1816 :			# Open the file.
1817 :			(open CONFIGFILE, "<$fileName") \|\| Confess("Could not open option file $fileName.");
1818 :			# Count the number of records read.
1819 :			my ($records, $comments) = 0;
1820 :			# Create the return hash.
1821 :			my %retVal = ();
1822 :			# Loop through the file, accumulating key-value pairs.
1823 :			while (my $line = <CONFIGFILE>) {
1824 :			# Denote we've read a line.
1825 :			$records++;
1826 :			# Determine the line type.
1827 :			if ($line =~ /^\s*[\n\r]/) {
1828 :			# A blank line is a comment.
1829 :			$comments++;
1830 :			} elsif ($line =~ /^\s([A-Za-z0-9_\.]+)=([^;]);/) {
1831 :			# Here we have an option assignment.
1832 :			retVal{$1} = $2;
1833 :			} elsif ($line =~ /^\s*;/) {
1834 :			# Here we have a text comment.
1835 :			$comments++;
1836 :	parrello	1.12	} else {
1837 :	parrello	1.93	# Here we have an invalid line.
1838 :			Trace("Invalid option statement in record $records.") if T(0);
1839 :	parrello	1.12	}
1840 :			}
1841 :	parrello	1.93	# Return the hash created.
1842 :			return %retVal;
1843 :	olson	1.1	}
1844 :
1845 :	parrello	1.93	=head3 GetOptions
1846 :	parrello	1.9
1847 :	parrello	1.93	Tracer::GetOptions(\%defaults, \%options);
1848 :	parrello	1.9
1849 :	parrello	1.93	Merge a specified set of options into a table of defaults. This method takes two hash references
1850 :			as input and uses the data from the second to update the first. If the second does not exist,
1851 :			there will be no effect. An error will be thrown if one of the entries in the second hash does not
1852 :			exist in the first.
1853 :	parrello	1.9
1854 :	parrello	1.93	Consider the following example.
1855 :	parrello	1.9
1856 :	parrello	1.93	my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1857 :	parrello	1.9
1858 :	parrello	1.93	In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1859 :			B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1860 :			B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1861 :			the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1862 :			will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1863 :	parrello	1.9
1864 :	parrello	1.93	{databaseType => 'Oracle'}
1865 :	parrello	1.9
1866 :	parrello	1.93	an error will occur because the B<databaseType> option does not exist.
1867 :	parrello	1.9
1868 :	parrello	1.93	=over 4
1869 :	parrello	1.9
1870 :	parrello	1.93	=item defaults
1871 :	parrello	1.9
1872 :	parrello	1.93	Table of default option values.
1873 :	parrello	1.9
1874 :	parrello	1.93	=item options
1875 :	olson	1.1
1876 :	parrello	1.93	Table of overrides, if any.
1877 :	olson	1.1
1878 :			=item RETURN
1879 :
1880 :	parrello	1.93	Returns a reference to the default table passed in as the first parameter.
1881 :	olson	1.1
1882 :			=back
1883 :
1884 :			=cut
1885 :
1886 :	parrello	1.93	sub GetOptions {
1887 :			# Get the parameters.
1888 :			my ($defaults, $options) = @_;
1889 :			# Check for overrides.
1890 :			if ($options) {
1891 :			# Loop through the overrides.
1892 :			while (my ($option, $setting) = each %{$options}) {
1893 :			# Insure this override exists.
1894 :			if (!exists $defaults->{$option}) {
1895 :			croak "Unrecognized option $option encountered.";
1896 :	parrello	1.12	} else {
1897 :	parrello	1.93	# Apply the override.
1898 :			$defaults->{$option} = $setting;
1899 :	parrello	1.12	}
1900 :			}
1901 :			}
1902 :	parrello	1.93	# Return the merged table.
1903 :			return $defaults;
1904 :	olson	1.1	}
1905 :
1906 :	parrello	1.93	=head3 MergeOptions
1907 :	olson	1.1
1908 :	parrello	1.93	Tracer::MergeOptions(\%table, \%defaults);
1909 :	olson	1.1
1910 :	parrello	1.93	Merge default values into a hash table. This method looks at the key-value pairs in the
1911 :			second (default) hash, and if a matching key is not found in the first hash, the default
1912 :			pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1913 :			checking and no return value.
1914 :	olson	1.1
1915 :			=over 4
1916 :
1917 :	parrello	1.93	=item table
1918 :	olson	1.1
1919 :	parrello	1.93	Hash table to be updated with the default values.
1920 :	olson	1.1
1921 :	parrello	1.93	=item defaults
1922 :	olson	1.1
1923 :	parrello	1.93	Default values to be merged into the first hash table if they are not already present.
1924 :	olson	1.1
1925 :			=back
1926 :
1927 :			=cut
1928 :
1929 :	parrello	1.93	sub MergeOptions {
1930 :			# Get the parameters.
1931 :			my ($table, $defaults) = @_;
1932 :			# Loop through the defaults.
1933 :			while (my ($key, $value) = each %{$defaults}) {
1934 :			if (!exists $table->{$key}) {
1935 :			$table->{$key} = $value;
1936 :			}
1937 :	parrello	1.12	}
1938 :	olson	1.1	}
1939 :
1940 :	parrello	1.93	=head3 ParseCommand
1941 :	olson	1.1
1942 :	parrello	1.93	my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1943 :	olson	1.1
1944 :	parrello	1.93	Parse a command line consisting of a list of parameters. The initial parameters may be option
1945 :			specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1946 :			off and merged into a table of default options. The remainder of the command line is
1947 :			returned as a list of positional arguments. For example, consider the following invocation.
1948 :	olson	1.1
1949 :	parrello	1.93	my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1950 :	olson	1.1
1951 :	parrello	1.93	In this case, the list @words will be treated as a command line and there are two options available,
1952 :			B<errors> and B<logFile>. If @words has the following format
1953 :	olson	1.1
1954 :	parrello	1.93	-logFile=error.log apple orange rutabaga
1955 :	olson	1.1
1956 :	parrello	1.93	then at the end of the invocation, C<$options> will be
1957 :	olson	1.1
1958 :	parrello	1.93	{ errors => 0, logFile => 'error.log' }
1959 :	olson	1.1
1960 :	parrello	1.93	and C<@arguments> will contain
1961 :	olson	1.1
1962 :	parrello	1.93	apple orange rutabaga
1963 :	olson	1.1
1964 :	parrello	1.93	The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1965 :			support for quote characters. Options can be specified with single or double hyphens.
1966 :	parrello	1.54
1967 :			=over 4
1968 :
1969 :	parrello	1.93	=item optionTable
1970 :	parrello	1.54
1971 :	parrello	1.93	Table of default options.
1972 :	parrello	1.54
1973 :	parrello	1.93	=item inputList
1974 :	parrello	1.54
1975 :	parrello	1.93	List of words on the command line.
1976 :	parrello	1.54
1977 :			=item RETURN
1978 :
1979 :	parrello	1.93	Returns a reference to the option table and a list of the positional arguments.
1980 :	parrello	1.54
1981 :			=back
1982 :
1983 :			=cut
1984 :
1985 :	parrello	1.93	sub ParseCommand {
1986 :	parrello	1.54	# Get the parameters.
1987 :	parrello	1.93	my ($optionTable, @inputList) = @_;
1988 :			# Process any options in the input list.
1989 :			my %overrides = ();
1990 :			while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1991 :			# Get the current option.
1992 :			my $arg = shift @inputList;
1993 :			# Pull out the option name.
1994 :			$arg =~ /^--?([^=]*)/g;
1995 :			my $name = $1;
1996 :			# Check for an option value.
1997 :			if ($arg =~ /\G=(.*)$/g) {
1998 :			# Here we have a value for the option.
1999 :			$overrides{$name} = UnEscape($1);
2000 :			} else {
2001 :			# Here there is no value, so we use 1.
2002 :			$overrides{$name} = 1;
2003 :			}
2004 :			}
2005 :			# Merge the options into the defaults.
2006 :			GetOptions($optionTable, \%overrides);
2007 :			# Translate the remaining parameters.
2008 :			my @retVal = ();
2009 :			for my $inputParm (@inputList) {
2010 :			push @retVal, UnEscape($inputParm);
2011 :	parrello	1.54	}
2012 :	parrello	1.93	# Return the results.
2013 :			return ($optionTable, @retVal);
2014 :	parrello	1.54	}
2015 :
2016 :	parrello	1.93
2017 :			=head2 File Utility Methods
2018 :
2019 :	olson	1.1	=head3 GetFile
2020 :
2021 :	parrello	1.92	my @fileContents = Tracer::GetFile($fileName);
2022 :	olson	1.1
2023 :	parrello	1.35	or
2024 :
2025 :	parrello	1.92	my $fileContents = Tracer::GetFile($fileName);
2026 :	parrello	1.35
2027 :			Return the entire contents of a file. In list context, line-ends are removed and
2028 :			each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2029 :	olson	1.1
2030 :			=over 4
2031 :
2032 :			=item fileName
2033 :
2034 :			Name of the file to read.
2035 :
2036 :			=item RETURN
2037 :
2038 :	parrello	1.6	In a list context, returns the entire file as a list with the line terminators removed.
2039 :	parrello	1.39	In a scalar context, returns the entire file as a string. If an error occurs opening
2040 :			the file, an empty list will be returned.
2041 :	olson	1.1
2042 :			=back
2043 :
2044 :			=cut
2045 :
2046 :			sub GetFile {
2047 :	parrello	1.12	# Get the parameters.
2048 :			my ($fileName) = @_;
2049 :			# Declare the return variable.
2050 :			my @retVal = ();
2051 :			# Open the file for input.
2052 :	parrello	1.60	my $handle = Open(undef, "<$fileName");
2053 :			# Read the whole file into the return variable, stripping off any terminator
2054 :			# characters.
2055 :			my $lineCount = 0;
2056 :			while (my $line = <$handle>) {
2057 :			$lineCount++;
2058 :			$line = Strip($line);
2059 :			push @retVal, $line;
2060 :			}
2061 :			# Close it.
2062 :			close $handle;
2063 :			my $actualLines = @retVal;
2064 :	parrello	1.77	Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2065 :	parrello	1.12	# Return the file's contents in the desired format.
2066 :	parrello	1.9	if (wantarray) {
2067 :	parrello	1.12	return @retVal;
2068 :	parrello	1.6	} else {
2069 :			return join "\n", @retVal;
2070 :			}
2071 :	olson	1.1	}
2072 :
2073 :	parrello	1.60	=head3 PutFile
2074 :
2075 :	parrello	1.92	Tracer::PutFile($fileName, \@lines);
2076 :	parrello	1.60
2077 :			Write out a file from a list of lines of text.
2078 :
2079 :			=over 4
2080 :
2081 :			=item fileName
2082 :
2083 :			Name of the output file.
2084 :
2085 :			=item lines
2086 :
2087 :			Reference to a list of text lines. The lines will be written to the file in order, with trailing
2088 :	parrello	1.66	new-line characters. Alternatively, may be a string, in which case the string will be written without
2089 :			modification.
2090 :	parrello	1.60
2091 :			=back
2092 :
2093 :			=cut
2094 :
2095 :			sub PutFile {
2096 :			# Get the parameters.
2097 :			my ($fileName, $lines) = @_;
2098 :			# Open the output file.
2099 :			my $handle = Open(undef, ">$fileName");
2100 :	parrello	1.77	# Count the lines written.
2101 :	parrello	1.66	if (ref $lines ne 'ARRAY') {
2102 :			# Here we have a scalar, so we write it raw.
2103 :			print $handle $lines;
2104 :	parrello	1.77	Trace("Scalar put to file $fileName.") if T(File => 3);
2105 :	parrello	1.66	} else {
2106 :			# Write the lines one at a time.
2107 :	parrello	1.77	my $count = 0;
2108 :	parrello	1.66	for my $line (@{$lines}) {
2109 :			print $handle "$line\n";
2110 :	parrello	1.77	$count++;
2111 :	parrello	1.66	}
2112 :	parrello	1.77	Trace("$count lines put to file $fileName.") if T(File => 3);
2113 :	parrello	1.60	}
2114 :			# Close the output file.
2115 :			close $handle;
2116 :			}
2117 :
2118 :	parrello	1.93	=head3 ParseRecord
2119 :	olson	1.1
2120 :	parrello	1.93	my @fields = Tracer::ParseRecord($line);
2121 :	olson	1.1
2122 :	parrello	1.93	Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2123 :			and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2124 :			These will automatically be converted.
2125 :	olson	1.1
2126 :			=over 4
2127 :
2128 :	parrello	1.93	=item line
2129 :
2130 :			Line of data containing the tab-delimited fields.
2131 :
2132 :			=item RETURN
2133 :	olson	1.1
2134 :	parrello	1.93	Returns a list of the fields found in the data line.
2135 :	olson	1.1
2136 :			=back
2137 :
2138 :			=cut
2139 :
2140 :	parrello	1.93	sub ParseRecord {
2141 :	parrello	1.12	# Get the parameter.
2142 :	parrello	1.93	my ($line) = @_;
2143 :			# Remove the trailing new-line, if any.
2144 :			chomp $line;
2145 :			# Split the line read into pieces using the tab character.
2146 :			my @retVal = split /\t/, $line;
2147 :			# Trim and fix the escapes in each piece.
2148 :			for my $value (@retVal) {
2149 :			# Trim leading whitespace.
2150 :			$value =~ s/^\s+//;
2151 :			# Trim trailing whitespace.
2152 :			$value =~ s/\s+$//;
2153 :			# Delete the carriage returns.
2154 :			$value =~ s/\r//g;
2155 :			# Convert the escapes into their real values.
2156 :			$value =~ s/\\t/"\t"/ge;
2157 :			$value =~ s/\\n/"\n"/ge;
2158 :			}
2159 :			# Return the result.
2160 :			return @retVal;
2161 :			}
2162 :
2163 :			=head3 Merge
2164 :
2165 :			my @mergedList = Tracer::Merge(@inputList);
2166 :
2167 :			Sort a list of strings and remove duplicates.
2168 :
2169 :			=over 4
2170 :
2171 :			=item inputList
2172 :
2173 :			List of scalars to sort and merge.
2174 :
2175 :			=item RETURN
2176 :
2177 :			Returns a list containing the same elements sorted in ascending order with duplicates
2178 :			removed.
2179 :
2180 :			=back
2181 :
2182 :			=cut
2183 :
2184 :			sub Merge {
2185 :			# Get the input list in sort order.
2186 :			my @inputList = sort @_;
2187 :			# Only proceed if the list has at least two elements.
2188 :			if (@inputList > 1) {
2189 :			# Now we want to move through the list splicing out duplicates.
2190 :			my $i = 0;
2191 :			while ($i < @inputList) {
2192 :			# Get the current entry.
2193 :			my $thisEntry = $inputList[$i];
2194 :			# Find out how many elements duplicate the current entry.
2195 :			my $j = $i + 1;
2196 :			my $dup1 = $i + 1;
2197 :			while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2198 :			# If the number is nonzero, splice out the duplicates found.
2199 :			if ($j > $dup1) {
2200 :			splice @inputList, $dup1, $j - $dup1;
2201 :	parrello	1.14	}
2202 :	parrello	1.93	# Now the element at position $dup1 is different from the element before it
2203 :			# at position $i. We push $i forward one position and start again.
2204 :			$i++;
2205 :	parrello	1.14	}
2206 :	parrello	1.12	}
2207 :	parrello	1.93	# Return the merged list.
2208 :			return @inputList;
2209 :	olson	1.1	}
2210 :
2211 :	parrello	1.93	=head3 Open
2212 :	olson	1.1
2213 :	parrello	1.93	my $handle = Open($fileHandle, $fileSpec, $message);
2214 :	olson	1.1
2215 :	parrello	1.93	Open a file.
2216 :	olson	1.1
2217 :	parrello	1.93	The I<$fileSpec> is essentially the second argument of the PERL C<open>
2218 :			function. The mode is specified using Unix-like shell information. So, for
2219 :			example,
2220 :	olson	1.1
2221 :	parrello	1.93	Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2222 :	olson	1.1
2223 :	parrello	1.93	would open for output appended to the specified file, and
2224 :	olson	1.1
2225 :	parrello	1.93	Open(\*DATASTREAM, "\| sort -u >$outputFile", "Could not open $outputFile.");
2226 :	olson	1.1
2227 :	parrello	1.93	would open a pipe that sorts the records written and removes duplicates. Note
2228 :			the use of file handle syntax in the Open call. To use anonymous file handles,
2229 :			code as follows.
2230 :	olson	1.1
2231 :	parrello	1.93	my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2232 :	olson	1.1
2233 :	parrello	1.93	The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2234 :			the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2235 :			failed open will throw an exception and the third parameter will be used to construct
2236 :			an error message. If the parameter is omitted, a standard message is constructed
2237 :			using the file spec.
2238 :	olson	1.1
2239 :	parrello	1.93	Could not open "/usr/spool/news/twitlog"
2240 :	olson	1.1
2241 :	parrello	1.93	Note that the mode characters are automatically cleaned from the file name.
2242 :			The actual error message from the file system will be captured and appended to the
2243 :			message in any case.
2244 :	parrello	1.6
2245 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": file not found.
2246 :	parrello	1.6
2247 :	parrello	1.93	In some versions of PERL the only error message we get is a number, which
2248 :			corresponds to the C++ C<errno> value.
2249 :	parrello	1.6
2250 :	parrello	1.93	Could not open "/usr/spool/news/twitlog": 6.
2251 :	parrello	1.6
2252 :	parrello	1.93	=over 4
2253 :	parrello	1.6
2254 :	parrello	1.93	=item fileHandle
2255 :	parrello	1.6
2256 :	parrello	1.93	File handle. If this parameter is C<undef>, a file handle will be generated
2257 :			and returned as the value of this method.
2258 :	olson	1.1
2259 :	parrello	1.93	=item fileSpec
2260 :	olson	1.1
2261 :	parrello	1.93	File name and mode, as per the PERL C<open> function.
2262 :	olson	1.1
2263 :	parrello	1.93	=item message (optional)
2264 :	olson	1.1
2265 :	parrello	1.93	Error message to use if the open fails. If omitted, a standard error message
2266 :			will be generated. In either case, the error information from the file system
2267 :			is appended to the message. To specify a conditional open that does not throw
2268 :			an error if it fails, use C<0>.
2269 :	olson	1.1
2270 :	parrello	1.93	=item RETURN
2271 :	olson	1.1
2272 :	parrello	1.93	Returns the name of the file handle assigned to the file, or C<undef> if the
2273 :			open failed.
2274 :	olson	1.1
2275 :			=back
2276 :
2277 :			=cut
2278 :
2279 :	parrello	1.93	sub Open {
2280 :	parrello	1.12	# Get the parameters.
2281 :	parrello	1.93	my ($fileHandle, $fileSpec, $message) = @_;
2282 :			# Attempt to open the file.
2283 :			my $rv = open $fileHandle, $fileSpec;
2284 :			# If the open failed, generate an error message.
2285 :			if (! $rv) {
2286 :			# Save the system error message.
2287 :			my $sysMessage = $!;
2288 :			# See if we need a default message.
2289 :			if (!$message) {
2290 :			# Clean any obvious mode characters and leading spaces from the
2291 :			# filename.
2292 :			my ($fileName) = FindNamePart($fileSpec);
2293 :			$message = "Could not open \"$fileName\"";
2294 :			}
2295 :			# Terminate with an error using the supplied message and the
2296 :			# error message from the file system.
2297 :			Confess("$message: $!");
2298 :	parrello	1.12	}
2299 :	parrello	1.93	# Return the file handle.
2300 :			return $fileHandle;
2301 :	olson	1.1	}
2302 :
2303 :	parrello	1.93	=head3 FindNamePart
2304 :
2305 :			my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2306 :
2307 :			Extract the portion of a file specification that contains the file name.
2308 :
2309 :			A file specification is the string passed to an C<open> call. It specifies the file
2310 :			mode and name. In a truly complex situation, it can specify a pipe sequence. This
2311 :			method assumes that the file name is whatever follows the first angle bracket
2312 :			sequence. So, for example, in the following strings the file name is
2313 :			C</usr/fig/myfile.txt>.
2314 :	parrello	1.5
2315 :	parrello	1.93	>>/usr/fig/myfile.txt
2316 :			</usr/fig/myfile.txt
2317 :			\| sort -u > /usr/fig/myfile.txt
2318 :	parrello	1.5
2319 :	parrello	1.93	If the method cannot find a file name using its normal methods, it will return the
2320 :			whole incoming string.
2321 :	parrello	1.5
2322 :			=over 4
2323 :
2324 :	parrello	1.93	=item fileSpec
2325 :	parrello	1.5
2326 :	parrello	1.93	File specification string from which the file name is to be extracted.
2327 :	parrello	1.5
2328 :			=item RETURN
2329 :
2330 :	parrello	1.93	Returns a three-element list. The first element contains the file name portion of
2331 :			the specified string, or the whole string if a file name cannot be found via normal
2332 :			methods. The second element contains the start position of the file name portion and
2333 :			the third element contains the length.
2334 :	parrello	1.5
2335 :			=back
2336 :
2337 :			=cut
2338 :	parrello	1.93	#: Return Type $;
2339 :			sub FindNamePart {
2340 :			# Get the parameters.
2341 :			my ($fileSpec) = @_;
2342 :			# Default to the whole input string.
2343 :			my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2344 :			# Parse out the file name if we can.
2345 :			if ($fileSpec =~ m/(<\|>>?)(.+?)(\s*)$/) {
2346 :			$retVal = $2;
2347 :			$len = length $retVal;
2348 :			$pos = (length $fileSpec) - (length $3) - $len;
2349 :	parrello	1.12	}
2350 :	parrello	1.93	# Return the result.
2351 :			return ($retVal, $pos, $len);
2352 :	parrello	1.5	}
2353 :
2354 :	parrello	1.93	=head3 OpenDir
2355 :	parrello	1.5
2356 :	parrello	1.93	my @files = OpenDir($dirName, $filtered, $flag);
2357 :	parrello	1.5
2358 :	parrello	1.93	Open a directory and return all the file names. This function essentially performs
2359 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2360 :			set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2361 :			or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2362 :			filtered out of the return list. If the directory does not open and I<$flag> is not
2363 :			set, an exception is thrown. So, for example,
2364 :	parrello	1.5
2365 :	parrello	1.93	my @files = OpenDir("/Volumes/fig/contigs", 1);
2366 :	parrello	1.5
2367 :	parrello	1.93	is effectively the same as
2368 :	parrello	1.5
2369 :	parrello	1.93	opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
2370 :			my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2371 :	parrello	1.5
2372 :	parrello	1.93	Similarly, the following code
2373 :	parrello	1.5
2374 :	parrello	1.93	my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2375 :	parrello	1.5
2376 :	parrello	1.93	Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2377 :			automatically returns an empty list if the directory fails to open.
2378 :	parrello	1.5
2379 :	parrello	1.93	=over 4
2380 :	parrello	1.5
2381 :	parrello	1.93	=item dirName
2382 :	parrello	1.5
2383 :	parrello	1.93	Name of the directory to open.
2384 :	parrello	1.5
2385 :	parrello	1.93	=item filtered
2386 :	parrello	1.5
2387 :	parrello	1.93	TRUE if files whose names begin with a period (C<.>) should be automatically removed
2388 :			from the list, else FALSE.
2389 :	parrello	1.5
2390 :	parrello	1.93	=item flag
2391 :	parrello	1.5
2392 :	parrello	1.93	TRUE if a failure to open is okay, else FALSE
2393 :	parrello	1.5
2394 :	parrello	1.93	=back
2395 :	parrello	1.5
2396 :	parrello	1.93	=cut
2397 :			#: Return Type @;
2398 :			sub OpenDir {
2399 :			# Get the parameters.
2400 :			my ($dirName, $filtered, $flag) = @_;
2401 :			# Declare the return variable.
2402 :			my @retVal = ();
2403 :			# Open the directory.
2404 :			if (opendir(my $dirHandle, $dirName)) {
2405 :			# The directory opened successfully. Get the appropriate list according to the
2406 :			# strictures of the filter parameter.
2407 :			if ($filtered) {
2408 :			@retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2409 :			} else {
2410 :			@retVal = readdir $dirHandle;
2411 :			}
2412 :			} elsif (! $flag) {
2413 :			# Here the directory would not open and it's considered an error.
2414 :			Confess("Could not open directory $dirName.");
2415 :			}
2416 :			# Return the result.
2417 :			return @retVal;
2418 :			}
2419 :	parrello	1.5
2420 :
2421 :	parrello	1.93	=head3 Insure
2422 :	parrello	1.5
2423 :	parrello	1.93	Insure($dirName, $chmod);
2424 :	parrello	1.5
2425 :	parrello	1.93	Insure a directory is present.
2426 :	parrello	1.5
2427 :	parrello	1.93	=over 4
2428 :	parrello	1.5
2429 :	parrello	1.93	=item dirName
2430 :	olson	1.1
2431 :	parrello	1.93	Name of the directory to check. If it does not exist, it will be created.
2432 :	parrello	1.7
2433 :	parrello	1.93	=item chmod (optional)
2434 :	parrello	1.7
2435 :	parrello	1.93	Security privileges to be given to the directory if it is created.
2436 :	parrello	1.7
2437 :	parrello	1.93	=back
2438 :	parrello	1.7
2439 :			=cut
2440 :
2441 :	parrello	1.93	sub Insure {
2442 :			my ($dirName, $chmod) = @_;
2443 :			if (! -d $dirName) {
2444 :			Trace("Creating $dirName directory.") if T(2);
2445 :			eval {
2446 :			mkpath $dirName;
2447 :			# If we have permissions specified, set them here.
2448 :			if (defined($chmod)) {
2449 :			chmod $chmod, $dirName;
2450 :			}
2451 :			};
2452 :			if ($@) {
2453 :			Confess("Error creating $dirName: $@");
2454 :			}
2455 :	parrello	1.12	}
2456 :	parrello	1.9	}
2457 :
2458 :	parrello	1.93	=head3 ChDir
2459 :	parrello	1.9
2460 :	parrello	1.93	ChDir($dirName);
2461 :	parrello	1.9
2462 :	parrello	1.93	Change to the specified directory.
2463 :	parrello	1.9
2464 :			=over 4
2465 :
2466 :	parrello	1.93	=item dirName
2467 :	parrello	1.9
2468 :	parrello	1.93	Name of the directory to which we want to change.
2469 :	parrello	1.9
2470 :			=back
2471 :
2472 :			=cut
2473 :
2474 :	parrello	1.93	sub ChDir {
2475 :			my ($dirName) = @_;
2476 :			if (! -d $dirName) {
2477 :			Confess("Cannot change to directory $dirName: no such directory.");
2478 :			} else {
2479 :			Trace("Changing to directory $dirName.") if T(File => 4);
2480 :			my $okFlag = chdir $dirName;
2481 :			if (! $okFlag) {
2482 :			Confess("Error switching to directory $dirName.");
2483 :			}
2484 :			}
2485 :	parrello	1.9	}
2486 :
2487 :	parrello	1.93	=head3 SetPermissions
2488 :
2489 :			Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2490 :	parrello	1.9
2491 :	parrello	1.93	Set the permissions for a directory and all the files and folders inside it.
2492 :			In addition, the group ownership will be changed to the specified value.
2493 :	parrello	1.9
2494 :	parrello	1.93	This method is more vulnerable than most to permission and compatability
2495 :			problems, so it does internal error recovery.
2496 :	parrello	1.9
2497 :			=over 4
2498 :
2499 :	parrello	1.93	=item dirName
2500 :
2501 :			Name of the directory to process.
2502 :
2503 :			=item group
2504 :	parrello	1.9
2505 :	parrello	1.93	Name of the group to be assigned.
2506 :	parrello	1.9
2507 :	parrello	1.93	=item mask
2508 :	parrello	1.9
2509 :	parrello	1.93	Permission mask. Bits that are C<1> in this mask will be ORed into the
2510 :			permission bits of any file or directory that does not already have them
2511 :			set to 1.
2512 :	parrello	1.9
2513 :	parrello	1.93	=item otherMasks
2514 :	parrello	1.9
2515 :	parrello	1.93	Map of search patterns to permission masks. If a directory name matches
2516 :			one of the patterns, that directory and all its members and subdirectories
2517 :			will be assigned the new pattern. For example, the following would
2518 :			assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2519 :	parrello	1.9
2520 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2521 :	parrello	1.9
2522 :	parrello	1.93	The list is ordered, so the following would use 0777 for C<tmp1> and
2523 :			0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2524 :	parrello	1.22
2525 :	parrello	1.93	Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2526 :			'^tmp' => 0666);
2527 :	parrello	1.9
2528 :	parrello	1.93	Note that the pattern matches are all case-insensitive, and only directory
2529 :			names are matched, not file names.
2530 :	parrello	1.9
2531 :			=back
2532 :
2533 :			=cut
2534 :
2535 :	parrello	1.93	sub SetPermissions {
2536 :	parrello	1.12	# Get the parameters.
2537 :	parrello	1.93	my ($dirName, $group, $mask, @otherMasks) = @_;
2538 :			# Set up for error recovery.
2539 :			eval {
2540 :			# Switch to the specified directory.
2541 :			ChDir($dirName);
2542 :			# Get the group ID.
2543 :			my $gid = getgrnam($group);
2544 :			# Get the mask for tracing.
2545 :			my $traceMask = sprintf("%04o", $mask) . "($mask)";
2546 :			Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2547 :			my $fixCount = 0;
2548 :			my $lookCount = 0;
2549 :			# @dirs will be a stack of directories to be processed.
2550 :			my @dirs = (getcwd());
2551 :			while (scalar(@dirs) > 0) {
2552 :			# Get the current directory.
2553 :			my $dir = pop @dirs;
2554 :			# Check for a match to one of the specified directory names. To do
2555 :			# that, we need to pull the individual part of the name off of the
2556 :			# whole path.
2557 :			my $simpleName = $dir;
2558 :			if ($dir =~ m!/([^/]+)$!) {
2559 :			$simpleName = $1;
2560 :			}
2561 :			Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2562 :			# Search for a match.
2563 :			my $match = 0;
2564 :			my $i;
2565 :			for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2566 :			my $pattern = $otherMasks[$i];
2567 :			if ($simpleName =~ /$pattern/i) {
2568 :			$match = 1;
2569 :			}
2570 :			}
2571 :			# Check for a match. Note we use $i-1 because the loop added 2
2572 :			# before terminating due to the match.
2573 :			if ($match && $otherMasks[$i-1] != $mask) {
2574 :			# This directory matches one of the incoming patterns, and it's
2575 :			# a different mask, so we process it recursively with that mask.
2576 :			SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2577 :			} else {
2578 :			# Here we can process normally. Get all of the non-hidden members.
2579 :			my @submems = OpenDir($dir, 1);
2580 :			for my $submem (@submems) {
2581 :			# Get the full name.
2582 :			my $thisMem = "$dir/$submem";
2583 :			Trace("Checking member $thisMem.") if T(4);
2584 :			$lookCount++;
2585 :			if ($lookCount % 1000 == 0) {
2586 :			Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2587 :			}
2588 :			# Fix the group.
2589 :			chown -1, $gid, $thisMem;
2590 :			# Insure this member is not a symlink.
2591 :			if (! -l $thisMem) {
2592 :			# Get its info.
2593 :			my $fileInfo = stat $thisMem;
2594 :			# Only proceed if we got the info. Otherwise, it's a hard link
2595 :			# and we want to skip it anyway.
2596 :			if ($fileInfo) {
2597 :			my $fileMode = $fileInfo->mode;
2598 :			if (($fileMode & $mask) != $mask) {
2599 :			# Fix this member.
2600 :			$fileMode \|= $mask;
2601 :			chmod $fileMode, $thisMem;
2602 :			$fixCount++;
2603 :			}
2604 :			# If it's a subdirectory, stack it.
2605 :			if (-d $thisMem) {
2606 :			push @dirs, $thisMem;
2607 :			}
2608 :			}
2609 :			}
2610 :			}
2611 :			}
2612 :	parrello	1.12	}
2613 :	parrello	1.93	Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2614 :			};
2615 :			# Check for an error.
2616 :			if ($@) {
2617 :			Confess("SetPermissions error: $@");
2618 :	parrello	1.12	}
2619 :	parrello	1.7	}
2620 :
2621 :	parrello	1.93	=head3 GetLine
2622 :	parrello	1.29
2623 :	parrello	1.93	my @data = Tracer::GetLine($handle);
2624 :	parrello	1.15
2625 :	parrello	1.93	Read a line of data from a tab-delimited file.
2626 :	parrello	1.15
2627 :			=over 4
2628 :
2629 :	parrello	1.93	=item handle
2630 :	parrello	1.15
2631 :	parrello	1.93	Open file handle from which to read.
2632 :	parrello	1.15
2633 :			=item RETURN
2634 :
2635 :	parrello	1.93	Returns a list of the fields in the record read. The fields are presumed to be
2636 :			tab-delimited. If we are at the end of the file, then an empty list will be
2637 :			returned. If an empty line is read, a single list item consisting of a null
2638 :			string will be returned.
2639 :	parrello	1.15
2640 :			=back
2641 :
2642 :			=cut
2643 :	parrello	1.93
2644 :			sub GetLine {
2645 :	parrello	1.15	# Get the parameters.
2646 :	parrello	1.93	my ($handle) = @_;
2647 :			# Declare the return variable.
2648 :			my @retVal = ();
2649 :			Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2650 :			# Read from the file.
2651 :			my $line = <$handle>;
2652 :			# Only proceed if we found something.
2653 :			if (defined $line) {
2654 :			# Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2655 :			# upload control and have a nonstandard EOL combination.
2656 :			$line =~ s/(\r\|\n)+$//;
2657 :			# Here we do some fancy tracing to help in debugging complicated EOL marks.
2658 :			if (T(File => 4)) {
2659 :			my $escapedLine = $line;
2660 :			$escapedLine =~ s/\n/\\n/g;
2661 :			$escapedLine =~ s/\r/\\r/g;
2662 :			$escapedLine =~ s/\t/\\t/g;
2663 :			Trace("Line read: -->$escapedLine<--");
2664 :			}
2665 :			# If the line is empty, return a single empty string; otherwise, parse
2666 :			# it into fields.
2667 :			if ($line eq "") {
2668 :			push @retVal, "";
2669 :			} else {
2670 :			push @retVal, split /\t/,$line;
2671 :			}
2672 :			} else {
2673 :			# Trace the reason the read failed.
2674 :			Trace("End of file: $!") if T(File => 3);
2675 :	parrello	1.15	}
2676 :	parrello	1.93	# Return the result.
2677 :			return @retVal;
2678 :	parrello	1.15	}
2679 :
2680 :	parrello	1.93	=head3 PutLine
2681 :
2682 :			Tracer::PutLine($handle, \@fields, $eol);
2683 :	parrello	1.35
2684 :	parrello	1.93	Write a line of data to a tab-delimited file. The specified field values will be
2685 :			output in tab-separated form, with a trailing new-line.
2686 :	parrello	1.35
2687 :	parrello	1.93	=over 4
2688 :	parrello	1.35
2689 :	parrello	1.93	=item handle
2690 :	parrello	1.69
2691 :	parrello	1.93	Output file handle.
2692 :	parrello	1.69
2693 :	parrello	1.93	=item fields
2694 :	parrello	1.69
2695 :	parrello	1.93	List of field values.
2696 :	parrello	1.69
2697 :	parrello	1.93	=item eol (optional)
2698 :	parrello	1.69
2699 :	parrello	1.93	End-of-line character (default is "\n").
2700 :	parrello	1.69
2701 :			=back
2702 :	parrello	1.35
2703 :			=cut
2704 :
2705 :	parrello	1.93	sub PutLine {
2706 :	parrello	1.69	# Get the parameters.
2707 :	parrello	1.93	my ($handle, $fields, $eol) = @_;
2708 :			# Write the data.
2709 :			print $handle join("\t", @{$fields}) . ($eol \|\| "\n");
2710 :	parrello	1.69	}
2711 :
2712 :
2713 :	parrello	1.97	=head3 PrintLine
2714 :
2715 :			Tracer::PrintLine($line);
2716 :
2717 :			Print a line of text with a trailing new-line.
2718 :
2719 :			=over 4
2720 :
2721 :			=item line
2722 :
2723 :			Line of text to print.
2724 :
2725 :			=back
2726 :
2727 :			=cut
2728 :
2729 :			sub PrintLine {
2730 :			# Get the parameters.
2731 :			my ($line) = @_;
2732 :			# Print the line.
2733 :			print "$line\n";
2734 :			}
2735 :
2736 :	parrello	1.69
2737 :	parrello	1.93	=head2 Other Useful Methods
2738 :
2739 :			=head3 ParseParm
2740 :
2741 :			my $listValue = Tracer::ParseParm($string);
2742 :
2743 :			Convert a parameter into a list reference. If the parameter is undefined,
2744 :			an undefined value will be returned. Otherwise, it will be parsed as a
2745 :			comma-separated list of values.
2746 :	parrello	1.69
2747 :			=over 4
2748 :
2749 :	parrello	1.93	=item string
2750 :
2751 :			Incoming string.
2752 :
2753 :			=item RETURN
2754 :	parrello	1.69
2755 :	parrello	1.93	Returns a reference to a list of values, or C<undef> if the incoming value
2756 :			was undefined.
2757 :	parrello	1.69
2758 :			=back
2759 :
2760 :			=cut
2761 :
2762 :	parrello	1.93	sub ParseParm {
2763 :			# Get the parameters.
2764 :			my ($string) = @_;
2765 :			# Declare the return variable.
2766 :			my $retVal;
2767 :			# Check for data.
2768 :			if (defined $string) {
2769 :			# We have some, so split it into a list.
2770 :			$retVal = [ split /\s,\s/, $string];
2771 :	parrello	1.72	}
2772 :	parrello	1.93	# Return the result.
2773 :			return $retVal;
2774 :	parrello	1.69	}
2775 :
2776 :	parrello	1.97	=head3 Now
2777 :
2778 :			my $string = Tracer::Now();
2779 :
2780 :			Return a displayable time stamp containing the local time. Whatever format this
2781 :			method produces must be parseable by L</ParseDate>.
2782 :
2783 :			=cut
2784 :
2785 :			sub Now {
2786 :			return DisplayTime(time);
2787 :			}
2788 :
2789 :			=head3 DisplayTime
2790 :
2791 :			my $string = Tracer::DisplayTime($time);
2792 :	parrello	1.69
2793 :	parrello	1.97	Convert a time value to a displayable time stamp. Whatever format this
2794 :			method produces must be parseable by L</ParseDate>.
2795 :
2796 :			=over 4
2797 :	parrello	1.69
2798 :	parrello	1.97	=item time
2799 :	parrello	1.69
2800 :	parrello	1.97	Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2801 :
2802 :			=item RETURN
2803 :	parrello	1.69
2804 :	parrello	1.97	Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2805 :	parrello	1.69
2806 :	parrello	1.97	=back
2807 :	parrello	1.69
2808 :	parrello	1.93	=cut
2809 :	parrello	1.69
2810 :	parrello	1.97	sub DisplayTime {
2811 :			my ($time) = @_;
2812 :			my $retVal = "(n/a)";
2813 :			if (defined $time) {
2814 :			my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2815 :			$retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2816 :			_p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2817 :			}
2818 :	parrello	1.93	return $retVal;
2819 :			}
2820 :	parrello	1.69
2821 :	parrello	1.93	# Pad a number to 2 digits.
2822 :			sub _p2 {
2823 :			my ($value) = @_;
2824 :			$value = "0$value" if ($value < 10);
2825 :			return $value;
2826 :	parrello	1.69	}
2827 :
2828 :	parrello	1.93	=head3 Escape
2829 :	parrello	1.69
2830 :	parrello	1.93	my $codedString = Tracer::Escape($realString);
2831 :	parrello	1.69
2832 :	parrello	1.93	Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2833 :			replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2834 :			result is to reverse the effect of L</UnEscape>.
2835 :	parrello	1.69
2836 :			=over 4
2837 :
2838 :	parrello	1.93	=item realString
2839 :	parrello	1.69
2840 :	parrello	1.93	String to escape.
2841 :	parrello	1.69
2842 :			=item RETURN
2843 :
2844 :	parrello	1.93	Escaped equivalent of the real string.
2845 :
2846 :			=back
2847 :
2848 :			=cut
2849 :
2850 :			sub Escape {
2851 :			# Get the parameter.
2852 :			my ($realString) = @_;
2853 :			# Initialize the return variable.
2854 :			my $retVal = "";
2855 :			# Loop through the parameter string, looking for sequences to escape.
2856 :			while (length $realString > 0) {
2857 :			# Look for the first sequence to escape.
2858 :			if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2859 :			# Here we found it. The text preceding the sequence is in $1. The sequence
2860 :			# itself is in $2. First, move the clear text to the return variable.
2861 :			$retVal .= $1;
2862 :			# Strip the processed section off the real string.
2863 :			$realString = substr $realString, (length $2) + (length $1);
2864 :			# Get the matched character.
2865 :			my $char = $2;
2866 :			# If we have a CR, we are done.
2867 :			if ($char ne "\r") {
2868 :			# It's not a CR, so encode the escape sequence.
2869 :			$char =~ tr/\t\n/tn/;
2870 :			$retVal .= "\\" . $char;
2871 :			}
2872 :			} else {
2873 :			# Here there are no more escape sequences. The rest of the string is
2874 :			# transferred unmodified.
2875 :			$retVal .= $realString;
2876 :			$realString = "";
2877 :			}
2878 :			}
2879 :			# Return the result.
2880 :			return $retVal;
2881 :	parrello	1.69	}
2882 :
2883 :	parrello	1.93	=head3 UnEscape
2884 :	parrello	1.69
2885 :	parrello	1.93	my $realString = Tracer::UnEscape($codedString);
2886 :	parrello	1.69
2887 :	parrello	1.93	Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2888 :			a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2889 :			be deleted.
2890 :	parrello	1.69
2891 :			=over 4
2892 :
2893 :	parrello	1.93	=item codedString
2894 :	parrello	1.69
2895 :	parrello	1.93	String to un-escape.
2896 :	parrello	1.69
2897 :			=item RETURN
2898 :
2899 :	parrello	1.93	Returns a copy of the original string with the escape sequences converted to their actual
2900 :			values.
2901 :	parrello	1.69
2902 :			=back
2903 :
2904 :			=cut
2905 :
2906 :	parrello	1.93	sub UnEscape {
2907 :			# Get the parameter.
2908 :			my ($codedString) = @_;
2909 :			# Initialize the return variable.
2910 :			my $retVal = "";
2911 :			# Only proceed if the incoming string is nonempty.
2912 :			if (defined $codedString) {
2913 :			# Loop through the parameter string, looking for escape sequences. We can't do
2914 :			# translating because it causes problems with the escaped slash. ("\\t" becomes
2915 :			# "\<tab>" no matter what we do.)
2916 :			while (length $codedString > 0) {
2917 :			# Look for the first escape sequence.
2918 :			if ($codedString =~ /^(.*?)\\(\\\|n\|t\|r)/) {
2919 :			# Here we found it. The text preceding the sequence is in $1. The sequence
2920 :			# itself is in $2. First, move the clear text to the return variable.
2921 :			$retVal .= $1;
2922 :			$codedString = substr $codedString, (2 + length $1);
2923 :			# Get the escape value.
2924 :			my $char = $2;
2925 :			# If we have a "\r", we are done.
2926 :			if ($char ne 'r') {
2927 :			# Here it's not an 'r', so we convert it.
2928 :			$char =~ tr/\\tn/\\\t\n/;
2929 :			$retVal .= $char;
2930 :			}
2931 :			} else {
2932 :			# Here there are no more escape sequences. The rest of the string is
2933 :			# transferred unmodified.
2934 :			$retVal .= $codedString;
2935 :			$codedString = "";
2936 :			}
2937 :			}
2938 :	parrello	1.35	}
2939 :	parrello	1.69	# Return the result.
2940 :			return $retVal;
2941 :			}
2942 :
2943 :	parrello	1.93	=head3 Percent
2944 :	parrello	1.69
2945 :	parrello	1.93	my $percent = Tracer::Percent($number, $base);
2946 :	parrello	1.69
2947 :	parrello	1.93	Returns the percent of the base represented by the given number. If the base
2948 :			is zero, returns zero.
2949 :	parrello	1.69
2950 :			=over 4
2951 :
2952 :	parrello	1.93	=item number
2953 :	parrello	1.69
2954 :	parrello	1.93	Percent numerator.
2955 :	parrello	1.69
2956 :	parrello	1.93	=item base
2957 :	parrello	1.69
2958 :	parrello	1.93	Percent base.
2959 :	parrello	1.69
2960 :	parrello	1.93	=item RETURN
2961 :	parrello	1.69
2962 :	parrello	1.93	Returns the percentage of the base represented by the numerator.
2963 :	parrello	1.69
2964 :			=back
2965 :
2966 :			=cut
2967 :
2968 :	parrello	1.93	sub Percent {
2969 :	parrello	1.69	# Get the parameters.
2970 :	parrello	1.93	my ($number, $base) = @_;
2971 :			# Declare the return variable.
2972 :			my $retVal = 0;
2973 :			# Compute the percent.
2974 :			if ($base != 0) {
2975 :			$retVal = $number * 100 / $base;
2976 :			}
2977 :			# Return the result.
2978 :			return $retVal;
2979 :	parrello	1.69	}
2980 :
2981 :	parrello	1.97	=head3 Constrain
2982 :
2983 :			my $constrained = Constrain($value, $min, $max);
2984 :
2985 :			Modify a numeric value to bring it to a point in between a maximum and a minimum.
2986 :
2987 :			=over 4
2988 :
2989 :			=item value
2990 :
2991 :			Value to constrain.
2992 :
2993 :			=item min (optional)
2994 :
2995 :			Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2996 :
2997 :			=item max (optional)
2998 :
2999 :			Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3000 :
3001 :			=item RETURN
3002 :
3003 :			Returns the incoming value, constrained according to the other parameters.
3004 :
3005 :			=back
3006 :
3007 :			=cut
3008 :
3009 :			sub Constrain {
3010 :			# Get the parameters.
3011 :			my ($value, $min, $max) = @_;
3012 :			# Declare the return variable.
3013 :			my $retVal = $value;
3014 :			# Apply the minimum constraint.
3015 :			if (defined $min && $retVal < $min) {
3016 :			$retVal = $min;
3017 :			}
3018 :			# Apply the maximum constraint.
3019 :			if (defined $max && $retVal > $max) {
3020 :			$retVal = $max;
3021 :			}
3022 :			# Return the result.
3023 :			return $retVal;
3024 :			}
3025 :
3026 :	parrello	1.93	=head3 Min
3027 :	parrello	1.69
3028 :	parrello	1.93	my $min = Min($value1, $value2, ... $valueN);
3029 :	parrello	1.69
3030 :	parrello	1.93	Return the minimum argument. The arguments are treated as numbers.
3031 :	parrello	1.69
3032 :			=over 4
3033 :
3034 :	parrello	1.93	=item $value1, $value2, ... $valueN
3035 :	parrello	1.69
3036 :	parrello	1.93	List of numbers to compare.
3037 :	parrello	1.69
3038 :			=item RETURN
3039 :
3040 :	parrello	1.93	Returns the lowest number in the list.
3041 :	parrello	1.69
3042 :			=back
3043 :
3044 :			=cut
3045 :
3046 :	parrello	1.93	sub Min {
3047 :			# Get the parameters. Note that we prime the return value with the first parameter.
3048 :			my ($retVal, @values) = @_;
3049 :			# Loop through the remaining parameters, looking for the lowest.
3050 :			for my $value (@values) {
3051 :			if ($value < $retVal) {
3052 :			$retVal = $value;
3053 :	parrello	1.72	}
3054 :			}
3055 :	parrello	1.93	# Return the minimum found.
3056 :	parrello	1.70	return $retVal;
3057 :	parrello	1.35	}
3058 :
3059 :	parrello	1.93	=head3 Max
3060 :
3061 :			my $max = Max($value1, $value2, ... $valueN);
3062 :	parrello	1.69
3063 :	parrello	1.93	Return the maximum argument. The arguments are treated as numbers.
3064 :	parrello	1.65
3065 :	parrello	1.93	=over 4
3066 :	parrello	1.65
3067 :	parrello	1.93	=item $value1, $value2, ... $valueN
3068 :	parrello	1.65
3069 :	parrello	1.93	List of numbers to compare.
3070 :	parrello	1.65
3071 :	parrello	1.93	=item RETURN
3072 :	parrello	1.65
3073 :	parrello	1.93	Returns the highest number in the list.
3074 :	parrello	1.65
3075 :			=back
3076 :
3077 :			=cut
3078 :
3079 :	parrello	1.93	sub Max {
3080 :			# Get the parameters. Note that we prime the return value with the first parameter.
3081 :			my ($retVal, @values) = @_;
3082 :			# Loop through the remaining parameters, looking for the highest.
3083 :			for my $value (@values) {
3084 :			if ($value > $retVal) {
3085 :			$retVal = $value;
3086 :	parrello	1.65	}
3087 :			}
3088 :	parrello	1.93	# Return the maximum found.
3089 :			return $retVal;
3090 :	parrello	1.65	}
3091 :
3092 :	parrello	1.93	=head3 Strip
3093 :	parrello	1.37
3094 :	parrello	1.93	my $string = Tracer::Strip($line);
3095 :	parrello	1.37
3096 :	parrello	1.93	Strip all line terminators off a string. This is necessary when dealing with files
3097 :			that may have been transferred back and forth several times among different
3098 :			operating environments.
3099 :	parrello	1.37
3100 :			=over 4
3101 :
3102 :	parrello	1.93	=item line
3103 :	parrello	1.37
3104 :	parrello	1.93	Line of text to be stripped.
3105 :	parrello	1.37
3106 :	parrello	1.93	=item RETURN
3107 :	parrello	1.91
3108 :	parrello	1.93	The same line of text with all the line-ending characters chopped from the end.
3109 :	parrello	1.91
3110 :	parrello	1.37	=back
3111 :
3112 :			=cut
3113 :
3114 :	parrello	1.93	sub Strip {
3115 :			# Get a copy of the parameter string.
3116 :			my ($string) = @_;
3117 :			my $retVal = (defined $string ? $string : "");
3118 :			# Strip the line terminator characters.
3119 :			$retVal =~ s/(\r\|\n)+$//g;
3120 :			# Return the result.
3121 :			return $retVal;
3122 :	parrello	1.43	}
3123 :
3124 :	parrello	1.93	=head3 Pad
3125 :	parrello	1.43
3126 :	parrello	1.93	my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3127 :	parrello	1.43
3128 :	parrello	1.93	Pad a string to a specified length. The pad character will be a
3129 :			space, and the padding will be on the right side unless specified
3130 :			in the third parameter.
3131 :	parrello	1.43
3132 :			=over 4
3133 :
3134 :	parrello	1.93	=item string
3135 :
3136 :			String to be padded.
3137 :
3138 :			=item len
3139 :
3140 :			Desired length of the padded string.
3141 :
3142 :			=item left (optional)
3143 :
3144 :			TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3145 :
3146 :			=item padChar (optional)
3147 :
3148 :			Character to use for padding. The default is a space.
3149 :
3150 :			=item RETURN
3151 :	parrello	1.43
3152 :	parrello	1.93	Returns a copy of the original string with the pad character added to the
3153 :			specified end so that it achieves the desired length.
3154 :	parrello	1.43
3155 :			=back
3156 :
3157 :			=cut
3158 :
3159 :	parrello	1.93	sub Pad {
3160 :			# Get the parameters.
3161 :			my ($string, $len, $left, $padChar) = @_;
3162 :			# Compute the padding character.
3163 :			if (! defined $padChar) {
3164 :			$padChar = " ";
3165 :			}
3166 :			# Compute the number of spaces needed.
3167 :			my $needed = $len - length $string;
3168 :			# Copy the string into the return variable.
3169 :			my $retVal = $string;
3170 :			# Only proceed if padding is needed.
3171 :			if ($needed > 0) {
3172 :			# Create the pad string.
3173 :			my $pad = $padChar x $needed;
3174 :			# Affix it to the return value.
3175 :			if ($left) {
3176 :			$retVal = $pad . $retVal;
3177 :			} else {
3178 :			$retVal .= $pad;
3179 :	parrello	1.43	}
3180 :	parrello	1.37	}
3181 :	parrello	1.93	# Return the result.
3182 :			return $retVal;
3183 :	parrello	1.37	}
3184 :
3185 :	parrello	1.93	=head3 EOF
3186 :
3187 :			This is a constant that is lexically greater than any useful string.
3188 :
3189 :			=cut
3190 :
3191 :			sub EOF {
3192 :			return "\xFF\xFF\xFF\xFF\xFF";
3193 :			}
3194 :	parrello	1.59
3195 :	parrello	1.93	=head3 TICK
3196 :	parrello	1.59
3197 :	parrello	1.93	my @results = TICK($commandString);
3198 :	parrello	1.59
3199 :	parrello	1.93	Perform a back-tick operation on a command. If this is a Windows environment, any leading
3200 :			dot-slash (C<./> will be removed. So, for example, if you were doing
3201 :	parrello	1.59
3202 :	parrello	1.93	`./protein.cgi`
3203 :	parrello	1.59
3204 :	parrello	1.93	from inside a CGI script, it would work fine in Unix, but would issue an error message
3205 :			in Windows complaining that C<'.'> is not a valid command. If instead you code
3206 :	parrello	1.59
3207 :	parrello	1.93	TICK("./protein.cgi")
3208 :	parrello	1.59
3209 :	parrello	1.93	it will work correctly in both environments.
3210 :	parrello	1.59
3211 :	parrello	1.93	=over 4
3212 :	parrello	1.59
3213 :	parrello	1.93	=item commandString
3214 :	parrello	1.59
3215 :	parrello	1.93	The command string to pass to the system.
3216 :	parrello	1.59
3217 :			=item RETURN
3218 :
3219 :	parrello	1.93	Returns the standard output from the specified command, as a list.
3220 :	parrello	1.59
3221 :			=back
3222 :
3223 :			=cut
3224 :	parrello	1.93	#: Return Type @;
3225 :			sub TICK {
3226 :	parrello	1.59	# Get the parameters.
3227 :	parrello	1.93	my ($commandString) = @_;
3228 :			# Chop off the dot-slash if this is Windows.
3229 :			if ($FIG_Config::win_mode) {
3230 :			$commandString =~ s!^\./!!;
3231 :	parrello	1.59	}
3232 :	parrello	1.93	# Activate the command and return the result.
3233 :			return `$commandString`;
3234 :	parrello	1.59	}
3235 :
3236 :	parrello	1.93
3237 :	parrello	1.55	=head3 CommaFormat
3238 :
3239 :	parrello	1.92	my $formatted = Tracer::CommaFormat($number);
3240 :	parrello	1.55
3241 :			Insert commas into a number.
3242 :
3243 :			=over 4
3244 :
3245 :			=item number
3246 :
3247 :			A sequence of digits.
3248 :
3249 :			=item RETURN
3250 :
3251 :			Returns the same digits with commas strategically inserted.
3252 :
3253 :			=back
3254 :
3255 :			=cut
3256 :
3257 :			sub CommaFormat {
3258 :			# Get the parameters.
3259 :			my ($number) = @_;
3260 :			# Pad the length up to a multiple of three.
3261 :			my $padded = "$number";
3262 :			$padded = " " . $padded while length($padded) % 3 != 0;
3263 :			# This is a fancy PERL trick. The parentheses in the SPLIT pattern
3264 :			# cause the delimiters to be included in the output stream. The
3265 :			# GREP removes the empty strings in between the delimiters.
3266 :			my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3267 :			# Clean out the spaces.
3268 :			$retVal =~ s/ //g;
3269 :			# Return the result.
3270 :			return $retVal;
3271 :			}
3272 :	parrello	1.46
3273 :
3274 :	parrello	1.62	=head3 CompareLists
3275 :
3276 :	parrello	1.92	my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3277 :	parrello	1.62
3278 :			Compare two lists of tuples, and return a hash analyzing the differences. The lists
3279 :			are presumed to be sorted alphabetically by the value in the $keyIndex column.
3280 :			The return value contains a list of items that are only in the new list
3281 :			(inserted) and only in the old list (deleted).
3282 :
3283 :			=over 4
3284 :
3285 :			=item newList
3286 :
3287 :			Reference to a list of new tuples.
3288 :
3289 :			=item oldList
3290 :
3291 :			Reference to a list of old tuples.
3292 :
3293 :			=item keyIndex (optional)
3294 :
3295 :			Index into each tuple of its key field. The default is 0.
3296 :
3297 :			=item RETURN
3298 :
3299 :			Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3300 :			list (inserted) followed by a reference to the list of items that are only in the old
3301 :			list (deleted).
3302 :
3303 :			=back
3304 :
3305 :			=cut
3306 :
3307 :			sub CompareLists {
3308 :			# Get the parameters.
3309 :			my ($newList, $oldList, $keyIndex) = @_;
3310 :			if (! defined $keyIndex) {
3311 :			$keyIndex = 0;
3312 :			}
3313 :			# Declare the return variables.
3314 :			my ($inserted, $deleted) = ([], []);
3315 :			# Loop through the two lists simultaneously.
3316 :			my ($newI, $oldI) = (0, 0);
3317 :			my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3318 :			while ($newI < $newN \|\| $oldI < $oldN) {
3319 :			# Get the current object in each list. Note that if one
3320 :			# of the lists is past the end, we'll get undef.
3321 :			my $newItem = $newList->[$newI];
3322 :			my $oldItem = $oldList->[$oldI];
3323 :	parrello	1.63	if (! defined($newItem) \|\| defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3324 :	parrello	1.62	# The old item is not in the new list, so mark it deleted.
3325 :			push @{$deleted}, $oldItem;
3326 :			$oldI++;
3327 :			} elsif (! defined($oldItem) \|\| $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3328 :			# The new item is not in the old list, so mark it inserted.
3329 :			push @{$inserted}, $newItem;
3330 :			$newI++;
3331 :			} else {
3332 :			# The item is in both lists, so push forward.
3333 :			$oldI++;
3334 :			$newI++;
3335 :			}
3336 :			}
3337 :			# Return the result.
3338 :			return ($inserted, $deleted);
3339 :			}
3340 :
3341 :	parrello	1.105	=head3 Cmp
3342 :
3343 :			my $cmp = Tracer::Cmp($a, $b);
3344 :
3345 :			This method performs a universal sort comparison. Each value coming in is
3346 :			separated into a leading text part and a trailing number part. The text
3347 :			part is string compared, and if both parts are equal, then the number
3348 :			parts are compared numerically. A stream of just numbers or a stream of
3349 :			just strings will sort correctly, and a mixed stream will sort with the
3350 :			numbers first. Strings with a label and a number will sort in the
3351 :			expected manner instead of lexically.
3352 :
3353 :			=over 4
3354 :
3355 :			=item a
3356 :
3357 :			First item to compare.
3358 :
3359 :			=item b
3360 :
3361 :			Second item to compare.
3362 :
3363 :			=item RETURN
3364 :
3365 :			Returns a negative number if the first item should sort first (is less), a positive
3366 :			number if the first item should sort second (is greater), and a zero if the items are
3367 :			equal.
3368 :
3369 :			=back
3370 :
3371 :			=cut
3372 :
3373 :			sub Cmp {
3374 :			# Get the parameters.
3375 :			my ($a, $b) = @_;
3376 :			# Declare the return value.
3377 :			my $retVal;
3378 :			# Check for nulls.
3379 :			if (! defined($a)) {
3380 :			$retVal = (! defined($b) ? 0 : -1);
3381 :			} elsif (! defined($b)) {
3382 :			$retVal = 1;
3383 :			} else {
3384 :			# Here we have two real values. Parse the two strings.
3385 :			$a =~ /^(\D)(\d)$/;
3386 :			my $aParsed = [$1, $2];
3387 :			$b =~ /^(\D)(\d)$/;
3388 :			my $bParsed = [$1, $2];
3389 :			# Compare the string parts.
3390 :			$retVal = $aParsed->[0] cmp $bParsed->[0];
3391 :			if (! $retVal) {
3392 :			$retVal = $aParsed->[1] <=> $bParsed->[1];
3393 :			}
3394 :			}
3395 :			# Return the result.
3396 :			return $retVal;
3397 :			}
3398 :
3399 :	parrello	1.108	=head3 ListEQ
3400 :
3401 :			my $flag = Tracer::ListEQ(\@a, \@b);
3402 :
3403 :			Return TRUE if the specified lists contain the same strings in the same
3404 :			order, else FALSE.
3405 :
3406 :			=over 4
3407 :
3408 :			=item a
3409 :
3410 :			Reference to the first list.
3411 :
3412 :			=item b
3413 :
3414 :			Reference to the second list.
3415 :
3416 :			=item RETURN
3417 :
3418 :			Returns TRUE if the two parameters are identical string lists, else FALSE.
3419 :
3420 :			=back
3421 :
3422 :			=cut
3423 :
3424 :			sub ListEQ {
3425 :			# Get the parameters.
3426 :			my ($a, $b) = @_;
3427 :			# Declare the return variable. Start by checking the lengths.
3428 :			my $n = scalar(@$a);
3429 :			my $retVal = ($n == scalar(@$b));
3430 :			# Now compare the list elements.
3431 :			for (my $i = 0; $retVal && $i < $n; $i++) {
3432 :			$retVal = ($a->[$i] eq $b->[$i]);
3433 :			}
3434 :			# Return the result.
3435 :			return $retVal;
3436 :			}
3437 :
3438 :	parrello	1.105	=head2 CGI Script Utilities
3439 :
3440 :			=head3 ScriptSetup (deprecated)
3441 :
3442 :			my ($cgi, $varHash) = ScriptSetup($noTrace);
3443 :
3444 :			Perform standard tracing and debugging setup for scripts. The value returned is
3445 :			the CGI object followed by a pre-built variable hash. At the end of the script,
3446 :			the client should call L</ScriptFinish> to output the web page.
3447 :
3448 :			This method calls L</ETracing> to configure tracing, which allows the tracing
3449 :			to be configured via the emergency tracing form on the debugging control panel.
3450 :			Tracing will then be turned on automatically for all programs that use the L</ETracing>
3451 :			method, which includes every program that uses this method or L</StandardSetup>.
3452 :
3453 :			=over 4
3454 :
3455 :			=item noTrace (optional)
3456 :
3457 :			If specified, tracing will be suppressed. This is useful if the script wants to set up
3458 :			tracing manually.
3459 :
3460 :			=item RETURN
3461 :
3462 :			Returns a two-element list consisting of a CGI query object and a variable hash for
3463 :			the output page.
3464 :
3465 :			=back
3466 :
3467 :			=cut
3468 :
3469 :			sub ScriptSetup {
3470 :			# Get the parameters.
3471 :			my ($noTrace) = @_;
3472 :			# Get the CGI query object.
3473 :			my $cgi = CGI->new();
3474 :			# Set up tracing if it's not suppressed.
3475 :			ETracing($cgi) unless $noTrace;
3476 :			# Create the variable hash.
3477 :			my $varHash = { results => '' };
3478 :			# Return the query object and variable hash.
3479 :			return ($cgi, $varHash);
3480 :			}
3481 :
3482 :			=head3 ScriptFinish (deprecated)
3483 :
3484 :			ScriptFinish($webData, $varHash);
3485 :
3486 :			Output a web page at the end of a script. Either the string to be output or the
3487 :			name of a template file can be specified. If the second parameter is omitted,
3488 :			it is assumed we have a string to be output; otherwise, it is assumed we have the
3489 :			name of a template file. The template should have the variable C<DebugData>
3490 :			specified in any form that invokes a standard script. If debugging mode is turned
3491 :			on, a form field will be put in that allows the user to enter tracing data.
3492 :			Trace messages will be placed immediately before the terminal C<BODY> tag in
3493 :			the output, formatted as a list.
3494 :
3495 :			A typical standard script would loook like the following.
3496 :
3497 :			BEGIN {
3498 :			# Print the HTML header.
3499 :			print "CONTENT-TYPE: text/html\n\n";
3500 :			}
3501 :			use Tracer;
3502 :			use CGI;
3503 :			use FIG;
3504 :			# ... more uses ...
3505 :
3506 :			my ($cgi, $varHash) = ScriptSetup();
3507 :			eval {
3508 :			# ... get data from $cgi, put it in $varHash ...
3509 :			};
3510 :			if ($@) {
3511 :			Trace("Script Error: $@") if T(0);
3512 :			}
3513 :			ScriptFinish("Html/MyTemplate.html", $varHash);
3514 :
3515 :			The idea here is that even if the script fails, you'll see trace messages and
3516 :			useful output.
3517 :
3518 :			=over 4
3519 :
3520 :			=item webData
3521 :
3522 :			A string containing either the full web page to be written to the output or the
3523 :			name of a template file from which the page is to be constructed. If the name
3524 :			of a template file is specified, then the second parameter must be present;
3525 :			otherwise, it must be absent.
3526 :
3527 :			=item varHash (optional)
3528 :
3529 :			If specified, then a reference to a hash mapping variable names for a template
3530 :			to their values. The template file will be read into memory, and variable markers
3531 :			will be replaced by data in this hash reference.
3532 :
3533 :			=back
3534 :
3535 :			=cut
3536 :
3537 :			sub ScriptFinish {
3538 :			# Get the parameters.
3539 :			my ($webData, $varHash) = @_;
3540 :			# Check for a template file situation.
3541 :			my $outputString;
3542 :			if (defined $varHash) {
3543 :			# Here we have a template file. We need to determine the template type.
3544 :			my $template;
3545 :			if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3546 :			$template = "$FIG_Config::template_url/$webData";
3547 :			} else {
3548 :			$template = "<<$webData";
3549 :			}
3550 :			$outputString = PageBuilder::Build($template, $varHash, "Html");
3551 :			} else {
3552 :			# Here the user gave us a raw string.
3553 :			$outputString = $webData;
3554 :			}
3555 :			# Check for trace messages.
3556 :			if ($Destination ne "NONE" && $TraceLevel > 0) {
3557 :			# We have trace messages, so we want to put them at the end of the body. This
3558 :			# is either at the end of the whole string or at the beginning of the BODY
3559 :			# end-tag.
3560 :			my $pos = length $outputString;
3561 :			if ($outputString =~ m#</body>#gi) {
3562 :			$pos = (pos $outputString) - 7;
3563 :			}
3564 :			# If the trace messages were queued, we unroll them. Otherwise, we display the
3565 :			# destination.
3566 :			my $traceHtml;
3567 :			if ($Destination eq "QUEUE") {
3568 :			$traceHtml = QTrace('Html');
3569 :			} elsif ($Destination =~ /^>>(.+)$/) {
3570 :			# Here the tracing output it to a file. We code it as a hyperlink so the user
3571 :			# can copy the file name into the clipboard easily.
3572 :			my $actualDest = $1;
3573 :			$traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3574 :			} else {
3575 :			# Here we have one of the special destinations.
3576 :			$traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3577 :			}
3578 :			substr $outputString, $pos, 0, $traceHtml;
3579 :			}
3580 :			# Write the output string.
3581 :			print $outputString;
3582 :			}
3583 :
3584 :	parrello	1.65	=head3 GenerateURL
3585 :
3586 :	parrello	1.92	my $queryUrl = Tracer::GenerateURL($page, %parameters);
3587 :	parrello	1.65
3588 :			Generate a GET-style URL for the specified page with the specified parameter
3589 :			names and values. The values will be URL-escaped automatically. So, for
3590 :			example
3591 :
3592 :			Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3593 :
3594 :			would return
3595 :
3596 :	parrello	1.79	form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3597 :	parrello	1.65
3598 :			=over 4
3599 :
3600 :			=item page
3601 :
3602 :			Page URL.
3603 :
3604 :			=item parameters
3605 :
3606 :			Hash mapping parameter names to parameter values.
3607 :
3608 :			=item RETURN
3609 :
3610 :			Returns a GET-style URL that goes to the specified page and passes in the
3611 :			specified parameters and values.
3612 :
3613 :			=back
3614 :
3615 :			=cut
3616 :
3617 :			sub GenerateURL {
3618 :			# Get the parameters.
3619 :			my ($page, %parameters) = @_;
3620 :			# Prime the return variable with the page URL.
3621 :			my $retVal = $page;
3622 :			# Loop through the parameters, creating parameter elements in a list.
3623 :			my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3624 :			# If the list is nonempty, tack it on.
3625 :			if (@parmList) {
3626 :	parrello	1.79	$retVal .= "?" . join(";", @parmList);
3627 :	parrello	1.65	}
3628 :			# Return the result.
3629 :			return $retVal;
3630 :			}
3631 :
3632 :	parrello	1.78	=head3 ApplyURL
3633 :
3634 :	parrello	1.92	Tracer::ApplyURL($table, $target, $url);
3635 :	parrello	1.78
3636 :			Run through a two-dimensional table (or more accurately, a list of lists), converting the
3637 :			I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3638 :			URL column will be deleted by this process and the target column will be HTML-escaped.
3639 :
3640 :			This provides a simple way to process the results of a database query into something
3641 :			displayable by combining a URL with text.
3642 :
3643 :			=over 4
3644 :
3645 :			=item table
3646 :
3647 :			Reference to a list of lists. The elements in the containing list will be updated by
3648 :			this method.
3649 :
3650 :			=item target
3651 :
3652 :			The index of the column to be converted into HTML.
3653 :
3654 :			=item url
3655 :
3656 :			The index of the column containing the URL. Note that the URL must have a recognizable
3657 :			C<http:> at the beginning.
3658 :
3659 :			=back
3660 :
3661 :			=cut
3662 :
3663 :			sub ApplyURL {
3664 :			# Get the parameters.
3665 :			my ($table, $target, $url) = @_;
3666 :			# Loop through the table.
3667 :			for my $row (@{$table}) {
3668 :			# Apply the URL to the target cell.
3669 :			$row->[$target] = CombineURL($row->[$target], $row->[$url]);
3670 :			# Delete the URL from the row.
3671 :			delete $row->[$url];
3672 :			}
3673 :			}
3674 :
3675 :			=head3 CombineURL
3676 :
3677 :	parrello	1.92	my $combinedHtml = Tracer::CombineURL($text, $url);
3678 :	parrello	1.78
3679 :			This method will convert the specified text into HTML hyperlinked to the specified
3680 :			URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3681 :			is defined and begins with an C<http:> header.
3682 :
3683 :			=over 4
3684 :
3685 :			=item text
3686 :
3687 :			Text to return. This will be HTML-escaped automatically.
3688 :
3689 :			=item url
3690 :
3691 :			A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3692 :			will be returned without any hyperlinking.
3693 :
3694 :			=item RETURN
3695 :
3696 :			Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3697 :			doesn't look right, the HTML-escaped text will be returned without any further
3698 :			modification.
3699 :
3700 :			=back
3701 :
3702 :			=cut
3703 :
3704 :			sub CombineURL {
3705 :			# Get the parameters.
3706 :			my ($text, $url) = @_;
3707 :			# Declare the return variable.
3708 :			my $retVal = CGI::escapeHTML($text);
3709 :			# Verify the URL.
3710 :			if (defined($url) && $url =~ m!http://!i) {
3711 :			# It's good, so we apply it to the text.
3712 :			$retVal = "<a href=\"$url\">$retVal</a>";
3713 :			}
3714 :			# Return the result.
3715 :			return $retVal;
3716 :			}
3717 :
3718 :	parrello	1.97	=head3 TrackingCode
3719 :
3720 :			my $html = Tracer::TrackingCode();
3721 :
3722 :			Returns the HTML code for doing web page traffic monitoring. If the
3723 :			current environment is a test system, then it returns a null string;
3724 :			otherwise, it returns a bunch of javascript containing code for turning
3725 :			on SiteMeter and Google Analytics.
3726 :
3727 :			=cut
3728 :
3729 :			sub TrackingCode {
3730 :			# Declare the return variable.
3731 :			my $retVal = "<!-- tracking off -->";
3732 :			# Determine if we're in production.
3733 :			if ($FIG_Config::site_meter) {
3734 :			$retVal = <<END_HTML
3735 :			<!-- Site Meter -->
3736 :			<script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3737 :			</script>
3738 :			<noscript>
3739 :			<a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3740 :			<img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3741 :			</noscript>
3742 :			<!-- Copyright (c)2006 Site Meter -->
3743 :			END_HTML
3744 :			}
3745 :			return $retVal;
3746 :			}
3747 :
3748 :	parrello	1.105	=head3 Clean
3749 :
3750 :			my $cleaned = Tracer::Clean($string);
3751 :
3752 :			Clean up a string for HTML display. This not only converts special
3753 :			characters to HTML entity names, it also removes control characters.
3754 :
3755 :			=over 4
3756 :
3757 :			=item string
3758 :
3759 :			String to convert.
3760 :
3761 :			=item RETURN
3762 :
3763 :			Returns the input string with anything that might disrupt an HTML literal removed. An
3764 :			undefined value will be converted to an empty string.
3765 :
3766 :			=back
3767 :
3768 :			=cut
3769 :
3770 :			sub Clean {
3771 :			# Get the parameters.
3772 :			my ($string) = @_;
3773 :			# Declare the return variable.
3774 :			my $retVal = "";
3775 :			# Only proceed if the value exists.
3776 :			if (defined $string) {
3777 :			# Get the string.
3778 :			$retVal = $string;
3779 :			# Clean the control characters.
3780 :			$retVal =~ tr/\x00-\x1F/?/;
3781 :			# Escape the rest.
3782 :			$retVal = CGI::escapeHTML($retVal);
3783 :			}
3784 :			# Return the result.
3785 :			return $retVal;
3786 :			}
3787 :
3788 :
3789 :
3790 :	parrello	1.97
3791 :	olson	1.88	1;

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