Annotation of /FigKernelPackages/Tracer.pm

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1 :	olson	1.30	#
2 :			# Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :			# for Interpretations of Genomes. All Rights Reserved.
4 :			#
5 :			# This file is part of the SEED Toolkit.
6 :			#
7 :			# The SEED Toolkit is free software. You can redistribute
8 :			# it and/or modify it under the terms of the SEED Toolkit
9 :			# Public License.
10 :			#
11 :			# You should have received a copy of the SEED Toolkit Public License
12 :			# along with this program; if not write to the University of Chicago
13 :			# at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :			# Genomes at veronika@thefig.info or download a copy from
15 :			# http://www.theseed.org/LICENSE.TXT.
16 :			#
17 :
18 :	olson	1.1	package Tracer;
19 :
20 :	parrello	1.12	require Exporter;
21 :			@ISA = ('Exporter');
22 :	parrello	1.45	@EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure ChDir);
23 :	parrello	1.12	@EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24 :			use strict;
25 :			use Carp qw(longmess croak);
26 :			use CGI;
27 :	parrello	1.47	use Cwd;
28 :	parrello	1.12	use FIG_Config;
29 :	parrello	1.9	use PageBuilder;
30 :	parrello	1.21	use Digest::MD5;
31 :	parrello	1.36	use File::Basename;
32 :	parrello	1.37	use File::Path;
33 :	parrello	1.48	use File::stat;
34 :	olson	1.1
35 :			=head1 Tracing and Debugging Helpers
36 :
37 :			=head2 Introduction
38 :
39 :			This package provides simple tracing for debugging and reporting purposes. To use it simply call the
40 :			L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace
41 :	parrello	1.2	message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself
42 :			has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
43 :	olson	1.1	level is less than or equal to this package's trace level and whose category is activated will
44 :	parrello	1.2	be written. Thus, a higher trace level on a message indicates that the message
45 :	parrello	1.10	is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
46 :	olson	1.1	appear. To generate a trace message, use the following syntax.
47 :
48 :			C<< Trace($message) if T(errors => 4); >>
49 :
50 :	parrello	1.2	This statement will produce a trace message if the trace level is 4 or more and the C<errors>
51 :	parrello	1.3	category is active. Note that the special category C<main> is always active, so
52 :	olson	1.1
53 :	parrello	1.3	C<< Trace($message) if T(main => 4); >>
54 :	olson	1.1
55 :			will trace if the trace level is 4 or more.
56 :
57 :			If the category name is the same as the package name, all you need is the number. So, if the
58 :			following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
59 :			active and the trace level is 2 or more.
60 :
61 :			C<< Trace($message) if T(2); >>
62 :
63 :	parrello	1.10	To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
64 :	olson	1.1	of category names, and a set of options. The trace level and list of category names are
65 :			specified as a space-delimited string. Thus
66 :
67 :			C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>
68 :
69 :	parrello	1.7	sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
70 :	parrello	1.12	specifies that messages should be output as HTML paragraphs.
71 :
72 :			To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
73 :			level 3 and writes the output to the standard error output. This sort of thing might be
74 :			useful in a CGI environment.
75 :
76 :			C<< TSetup('3 *', 'WARN'); >>
77 :	olson	1.1
78 :			In addition to HTML and file output for trace messages, you can specify that the trace messages
79 :			be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
80 :			is useful if you are building a web page. Instead of having the trace messages interspersed with
81 :			the page output, they can be gathered together and displayed at the end of the page. This makes
82 :			it easier to debug page formatting problems.
83 :
84 :	parrello	1.4	Finally, you can specify that all trace messages be emitted as warnings.
85 :
86 :	olson	1.1	The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
87 :			Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
88 :			Thus, debugging information is available and easily retrieved even when the application is
89 :			being used out in the field.
90 :
91 :	parrello	1.10	There is no hard and fast rule on how to use trace levels. The following is therefore only
92 :			a suggestion.
93 :
94 :			=over 4
95 :
96 :	parrello	1.32	=item Error 0
97 :	parrello	1.10
98 :			Message indicates an error that may lead to incorrect results or that has stopped the
99 :			application entirely.
100 :
101 :	parrello	1.32	=item Warning 1
102 :	parrello	1.10
103 :			Message indicates something that is unexpected but that probably did not interfere
104 :			with program execution.
105 :
106 :	parrello	1.32	=item Notice 2
107 :	parrello	1.10
108 :			Message indicates the beginning or end of a major task.
109 :
110 :	parrello	1.32	=item Information 3
111 :	parrello	1.10
112 :			Message indicates a subtask. In the FIG system, a subtask generally relates to a single
113 :			genome. This would be a big loop that is not expected to execute more than 500 times or so.
114 :
115 :	parrello	1.32	=item Detail 4
116 :	parrello	1.10
117 :			Message indicates a low-level loop iteration.
118 :
119 :			=back
120 :
121 :	olson	1.1	=cut
122 :	parrello	1.2
123 :	olson	1.1	# Declare the configuration variables.
124 :
125 :	parrello	1.12	my $Destination = "NONE"; # Description of where to send the trace output.
126 :			my $TeeFlag = 0; # TRUE if output is going to a file and to the
127 :			# standard output
128 :	parrello	1.3	my %Categories = ( main => 1 );
129 :	parrello	1.12	# hash of active category names
130 :			my $TraceLevel = 0; # trace level; a higher trace level produces more
131 :			# messages
132 :			my @Queue = (); # queued list of trace messages.
133 :	parrello	1.7	my $LastCategory = "main"; # name of the last category interrogated
134 :	parrello	1.11	my $SetupCount = 0; # number of times TSetup called
135 :	parrello	1.12	my $AllTrace = 0; # TRUE if we are tracing all categories.
136 :	olson	1.1
137 :			=head2 Public Methods
138 :
139 :			=head3 TSetup
140 :
141 :			C<< TSetup($categoryList, $target); >>
142 :
143 :			This method is used to specify the trace options. The options are stored as package data
144 :			and interrogated by the L</Trace> and L</T> methods.
145 :
146 :			=over 4
147 :
148 :			=item categoryList
149 :
150 :			A string specifying the trace level and the categories to be traced, separated by spaces.
151 :			The trace level must come first.
152 :
153 :			=item target
154 :
155 :			The destination for the trace output. To send the trace output to a file, specify the file
156 :			name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
157 :	parrello	1.10	to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
158 :			symbol with a C<+> to echo output to a file AND to the standard output. In addition to
159 :			sending the trace messages to a file, you can specify a special destination. C<HTML> will
160 :			cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
161 :	parrello	1.5	will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
162 :	parrello	1.9	messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
163 :	parrello	1.6	messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
164 :	parrello	1.9	cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
165 :	parrello	1.6	cause tracing to be suppressed.
166 :	olson	1.1
167 :			=back
168 :
169 :			=cut
170 :
171 :			sub TSetup {
172 :	parrello	1.12	# Get the parameters.
173 :			my ($categoryList, $target) = @_;
174 :			# Parse the category list.
175 :			my @categoryData = split /\s+/, $categoryList;
176 :			# Extract the trace level.
177 :			$TraceLevel = shift @categoryData;
178 :			# Presume category-based tracing until we learn otherwise.
179 :			$AllTrace = 0;
180 :			# Build the category hash. Note that if we find a "*", we turn on non-category
181 :	parrello	1.33	# tracing. We must also clear away any pre-existing data.
182 :	parrello	1.34	%Categories = ( main => 1 );
183 :	parrello	1.12	for my $category (@categoryData) {
184 :			if ($category eq '*') {
185 :			$AllTrace = 1;
186 :			} else {
187 :	parrello	1.13	$Categories{lc $category} = 1;
188 :	parrello	1.12	}
189 :			}
190 :			# Now we need to process the destination information. The most important special
191 :			# cases are the single ">", which requires we clear the file first, and the
192 :			# "+" prefix which indicates a double echo.
193 :			if ($target =~ m/^\+?>>?/) {
194 :			if ($target =~ m/^\+/) {
195 :			$TeeFlag = 1;
196 :			$target = substr($target, 1);
197 :			}
198 :			if ($target =~ m/^>[^>]/) {
199 :			open TRACEFILE, $target;
200 :			print TRACEFILE Now() . " Tracing initialized.\n";
201 :			close TRACEFILE;
202 :			$Destination = ">$target";
203 :			} else {
204 :			$Destination = $target;
205 :			}
206 :			} else {
207 :			$Destination = uc($target);
208 :			}
209 :			# Increment the setup counter.
210 :			$SetupCount++;
211 :	parrello	1.11	}
212 :
213 :	parrello	1.31	=head3 StandardSetup
214 :
215 :	parrello	1.36	C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
216 :	parrello	1.31
217 :			This method performs standard command-line parsing and tracing setup. The return
218 :			values are a hash of the command-line options and a list of the positional
219 :			parameters. Tracing is automatically set up and the command-line options are
220 :			validated.
221 :
222 :			This is a complex method that does a lot of grunt work. The parameters can
223 :			be more easily understood, however, once they are examined individually.
224 :
225 :			The I<categories> parameter is the most obtuse. It is a reference to a list of
226 :			special-purpose tracing categories. Most tracing categories are PERL package
227 :			names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
228 :			B<ERDB>, and B<SproutLoad> packages, you would specify the categories
229 :
230 :			["Sprout", "SproutLoad", "ERDB"]
231 :
232 :			This would cause trace messages in the specified three packages to appear in
233 :			the output. There are threer special tracing categories that are automatically
234 :			handled by this method. In other words, if you used L</TSetup> you would need
235 :			to include these categories manually, but if you use this method they are turned
236 :			on automatically.
237 :
238 :			=over 4
239 :
240 :			=item FIG
241 :
242 :			Turns on trace messages inside the B<FIG> package.
243 :
244 :			=item SQL
245 :
246 :			Traces SQL commands and activity.
247 :
248 :			=item Tracer
249 :
250 :			Traces error messages and call stacks.
251 :
252 :			=back
253 :
254 :			C<SQL> is only turned on if the C<-sql> option is specified in the command line.
255 :			The trace level is specified using the C<-trace> command-line option. For example,
256 :			the following command line for C<TransactFeatures> turns on SQL tracing and runs
257 :			all tracing at level 3.
258 :
259 :			TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
260 :
261 :			Standard tracing is output to the standard output and echoed to the file
262 :	parrello	1.38	C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
263 :			process ID. You can also specify the C<user> parameter to put a user ID
264 :			instead of a process ID in the trace file name. So, for example
265 :	parrello	1.31
266 :	parrello	1.35	The default trace level is 2. To get all messages, specify a trace level of 4.
267 :			For a genome-by-genome update, use 3.
268 :	parrello	1.31
269 :	parrello	1.38	TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
270 :
271 :			would send the trace output to C<traceBruce.log> in the temporary directory.
272 :
273 :	parrello	1.31	The I<options> parameter is a reference to a hash containing the command-line
274 :	parrello	1.36	options, their default values, and an explanation of what they mean. Command-line
275 :			options may be in the form of switches or keywords. In the case of a switch, the
276 :			option value is 1 if it is specified and 0 if it is not specified. In the case
277 :			of a keyword, the value is separated from the option name by an equal sign. You
278 :			can see this last in the command-line example above.
279 :	parrello	1.31
280 :	parrello	1.42	You can specify a different default trace level by setting C<$options->{trace}>
281 :			prior to calling this method.
282 :
283 :	parrello	1.31	An example at this point would help. Consider, for example, the command-line utility
284 :			C<TransactFeatures>. It accepts a list of positional parameters plus the options
285 :			C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
286 :			the following code.
287 :
288 :			my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
289 :	parrello	1.36	{ safe => [0, "use database transactions"],
290 :			noAlias => [0, "do not expect aliases in CHANGE transactions"],
291 :			start => [' ', "start with this genome"],
292 :			tblFiles => [0, "output TBL files containing the corrected IDs"] },
293 :			"command transactionDirectory IDfile",
294 :			@ARGV);
295 :	parrello	1.31
296 :
297 :			The call to C<ParseCommand> specifies the default values for the options and
298 :			stores the actual options in a hash that is returned as C<$options>. The
299 :			positional parameters are returned in C<@parameters>.
300 :
301 :			The following is a sample command line for C<TransactFeatures>.
302 :
303 :			TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
304 :
305 :			In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
306 :			parameters, and would find themselves in I<@parameters> after executing the
307 :			above code fragment. The tracing would be set to level 2, and the categories
308 :			would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
309 :			and C<DocUtils> was included because it came in within the first parameter
310 :			to this method. The I<$options> hash would be
311 :
312 :			{ trace => 2, sql => 0, safe => 0,
313 :			noAlias => 1, start => ' ', tblFiles => 0 }
314 :
315 :			Use of C<StandardSetup> in this way provides a simple way of performing
316 :			standard tracing setup and command-line parsing. Note that the caller is
317 :			not even aware of the command-line switches C<-trace> and C<-sql>, which
318 :			are used by this method to control the tracing. If additional tracing features
319 :			need to be added in the future, they can be processed by this method without
320 :			upsetting the command-line utilities.
321 :
322 :	parrello	1.42	If the C<background> option is specified on the command line, then the
323 :			standard and error outputs will be directed to files in the temporary
324 :			directory, using the same suffix as the trace file. So, if the command
325 :			line specified
326 :
327 :			-user=Bruce -background
328 :
329 :			then the trace output would go to C<traceBruce.log>, the standard output to
330 :			C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
331 :			simplify starting a command in the background.
332 :
333 :	parrello	1.36	Finally, if the special option C<-h> is specified, the option names will
334 :			be traced at level 0 and the program will exit without processing.
335 :			This provides a limited help capability. For example, if the user enters
336 :
337 :			TransactFeatures -h
338 :
339 :			he would see the following output.
340 :
341 :			TransactFeatures [options] command transactionDirectory IDfile
342 :			-trace tracing level (default 2)
343 :			-sql trace SQL commands
344 :			-safe use database transactions
345 :			-noAlias do not expect aliases in CHANGE transactions
346 :			-start start with this genome
347 :			-tblFiles output TBL files containing the corrected IDs
348 :
349 :	parrello	1.44	The caller has the option of modifying the tracing scheme by placing a value
350 :			for C<trace> in the incoming options hash. The default value can be overridden,
351 :			or the tracing to the standard output can be turned off by suffixing a minus
352 :			sign to the trace level. So, for example,
353 :
354 :			{ trace => [0, "tracing level (default 0)"],
355 :			...
356 :
357 :			would set the default trace level to 0 instead of 2, while
358 :
359 :			{ trace => ["2-", "tracing level (default 2)"],
360 :			...
361 :
362 :			would leave the default at 2, but trace only to the log file, not to the
363 :			standard output.
364 :
365 :	parrello	1.31	The parameters to this method are as follows.
366 :
367 :			=over 4
368 :
369 :			=item categories
370 :
371 :			Reference to a list of tracing category names. These should be names of
372 :			packages whose internal workings will need to be debugged to get the
373 :			command working.
374 :
375 :			=item options
376 :
377 :			Reference to a hash containing the legal options for the current command mapped
378 :	parrello	1.36	to their default values and descriptions. The user can override the defaults
379 :			by specifying the options as command-line switches prefixed by a hyphen.
380 :			Tracing-related options may be added to this hash. If the C<-h> option is
381 :			specified on the command line, the option descriptions will be used to
382 :	parrello	1.44	explain the options. To turn off tracing to the standard output, add a
383 :			minus sign to the value for C<trace> (see above).
384 :	parrello	1.36
385 :			=item parmHelp
386 :
387 :			A string that vaguely describes the positional parameters. This is used
388 :			if the user specifies the C<-h> option.
389 :	parrello	1.31
390 :	parrello	1.44	=item argv
391 :	parrello	1.31
392 :			List of command line parameters, including the option switches, which must
393 :			precede the positional parameters and be prefixed by a hyphen.
394 :
395 :			=item RETURN
396 :
397 :			Returns a list. The first element of the list is the reference to a hash that
398 :			maps the command-line option switches to their values. These will either be the
399 :			default values or overrides specified on the command line. The remaining
400 :			elements of the list are the position parameters, in order.
401 :
402 :			=back
403 :
404 :			=cut
405 :
406 :			sub StandardSetup {
407 :			# Get the parameters.
408 :	parrello	1.36	my ($categories, $options, $parmHelp, @argv) = @_;
409 :	parrello	1.31	# Add the tracing options.
410 :	parrello	1.41	if (! exists $options->{trace}) {
411 :			$options->{trace} = [2, "tracing level"];
412 :			}
413 :	parrello	1.36	$options->{sql} = [0, "turn on SQL tracing"];
414 :			$options->{h} = [0, "display command-line options"];
415 :	parrello	1.38	$options->{user} = [$$, "trace log file name suffix"];
416 :	parrello	1.42	$options->{background} = [0, "spool standard and error output"];
417 :	parrello	1.36	# Create a parsing hash from the options hash. The parsing hash
418 :			# contains the default values rather than the default value
419 :			# and the description. While we're at it, we'll memorize the
420 :			# length of the longest option name.
421 :			my $longestName = 0;
422 :			my %parseOptions = ();
423 :			for my $key (keys %{$options}) {
424 :			if (length $key > $longestName) {
425 :			$longestName = length $key;
426 :			}
427 :			$parseOptions{$key} = $options->{$key}->[0];
428 :			}
429 :	parrello	1.31	# Parse the command line.
430 :	parrello	1.36	my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
431 :	parrello	1.42	# Get the logfile suffix.
432 :			my $suffix = $retOptions->{user};
433 :			# Check for background mode.
434 :			if ($retOptions->{background}) {
435 :			my $outFileName = "$FIG_Config::temp/out$suffix.log";
436 :			my $errFileName = "$FIG_Config::temp/err$suffix.log";
437 :			open STDOUT, ">$outFileName";
438 :			open STDERR, ">$errFileName";
439 :			}
440 :	parrello	1.31	# Now we want to set up tracing. First, we need to know if SQL is to
441 :			# be traced.
442 :			my @cats = @{$categories};
443 :			if ($retOptions->{sql}) {
444 :			push @cats, "SQL";
445 :			}
446 :			# Add the default categories.
447 :			push @cats, "Tracer", "FIG";
448 :	parrello	1.44	# Next, we create the category string by joining the categories.
449 :			my $cats = join(" ", @cats);
450 :			# Check to determine whether or not the caller wants to turn off tracing
451 :			# to the standard output.
452 :			my $traceLevel = $retOptions->{trace};
453 :			my $textOKFlag = 1;
454 :			if ($traceLevel =~ /^(.)-/) {
455 :			$traceLevel = $1;
456 :			$textOKFlag = 0;
457 :			}
458 :			# Now we set up the trace mode.
459 :			my $traceMode;
460 :			# Verify that we can open a file in the FIG temporary directory.
461 :	parrello	1.40	my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
462 :			if (open TESTTRACE, ">$traceFileName") {
463 :	parrello	1.44	# Here we can trace to a file.
464 :			$traceMode = ">$traceFileName";
465 :			if ($textOKFlag) {
466 :			# Echo to standard output if the text-OK flag is set.
467 :			$traceMode = "+$traceMode";
468 :			}
469 :			# Close the test file.
470 :	parrello	1.40	close TESTTRACE;
471 :	parrello	1.44	} else {
472 :			# Here we can't trace to a file. We trace to the standard output if it's
473 :			# okay, and the error log otherwise.
474 :			if ($textOKFlag) {
475 :			$traceMode = "TEXT";
476 :			} else {
477 :			$traceMode = "WARN";
478 :			}
479 :	parrello	1.40	}
480 :	parrello	1.31	# Now set up the tracing.
481 :	parrello	1.44	TSetup("$traceLevel $cats", $traceMode);
482 :	parrello	1.36	# Check for the "h" option. If it is specified, dump the command-line
483 :			# options and exit the program.
484 :			if ($retOptions->{h}) {
485 :			$0 =~ m#[/\\](\w+)(\.pl)?$#i;
486 :			Trace("$1 [options] $parmHelp") if T(0);
487 :			for my $key (sort keys %{$options}) {
488 :			my $name = Pad($key, $longestName, 0, ' ');
489 :			my $desc = $options->{$key}->[1];
490 :			if ($options->{$key}->[0]) {
491 :			$desc .= " (default " . $options->{$key}->[0] . ")";
492 :			}
493 :			Trace(" $name $desc") if T(0);
494 :			}
495 :			exit(0);
496 :			}
497 :	parrello	1.31	# Return the parsed parameters.
498 :			return ($retOptions, @retParameters);
499 :			}
500 :
501 :	parrello	1.11	=head3 Setups
502 :
503 :			C<< my $count = Tracer::Setups(); >>
504 :
505 :			Return the number of times L</TSetup> has been called.
506 :
507 :			This method allows for the creation of conditional tracing setups where, for example, we
508 :			may want to set up tracing if nobody else has done it before us.
509 :
510 :			=cut
511 :
512 :			sub Setups {
513 :	parrello	1.12	return $SetupCount;
514 :	olson	1.1	}
515 :
516 :	parrello	1.10	=head3 Open
517 :
518 :			C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
519 :
520 :	parrello	1.11	Open a file.
521 :	parrello	1.10
522 :			The I<$fileSpec> is essentially the second argument of the PERL C<open>
523 :			function. The mode is specified using Unix-like shell information. So, for
524 :			example,
525 :
526 :	parrello	1.12	Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
527 :	parrello	1.10
528 :			would open for output appended to the specified file, and
529 :
530 :	parrello	1.12	Open(\*DATASTREAM, "\| sort -u >$outputFile", "Could not open $outputFile.");
531 :	parrello	1.10
532 :			would open a pipe that sorts the records written and removes duplicates. Note
533 :	parrello	1.11	the use of file handle syntax in the Open call. To use anonymous file handles,
534 :			code as follows.
535 :	parrello	1.10
536 :	parrello	1.12	my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
537 :	parrello	1.10
538 :	parrello	1.11	The I<$message> parameter is used if the open fails. If it is set to C<0>, then
539 :			the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
540 :			failed open will throw an exception and the third parameter will be used to construct
541 :			an error message. If the parameter is omitted, a standard message is constructed
542 :			using the file spec.
543 :	parrello	1.10
544 :	parrello	1.12	Could not open "/usr/spool/news/twitlog"
545 :	parrello	1.10
546 :			Note that the mode characters are automatically cleaned from the file name.
547 :			The actual error message from the file system will be captured and appended to the
548 :			message in any case.
549 :
550 :	parrello	1.12	Could not open "/usr/spool/news/twitlog": file not found.
551 :	parrello	1.10
552 :			In some versions of PERL the only error message we get is a number, which
553 :			corresponds to the C++ C<errno> value.
554 :
555 :	parrello	1.12	Could not open "/usr/spool/news/twitlog": 6.
556 :	parrello	1.10
557 :			=over 4
558 :
559 :			=item fileHandle
560 :
561 :			File handle. If this parameter is C<undef>, a file handle will be generated
562 :			and returned as the value of this method.
563 :
564 :			=item fileSpec
565 :
566 :			File name and mode, as per the PERL C<open> function.
567 :
568 :			=item message (optional)
569 :
570 :			Error message to use if the open fails. If omitted, a standard error message
571 :			will be generated. In either case, the error information from the file system
572 :	parrello	1.11	is appended to the message. To specify a conditional open that does not throw
573 :			an error if it fails, use C<0>.
574 :	parrello	1.10
575 :			=item RETURN
576 :
577 :	parrello	1.11	Returns the name of the file handle assigned to the file, or C<undef> if the
578 :			open failed.
579 :	parrello	1.10
580 :			=back
581 :
582 :			=cut
583 :
584 :			sub Open {
585 :	parrello	1.12	# Get the parameters.
586 :			my ($fileHandle, $fileSpec, $message) = @_;
587 :			# Attempt to open the file.
588 :			my $rv = open $fileHandle, $fileSpec;
589 :			# If the open failed, generate an error message.
590 :			if (! $rv) {
591 :			# Save the system error message.
592 :			my $sysMessage = $!;
593 :			# See if we need a default message.
594 :			if (!$message) {
595 :			# Clean any obvious mode characters and leading spaces from the
596 :			# filename.
597 :			my ($fileName) = FindNamePart($fileSpec);
598 :			$message = "Could not open \"$fileName\"";
599 :			}
600 :			# Terminate with an error using the supplied message and the
601 :			# error message from the file system.
602 :			Confess("$message: $!");
603 :			}
604 :			# Return the file handle.
605 :			return $fileHandle;
606 :	parrello	1.10	}
607 :
608 :	parrello	1.11	=head3 FindNamePart
609 :
610 :			C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
611 :
612 :			Extract the portion of a file specification that contains the file name.
613 :
614 :			A file specification is the string passed to an C<open> call. It specifies the file
615 :			mode and name. In a truly complex situation, it can specify a pipe sequence. This
616 :			method assumes that the file name is whatever follows the first angle bracket
617 :			sequence. So, for example, in the following strings the file name is
618 :			C</usr/fig/myfile.txt>.
619 :
620 :			>>/usr/fig/myfile.txt
621 :			</usr/fig/myfile.txt
622 :			\| sort -u > /usr/fig/myfile.txt
623 :
624 :			If the method cannot find a file name using its normal methods, it will return the
625 :			whole incoming string.
626 :
627 :			=over 4
628 :
629 :			=item fileSpec
630 :
631 :			File specification string from which the file name is to be extracted.
632 :
633 :			=item RETURN
634 :
635 :			Returns a three-element list. The first element contains the file name portion of
636 :			the specified string, or the whole string if a file name cannot be found via normal
637 :			methods. The second element contains the start position of the file name portion and
638 :			the third element contains the length.
639 :
640 :			=back
641 :
642 :			=cut
643 :			#: Return Type $;
644 :			sub FindNamePart {
645 :			# Get the parameters.
646 :			my ($fileSpec) = @_;
647 :	parrello	1.12	# Default to the whole input string.
648 :			my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
649 :	parrello	1.11	# Parse out the file name if we can.
650 :	parrello	1.12	if ($fileSpec =~ m/(<\|>>?)(.+?)(\s*)$/) {
651 :			$retVal = $2;
652 :			$len = length $retVal;
653 :			$pos = (length $fileSpec) - (length $3) - $len;
654 :			}
655 :	parrello	1.11	# Return the result.
656 :			return ($retVal, $pos, $len);
657 :			}
658 :
659 :			=head3 OpenDir
660 :
661 :	parrello	1.31	C<< my @files = OpenDir($dirName, $filtered, $flag); >>
662 :	parrello	1.11
663 :			Open a directory and return all the file names. This function essentially performs
664 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
665 :	parrello	1.31	set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
666 :	parrello	1.33	or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
667 :			filtered out of the return list. If the directory does not open and I<$flag> is not
668 :			set, an exception is thrown. So, for example,
669 :	parrello	1.11
670 :	parrello	1.12	my @files = OpenDir("/Volumes/fig/contigs", 1);
671 :	parrello	1.29
672 :	parrello	1.11	is effectively the same as
673 :
674 :	parrello	1.12	opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
675 :	parrello	1.33	my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
676 :	parrello	1.11
677 :			Similarly, the following code
678 :
679 :	parrello	1.31	my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
680 :	parrello	1.29
681 :	parrello	1.11	Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
682 :	parrello	1.31	automatically returns an empty list if the directory fails to open.
683 :	parrello	1.11
684 :			=over 4
685 :
686 :			=item dirName
687 :
688 :			Name of the directory to open.
689 :
690 :			=item filtered
691 :
692 :			TRUE if files whose names begin with a period (C<.>) should be automatically removed
693 :			from the list, else FALSE.
694 :
695 :	parrello	1.31	=item flag
696 :
697 :			TRUE if a failure to open is okay, else FALSE
698 :
699 :	parrello	1.11	=back
700 :
701 :			=cut
702 :			#: Return Type @;
703 :			sub OpenDir {
704 :			# Get the parameters.
705 :	parrello	1.31	my ($dirName, $filtered, $flag) = @_;
706 :	parrello	1.11	# Declare the return variable.
707 :	parrello	1.31	my @retVal = ();
708 :	parrello	1.12	# Open the directory.
709 :			if (opendir(my $dirHandle, $dirName)) {
710 :			# The directory opened successfully. Get the appropriate list according to the
711 :			# strictures of the filter parameter.
712 :			if ($filtered) {
713 :	parrello	1.33	@retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
714 :	parrello	1.12	} else {
715 :			@retVal = readdir $dirHandle;
716 :			}
717 :	parrello	1.31	} elsif (! $flag) {
718 :			# Here the directory would not open and it's considered an error.
719 :	parrello	1.12	Confess("Could not open directory $dirName.");
720 :			}
721 :	parrello	1.11	# Return the result.
722 :			return @retVal;
723 :			}
724 :
725 :	parrello	1.6	=head3 SetLevel
726 :
727 :			C<< Tracer::SetLevel($newLevel); >>
728 :
729 :			Modify the trace level. A higher trace level will cause more messages to appear.
730 :
731 :			=over 4
732 :
733 :			=item newLevel
734 :
735 :			Proposed new trace level.
736 :
737 :			=back
738 :
739 :			=cut
740 :
741 :			sub SetLevel {
742 :			$TraceLevel = $_[0];
743 :			}
744 :
745 :	olson	1.1	=head3 Now
746 :
747 :			C<< my $string = Tracer::Now(); >>
748 :
749 :			Return a displayable time stamp containing the local time.
750 :
751 :			=cut
752 :
753 :			sub Now {
754 :	parrello	1.12	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
755 :			my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
756 :			_p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
757 :			return $retVal;
758 :	olson	1.1	}
759 :
760 :			# Pad a number to 2 digits.
761 :			sub _p2 {
762 :	parrello	1.12	my ($value) = @_;
763 :			$value = "0$value" if ($value < 10);
764 :			return $value;
765 :	olson	1.1	}
766 :
767 :			=head3 LogErrors
768 :
769 :			C<< Tracer::LogErrors($fileName); >>
770 :
771 :			Route the standard error output to a log file.
772 :
773 :			=over 4
774 :
775 :			=item fileName
776 :
777 :			Name of the file to receive the error output.
778 :
779 :			=back
780 :
781 :			=cut
782 :
783 :			sub LogErrors {
784 :	parrello	1.12	# Get the file name.
785 :			my ($fileName) = @_;
786 :			# Open the file as the standard error output.
787 :			open STDERR, '>', $fileName;
788 :	olson	1.1	}
789 :
790 :	parrello	1.5	=head3 ReadOptions
791 :
792 :			C<< my %options = Tracer::ReadOptions($fileName); >>
793 :
794 :			Read a set of options from a file. Each option is encoded in a line of text that has the
795 :			format
796 :
797 :			I<optionName>C<=>I<optionValue>C<; >I<comment>
798 :
799 :			The option name must consist entirely of letters, digits, and the punctuation characters
800 :	parrello	1.9	C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
801 :			character is a semi-colon will be ignored. The return hash will map each option name to
802 :	parrello	1.5	the corresponding option value.
803 :
804 :			=over 4
805 :
806 :			=item fileName
807 :
808 :			Name of the file containing the option data.
809 :
810 :			=item RETURN
811 :
812 :			Returns a hash mapping the option names specified in the file to their corresponding option
813 :			value.
814 :
815 :			=back
816 :
817 :			=cut
818 :
819 :			sub ReadOptions {
820 :	parrello	1.12	# Get the parameters.
821 :			my ($fileName) = @_;
822 :			# Open the file.
823 :			(open CONFIGFILE, "<$fileName") \|\| Confess("Could not open option file $fileName.");
824 :			# Count the number of records read.
825 :			my ($records, $comments) = 0;
826 :			# Create the return hash.
827 :			my %retVal = ();
828 :			# Loop through the file, accumulating key-value pairs.
829 :			while (my $line = <CONFIGFILE>) {
830 :			# Denote we've read a line.
831 :			$records++;
832 :			# Determine the line type.
833 :			if ($line =~ /^\s*[\n\r]/) {
834 :			# A blank line is a comment.
835 :			$comments++;
836 :			} elsif ($line =~ /^\s([A-Za-z0-9_\.]+)=([^;]);/) {
837 :			# Here we have an option assignment.
838 :			retVal{$1} = $2;
839 :			} elsif ($line =~ /^\s*;/) {
840 :			# Here we have a text comment.
841 :			$comments++;
842 :			} else {
843 :			# Here we have an invalid line.
844 :			Trace("Invalid option statement in record $records.") if T(0);
845 :			}
846 :			}
847 :			# Return the hash created.
848 :			return %retVal;
849 :	parrello	1.5	}
850 :
851 :	olson	1.1	=head3 GetOptions
852 :
853 :			C<< Tracer::GetOptions(\%defaults, \%options); >>
854 :
855 :			Merge a specified set of options into a table of defaults. This method takes two hash references
856 :			as input and uses the data from the second to update the first. If the second does not exist,
857 :			there will be no effect. An error will be thrown if one of the entries in the second hash does not
858 :			exist in the first.
859 :
860 :			Consider the following example.
861 :
862 :			C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
863 :
864 :			In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
865 :			B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
866 :			B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
867 :			the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
868 :			will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
869 :
870 :			C<< {databaseType => 'Oracle'} >>
871 :
872 :			an error will occur because the B<databaseType> option does not exist.
873 :
874 :			=over 4
875 :
876 :			=item defaults
877 :
878 :			Table of default option values.
879 :
880 :			=item options
881 :
882 :			Table of overrides, if any.
883 :
884 :			=item RETURN
885 :
886 :			Returns a reference to the default table passed in as the first parameter.
887 :
888 :			=back
889 :
890 :			=cut
891 :
892 :			sub GetOptions {
893 :	parrello	1.12	# Get the parameters.
894 :			my ($defaults, $options) = @_;
895 :			# Check for overrides.
896 :			if ($options) {
897 :			# Loop through the overrides.
898 :			while (my ($option, $setting) = each %{$options}) {
899 :			# Insure this override exists.
900 :			if (!exists $defaults->{$option}) {
901 :			croak "Unrecognized option $option encountered.";
902 :			} else {
903 :			# Apply the override.
904 :			$defaults->{$option} = $setting;
905 :			}
906 :			}
907 :			}
908 :			# Return the merged table.
909 :			return $defaults;
910 :	olson	1.1	}
911 :
912 :			=head3 MergeOptions
913 :
914 :			C<< Tracer::MergeOptions(\%table, \%defaults); >>
915 :
916 :			Merge default values into a hash table. This method looks at the key-value pairs in the
917 :			second (default) hash, and if a matching key is not found in the first hash, the default
918 :			pair is copied in. The process is similar to L</GetOptions>, but there is no error-
919 :			checking and no return value.
920 :
921 :			=over 4
922 :
923 :			=item table
924 :
925 :			Hash table to be updated with the default values.
926 :
927 :			=item defaults
928 :
929 :			Default values to be merged into the first hash table if they are not already present.
930 :
931 :			=back
932 :
933 :			=cut
934 :
935 :			sub MergeOptions {
936 :	parrello	1.12	# Get the parameters.
937 :			my ($table, $defaults) = @_;
938 :			# Loop through the defaults.
939 :			while (my ($key, $value) = each %{$defaults}) {
940 :			if (!exists $table->{$key}) {
941 :			$table->{$key} = $value;
942 :			}
943 :			}
944 :	olson	1.1	}
945 :
946 :			=head3 Trace
947 :
948 :			C<< Trace($message); >>
949 :
950 :			Write a trace message to the target location specified in L</TSetup>. If there has not been
951 :			any prior call to B<TSetup>.
952 :
953 :			=over 4
954 :
955 :			=item message
956 :
957 :			Message to write.
958 :
959 :			=back
960 :
961 :			=cut
962 :
963 :			sub Trace {
964 :	parrello	1.12	# Get the parameters.
965 :			my ($message) = @_;
966 :			# Get the timestamp.
967 :			my $timeStamp = Now();
968 :			# Format the message. Note we strip off any line terminators at the end.
969 :			my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);
970 :			# Process according to the destination.
971 :			if ($Destination eq "TEXT") {
972 :			# Write the message to the standard output.
973 :			print "$formatted\n";
974 :			} elsif ($Destination eq "ERROR") {
975 :			# Write the message to the error output.
976 :			print STDERR "$formatted\n";
977 :			} elsif ($Destination eq "QUEUE") {
978 :			# Push the message into the queue.
979 :			push @Queue, "$formatted";
980 :			} elsif ($Destination eq "HTML") {
981 :			# Convert the message to HTML and write it to the standard output.
982 :			my $escapedMessage = CGI::escapeHTML($message);
983 :			print "<p>$formatted</p>\n";
984 :	parrello	1.4	} elsif ($Destination eq "WARN") {
985 :			# Emit the message as a warning.
986 :			warn $message;
987 :	parrello	1.12	} elsif ($Destination =~ m/^>>/) {
988 :			# Write the trace message to an output file.
989 :	parrello	1.14	(open TRACING, $Destination) \|\| die "Tracing open for \"$Destination\" failed: $!";
990 :	parrello	1.12	print TRACING "$formatted\n";
991 :			close TRACING;
992 :			# If the Tee flag is on, echo it to the standard output.
993 :			if ($TeeFlag) {
994 :			print "$formatted\n";
995 :			}
996 :			}
997 :	olson	1.1	}
998 :
999 :			=head3 T
1000 :
1001 :	parrello	1.2	C<< my $switch = T($category, $traceLevel); >>
1002 :	olson	1.1
1003 :	parrello	1.12	or
1004 :	parrello	1.2
1005 :	olson	1.1	C<< my $switch = T($traceLevel); >>
1006 :
1007 :			Return TRUE if the trace level is at or above a specified value and the specified category
1008 :			is active, else FALSE. If no category is specified, the caller's package name is used.
1009 :
1010 :			=over 4
1011 :
1012 :			=item category
1013 :
1014 :			Category to which the message belongs. If not specified, the caller's package name is
1015 :			used.
1016 :
1017 :			=item traceLevel
1018 :
1019 :			Relevant tracing level.
1020 :
1021 :			=item RETURN
1022 :
1023 :			TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1024 :
1025 :			=back
1026 :
1027 :			=cut
1028 :
1029 :			sub T {
1030 :	parrello	1.12	# Declare the return variable.
1031 :			my $retVal = 0;
1032 :			# Only proceed if tracing is turned on.
1033 :			if ($Destination ne "NONE") {
1034 :			# Get the parameters.
1035 :			my ($category, $traceLevel) = @_;
1036 :			if (!defined $traceLevel) {
1037 :			# Here we have no category, so we need to get the calling package.
1038 :			# The calling package is normally the first parameter. If it is
1039 :			# omitted, the first parameter will be the tracelevel. So, the
1040 :			# first thing we do is shift the so-called category into the
1041 :			# $traceLevel variable where it belongs.
1042 :			$traceLevel = $category;
1043 :			my ($package, $fileName, $line) = caller;
1044 :	parrello	1.3	# If there is no calling package, we default to "main".
1045 :	parrello	1.12	if (!$package) {
1046 :	parrello	1.3	$category = "main";
1047 :	parrello	1.12	} else {
1048 :			$category = $package;
1049 :			}
1050 :			}
1051 :	parrello	1.7	# Save the category name.
1052 :			$LastCategory = $category;
1053 :	parrello	1.13	# Convert it to lower case before we hash it.
1054 :			$category = lc $category;
1055 :	parrello	1.12	# Use the category and tracelevel to compute the result.
1056 :	parrello	1.36	if (ref $traceLevel) {
1057 :			Confess("Bad trace level.");
1058 :			} elsif (ref $TraceLevel) {
1059 :			Confess("Bad trace config.");
1060 :			}
1061 :	parrello	1.12	$retVal = ($traceLevel <= $TraceLevel && ($AllTrace \|\| exists $Categories{$category}));
1062 :	parrello	1.3	}
1063 :	parrello	1.12	# Return the computed result.
1064 :	parrello	1.3	return $retVal;
1065 :	olson	1.1	}
1066 :
1067 :			=head3 ParseCommand
1068 :
1069 :			C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1070 :
1071 :			Parse a command line consisting of a list of parameters. The initial parameters may be option
1072 :	parrello	1.2	specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1073 :			off and merged into a table of default options. The remainder of the command line is
1074 :	olson	1.1	returned as a list of positional arguments. For example, consider the following invocation.
1075 :
1076 :			C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1077 :
1078 :			In this case, the list @words will be treated as a command line. There are two options available,
1079 :			B<errors> and B<logFile>. If @words has the following format
1080 :
1081 :			C<< -logFile=error.log apple orange rutabaga >>
1082 :
1083 :			then at the end of the invocation, C<$options> will be
1084 :
1085 :			C<< { errors => 0, logFile => 'error.log' } >>
1086 :
1087 :			and C<@arguments> will contain
1088 :
1089 :			C<< apple orange rutabaga >>
1090 :
1091 :	parrello	1.2	The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1092 :	olson	1.1	support for quote characters.
1093 :
1094 :			=over 4
1095 :
1096 :			=item optionTable
1097 :
1098 :			Table of default options.
1099 :
1100 :			=item inputList
1101 :
1102 :			List of words on the command line.
1103 :
1104 :			=item RETURN
1105 :
1106 :			Returns a reference to the option table and a list of the positional arguments.
1107 :
1108 :			=back
1109 :
1110 :			=cut
1111 :
1112 :			sub ParseCommand {
1113 :	parrello	1.12	# Get the parameters.
1114 :			my ($optionTable, @inputList) = @_;
1115 :			# Process any options in the input list.
1116 :			my %overrides = ();
1117 :			while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1118 :			# Get the current option.
1119 :			my $arg = shift @inputList;
1120 :			# Pull out the option name.
1121 :			$arg =~ /^-([^=]*)/g;
1122 :			my $name = $1;
1123 :			# Check for an option value.
1124 :			if ($arg =~ /\G=(.*)$/g) {
1125 :			# Here we have a value for the option.
1126 :			$overrides{$name} = UnEscape($1);
1127 :			} else {
1128 :			# Here there is no value, so we use 1.
1129 :			$overrides{$name} = 1;
1130 :			}
1131 :			}
1132 :			# Merge the options into the defaults.
1133 :			GetOptions($optionTable, \%overrides);
1134 :			# Translate the remaining parameters.
1135 :			my @retVal = ();
1136 :			for my $inputParm (@inputList) {
1137 :			push @retVal, UnEscape($inputParm);
1138 :			}
1139 :			# Return the results.
1140 :			return ($optionTable, @retVal);
1141 :	olson	1.1	}
1142 :
1143 :	parrello	1.9	=head3 Escape
1144 :
1145 :			C<< my $codedString = Tracer::Escape($realString); >>
1146 :
1147 :	parrello	1.25	Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1148 :	parrello	1.28	replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1149 :			result is to reverse the effect of L</UnEscape>.
1150 :	parrello	1.9
1151 :			=over 4
1152 :
1153 :			=item realString
1154 :
1155 :			String to escape.
1156 :
1157 :			=item RETURN
1158 :
1159 :			Escaped equivalent of the real string.
1160 :
1161 :			=back
1162 :
1163 :			=cut
1164 :
1165 :			sub Escape {
1166 :	parrello	1.12	# Get the parameter.
1167 :			my ($realString) = @_;
1168 :			# Initialize the return variable.
1169 :			my $retVal = "";
1170 :			# Loop through the parameter string, looking for sequences to escape.
1171 :			while (length $realString > 0) {
1172 :			# Look for the first sequence to escape.
1173 :	parrello	1.27	if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1174 :	parrello	1.12	# Here we found it. The text preceding the sequence is in $1. The sequence
1175 :			# itself is in $2. First, move the clear text to the return variable.
1176 :			$retVal .= $1;
1177 :	parrello	1.14	# Strip the processed section off the real string.
1178 :			$realString = substr $realString, (length $2) + (length $1);
1179 :	parrello	1.28	# Get the matched character.
1180 :	parrello	1.12	my $char = $2;
1181 :	parrello	1.28	# If we have a CR, we are done.
1182 :			if ($char ne "\r") {
1183 :			# It's not a CR, so encode the escape sequence.
1184 :			$char =~ tr/\t\n/tn/;
1185 :			$retVal .= "\\" . $char;
1186 :			}
1187 :	parrello	1.12	} else {
1188 :			# Here there are no more escape sequences. The rest of the string is
1189 :			# transferred unmodified.
1190 :			$retVal .= $realString;
1191 :			$realString = "";
1192 :			}
1193 :			}
1194 :			# Return the result.
1195 :			return $retVal;
1196 :	parrello	1.9	}
1197 :
1198 :	olson	1.1	=head3 UnEscape
1199 :
1200 :			C<< my $realString = Tracer::UnEscape($codedString); >>
1201 :
1202 :	parrello	1.25	Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1203 :	parrello	1.28	a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1204 :			be deleted.
1205 :	olson	1.1
1206 :			=over 4
1207 :
1208 :			=item codedString
1209 :
1210 :			String to un-escape.
1211 :
1212 :			=item RETURN
1213 :
1214 :			Returns a copy of the original string with the escape sequences converted to their actual
1215 :			values.
1216 :
1217 :			=back
1218 :
1219 :			=cut
1220 :
1221 :			sub UnEscape {
1222 :	parrello	1.12	# Get the parameter.
1223 :			my ($codedString) = @_;
1224 :			# Initialize the return variable.
1225 :			my $retVal = "";
1226 :			# Only proceed if the incoming string is nonempty.
1227 :			if (defined $codedString) {
1228 :			# Loop through the parameter string, looking for escape sequences. We can't do
1229 :	parrello	1.25	# translating because it causes problems with the escaped slash. ("\\t" becomes
1230 :			# "\<tab>" no matter what we do.)
1231 :	parrello	1.12	while (length $codedString > 0) {
1232 :			# Look for the first escape sequence.
1233 :	parrello	1.27	if ($codedString =~ /^(.*?)\\(\\\|n\|t\|r)/) {
1234 :	parrello	1.12	# Here we found it. The text preceding the sequence is in $1. The sequence
1235 :			# itself is in $2. First, move the clear text to the return variable.
1236 :			$retVal .= $1;
1237 :			$codedString = substr $codedString, (2 + length $1);
1238 :	parrello	1.28	# Get the escape value.
1239 :	parrello	1.12	my $char = $2;
1240 :	parrello	1.28	# If we have a "\r", we are done.
1241 :			if ($char ne 'r') {
1242 :			# Here it's not an 'r', so we convert it.
1243 :			$char =~ tr/\\tn/\\\t\n/;
1244 :			$retVal .= $char;
1245 :			}
1246 :	parrello	1.12	} else {
1247 :			# Here there are no more escape sequences. The rest of the string is
1248 :			# transferred unmodified.
1249 :			$retVal .= $codedString;
1250 :			$codedString = "";
1251 :			}
1252 :			}
1253 :			}
1254 :			# Return the result.
1255 :			return $retVal;
1256 :	olson	1.1	}
1257 :
1258 :			=head3 ParseRecord
1259 :
1260 :			C<< my @fields = Tracer::ParseRecord($line); >>
1261 :
1262 :			Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1263 :			and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1264 :			These will automatically be converted.
1265 :
1266 :			=over 4
1267 :
1268 :			=item line
1269 :
1270 :			Line of data containing the tab-delimited fields.
1271 :
1272 :			=item RETURN
1273 :
1274 :			Returns a list of the fields found in the data line.
1275 :
1276 :			=back
1277 :
1278 :			=cut
1279 :
1280 :			sub ParseRecord {
1281 :	parrello	1.12	# Get the parameter.
1282 :			my ($line) = @_;
1283 :			# Remove the trailing new-line, if any.
1284 :			chomp $line;
1285 :			# Split the line read into pieces using the tab character.
1286 :			my @retVal = split /\t/, $line;
1287 :			# Trim and fix the escapes in each piece.
1288 :			for my $value (@retVal) {
1289 :			# Trim leading whitespace.
1290 :			$value =~ s/^\s+//;
1291 :			# Trim trailing whitespace.
1292 :			$value =~ s/\s+$//;
1293 :			# Delete the carriage returns.
1294 :			$value =~ s/\r//g;
1295 :			# Convert the escapes into their real values.
1296 :			$value =~ s/\\t/"\t"/ge;
1297 :			$value =~ s/\\n/"\n"/ge;
1298 :			}
1299 :			# Return the result.
1300 :			return @retVal;
1301 :	olson	1.1	}
1302 :
1303 :			=head3 Merge
1304 :
1305 :			C<< my @mergedList = Tracer::Merge(@inputList); >>
1306 :
1307 :			Sort a list of strings and remove duplicates.
1308 :
1309 :			=over 4
1310 :
1311 :			=item inputList
1312 :
1313 :			List of scalars to sort and merge.
1314 :
1315 :			=item RETURN
1316 :
1317 :			Returns a list containing the same elements sorted in ascending order with duplicates
1318 :			removed.
1319 :
1320 :			=back
1321 :
1322 :			=cut
1323 :
1324 :			sub Merge {
1325 :	parrello	1.12	# Get the input list in sort order.
1326 :			my @inputList = sort @_;
1327 :			# Only proceed if the list has at least two elements.
1328 :			if (@inputList > 1) {
1329 :			# Now we want to move through the list splicing out duplicates.
1330 :			my $i = 0;
1331 :			while ($i < @inputList) {
1332 :			# Get the current entry.
1333 :			my $thisEntry = $inputList[$i];
1334 :			# Find out how many elements duplicate the current entry.
1335 :			my $j = $i + 1;
1336 :			my $dup1 = $i + 1;
1337 :			while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1338 :			# If the number is nonzero, splice out the duplicates found.
1339 :			if ($j > $dup1) {
1340 :			splice @inputList, $dup1, $j - $dup1;
1341 :			}
1342 :			# Now the element at position $dup1 is different from the element before it
1343 :			# at position $i. We push $i forward one position and start again.
1344 :			$i++;
1345 :			}
1346 :			}
1347 :			# Return the merged list.
1348 :			return @inputList;
1349 :	olson	1.1	}
1350 :
1351 :			=head3 GetFile
1352 :
1353 :	parrello	1.6	C<< my @fileContents = Tracer::GetFile($fileName); >>
1354 :	olson	1.1
1355 :	parrello	1.35	or
1356 :
1357 :			C<< my $fileContents = Tracer::GetFile($fileName); >>
1358 :
1359 :			Return the entire contents of a file. In list context, line-ends are removed and
1360 :			each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1361 :	olson	1.1
1362 :			=over 4
1363 :
1364 :			=item fileName
1365 :
1366 :			Name of the file to read.
1367 :
1368 :			=item RETURN
1369 :
1370 :	parrello	1.6	In a list context, returns the entire file as a list with the line terminators removed.
1371 :	parrello	1.39	In a scalar context, returns the entire file as a string. If an error occurs opening
1372 :			the file, an empty list will be returned.
1373 :	olson	1.1
1374 :			=back
1375 :
1376 :			=cut
1377 :
1378 :			sub GetFile {
1379 :	parrello	1.12	# Get the parameters.
1380 :			my ($fileName) = @_;
1381 :			# Declare the return variable.
1382 :			my @retVal = ();
1383 :			# Open the file for input.
1384 :			my $ok = open INPUTFILE, "<$fileName";
1385 :			if (!$ok) {
1386 :			# If we had an error, trace it. We will automatically return a null value.
1387 :	parrello	1.16	Trace("Could not open \"$fileName\" for input: $!") if T(0);
1388 :	parrello	1.12	} else {
1389 :			# Read the whole file into the return variable, stripping off any terminator
1390 :	parrello	1.6	# characters.
1391 :			my $lineCount = 0;
1392 :	parrello	1.12	while (my $line = <INPUTFILE>) {
1393 :	parrello	1.6	$lineCount++;
1394 :	parrello	1.9	$line = Strip($line);
1395 :	parrello	1.12	push @retVal, $line;
1396 :			}
1397 :			# Close it.
1398 :			close INPUTFILE;
1399 :	parrello	1.6	my $actualLines = @retVal;
1400 :	parrello	1.12	}
1401 :			# Return the file's contents in the desired format.
1402 :	parrello	1.9	if (wantarray) {
1403 :	parrello	1.12	return @retVal;
1404 :	parrello	1.6	} else {
1405 :			return join "\n", @retVal;
1406 :			}
1407 :	olson	1.1	}
1408 :
1409 :			=head3 QTrace
1410 :
1411 :			C<< my $data = QTrace($format); >>
1412 :
1413 :			Return the queued trace data in the specified format.
1414 :
1415 :			=over 4
1416 :
1417 :			=item format
1418 :
1419 :			C<html> to format the data as an HTML list, C<text> to format it as straight text.
1420 :
1421 :			=back
1422 :
1423 :			=cut
1424 :
1425 :			sub QTrace {
1426 :	parrello	1.12	# Get the parameter.
1427 :			my ($format) = @_;
1428 :			# Create the return variable.
1429 :			my $retVal = "";
1430 :	parrello	1.14	# Only proceed if there is an actual queue.
1431 :			if (@Queue) {
1432 :			# Process according to the format.
1433 :			if ($format =~ m/^HTML$/i) {
1434 :			# Convert the queue into an HTML list.
1435 :			$retVal = "<ul>\n";
1436 :			for my $line (@Queue) {
1437 :			my $escapedLine = CGI::escapeHTML($line);
1438 :			$retVal .= "<li>$escapedLine</li>\n";
1439 :			}
1440 :			$retVal .= "</ul>\n";
1441 :			} elsif ($format =~ m/^TEXT$/i) {
1442 :			# Convert the queue into a list of text lines.
1443 :			$retVal = join("\n", @Queue) . "\n";
1444 :			}
1445 :			# Clear the queue.
1446 :			@Queue = ();
1447 :	parrello	1.12	}
1448 :			# Return the formatted list.
1449 :			return $retVal;
1450 :	olson	1.1	}
1451 :
1452 :			=head3 Confess
1453 :
1454 :			C<< Confess($message); >>
1455 :
1456 :	parrello	1.22	Trace the call stack and abort the program with the specified message. When used with
1457 :	parrello	1.9	the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1458 :	parrello	1.6	So, for example
1459 :	olson	1.1
1460 :	parrello	1.6	C<< Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum."); >>
1461 :	olson	1.1
1462 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
1463 :
1464 :			=over 4
1465 :
1466 :			=item message
1467 :
1468 :			Message to include in the trace.
1469 :
1470 :			=back
1471 :
1472 :			=cut
1473 :
1474 :			sub Confess {
1475 :	parrello	1.12	# Get the parameters.
1476 :			my ($message) = @_;
1477 :			# Trace the call stack.
1478 :	parrello	1.22	Cluck($message);
1479 :	parrello	1.12	# Abort the program.
1480 :			croak(">>> $message");
1481 :	olson	1.1	}
1482 :
1483 :	parrello	1.6	=head3 Assert
1484 :
1485 :			C<< Assert($condition1, $condition2, ... $conditionN); >>
1486 :
1487 :			Return TRUE if all the conditions are true. This method can be used in conjunction with
1488 :	parrello	1.29	the OR operator and the L</Confess> method as a debugging assert.
1489 :	parrello	1.6	So, for example
1490 :
1491 :			C<< Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum."); >>
1492 :
1493 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
1494 :
1495 :			=cut
1496 :			sub Assert {
1497 :			my $retVal = 1;
1498 :			LOOP: for my $condition (@_) {
1499 :			if (! $condition) {
1500 :			$retVal = 0;
1501 :			last LOOP;
1502 :			}
1503 :			}
1504 :			return $retVal;
1505 :			}
1506 :
1507 :	olson	1.1	=head3 Cluck
1508 :
1509 :			C<< Cluck($message); >>
1510 :
1511 :			Trace the call stack. Note that for best results, you should qualify the call with a
1512 :			trace condition. For example,
1513 :
1514 :			C<< Cluck("Starting record parse.") if T(3); >>
1515 :
1516 :			will only trace the stack if the trace level for the package is 3 or more.
1517 :
1518 :			=over 4
1519 :
1520 :			=item message
1521 :
1522 :			Message to include in the trace.
1523 :
1524 :			=back
1525 :
1526 :			=cut
1527 :
1528 :			sub Cluck {
1529 :	parrello	1.12	# Get the parameters.
1530 :			my ($message) = @_;
1531 :	parrello	1.5	# Trace what's happening.
1532 :			Trace("Stack trace for event: $message");
1533 :	parrello	1.12	my $confession = longmess($message);
1534 :			# Convert the confession to a series of trace messages. Note we skip any
1535 :	parrello	1.5	# messages relating to calls into Tracer.
1536 :	parrello	1.12	for my $line (split /\s*\n/, $confession) {
1537 :			Trace($line) if ($line !~ /Tracer\.pm/);
1538 :			}
1539 :	olson	1.1	}
1540 :
1541 :	parrello	1.5	=head3 Min
1542 :
1543 :			C<< my $min = Min($value1, $value2, ... $valueN); >>
1544 :
1545 :			Return the minimum argument. The arguments are treated as numbers.
1546 :
1547 :			=over 4
1548 :
1549 :			=item $value1, $value2, ... $valueN
1550 :
1551 :			List of numbers to compare.
1552 :
1553 :			=item RETURN
1554 :
1555 :			Returns the lowest number in the list.
1556 :
1557 :			=back
1558 :
1559 :			=cut
1560 :
1561 :			sub Min {
1562 :	parrello	1.12	# Get the parameters. Note that we prime the return value with the first parameter.
1563 :			my ($retVal, @values) = @_;
1564 :			# Loop through the remaining parameters, looking for the lowest.
1565 :			for my $value (@values) {
1566 :			if ($value < $retVal) {
1567 :			$retVal = $value;
1568 :			}
1569 :			}
1570 :			# Return the minimum found.
1571 :			return $retVal;
1572 :	parrello	1.5	}
1573 :
1574 :			=head3 Max
1575 :
1576 :			C<< my $max = Max($value1, $value2, ... $valueN); >>
1577 :
1578 :			Return the maximum argument. The arguments are treated as numbers.
1579 :
1580 :			=over 4
1581 :
1582 :			=item $value1, $value2, ... $valueN
1583 :
1584 :			List of numbers to compare.
1585 :
1586 :			=item RETURN
1587 :
1588 :			Returns the highest number in the list.
1589 :
1590 :			=back
1591 :
1592 :			=cut
1593 :
1594 :			sub Max {
1595 :	parrello	1.12	# Get the parameters. Note that we prime the return value with the first parameter.
1596 :			my ($retVal, @values) = @_;
1597 :			# Loop through the remaining parameters, looking for the highest.
1598 :			for my $value (@values) {
1599 :			if ($value > $retVal) {
1600 :			$retVal = $value;
1601 :			}
1602 :			}
1603 :			# Return the maximum found.
1604 :			return $retVal;
1605 :	parrello	1.5	}
1606 :
1607 :			=head3 AddToListMap
1608 :
1609 :			C<< Tracer::AddToListMap(\%hash, $key, $value); >>
1610 :
1611 :			Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1612 :			is created for the key. Otherwise, the new value is pushed onto the list.
1613 :
1614 :			=over 4
1615 :
1616 :			=item hash
1617 :
1618 :			Reference to the target hash.
1619 :
1620 :			=item key
1621 :
1622 :			Key for which the value is to be added.
1623 :
1624 :			=item value
1625 :
1626 :			Value to add to the key's value list.
1627 :
1628 :			=back
1629 :
1630 :			=cut
1631 :
1632 :			sub AddToListMap {
1633 :			# Get the parameters.
1634 :			my ($hash, $key, $value) = @_;
1635 :			# Process according to whether or not the key already has a value.
1636 :			if (! exists $hash->{$key}) {
1637 :			$hash->{$key} = [$value];
1638 :			} else {
1639 :			push @{$hash->{$key}}, $value;
1640 :			}
1641 :			}
1642 :	olson	1.1
1643 :	parrello	1.7	=head3 DebugMode
1644 :
1645 :			C<< if (Tracer::DebugMode) { ...code... } >>
1646 :
1647 :	parrello	1.22	Return TRUE if debug mode has been turned on, else output an error
1648 :			page and return FALSE.
1649 :	parrello	1.7
1650 :			Certain CGI scripts are too dangerous to exist in the production
1651 :			environment. This method provides a simple way to prevent them
1652 :	parrello	1.21	from working unless they are explicitly turned on by creating a password
1653 :			cookie via the B<SetPassword> script. If debugging mode
1654 :	parrello	1.22	is not turned on, an error web page will be output directing the
1655 :			user to enter in the correct password.
1656 :	parrello	1.7
1657 :			=cut
1658 :
1659 :			sub DebugMode {
1660 :	parrello	1.12	# Declare the return variable.
1661 :	parrello	1.21	my $retVal = 0;
1662 :	parrello	1.12	# Check the debug configuration.
1663 :	parrello	1.21	my $password = CGI::cookie("DebugMode");
1664 :			my $encrypted = Digest::MD5::md5_hex($password);
1665 :			if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1666 :	parrello	1.12	$retVal = 1;
1667 :			} else {
1668 :			# Here debug mode is off, so we generate an error page.
1669 :	parrello	1.9	my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");
1670 :	parrello	1.12	print $pageString;
1671 :			}
1672 :			# Return the determination indicator.
1673 :	parrello	1.18	return $retVal;
1674 :	parrello	1.9	}
1675 :
1676 :			=head3 Strip
1677 :
1678 :			C<< my $string = Tracer::Strip($line); >>
1679 :
1680 :			Strip all line terminators off a string. This is necessary when dealing with files
1681 :			that may have been transferred back and forth several times among different
1682 :			operating environments.
1683 :
1684 :			=over 4
1685 :
1686 :			=item line
1687 :
1688 :			Line of text to be stripped.
1689 :
1690 :			=item RETURN
1691 :
1692 :			The same line of text with all the line-ending characters chopped from the end.
1693 :
1694 :			=back
1695 :
1696 :			=cut
1697 :
1698 :			sub Strip {
1699 :	parrello	1.12	# Get a copy of the parameter string.
1700 :			my ($string) = @_;
1701 :	parrello	1.29	my $retVal = (defined $string ? $string : "");
1702 :	parrello	1.9	# Strip the line terminator characters.
1703 :			$retVal =~ s/(\r\|\n)+$//g;
1704 :	parrello	1.12	# Return the result.
1705 :			return $retVal;
1706 :	parrello	1.9	}
1707 :
1708 :			=head3 Pad
1709 :
1710 :			C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1711 :
1712 :			Pad a string to a specified length. The pad character will be a
1713 :			space, and the padding will be on the right side unless specified
1714 :			in the third parameter.
1715 :
1716 :			=over 4
1717 :
1718 :			=item string
1719 :
1720 :			String to be padded.
1721 :
1722 :			=item len
1723 :
1724 :			Desired length of the padded string.
1725 :
1726 :			=item left (optional)
1727 :
1728 :			TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1729 :
1730 :			=item padChar (optional)
1731 :
1732 :	parrello	1.22	Character to use for padding. The default is a space.
1733 :
1734 :	parrello	1.9	=item RETURN
1735 :
1736 :	parrello	1.22	Returns a copy of the original string with the pad character added to the
1737 :			specified end so that it achieves the desired length.
1738 :	parrello	1.9
1739 :			=back
1740 :
1741 :			=cut
1742 :
1743 :			sub Pad {
1744 :	parrello	1.12	# Get the parameters.
1745 :			my ($string, $len, $left, $padChar) = @_;
1746 :			# Compute the padding character.
1747 :			if (! defined $padChar) {
1748 :			$padChar = " ";
1749 :			}
1750 :			# Compute the number of spaces needed.
1751 :			my $needed = $len - length $string;
1752 :			# Copy the string into the return variable.
1753 :			my $retVal = $string;
1754 :			# Only proceed if padding is needed.
1755 :			if ($needed > 0) {
1756 :			# Create the pad string.
1757 :			my $pad = $padChar x $needed;
1758 :			# Affix it to the return value.
1759 :			if ($left) {
1760 :			$retVal = $pad . $retVal;
1761 :			} else {
1762 :			$retVal .= $pad;
1763 :			}
1764 :			}
1765 :			# Return the result.
1766 :			return $retVal;
1767 :	parrello	1.7	}
1768 :
1769 :	parrello	1.29	=head3 EOF
1770 :
1771 :			This is a constant that is lexically greater than any useful string.
1772 :
1773 :			=cut
1774 :
1775 :			sub EOF {
1776 :			return "\xFF\xFF\xFF\xFF\xFF";
1777 :			}
1778 :
1779 :	parrello	1.15	=head3 TICK
1780 :
1781 :			C<< my @results = TICK($commandString); >>
1782 :
1783 :			Perform a back-tick operation on a command. If this is a Windows environment, any leading
1784 :			dot-slash (C<./> will be removed. So, for example, if you were doing
1785 :
1786 :			`./protein.cgi`
1787 :
1788 :			from inside a CGI script, it would work fine in Unix, but would issue an error message
1789 :			in Windows complaining that C<'.'> is not a valid command. If instead you code
1790 :
1791 :			TICK("./protein.cgi")
1792 :
1793 :			it will work correctly in both environments.
1794 :
1795 :			=over 4
1796 :
1797 :			=item commandString
1798 :
1799 :			The command string to pass to the system.
1800 :
1801 :			=item RETURN
1802 :
1803 :			Returns the standard output from the specified command, as a list.
1804 :
1805 :			=back
1806 :
1807 :			=cut
1808 :			#: Return Type @;
1809 :			sub TICK {
1810 :			# Get the parameters.
1811 :			my ($commandString) = @_;
1812 :			# Chop off the dot-slash if this is Windows.
1813 :			if ($FIG_Config::win_mode) {
1814 :			$commandString =~ s!^\./!!;
1815 :			}
1816 :			# Activate the command and return the result.
1817 :			return `$commandString`;
1818 :			}
1819 :
1820 :	parrello	1.35	=head3 ScriptSetup
1821 :
1822 :			C<< my ($query, $varHash) = ScriptSetup(); >>
1823 :
1824 :			Perform standard tracing and debugging setup for scripts. The value returned is
1825 :			the CGI object followed by a pre-built variable hash.
1826 :
1827 :			The C<Trace> query parameter is used to determine whether or not tracing is active and
1828 :			which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1829 :			the C<CGI> trace module will trace parameter and environment information. Parameters are
1830 :			traced at level 3 and environment variables at level 4. At the end of the script, the
1831 :			client should call L</ScriptFinish> to output the web page.
1832 :
1833 :			=cut
1834 :
1835 :			sub ScriptSetup {
1836 :			# Get the CGI query object.
1837 :			my $query = CGI->new();
1838 :			# Check for tracing. Set it up if the user asked for it.
1839 :			if ($query->param('Trace')) {
1840 :			# Set up tracing to be queued for display at the bottom of the web page.
1841 :			TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1842 :			# Trace the parameter and environment data.
1843 :			if (T(CGI => 3)) {
1844 :			# Here we want to trace the parameter data.
1845 :			my @names = $query->param;
1846 :			for my $parmName (sort @names) {
1847 :			# Note we skip "Trace", which is for our use only.
1848 :			if ($parmName ne 'Trace') {
1849 :			my @values = $query->param($parmName);
1850 :			Trace("CGI: $parmName = " . join(", ", @values));
1851 :			}
1852 :			}
1853 :			}
1854 :			if (T(CGI => 4)) {
1855 :			# Here we want the environment data too.
1856 :			for my $envName (sort keys %ENV) {
1857 :			Trace("ENV: $envName = $ENV{$envName}");
1858 :			}
1859 :			}
1860 :			} else {
1861 :			# Here tracing is to be turned off. All we allow is errors traced into the
1862 :			# error log.
1863 :			TSetup("0", "WARN");
1864 :			}
1865 :			# Create the variable hash.
1866 :			my $varHash = { DebugData => '' };
1867 :			# If we're in DEBUG mode, set up the debug mode data for forms.
1868 :			if (Tracer::DebugMode) {
1869 :			$varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1870 :			}
1871 :			# Return the query object and variable hash.
1872 :			return ($query, $varHash);
1873 :			}
1874 :
1875 :			=head3 ScriptFinish
1876 :
1877 :			C<< ScriptFinish($webData, $varHash); >>
1878 :
1879 :			Output a web page at the end of a script. Either the string to be output or the
1880 :			name of a template file can be specified. If the second parameter is omitted,
1881 :			it is assumed we have a string to be output; otherwise, it is assumed we have the
1882 :			name of a template file. The template should have the variable C<DebugData>
1883 :			specified in any form that invokes a standard script. If debugging mode is turned
1884 :			on, a form field will be put in that allows the user to enter tracing data.
1885 :			Trace messages will be placed immediately before the terminal C<BODY> tag in
1886 :			the output, formatted as a list.
1887 :
1888 :			A typical standard script would loook like the following.
1889 :
1890 :			BEGIN {
1891 :			# Print the HTML header.
1892 :			print "CONTENT-TYPE: text/html\n\n";
1893 :			}
1894 :			use Tracer;
1895 :			use CGI;
1896 :			use FIG;
1897 :			# ... more uses ...
1898 :
1899 :			my ($query, $varHash) = ScriptSetup();
1900 :			eval {
1901 :			# ... get data from $query, put it in $varHash ...
1902 :			};
1903 :			if ($@) {
1904 :			Trace("Script Error: $@") if T(0);
1905 :			}
1906 :			ScriptFinish("Html/MyTemplate.html", $varHash);
1907 :
1908 :			The idea here is that even if the script fails, you'll see trace messages and
1909 :			useful output.
1910 :
1911 :			=over 4
1912 :
1913 :			=item webData
1914 :
1915 :			A string containing either the full web page to be written to the output or the
1916 :			name of a template file from which the page is to be constructed. If the name
1917 :			of a template file is specified, then the second parameter must be present;
1918 :			otherwise, it must be absent.
1919 :
1920 :			=item varHash (optional)
1921 :
1922 :			If specified, then a reference to a hash mapping variable names for a template
1923 :			to their values. The template file will be read into memory, and variable markers
1924 :			will be replaced by data in this hash reference.
1925 :
1926 :	parrello	1.37	=back
1927 :
1928 :	parrello	1.35	=cut
1929 :
1930 :			sub ScriptFinish {
1931 :			# Get the parameters.
1932 :			my ($webData, $varHash) = @_;
1933 :			# Check for a template file situation.
1934 :			my $outputString;
1935 :			if (defined $varHash) {
1936 :			# Here we have a template file. We need to apply the variables to the template.
1937 :			$outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1938 :			} else {
1939 :			# Here the user gave us a raw string.
1940 :			$outputString = $webData;
1941 :			}
1942 :			# Check for trace messages.
1943 :			if ($Destination eq "QUEUE") {
1944 :			# We have trace messages, so we want to put them at the end of the body. This
1945 :			# is either at the end of the whole string or at the beginning of the BODY
1946 :			# end-tag.
1947 :			my $pos = length $outputString;
1948 :			if ($outputString =~ m#</body>#gi) {
1949 :			$pos = (pos $outputString) - 7;
1950 :			}
1951 :			substr $outputString, $pos, 0, QTrace('Html');
1952 :			}
1953 :			# Write the output string.
1954 :			print $outputString;
1955 :			}
1956 :
1957 :	parrello	1.37	=head3 Insure
1958 :
1959 :			C<< Insure($dirName); >>
1960 :
1961 :			Insure a directory is present.
1962 :
1963 :			=over 4
1964 :
1965 :			=item dirName
1966 :
1967 :			Name of the directory to check. If it does not exist, it will be created.
1968 :
1969 :			=back
1970 :
1971 :			=cut
1972 :
1973 :			sub Insure {
1974 :			my ($dirName) = @_;
1975 :			if (! -d $dirName) {
1976 :			Trace("Creating $dirName directory.") if T(2);
1977 :	parrello	1.43	eval { mkpath $dirName; };
1978 :			if ($@) {
1979 :			Confess("Error creating $dirName: $@");
1980 :			}
1981 :			}
1982 :			}
1983 :
1984 :			=head3 ChDir
1985 :
1986 :			C<< ChDir($dirName); >>
1987 :
1988 :			Change to the specified directory.
1989 :
1990 :			=over 4
1991 :
1992 :			=item dirName
1993 :
1994 :			Name of the directory to which we want to change.
1995 :
1996 :			=back
1997 :
1998 :			=cut
1999 :
2000 :			sub ChDir {
2001 :			my ($dirName) = @_;
2002 :			if (! -d $dirName) {
2003 :			Confess("Cannot change to directory $dirName: no such directory.");
2004 :			} else {
2005 :			Trace("Changing to directory $dirName.") if T(4);
2006 :			my $okFlag = chdir $dirName;
2007 :			if (! $okFlag) {
2008 :			Confess("Error switching to directory $dirName.");
2009 :			}
2010 :	parrello	1.37	}
2011 :			}
2012 :
2013 :	parrello	1.46	=head3 SetPermissions
2014 :
2015 :	parrello	1.49	C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2016 :	parrello	1.46
2017 :			Set the permissions for a directory and all the files and folders inside it.
2018 :			In addition, the group ownership will be changed to the specified value.
2019 :
2020 :			This method is more vulnerable than most to permission and compatability
2021 :			problems, so it does internal error recovery.
2022 :
2023 :			=over 4
2024 :
2025 :			=item dirName
2026 :
2027 :			Name of the directory to process.
2028 :
2029 :			=item group
2030 :
2031 :			Name of the group to be assigned.
2032 :
2033 :			=item mask
2034 :
2035 :			Permission mask. Bits that are C<1> in this mask will be ORed into the
2036 :			permission bits of any file or directory that does not already have them
2037 :			set to 1.
2038 :
2039 :	parrello	1.49	=item otherMasks
2040 :
2041 :			Map of search patterns to permission masks. If a directory name matches
2042 :			one of the patterns, that directory and all its members and subdirectories
2043 :			will be assigned the new pattern. For example, the following would
2044 :			assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2045 :
2046 :			Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2047 :
2048 :			The list is ordered, so the following would use 0777 for C<tmp1> and
2049 :			0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2050 :
2051 :			Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2052 :			'^tmp' => 0666);
2053 :
2054 :			Note that the pattern matches are all case-insensitive, and only directory
2055 :			names are matched, not file names.
2056 :
2057 :	parrello	1.46	=back
2058 :
2059 :			=cut
2060 :
2061 :			sub SetPermissions {
2062 :			# Get the parameters.
2063 :	parrello	1.49	my ($dirName, $group, $mask, @otherMasks) = @_;
2064 :	parrello	1.46	# Set up for error recovery.
2065 :			eval {
2066 :	parrello	1.49	# Switch to the specified directory.
2067 :	parrello	1.46	ChDir($dirName);
2068 :			# Get the group ID.
2069 :			my $gid = getgrnam($group);
2070 :	parrello	1.50	# Get the mask for tracing.
2071 :			my $traceMask = sprintf("%04o", $mask);
2072 :			Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(2);
2073 :	parrello	1.46	my $fixCount = 0;
2074 :			my $lookCount = 0;
2075 :			# @dirs will be a stack of directories to be processed.
2076 :			my @dirs = (getcwd());
2077 :			while (scalar(@dirs) > 0) {
2078 :			# Get the current directory.
2079 :			my $dir = pop @dirs;
2080 :	parrello	1.49	# Check for a match to one of the specified directory names. To do
2081 :			# that, we need to pull the individual part of the name off of the
2082 :			# whole path.
2083 :			my $simpleName = $dir;
2084 :			if ($dir =~ m!/(.+)$!) {
2085 :			$simpleName = $1;
2086 :			}
2087 :			# Search for a match.
2088 :			my $match = 0;
2089 :			my $i;
2090 :			for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2091 :			my $pattern = $otherMasks[$i];
2092 :			if ($simpleName =~ /$pattern/i) {
2093 :			$match = 1;
2094 :	parrello	1.46	}
2095 :	parrello	1.49	}
2096 :			# Check for a match.
2097 :			if ($match && $otherMasks[$i+1] != $mask) {
2098 :			# This directory matches one of the incoming patterns, and it's
2099 :			# a different mask, so we process it recursively with that mask.
2100 :			SetPermissions($dir, $group, $otherMasks[$i+1], @otherMasks);
2101 :			} else {
2102 :			# Here we can process normally. Get all of the non-hidden members.
2103 :			my @submems = OpenDir($dir, 1);
2104 :			for my $submem (@submems) {
2105 :			# Get the full name.
2106 :			my $thisMem = "$dir/$submem";
2107 :			Trace("Checking member $thisMem.") if T(4);
2108 :			$lookCount++;
2109 :			if ($lookCount % 1000 == 0) {
2110 :	parrello	1.50	Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(3);
2111 :	parrello	1.49	}
2112 :			# Fix the group.
2113 :			chown -1, $gid, $thisMem;
2114 :			# Insure this member is not a symlink.
2115 :			if (! -l $thisMem) {
2116 :			# Get its info.
2117 :			my $fileInfo = stat $thisMem;
2118 :			# Only proceed if we got the info. Otherwise, it's a hard link
2119 :			# and we want to skip it anyway.
2120 :			if ($fileInfo) {
2121 :			my $fileMode = $fileInfo->mode;
2122 :			if (($fileMode & $mask) == 0) {
2123 :			# Fix this member.
2124 :			$fileMode \|= $mask;
2125 :			chmod $fileMode, $thisMem;
2126 :			$fixCount++;
2127 :			}
2128 :			# If it's a subdirectory, stack it.
2129 :			if (-d $thisMem) {
2130 :			push @dirs, $thisMem;
2131 :			}
2132 :	parrello	1.46	}
2133 :			}
2134 :			}
2135 :			}
2136 :			}
2137 :			Trace("$lookCount files and directories processed, $fixCount fixed.") if T(2);
2138 :			};
2139 :			# Check for an error.
2140 :			if ($@) {
2141 :			Confess("SetPermissions error: $@");
2142 :			}
2143 :			}
2144 :
2145 :	redwards	1.8	1;

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