Annotation of /FigKernelPackages/Tracer.pm

Revision 1.84 - (view) (download) (as text)

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 :	parrello	1.61	#
7 :	olson	1.30	# The SEED Toolkit is free software. You can redistribute
8 :			# it and/or modify it under the terms of the SEED Toolkit
9 :	parrello	1.61	# Public License.
10 :	olson	1.30	#
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	1.72	@EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing ScriptSetup ScriptFinish Insure ChDir Emergency);
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 :	parrello	1.59	use LWP::UserAgent;
35 :	parrello	1.64	use Time::HiRes 'gettimeofday';
36 :	parrello	1.65	use URI::Escape;
37 :	parrello	1.74	use Time::Local;
38 :	olson	1.1
39 :			=head1 Tracing and Debugging Helpers
40 :
41 :	parrello	1.72	=head2 Tracing
42 :	olson	1.1
43 :			This package provides simple tracing for debugging and reporting purposes. To use it simply call the
44 :	parrello	1.72	L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
45 :			L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
46 :			each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
47 :			level is less than or equal to the setup trace level and whose category is activated will
48 :	parrello	1.2	be written. Thus, a higher trace level on a message indicates that the message
49 :	parrello	1.72	is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
50 :			appear.
51 :	olson	1.1
52 :	parrello	1.72	=head3 Putting Trace Messages in Your Code
53 :
54 :			To generate a trace message, use the following syntax.
55 :
56 :			Trace($message) if T(errors => 4);
57 :	olson	1.1
58 :	parrello	1.2	This statement will produce a trace message if the trace level is 4 or more and the C<errors>
59 :	parrello	1.72	category is active. There is a special category C<main> that is always active, so
60 :	olson	1.1
61 :	parrello	1.72	Trace($message) if T(main => 4);
62 :	olson	1.1
63 :			will trace if the trace level is 4 or more.
64 :
65 :			If the category name is the same as the package name, all you need is the number. So, if the
66 :			following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
67 :			active and the trace level is 2 or more.
68 :
69 :	parrello	1.72	Trace($message) if T(2);
70 :
71 :			In scripts, where no package name is available, the category defaults to C<main>.
72 :
73 :			=head3 Custom Tracing
74 :
75 :			Many programs have customized tracing configured using the L</TSetup> method. This is no longer
76 :			the preferred method, but a knowledge of how custom tracing works can make the more modern
77 :			L</Emergency Tracing> easier to understand.
78 :	olson	1.1
79 :	parrello	1.72	To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
80 :			a list of category names, and a destination. The trace level and list of category names are
81 :	olson	1.1	specified as a space-delimited string. Thus
82 :
83 :	parrello	1.72	TSetup('3 errors Sprout ERDB', 'TEXT');
84 :	olson	1.1
85 :	parrello	1.7	sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
86 :	parrello	1.72	specifies that messages should be sent to the standard output.
87 :	parrello	1.12
88 :			To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
89 :			level 3 and writes the output to the standard error output. This sort of thing might be
90 :			useful in a CGI environment.
91 :
92 :	parrello	1.72	TSetup('3 *', 'WARN');
93 :	olson	1.1
94 :	parrello	1.72	In addition standard error and file output for trace messages, you can specify that the trace messages
95 :	olson	1.1	be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
96 :			is useful if you are building a web page. Instead of having the trace messages interspersed with
97 :			the page output, they can be gathered together and displayed at the end of the page. This makes
98 :			it easier to debug page formatting problems.
99 :
100 :	parrello	1.72	Finally, you can specify that all trace messages be emitted to a file, or the standard output and
101 :			a file at the same time. To trace to a file, specify the filename with an output character in front
102 :			of it.
103 :
104 :			TSetup('4 SQL', ">$fileName");
105 :
106 :			To trace to the standard output and a file at the same time, put a C<+> in front of the angle
107 :			bracket.
108 :
109 :			TSetup('3 *', "+>$fileName");
110 :	parrello	1.4
111 :	olson	1.1	The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
112 :			Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
113 :			Thus, debugging information is available and easily retrieved even when the application is
114 :			being used out in the field.
115 :
116 :	parrello	1.72	=head3 Trace Levels
117 :
118 :	parrello	1.10	There is no hard and fast rule on how to use trace levels. The following is therefore only
119 :			a suggestion.
120 :
121 :			=over 4
122 :
123 :	parrello	1.32	=item Error 0
124 :	parrello	1.10
125 :			Message indicates an error that may lead to incorrect results or that has stopped the
126 :			application entirely.
127 :
128 :	parrello	1.32	=item Warning 1
129 :	parrello	1.10
130 :			Message indicates something that is unexpected but that probably did not interfere
131 :			with program execution.
132 :
133 :	parrello	1.32	=item Notice 2
134 :	parrello	1.10
135 :			Message indicates the beginning or end of a major task.
136 :
137 :	parrello	1.32	=item Information 3
138 :	parrello	1.10
139 :			Message indicates a subtask. In the FIG system, a subtask generally relates to a single
140 :			genome. This would be a big loop that is not expected to execute more than 500 times or so.
141 :
142 :	parrello	1.32	=item Detail 4
143 :	parrello	1.10
144 :			Message indicates a low-level loop iteration.
145 :
146 :			=back
147 :
148 :	parrello	1.69	The format of trace messages is important because some utilities analyze trace files.
149 :	parrello	1.72	There are three fields-- the time stamp, the category name, and the text.
150 :			The time stamp is between square brackets and the category name between angle brackets.
151 :			After the category name there is a colon (C<:>) followed by the message text.
152 :			If the square brackets or angle brackets are missing, then the trace management
153 :			utilities assume that they are encountering a set of pre-formatted lines.
154 :
155 :			Note, however, that this formatting is done automatically by the tracing functions. You
156 :			only need to know about it if you want to parse a trace file.
157 :
158 :			=head3 Emergency Tracing
159 :
160 :			Sometimes, you need a way for tracing to happen automatically without putting parameters
161 :			in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
162 :			from the debug form, which is accessed from I<MySeedInstance>C</FIG/Html/SetPassword.html>.
163 :			Emergency tracing requires you specify a tracing key. For command-line tools, the key is
164 :			taken from the C<TRACING> environment variable. For web services, the key is taken from
165 :			a cookie. Either way, the key tells the tracing facility who you are, so that you control
166 :			the tracing in your environment without stepping on other users.
167 :
168 :			The key can be anything you want. If you don't have a key, the C<SetPassword> page will
169 :			generate one for you.
170 :
171 :			You can activate and de-activate emergency tracing from the debugging control panel, as
172 :			well as display the trace file itself.
173 :
174 :			To enable emergency tracing in your code, call
175 :
176 :			ETracing($cgi)
177 :
178 :			from a web script and
179 :
180 :			ETracing()
181 :
182 :			from a command-line script.
183 :
184 :			The web script will look for the tracing key in the cookies, and the command-line
185 :			script will look for it in the C<TRACING> environment variable. If you are
186 :			using the L</StandardScript> or L</StandardSetup> methods, emergency tracing
187 :			will be configured automatically.
188 :
189 :	parrello	1.84	NOTE: to configure emergency tracing from the command line instead of the Debugging
190 :			Control Panel (see below), use the C<trace.pl> script.
191 :
192 :	parrello	1.72	=head3 Debugging Control Panel
193 :
194 :			The debugging control panel provides several tools to assist in development of
195 :			SEED and Sprout software. You access the debugging control panel from the URL
196 :			C</FIG/Html/SetPassword.html> in whichever seed instance you're using. (So,
197 :			for example, the panel access point for the development NMPDR system is
198 :			C<http://web-1.nmpdr.org/next/FIG/Html/SetPassword.html>. Contact Bruce to
199 :			find out what the password is. From this page, you can also specify a tracing
200 :			key. If you don't specify a key, one will be generated for you.
201 :
202 :			=head4 Emergency Tracing Form
203 :
204 :			At the bottom of the debugging control panel is a form that allows you to
205 :			specify a trace level and tracing categories. Special and common categories
206 :			are listed with check boxes. You can hold your mouse over a check box to see
207 :			what its category does. In general, however, a category name is the same as
208 :			the name of the package in which the trace message occurs.
209 :
210 :			Additional categories can be entered in an input box, delimited by spaces or commas.
211 :
212 :			The B<Activate> button turns on Emergency tracing at the level you specify with the
213 :			specified categories active. The B<Terminate> button turns tracing off. The
214 :			B<Show File> button displays the current contents of the trace file. The tracing
215 :			form at the bottom of the control panel is designed for emergency tracing, so it
216 :			will only affect programs that call L</ETracing>, L</StandardScript>,
217 :			or L</StandardSetup>.
218 :
219 :			=head4 Script Form
220 :
221 :			The top form of the debugging control panel allows you to enter a tiny script and
222 :			have the output generated in a formatted table. Certain object variables are
223 :			predefined in the script, including a FIG object (C<$fig>), a CGI object (C<$cgi>),
224 :			and-- if Sprout is active-- Sprout (C<$sprout>) and SFXlate (C<$sfx>) objects.
225 :
226 :			The last line of the script must be a scalar, but it can be a reference to a hash,
227 :			a list, a list of lists, and various other combinations. If you select the appropriate
228 :			data type in the dropdown box, the output will be formatted accordingly. The form
229 :			also has controls for specifying tracing. These controls override any emergency
230 :			tracing in effect.
231 :
232 :			=head4 Database Query Forms
233 :
234 :			The forms between the script form and the emergency tracing form allow you to
235 :			make queries against the database. The FIG query form allows simple queries against
236 :			a single FIG table. The Sprout query form uses the B<GetAll> method to do a
237 :			multi-table query against the Sprout database. B<GetAll> is located in the B<ERDB>
238 :			package, and it takes five parameters.
239 :
240 :			GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count);
241 :
242 :			Each of the five parameters corresponds to a text box on the query form:
243 :
244 :			=over 4
245 :
246 :			=item Objects
247 :
248 :			Comma-separated list containing the names of the entity and relationship objects to be retrieved.
249 :
250 :			=item Filter
251 :
252 :			WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can
253 :			be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form
254 :			B<I<objectName>(I<fieldName>)> or B<$I<number>(I<fieldName>)> where I<fieldName> is the name of a
255 :			field, I<objectName> is the name of the entity or relationship object containing the field, and
256 :			I<number> is the 1-based position of the object in the object list. Any parameters
257 :			specified in the filter clause should be specified in the B<Params> field.
258 :			The fields in a filter clause can come from primary entity relations,
259 :			relationship relations, or secondary entity relations; however, all of the
260 :			entities and relationships involved must be included in the list of object names.
261 :
262 :			=item Params
263 :
264 :			List of the parameters to be substituted in for the parameters marks in the filter clause. This
265 :			is a comma-separated list without any quoting or escaping.
266 :
267 :			=item fields
268 :
269 :			Comma-separated list of the fields to be returned in each element of the list returned. Fields
270 :			are specified in the same manner as in the filter clause.
271 :
272 :			=item count
273 :
274 :			Maximum number of records to return. If omitted or 0, all available records will be returned.
275 :
276 :			=back
277 :
278 :			B<GetAll> automatically joins together the entities and relationships listed in the object
279 :			names. This simplifies the coding of the filter clause, but it means that some queries are
280 :			not possible, since they cannot be expressed in a linear sequence of joins. This is a limitation
281 :			that has yet to be addressed.
282 :	parrello	1.69
283 :	olson	1.1	=cut
284 :	parrello	1.2
285 :	olson	1.1	# Declare the configuration variables.
286 :
287 :	parrello	1.12	my $Destination = "NONE"; # Description of where to send the trace output.
288 :			my $TeeFlag = 0; # TRUE if output is going to a file and to the
289 :			# standard output
290 :	parrello	1.3	my %Categories = ( main => 1 );
291 :	parrello	1.12	# hash of active category names
292 :			my $TraceLevel = 0; # trace level; a higher trace level produces more
293 :			# messages
294 :			my @Queue = (); # queued list of trace messages.
295 :	parrello	1.7	my $LastCategory = "main"; # name of the last category interrogated
296 :	parrello	1.11	my $SetupCount = 0; # number of times TSetup called
297 :	parrello	1.12	my $AllTrace = 0; # TRUE if we are tracing all categories.
298 :	olson	1.1
299 :			=head2 Public Methods
300 :
301 :			=head3 TSetup
302 :
303 :			C<< TSetup($categoryList, $target); >>
304 :
305 :			This method is used to specify the trace options. The options are stored as package data
306 :			and interrogated by the L</Trace> and L</T> methods.
307 :
308 :			=over 4
309 :
310 :			=item categoryList
311 :
312 :			A string specifying the trace level and the categories to be traced, separated by spaces.
313 :			The trace level must come first.
314 :
315 :			=item target
316 :
317 :			The destination for the trace output. To send the trace output to a file, specify the file
318 :			name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
319 :	parrello	1.10	to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
320 :			symbol with a C<+> to echo output to a file AND to the standard output. In addition to
321 :			sending the trace messages to a file, you can specify a special destination. C<HTML> will
322 :			cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
323 :	parrello	1.5	will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
324 :	parrello	1.9	messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
325 :	parrello	1.6	messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
326 :	parrello	1.9	cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
327 :	parrello	1.6	cause tracing to be suppressed.
328 :	olson	1.1
329 :			=back
330 :
331 :			=cut
332 :
333 :			sub TSetup {
334 :	parrello	1.12	# Get the parameters.
335 :			my ($categoryList, $target) = @_;
336 :			# Parse the category list.
337 :			my @categoryData = split /\s+/, $categoryList;
338 :			# Extract the trace level.
339 :			$TraceLevel = shift @categoryData;
340 :			# Presume category-based tracing until we learn otherwise.
341 :			$AllTrace = 0;
342 :			# Build the category hash. Note that if we find a "*", we turn on non-category
343 :	parrello	1.33	# tracing. We must also clear away any pre-existing data.
344 :	parrello	1.34	%Categories = ( main => 1 );
345 :	parrello	1.12	for my $category (@categoryData) {
346 :			if ($category eq '*') {
347 :			$AllTrace = 1;
348 :			} else {
349 :	parrello	1.13	$Categories{lc $category} = 1;
350 :	parrello	1.12	}
351 :			}
352 :			# Now we need to process the destination information. The most important special
353 :			# cases are the single ">", which requires we clear the file first, and the
354 :			# "+" prefix which indicates a double echo.
355 :			if ($target =~ m/^\+?>>?/) {
356 :			if ($target =~ m/^\+/) {
357 :			$TeeFlag = 1;
358 :			$target = substr($target, 1);
359 :			}
360 :			if ($target =~ m/^>[^>]/) {
361 :			open TRACEFILE, $target;
362 :	parrello	1.69	print TRACEFILE "[" . Now() . "] <Tracer>: Tracing initialized.\n";
363 :	parrello	1.12	close TRACEFILE;
364 :			$Destination = ">$target";
365 :			} else {
366 :			$Destination = $target;
367 :			}
368 :			} else {
369 :			$Destination = uc($target);
370 :			}
371 :			# Increment the setup counter.
372 :			$SetupCount++;
373 :	parrello	1.11	}
374 :
375 :	parrello	1.31	=head3 StandardSetup
376 :
377 :	parrello	1.36	C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
378 :	parrello	1.31
379 :			This method performs standard command-line parsing and tracing setup. The return
380 :			values are a hash of the command-line options and a list of the positional
381 :			parameters. Tracing is automatically set up and the command-line options are
382 :			validated.
383 :
384 :			This is a complex method that does a lot of grunt work. The parameters can
385 :			be more easily understood, however, once they are examined individually.
386 :
387 :			The I<categories> parameter is the most obtuse. It is a reference to a list of
388 :			special-purpose tracing categories. Most tracing categories are PERL package
389 :			names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
390 :			B<ERDB>, and B<SproutLoad> packages, you would specify the categories
391 :
392 :			["Sprout", "SproutLoad", "ERDB"]
393 :
394 :			This would cause trace messages in the specified three packages to appear in
395 :	parrello	1.69	the output. There are two special tracing categories that are automatically
396 :	parrello	1.31	handled by this method. In other words, if you used L</TSetup> you would need
397 :			to include these categories manually, but if you use this method they are turned
398 :			on automatically.
399 :
400 :			=over 4
401 :
402 :			=item SQL
403 :
404 :			Traces SQL commands and activity.
405 :
406 :			=item Tracer
407 :
408 :			Traces error messages and call stacks.
409 :
410 :			=back
411 :
412 :			C<SQL> is only turned on if the C<-sql> option is specified in the command line.
413 :			The trace level is specified using the C<-trace> command-line option. For example,
414 :			the following command line for C<TransactFeatures> turns on SQL tracing and runs
415 :			all tracing at level 3.
416 :
417 :			TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
418 :
419 :			Standard tracing is output to the standard output and echoed to the file
420 :	parrello	1.38	C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
421 :			process ID. You can also specify the C<user> parameter to put a user ID
422 :			instead of a process ID in the trace file name. So, for example
423 :	parrello	1.31
424 :	parrello	1.35	The default trace level is 2. To get all messages, specify a trace level of 4.
425 :			For a genome-by-genome update, use 3.
426 :	parrello	1.31
427 :	parrello	1.38	TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
428 :
429 :			would send the trace output to C<traceBruce.log> in the temporary directory.
430 :
431 :	parrello	1.31	The I<options> parameter is a reference to a hash containing the command-line
432 :	parrello	1.36	options, their default values, and an explanation of what they mean. Command-line
433 :			options may be in the form of switches or keywords. In the case of a switch, the
434 :			option value is 1 if it is specified and 0 if it is not specified. In the case
435 :			of a keyword, the value is separated from the option name by an equal sign. You
436 :			can see this last in the command-line example above.
437 :	parrello	1.31
438 :	parrello	1.42	You can specify a different default trace level by setting C<$options->{trace}>
439 :			prior to calling this method.
440 :
441 :	parrello	1.31	An example at this point would help. Consider, for example, the command-line utility
442 :			C<TransactFeatures>. It accepts a list of positional parameters plus the options
443 :			C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
444 :			the following code.
445 :
446 :			my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
447 :	parrello	1.36	{ safe => [0, "use database transactions"],
448 :			noAlias => [0, "do not expect aliases in CHANGE transactions"],
449 :			start => [' ', "start with this genome"],
450 :			tblFiles => [0, "output TBL files containing the corrected IDs"] },
451 :	parrello	1.84	"<command> <transactionDirectory> <IDfile>",
452 :	parrello	1.36	@ARGV);
453 :	parrello	1.31
454 :
455 :			The call to C<ParseCommand> specifies the default values for the options and
456 :			stores the actual options in a hash that is returned as C<$options>. The
457 :	parrello	1.61	positional parameters are returned in C<@parameters>.
458 :	parrello	1.31
459 :			The following is a sample command line for C<TransactFeatures>.
460 :
461 :			TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
462 :
463 :	parrello	1.84	Single and double hyphens are equivalent. So, you could also code the
464 :			above command as
465 :
466 :			TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
467 :
468 :	parrello	1.31	In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
469 :			parameters, and would find themselves in I<@parameters> after executing the
470 :			above code fragment. The tracing would be set to level 2, and the categories
471 :	parrello	1.69	would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
472 :	parrello	1.31	and C<DocUtils> was included because it came in within the first parameter
473 :			to this method. The I<$options> hash would be
474 :
475 :			{ trace => 2, sql => 0, safe => 0,
476 :			noAlias => 1, start => ' ', tblFiles => 0 }
477 :
478 :			Use of C<StandardSetup> in this way provides a simple way of performing
479 :			standard tracing setup and command-line parsing. Note that the caller is
480 :			not even aware of the command-line switches C<-trace> and C<-sql>, which
481 :			are used by this method to control the tracing. If additional tracing features
482 :			need to be added in the future, they can be processed by this method without
483 :			upsetting the command-line utilities.
484 :
485 :	parrello	1.42	If the C<background> option is specified on the command line, then the
486 :			standard and error outputs will be directed to files in the temporary
487 :			directory, using the same suffix as the trace file. So, if the command
488 :			line specified
489 :
490 :			-user=Bruce -background
491 :
492 :			then the trace output would go to C<traceBruce.log>, the standard output to
493 :			C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
494 :			simplify starting a command in the background.
495 :
496 :	parrello	1.72	The user name is also used as the tracing key for L</Emergency Tracing>.
497 :			Specifying a value of C<E> for the trace level causes emergency tracing to
498 :			be used instead of custom tracing. If the user name is not specified,
499 :			the tracing key is taken from the C<Tracing> environment variable. If there
500 :			is no value for that variable, the tracing key will be computed from the PID.
501 :
502 :	parrello	1.84	Finally, if the special option C<-help> is specified, the option
503 :			names will be traced at level 0 and the program will exit without processing.
504 :	parrello	1.36	This provides a limited help capability. For example, if the user enters
505 :
506 :	parrello	1.84	TransactFeatures -help
507 :	parrello	1.36
508 :			he would see the following output.
509 :
510 :	parrello	1.84	TransactFeatures [options] <command> <transactionDirectory> <IDfile>
511 :	parrello	1.72	-trace tracing level (default E)
512 :	parrello	1.36	-sql trace SQL commands
513 :			-safe use database transactions
514 :			-noAlias do not expect aliases in CHANGE transactions
515 :			-start start with this genome
516 :			-tblFiles output TBL files containing the corrected IDs
517 :
518 :	parrello	1.44	The caller has the option of modifying the tracing scheme by placing a value
519 :			for C<trace> in the incoming options hash. The default value can be overridden,
520 :			or the tracing to the standard output can be turned off by suffixing a minus
521 :	parrello	1.61	sign to the trace level. So, for example,
522 :	parrello	1.44
523 :			{ trace => [0, "tracing level (default 0)"],
524 :			...
525 :
526 :	parrello	1.72	would set the default trace level to 0 instead of E, while
527 :	parrello	1.44
528 :			{ trace => ["2-", "tracing level (default 2)"],
529 :			...
530 :
531 :	parrello	1.72	would set the default to 2, but trace only to the log file, not to the
532 :	parrello	1.44	standard output.
533 :
534 :	parrello	1.31	The parameters to this method are as follows.
535 :
536 :			=over 4
537 :
538 :			=item categories
539 :
540 :			Reference to a list of tracing category names. These should be names of
541 :			packages whose internal workings will need to be debugged to get the
542 :			command working.
543 :
544 :			=item options
545 :
546 :			Reference to a hash containing the legal options for the current command mapped
547 :	parrello	1.36	to their default values and descriptions. The user can override the defaults
548 :			by specifying the options as command-line switches prefixed by a hyphen.
549 :			Tracing-related options may be added to this hash. If the C<-h> option is
550 :			specified on the command line, the option descriptions will be used to
551 :	parrello	1.44	explain the options. To turn off tracing to the standard output, add a
552 :			minus sign to the value for C<trace> (see above).
553 :	parrello	1.36
554 :			=item parmHelp
555 :
556 :			A string that vaguely describes the positional parameters. This is used
557 :			if the user specifies the C<-h> option.
558 :	parrello	1.31
559 :	parrello	1.44	=item argv
560 :	parrello	1.31
561 :			List of command line parameters, including the option switches, which must
562 :			precede the positional parameters and be prefixed by a hyphen.
563 :
564 :			=item RETURN
565 :
566 :			Returns a list. The first element of the list is the reference to a hash that
567 :			maps the command-line option switches to their values. These will either be the
568 :			default values or overrides specified on the command line. The remaining
569 :			elements of the list are the position parameters, in order.
570 :
571 :			=back
572 :
573 :			=cut
574 :
575 :			sub StandardSetup {
576 :			# Get the parameters.
577 :	parrello	1.36	my ($categories, $options, $parmHelp, @argv) = @_;
578 :	parrello	1.72	# Get the default tracing key.
579 :			my $tkey = EmergencyKey();
580 :	parrello	1.31	# Add the tracing options.
581 :	parrello	1.41	if (! exists $options->{trace}) {
582 :	parrello	1.72	$options->{trace} = ['E', "tracing level (E for emergency tracing)"];
583 :	parrello	1.41	}
584 :	parrello	1.36	$options->{sql} = [0, "turn on SQL tracing"];
585 :	parrello	1.84	$options->{help} = [0, "display command-line options"];
586 :	parrello	1.72	$options->{user} = [$tkey, "tracing key"];
587 :	parrello	1.42	$options->{background} = [0, "spool standard and error output"];
588 :	parrello	1.36	# Create a parsing hash from the options hash. The parsing hash
589 :			# contains the default values rather than the default value
590 :			# and the description. While we're at it, we'll memorize the
591 :			# length of the longest option name.
592 :			my $longestName = 0;
593 :			my %parseOptions = ();
594 :			for my $key (keys %{$options}) {
595 :			if (length $key > $longestName) {
596 :			$longestName = length $key;
597 :			}
598 :			$parseOptions{$key} = $options->{$key}->[0];
599 :			}
600 :	parrello	1.31	# Parse the command line.
601 :	parrello	1.36	my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
602 :	parrello	1.42	# Get the logfile suffix.
603 :			my $suffix = $retOptions->{user};
604 :			# Check for background mode.
605 :			if ($retOptions->{background}) {
606 :			my $outFileName = "$FIG_Config::temp/out$suffix.log";
607 :			my $errFileName = "$FIG_Config::temp/err$suffix.log";
608 :			open STDOUT, ">$outFileName";
609 :			open STDERR, ">$errFileName";
610 :			}
611 :	parrello	1.72	# Now we want to set up tracing. First, we need to know if the user
612 :			# wants emergency tracing.
613 :			if ($retOptions->{trace} eq 'E') {
614 :			ETracing($retOptions->{user});
615 :	parrello	1.44	} else {
616 :	parrello	1.72	# Here the tracing is controlled from the command line.
617 :			my @cats = @{$categories};
618 :			if ($retOptions->{sql}) {
619 :			push @cats, "SQL";
620 :			}
621 :			# Add the default categories.
622 :			push @cats, "Tracer";
623 :			# Next, we create the category string by joining the categories.
624 :			my $cats = join(" ", @cats);
625 :			# Check to determine whether or not the caller wants to turn off tracing
626 :			# to the standard output.
627 :			my $traceLevel = $retOptions->{trace};
628 :			my $textOKFlag = 1;
629 :			if ($traceLevel =~ /^(.)-/) {
630 :			$traceLevel = $1;
631 :			$textOKFlag = 0;
632 :			}
633 :			# Now we set up the trace mode.
634 :			my $traceMode;
635 :			# Verify that we can open a file in the FIG temporary directory.
636 :			my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
637 :			if (open TESTTRACE, ">$traceFileName") {
638 :			# Here we can trace to a file.
639 :			$traceMode = ">$traceFileName";
640 :			if ($textOKFlag) {
641 :			# Echo to standard output if the text-OK flag is set.
642 :			$traceMode = "+$traceMode";
643 :			}
644 :			# Close the test file.
645 :			close TESTTRACE;
646 :	parrello	1.44	} else {
647 :	parrello	1.72	# Here we can't trace to a file. We trace to the standard output if it's
648 :			# okay, and the error log otherwise.
649 :			if ($textOKFlag) {
650 :			$traceMode = "TEXT";
651 :			} else {
652 :			$traceMode = "WARN";
653 :			}
654 :	parrello	1.44	}
655 :	parrello	1.72	# Now set up the tracing.
656 :			TSetup("$traceLevel $cats", $traceMode);
657 :	parrello	1.40	}
658 :	parrello	1.36	# Check for the "h" option. If it is specified, dump the command-line
659 :			# options and exit the program.
660 :	parrello	1.84	if ($retOptions->{help}) {
661 :	parrello	1.36	$0 =~ m#[/\\](\w+)(\.pl)?$#i;
662 :	parrello	1.69	print "$1 [options] $parmHelp\n";
663 :	parrello	1.36	for my $key (sort keys %{$options}) {
664 :			my $name = Pad($key, $longestName, 0, ' ');
665 :			my $desc = $options->{$key}->[1];
666 :			if ($options->{$key}->[0]) {
667 :			$desc .= " (default " . $options->{$key}->[0] . ")";
668 :			}
669 :	parrello	1.69	print " $name $desc\n";
670 :	parrello	1.36	}
671 :			exit(0);
672 :			}
673 :	parrello	1.83	# Trace the options, if applicable.
674 :			if (T(3)) {
675 :			my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
676 :			Trace("Selected options: " . join(", ", sort @parms) . ".");
677 :			}
678 :	parrello	1.31	# Return the parsed parameters.
679 :			return ($retOptions, @retParameters);
680 :			}
681 :
682 :	parrello	1.11	=head3 Setups
683 :
684 :			C<< my $count = Tracer::Setups(); >>
685 :
686 :			Return the number of times L</TSetup> has been called.
687 :
688 :			This method allows for the creation of conditional tracing setups where, for example, we
689 :			may want to set up tracing if nobody else has done it before us.
690 :
691 :			=cut
692 :
693 :			sub Setups {
694 :	parrello	1.12	return $SetupCount;
695 :	olson	1.1	}
696 :
697 :	parrello	1.10	=head3 Open
698 :
699 :			C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
700 :
701 :	parrello	1.11	Open a file.
702 :	parrello	1.10
703 :			The I<$fileSpec> is essentially the second argument of the PERL C<open>
704 :			function. The mode is specified using Unix-like shell information. So, for
705 :			example,
706 :
707 :	parrello	1.12	Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
708 :	parrello	1.10
709 :			would open for output appended to the specified file, and
710 :
711 :	parrello	1.12	Open(\*DATASTREAM, "\| sort -u >$outputFile", "Could not open $outputFile.");
712 :	parrello	1.10
713 :			would open a pipe that sorts the records written and removes duplicates. Note
714 :	parrello	1.11	the use of file handle syntax in the Open call. To use anonymous file handles,
715 :			code as follows.
716 :	parrello	1.10
717 :	parrello	1.12	my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
718 :	parrello	1.10
719 :	parrello	1.11	The I<$message> parameter is used if the open fails. If it is set to C<0>, then
720 :			the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
721 :			failed open will throw an exception and the third parameter will be used to construct
722 :			an error message. If the parameter is omitted, a standard message is constructed
723 :			using the file spec.
724 :	parrello	1.10
725 :	parrello	1.12	Could not open "/usr/spool/news/twitlog"
726 :	parrello	1.10
727 :			Note that the mode characters are automatically cleaned from the file name.
728 :			The actual error message from the file system will be captured and appended to the
729 :			message in any case.
730 :
731 :	parrello	1.12	Could not open "/usr/spool/news/twitlog": file not found.
732 :	parrello	1.10
733 :			In some versions of PERL the only error message we get is a number, which
734 :			corresponds to the C++ C<errno> value.
735 :
736 :	parrello	1.12	Could not open "/usr/spool/news/twitlog": 6.
737 :	parrello	1.10
738 :			=over 4
739 :
740 :			=item fileHandle
741 :
742 :			File handle. If this parameter is C<undef>, a file handle will be generated
743 :			and returned as the value of this method.
744 :
745 :			=item fileSpec
746 :
747 :			File name and mode, as per the PERL C<open> function.
748 :
749 :			=item message (optional)
750 :
751 :			Error message to use if the open fails. If omitted, a standard error message
752 :			will be generated. In either case, the error information from the file system
753 :	parrello	1.11	is appended to the message. To specify a conditional open that does not throw
754 :			an error if it fails, use C<0>.
755 :	parrello	1.10
756 :			=item RETURN
757 :
758 :	parrello	1.11	Returns the name of the file handle assigned to the file, or C<undef> if the
759 :			open failed.
760 :	parrello	1.10
761 :			=back
762 :
763 :			=cut
764 :
765 :			sub Open {
766 :	parrello	1.12	# Get the parameters.
767 :			my ($fileHandle, $fileSpec, $message) = @_;
768 :			# Attempt to open the file.
769 :			my $rv = open $fileHandle, $fileSpec;
770 :			# If the open failed, generate an error message.
771 :			if (! $rv) {
772 :			# Save the system error message.
773 :			my $sysMessage = $!;
774 :			# See if we need a default message.
775 :			if (!$message) {
776 :			# Clean any obvious mode characters and leading spaces from the
777 :			# filename.
778 :			my ($fileName) = FindNamePart($fileSpec);
779 :			$message = "Could not open \"$fileName\"";
780 :			}
781 :			# Terminate with an error using the supplied message and the
782 :			# error message from the file system.
783 :			Confess("$message: $!");
784 :			}
785 :			# Return the file handle.
786 :			return $fileHandle;
787 :	parrello	1.10	}
788 :
789 :	parrello	1.11	=head3 FindNamePart
790 :
791 :			C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
792 :
793 :			Extract the portion of a file specification that contains the file name.
794 :
795 :			A file specification is the string passed to an C<open> call. It specifies the file
796 :			mode and name. In a truly complex situation, it can specify a pipe sequence. This
797 :			method assumes that the file name is whatever follows the first angle bracket
798 :			sequence. So, for example, in the following strings the file name is
799 :			C</usr/fig/myfile.txt>.
800 :
801 :			>>/usr/fig/myfile.txt
802 :			</usr/fig/myfile.txt
803 :			\| sort -u > /usr/fig/myfile.txt
804 :
805 :			If the method cannot find a file name using its normal methods, it will return the
806 :			whole incoming string.
807 :
808 :			=over 4
809 :
810 :			=item fileSpec
811 :
812 :			File specification string from which the file name is to be extracted.
813 :
814 :			=item RETURN
815 :
816 :			Returns a three-element list. The first element contains the file name portion of
817 :			the specified string, or the whole string if a file name cannot be found via normal
818 :			methods. The second element contains the start position of the file name portion and
819 :			the third element contains the length.
820 :
821 :			=back
822 :
823 :			=cut
824 :			#: Return Type $;
825 :			sub FindNamePart {
826 :			# Get the parameters.
827 :			my ($fileSpec) = @_;
828 :	parrello	1.12	# Default to the whole input string.
829 :			my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
830 :	parrello	1.11	# Parse out the file name if we can.
831 :	parrello	1.12	if ($fileSpec =~ m/(<\|>>?)(.+?)(\s*)$/) {
832 :			$retVal = $2;
833 :			$len = length $retVal;
834 :			$pos = (length $fileSpec) - (length $3) - $len;
835 :			}
836 :	parrello	1.11	# Return the result.
837 :			return ($retVal, $pos, $len);
838 :			}
839 :
840 :			=head3 OpenDir
841 :
842 :	parrello	1.31	C<< my @files = OpenDir($dirName, $filtered, $flag); >>
843 :	parrello	1.11
844 :			Open a directory and return all the file names. This function essentially performs
845 :			the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
846 :	parrello	1.31	set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
847 :	parrello	1.33	or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
848 :			filtered out of the return list. If the directory does not open and I<$flag> is not
849 :			set, an exception is thrown. So, for example,
850 :	parrello	1.11
851 :	parrello	1.12	my @files = OpenDir("/Volumes/fig/contigs", 1);
852 :	parrello	1.29
853 :	parrello	1.11	is effectively the same as
854 :
855 :	parrello	1.12	opendir(TMP, "/Volumes/fig/contigs") \|\| Confess("Could not open /Volumes/fig/contigs.");
856 :	parrello	1.33	my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
857 :	parrello	1.11
858 :			Similarly, the following code
859 :
860 :	parrello	1.31	my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
861 :	parrello	1.29
862 :	parrello	1.11	Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
863 :	parrello	1.31	automatically returns an empty list if the directory fails to open.
864 :	parrello	1.11
865 :			=over 4
866 :
867 :			=item dirName
868 :
869 :			Name of the directory to open.
870 :
871 :			=item filtered
872 :
873 :			TRUE if files whose names begin with a period (C<.>) should be automatically removed
874 :			from the list, else FALSE.
875 :
876 :	parrello	1.31	=item flag
877 :
878 :			TRUE if a failure to open is okay, else FALSE
879 :
880 :	parrello	1.11	=back
881 :
882 :			=cut
883 :			#: Return Type @;
884 :			sub OpenDir {
885 :			# Get the parameters.
886 :	parrello	1.31	my ($dirName, $filtered, $flag) = @_;
887 :	parrello	1.11	# Declare the return variable.
888 :	parrello	1.31	my @retVal = ();
889 :	parrello	1.12	# Open the directory.
890 :			if (opendir(my $dirHandle, $dirName)) {
891 :			# The directory opened successfully. Get the appropriate list according to the
892 :			# strictures of the filter parameter.
893 :			if ($filtered) {
894 :	parrello	1.33	@retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
895 :	parrello	1.12	} else {
896 :			@retVal = readdir $dirHandle;
897 :			}
898 :	parrello	1.31	} elsif (! $flag) {
899 :			# Here the directory would not open and it's considered an error.
900 :	parrello	1.12	Confess("Could not open directory $dirName.");
901 :			}
902 :	parrello	1.11	# Return the result.
903 :			return @retVal;
904 :			}
905 :
906 :	parrello	1.6	=head3 SetLevel
907 :
908 :			C<< Tracer::SetLevel($newLevel); >>
909 :
910 :			Modify the trace level. A higher trace level will cause more messages to appear.
911 :
912 :			=over 4
913 :
914 :			=item newLevel
915 :
916 :			Proposed new trace level.
917 :
918 :			=back
919 :
920 :			=cut
921 :
922 :			sub SetLevel {
923 :			$TraceLevel = $_[0];
924 :			}
925 :
926 :	olson	1.1	=head3 Now
927 :
928 :			C<< my $string = Tracer::Now(); >>
929 :
930 :			Return a displayable time stamp containing the local time.
931 :
932 :			=cut
933 :
934 :			sub Now {
935 :	parrello	1.12	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
936 :			my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
937 :			_p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
938 :			return $retVal;
939 :	olson	1.1	}
940 :
941 :			# Pad a number to 2 digits.
942 :			sub _p2 {
943 :	parrello	1.12	my ($value) = @_;
944 :			$value = "0$value" if ($value < 10);
945 :			return $value;
946 :	olson	1.1	}
947 :
948 :	parrello	1.74	=head3 ParseTraceDate
949 :
950 :			C<< my $time = Tracer::ParseTraceDate($dateString); >>
951 :
952 :			Convert a date from the trace file into a PERL timestamp.
953 :
954 :			=over 4
955 :
956 :			=item dateString
957 :
958 :			The date string from the trace file. The format of the string is determined by the
959 :			L</Now> method.
960 :
961 :			=item RETURN
962 :
963 :			Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
964 :			the time string is invalid.
965 :
966 :	parrello	1.78	=back
967 :
968 :	parrello	1.74	=cut
969 :
970 :			sub ParseTraceDate {
971 :			# Get the parameters.
972 :			my ($dateString) = @_;
973 :			# Declare the return variable.
974 :			my $retVal;
975 :			# Parse the date.
976 :			if ($dateString =~ m#(\d+)/(\d+)/(\d+)\s+(\d+):(\d+):(\d+)#) {
977 :	parrello	1.76	# Create a time object. Note we need to convert the day, month,
978 :			# and year to a different base. Years count from 1900, and
979 :			# the internal month value is relocated to January = 0.
980 :			$retVal = timelocal($6, $5, $4, $2, $1 - 1, $3 - 1900);
981 :	parrello	1.74	}
982 :			# Return the result.
983 :			return $retVal;
984 :			}
985 :
986 :	olson	1.1	=head3 LogErrors
987 :
988 :			C<< Tracer::LogErrors($fileName); >>
989 :
990 :			Route the standard error output to a log file.
991 :
992 :			=over 4
993 :
994 :			=item fileName
995 :
996 :			Name of the file to receive the error output.
997 :
998 :			=back
999 :
1000 :			=cut
1001 :
1002 :			sub LogErrors {
1003 :	parrello	1.12	# Get the file name.
1004 :			my ($fileName) = @_;
1005 :			# Open the file as the standard error output.
1006 :			open STDERR, '>', $fileName;
1007 :	olson	1.1	}
1008 :
1009 :	parrello	1.5	=head3 ReadOptions
1010 :
1011 :			C<< my %options = Tracer::ReadOptions($fileName); >>
1012 :
1013 :			Read a set of options from a file. Each option is encoded in a line of text that has the
1014 :			format
1015 :
1016 :			I<optionName>C<=>I<optionValue>C<; >I<comment>
1017 :
1018 :			The option name must consist entirely of letters, digits, and the punctuation characters
1019 :	parrello	1.9	C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1020 :			character is a semi-colon will be ignored. The return hash will map each option name to
1021 :	parrello	1.5	the corresponding option value.
1022 :
1023 :			=over 4
1024 :
1025 :			=item fileName
1026 :
1027 :			Name of the file containing the option data.
1028 :
1029 :			=item RETURN
1030 :
1031 :			Returns a hash mapping the option names specified in the file to their corresponding option
1032 :			value.
1033 :
1034 :			=back
1035 :
1036 :			=cut
1037 :
1038 :			sub ReadOptions {
1039 :	parrello	1.12	# Get the parameters.
1040 :			my ($fileName) = @_;
1041 :			# Open the file.
1042 :			(open CONFIGFILE, "<$fileName") \|\| Confess("Could not open option file $fileName.");
1043 :			# Count the number of records read.
1044 :			my ($records, $comments) = 0;
1045 :			# Create the return hash.
1046 :			my %retVal = ();
1047 :			# Loop through the file, accumulating key-value pairs.
1048 :			while (my $line = <CONFIGFILE>) {
1049 :			# Denote we've read a line.
1050 :			$records++;
1051 :			# Determine the line type.
1052 :			if ($line =~ /^\s*[\n\r]/) {
1053 :			# A blank line is a comment.
1054 :			$comments++;
1055 :			} elsif ($line =~ /^\s([A-Za-z0-9_\.]+)=([^;]);/) {
1056 :			# Here we have an option assignment.
1057 :			retVal{$1} = $2;
1058 :			} elsif ($line =~ /^\s*;/) {
1059 :			# Here we have a text comment.
1060 :			$comments++;
1061 :			} else {
1062 :			# Here we have an invalid line.
1063 :			Trace("Invalid option statement in record $records.") if T(0);
1064 :			}
1065 :			}
1066 :			# Return the hash created.
1067 :			return %retVal;
1068 :	parrello	1.5	}
1069 :
1070 :	olson	1.1	=head3 GetOptions
1071 :
1072 :			C<< Tracer::GetOptions(\%defaults, \%options); >>
1073 :
1074 :			Merge a specified set of options into a table of defaults. This method takes two hash references
1075 :			as input and uses the data from the second to update the first. If the second does not exist,
1076 :			there will be no effect. An error will be thrown if one of the entries in the second hash does not
1077 :			exist in the first.
1078 :
1079 :			Consider the following example.
1080 :
1081 :			C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
1082 :
1083 :			In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1084 :			B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1085 :			B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1086 :			the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1087 :			will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1088 :
1089 :			C<< {databaseType => 'Oracle'} >>
1090 :
1091 :			an error will occur because the B<databaseType> option does not exist.
1092 :
1093 :			=over 4
1094 :
1095 :			=item defaults
1096 :
1097 :			Table of default option values.
1098 :
1099 :			=item options
1100 :
1101 :			Table of overrides, if any.
1102 :
1103 :			=item RETURN
1104 :
1105 :			Returns a reference to the default table passed in as the first parameter.
1106 :
1107 :			=back
1108 :
1109 :			=cut
1110 :
1111 :			sub GetOptions {
1112 :	parrello	1.12	# Get the parameters.
1113 :			my ($defaults, $options) = @_;
1114 :			# Check for overrides.
1115 :			if ($options) {
1116 :			# Loop through the overrides.
1117 :			while (my ($option, $setting) = each %{$options}) {
1118 :			# Insure this override exists.
1119 :			if (!exists $defaults->{$option}) {
1120 :			croak "Unrecognized option $option encountered.";
1121 :			} else {
1122 :			# Apply the override.
1123 :			$defaults->{$option} = $setting;
1124 :			}
1125 :			}
1126 :			}
1127 :			# Return the merged table.
1128 :			return $defaults;
1129 :	olson	1.1	}
1130 :
1131 :			=head3 MergeOptions
1132 :
1133 :			C<< Tracer::MergeOptions(\%table, \%defaults); >>
1134 :
1135 :			Merge default values into a hash table. This method looks at the key-value pairs in the
1136 :			second (default) hash, and if a matching key is not found in the first hash, the default
1137 :			pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1138 :			checking and no return value.
1139 :
1140 :			=over 4
1141 :
1142 :			=item table
1143 :
1144 :			Hash table to be updated with the default values.
1145 :
1146 :			=item defaults
1147 :
1148 :			Default values to be merged into the first hash table if they are not already present.
1149 :
1150 :			=back
1151 :
1152 :			=cut
1153 :
1154 :			sub MergeOptions {
1155 :	parrello	1.12	# Get the parameters.
1156 :			my ($table, $defaults) = @_;
1157 :			# Loop through the defaults.
1158 :			while (my ($key, $value) = each %{$defaults}) {
1159 :			if (!exists $table->{$key}) {
1160 :			$table->{$key} = $value;
1161 :			}
1162 :			}
1163 :	olson	1.1	}
1164 :
1165 :			=head3 Trace
1166 :
1167 :			C<< Trace($message); >>
1168 :
1169 :			Write a trace message to the target location specified in L</TSetup>. If there has not been
1170 :			any prior call to B<TSetup>.
1171 :
1172 :			=over 4
1173 :
1174 :			=item message
1175 :
1176 :			Message to write.
1177 :
1178 :			=back
1179 :
1180 :			=cut
1181 :
1182 :			sub Trace {
1183 :	parrello	1.12	# Get the parameters.
1184 :			my ($message) = @_;
1185 :			# Get the timestamp.
1186 :			my $timeStamp = Now();
1187 :			# Format the message. Note we strip off any line terminators at the end.
1188 :	parrello	1.69	my $formatted = "[$timeStamp] <$LastCategory>: " . Strip($message);
1189 :	parrello	1.12	# Process according to the destination.
1190 :			if ($Destination eq "TEXT") {
1191 :			# Write the message to the standard output.
1192 :			print "$formatted\n";
1193 :			} elsif ($Destination eq "ERROR") {
1194 :			# Write the message to the error output.
1195 :			print STDERR "$formatted\n";
1196 :			} elsif ($Destination eq "QUEUE") {
1197 :			# Push the message into the queue.
1198 :			push @Queue, "$formatted";
1199 :			} elsif ($Destination eq "HTML") {
1200 :			# Convert the message to HTML and write it to the standard output.
1201 :			my $escapedMessage = CGI::escapeHTML($message);
1202 :			print "<p>$formatted</p>\n";
1203 :	parrello	1.4	} elsif ($Destination eq "WARN") {
1204 :			# Emit the message as a warning.
1205 :			warn $message;
1206 :	parrello	1.12	} elsif ($Destination =~ m/^>>/) {
1207 :			# Write the trace message to an output file.
1208 :	parrello	1.14	(open TRACING, $Destination) \|\| die "Tracing open for \"$Destination\" failed: $!";
1209 :	parrello	1.12	print TRACING "$formatted\n";
1210 :			close TRACING;
1211 :			# If the Tee flag is on, echo it to the standard output.
1212 :			if ($TeeFlag) {
1213 :			print "$formatted\n";
1214 :			}
1215 :			}
1216 :	olson	1.1	}
1217 :
1218 :			=head3 T
1219 :
1220 :	parrello	1.2	C<< my $switch = T($category, $traceLevel); >>
1221 :	olson	1.1
1222 :	parrello	1.12	or
1223 :	parrello	1.2
1224 :	olson	1.1	C<< my $switch = T($traceLevel); >>
1225 :
1226 :			Return TRUE if the trace level is at or above a specified value and the specified category
1227 :			is active, else FALSE. If no category is specified, the caller's package name is used.
1228 :
1229 :			=over 4
1230 :
1231 :			=item category
1232 :
1233 :			Category to which the message belongs. If not specified, the caller's package name is
1234 :			used.
1235 :
1236 :			=item traceLevel
1237 :
1238 :			Relevant tracing level.
1239 :
1240 :			=item RETURN
1241 :
1242 :			TRUE if a message at the specified trace level would appear in the trace, else FALSE.
1243 :
1244 :			=back
1245 :
1246 :			=cut
1247 :
1248 :			sub T {
1249 :	parrello	1.12	# Declare the return variable.
1250 :			my $retVal = 0;
1251 :			# Only proceed if tracing is turned on.
1252 :			if ($Destination ne "NONE") {
1253 :			# Get the parameters.
1254 :			my ($category, $traceLevel) = @_;
1255 :			if (!defined $traceLevel) {
1256 :			# Here we have no category, so we need to get the calling package.
1257 :			# The calling package is normally the first parameter. If it is
1258 :			# omitted, the first parameter will be the tracelevel. So, the
1259 :			# first thing we do is shift the so-called category into the
1260 :			# $traceLevel variable where it belongs.
1261 :			$traceLevel = $category;
1262 :			my ($package, $fileName, $line) = caller;
1263 :	parrello	1.3	# If there is no calling package, we default to "main".
1264 :	parrello	1.12	if (!$package) {
1265 :	parrello	1.3	$category = "main";
1266 :	parrello	1.12	} else {
1267 :			$category = $package;
1268 :			}
1269 :			}
1270 :	parrello	1.7	# Save the category name.
1271 :			$LastCategory = $category;
1272 :	parrello	1.13	# Convert it to lower case before we hash it.
1273 :			$category = lc $category;
1274 :	parrello	1.12	# Use the category and tracelevel to compute the result.
1275 :	parrello	1.36	if (ref $traceLevel) {
1276 :			Confess("Bad trace level.");
1277 :			} elsif (ref $TraceLevel) {
1278 :			Confess("Bad trace config.");
1279 :			}
1280 :	parrello	1.12	$retVal = ($traceLevel <= $TraceLevel && ($AllTrace \|\| exists $Categories{$category}));
1281 :	parrello	1.3	}
1282 :	parrello	1.12	# Return the computed result.
1283 :	parrello	1.3	return $retVal;
1284 :	olson	1.1	}
1285 :
1286 :			=head3 ParseCommand
1287 :
1288 :			C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1289 :
1290 :			Parse a command line consisting of a list of parameters. The initial parameters may be option
1291 :	parrello	1.2	specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1292 :			off and merged into a table of default options. The remainder of the command line is
1293 :	olson	1.1	returned as a list of positional arguments. For example, consider the following invocation.
1294 :
1295 :			C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1296 :
1297 :	parrello	1.84	In this case, the list @words will be treated as a command line and there are two options available,
1298 :	olson	1.1	B<errors> and B<logFile>. If @words has the following format
1299 :
1300 :			C<< -logFile=error.log apple orange rutabaga >>
1301 :
1302 :			then at the end of the invocation, C<$options> will be
1303 :
1304 :			C<< { errors => 0, logFile => 'error.log' } >>
1305 :
1306 :			and C<@arguments> will contain
1307 :
1308 :			C<< apple orange rutabaga >>
1309 :
1310 :	parrello	1.2	The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1311 :	parrello	1.84	support for quote characters. Options can be specified with single or double hyphens.
1312 :	olson	1.1
1313 :			=over 4
1314 :
1315 :			=item optionTable
1316 :
1317 :			Table of default options.
1318 :
1319 :			=item inputList
1320 :
1321 :			List of words on the command line.
1322 :
1323 :			=item RETURN
1324 :
1325 :			Returns a reference to the option table and a list of the positional arguments.
1326 :
1327 :			=back
1328 :
1329 :			=cut
1330 :
1331 :			sub ParseCommand {
1332 :	parrello	1.12	# Get the parameters.
1333 :			my ($optionTable, @inputList) = @_;
1334 :			# Process any options in the input list.
1335 :			my %overrides = ();
1336 :	parrello	1.84	while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1337 :	parrello	1.12	# Get the current option.
1338 :			my $arg = shift @inputList;
1339 :			# Pull out the option name.
1340 :	parrello	1.84	$arg =~ /^--?([^=]*)/g;
1341 :	parrello	1.12	my $name = $1;
1342 :			# Check for an option value.
1343 :			if ($arg =~ /\G=(.*)$/g) {
1344 :			# Here we have a value for the option.
1345 :			$overrides{$name} = UnEscape($1);
1346 :			} else {
1347 :			# Here there is no value, so we use 1.
1348 :			$overrides{$name} = 1;
1349 :			}
1350 :			}
1351 :			# Merge the options into the defaults.
1352 :			GetOptions($optionTable, \%overrides);
1353 :			# Translate the remaining parameters.
1354 :			my @retVal = ();
1355 :			for my $inputParm (@inputList) {
1356 :			push @retVal, UnEscape($inputParm);
1357 :			}
1358 :			# Return the results.
1359 :			return ($optionTable, @retVal);
1360 :	olson	1.1	}
1361 :
1362 :	parrello	1.9	=head3 Escape
1363 :
1364 :			C<< my $codedString = Tracer::Escape($realString); >>
1365 :
1366 :	parrello	1.25	Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1367 :	parrello	1.28	replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1368 :			result is to reverse the effect of L</UnEscape>.
1369 :	parrello	1.9
1370 :			=over 4
1371 :
1372 :			=item realString
1373 :
1374 :			String to escape.
1375 :
1376 :			=item RETURN
1377 :
1378 :			Escaped equivalent of the real string.
1379 :
1380 :			=back
1381 :
1382 :			=cut
1383 :
1384 :			sub Escape {
1385 :	parrello	1.12	# Get the parameter.
1386 :			my ($realString) = @_;
1387 :			# Initialize the return variable.
1388 :			my $retVal = "";
1389 :			# Loop through the parameter string, looking for sequences to escape.
1390 :			while (length $realString > 0) {
1391 :			# Look for the first sequence to escape.
1392 :	parrello	1.27	if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1393 :	parrello	1.12	# Here we found it. The text preceding the sequence is in $1. The sequence
1394 :			# itself is in $2. First, move the clear text to the return variable.
1395 :			$retVal .= $1;
1396 :	parrello	1.14	# Strip the processed section off the real string.
1397 :			$realString = substr $realString, (length $2) + (length $1);
1398 :	parrello	1.28	# Get the matched character.
1399 :	parrello	1.12	my $char = $2;
1400 :	parrello	1.28	# If we have a CR, we are done.
1401 :			if ($char ne "\r") {
1402 :			# It's not a CR, so encode the escape sequence.
1403 :			$char =~ tr/\t\n/tn/;
1404 :			$retVal .= "\\" . $char;
1405 :			}
1406 :	parrello	1.12	} else {
1407 :			# Here there are no more escape sequences. The rest of the string is
1408 :			# transferred unmodified.
1409 :			$retVal .= $realString;
1410 :			$realString = "";
1411 :			}
1412 :			}
1413 :			# Return the result.
1414 :			return $retVal;
1415 :	parrello	1.9	}
1416 :
1417 :	olson	1.1	=head3 UnEscape
1418 :
1419 :			C<< my $realString = Tracer::UnEscape($codedString); >>
1420 :
1421 :	parrello	1.25	Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1422 :	parrello	1.28	a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1423 :			be deleted.
1424 :	olson	1.1
1425 :			=over 4
1426 :
1427 :			=item codedString
1428 :
1429 :			String to un-escape.
1430 :
1431 :			=item RETURN
1432 :
1433 :			Returns a copy of the original string with the escape sequences converted to their actual
1434 :			values.
1435 :
1436 :			=back
1437 :
1438 :			=cut
1439 :
1440 :			sub UnEscape {
1441 :	parrello	1.12	# Get the parameter.
1442 :			my ($codedString) = @_;
1443 :			# Initialize the return variable.
1444 :			my $retVal = "";
1445 :			# Only proceed if the incoming string is nonempty.
1446 :			if (defined $codedString) {
1447 :			# Loop through the parameter string, looking for escape sequences. We can't do
1448 :	parrello	1.25	# translating because it causes problems with the escaped slash. ("\\t" becomes
1449 :			# "\<tab>" no matter what we do.)
1450 :	parrello	1.12	while (length $codedString > 0) {
1451 :			# Look for the first escape sequence.
1452 :	parrello	1.27	if ($codedString =~ /^(.*?)\\(\\\|n\|t\|r)/) {
1453 :	parrello	1.12	# Here we found it. The text preceding the sequence is in $1. The sequence
1454 :			# itself is in $2. First, move the clear text to the return variable.
1455 :			$retVal .= $1;
1456 :			$codedString = substr $codedString, (2 + length $1);
1457 :	parrello	1.28	# Get the escape value.
1458 :	parrello	1.12	my $char = $2;
1459 :	parrello	1.28	# If we have a "\r", we are done.
1460 :			if ($char ne 'r') {
1461 :			# Here it's not an 'r', so we convert it.
1462 :			$char =~ tr/\\tn/\\\t\n/;
1463 :			$retVal .= $char;
1464 :			}
1465 :	parrello	1.12	} else {
1466 :			# Here there are no more escape sequences. The rest of the string is
1467 :			# transferred unmodified.
1468 :			$retVal .= $codedString;
1469 :			$codedString = "";
1470 :			}
1471 :			}
1472 :			}
1473 :			# Return the result.
1474 :			return $retVal;
1475 :	olson	1.1	}
1476 :
1477 :			=head3 ParseRecord
1478 :
1479 :			C<< my @fields = Tracer::ParseRecord($line); >>
1480 :
1481 :			Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1482 :			and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1483 :			These will automatically be converted.
1484 :
1485 :			=over 4
1486 :
1487 :			=item line
1488 :
1489 :			Line of data containing the tab-delimited fields.
1490 :
1491 :			=item RETURN
1492 :
1493 :			Returns a list of the fields found in the data line.
1494 :
1495 :			=back
1496 :
1497 :			=cut
1498 :
1499 :			sub ParseRecord {
1500 :	parrello	1.12	# Get the parameter.
1501 :			my ($line) = @_;
1502 :			# Remove the trailing new-line, if any.
1503 :			chomp $line;
1504 :			# Split the line read into pieces using the tab character.
1505 :			my @retVal = split /\t/, $line;
1506 :			# Trim and fix the escapes in each piece.
1507 :			for my $value (@retVal) {
1508 :			# Trim leading whitespace.
1509 :			$value =~ s/^\s+//;
1510 :			# Trim trailing whitespace.
1511 :			$value =~ s/\s+$//;
1512 :			# Delete the carriage returns.
1513 :			$value =~ s/\r//g;
1514 :			# Convert the escapes into their real values.
1515 :			$value =~ s/\\t/"\t"/ge;
1516 :			$value =~ s/\\n/"\n"/ge;
1517 :			}
1518 :			# Return the result.
1519 :			return @retVal;
1520 :	olson	1.1	}
1521 :
1522 :			=head3 Merge
1523 :
1524 :			C<< my @mergedList = Tracer::Merge(@inputList); >>
1525 :
1526 :			Sort a list of strings and remove duplicates.
1527 :
1528 :			=over 4
1529 :
1530 :			=item inputList
1531 :
1532 :			List of scalars to sort and merge.
1533 :
1534 :			=item RETURN
1535 :
1536 :			Returns a list containing the same elements sorted in ascending order with duplicates
1537 :			removed.
1538 :
1539 :			=back
1540 :
1541 :			=cut
1542 :
1543 :			sub Merge {
1544 :	parrello	1.12	# Get the input list in sort order.
1545 :			my @inputList = sort @_;
1546 :			# Only proceed if the list has at least two elements.
1547 :			if (@inputList > 1) {
1548 :			# Now we want to move through the list splicing out duplicates.
1549 :			my $i = 0;
1550 :			while ($i < @inputList) {
1551 :			# Get the current entry.
1552 :			my $thisEntry = $inputList[$i];
1553 :			# Find out how many elements duplicate the current entry.
1554 :			my $j = $i + 1;
1555 :			my $dup1 = $i + 1;
1556 :			while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1557 :			# If the number is nonzero, splice out the duplicates found.
1558 :			if ($j > $dup1) {
1559 :			splice @inputList, $dup1, $j - $dup1;
1560 :			}
1561 :			# Now the element at position $dup1 is different from the element before it
1562 :			# at position $i. We push $i forward one position and start again.
1563 :			$i++;
1564 :			}
1565 :			}
1566 :			# Return the merged list.
1567 :			return @inputList;
1568 :	olson	1.1	}
1569 :
1570 :	parrello	1.54	=head3 Percent
1571 :
1572 :			C<< my $percent = Tracer::Percent($number, $base); >>
1573 :
1574 :			Returns the percent of the base represented by the given number. If the base
1575 :			is zero, returns zero.
1576 :
1577 :			=over 4
1578 :
1579 :			=item number
1580 :
1581 :			Percent numerator.
1582 :
1583 :			=item base
1584 :
1585 :			Percent base.
1586 :
1587 :			=item RETURN
1588 :
1589 :			Returns the percentage of the base represented by the numerator.
1590 :
1591 :			=back
1592 :
1593 :			=cut
1594 :
1595 :			sub Percent {
1596 :			# Get the parameters.
1597 :			my ($number, $base) = @_;
1598 :			# Declare the return variable.
1599 :			my $retVal = 0;
1600 :			# Compute the percent.
1601 :			if ($base != 0) {
1602 :			$retVal = $number * 100 / $base;
1603 :			}
1604 :			# Return the result.
1605 :			return $retVal;
1606 :			}
1607 :
1608 :	olson	1.1	=head3 GetFile
1609 :
1610 :	parrello	1.6	C<< my @fileContents = Tracer::GetFile($fileName); >>
1611 :	olson	1.1
1612 :	parrello	1.35	or
1613 :
1614 :			C<< my $fileContents = Tracer::GetFile($fileName); >>
1615 :
1616 :			Return the entire contents of a file. In list context, line-ends are removed and
1617 :			each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1618 :	olson	1.1
1619 :			=over 4
1620 :
1621 :			=item fileName
1622 :
1623 :			Name of the file to read.
1624 :
1625 :			=item RETURN
1626 :
1627 :	parrello	1.6	In a list context, returns the entire file as a list with the line terminators removed.
1628 :	parrello	1.39	In a scalar context, returns the entire file as a string. If an error occurs opening
1629 :			the file, an empty list will be returned.
1630 :	olson	1.1
1631 :			=back
1632 :
1633 :			=cut
1634 :
1635 :			sub GetFile {
1636 :	parrello	1.12	# Get the parameters.
1637 :			my ($fileName) = @_;
1638 :			# Declare the return variable.
1639 :			my @retVal = ();
1640 :			# Open the file for input.
1641 :	parrello	1.60	my $handle = Open(undef, "<$fileName");
1642 :			# Read the whole file into the return variable, stripping off any terminator
1643 :			# characters.
1644 :			my $lineCount = 0;
1645 :			while (my $line = <$handle>) {
1646 :			$lineCount++;
1647 :			$line = Strip($line);
1648 :			push @retVal, $line;
1649 :			}
1650 :			# Close it.
1651 :			close $handle;
1652 :			my $actualLines = @retVal;
1653 :	parrello	1.77	Trace("$actualLines lines read from file $fileName.") if T(File => 2);
1654 :	parrello	1.12	# Return the file's contents in the desired format.
1655 :	parrello	1.9	if (wantarray) {
1656 :	parrello	1.12	return @retVal;
1657 :	parrello	1.6	} else {
1658 :			return join "\n", @retVal;
1659 :			}
1660 :	olson	1.1	}
1661 :
1662 :	parrello	1.60	=head3 PutFile
1663 :
1664 :			C<< Tracer::PutFile($fileName, \@lines); >>
1665 :
1666 :			Write out a file from a list of lines of text.
1667 :
1668 :			=over 4
1669 :
1670 :			=item fileName
1671 :
1672 :			Name of the output file.
1673 :
1674 :			=item lines
1675 :
1676 :			Reference to a list of text lines. The lines will be written to the file in order, with trailing
1677 :	parrello	1.66	new-line characters. Alternatively, may be a string, in which case the string will be written without
1678 :			modification.
1679 :	parrello	1.60
1680 :			=back
1681 :
1682 :			=cut
1683 :
1684 :			sub PutFile {
1685 :			# Get the parameters.
1686 :			my ($fileName, $lines) = @_;
1687 :			# Open the output file.
1688 :			my $handle = Open(undef, ">$fileName");
1689 :	parrello	1.77	# Count the lines written.
1690 :	parrello	1.66	if (ref $lines ne 'ARRAY') {
1691 :			# Here we have a scalar, so we write it raw.
1692 :			print $handle $lines;
1693 :	parrello	1.77	Trace("Scalar put to file $fileName.") if T(File => 3);
1694 :	parrello	1.66	} else {
1695 :			# Write the lines one at a time.
1696 :	parrello	1.77	my $count = 0;
1697 :	parrello	1.66	for my $line (@{$lines}) {
1698 :			print $handle "$line\n";
1699 :	parrello	1.77	$count++;
1700 :	parrello	1.66	}
1701 :	parrello	1.77	Trace("$count lines put to file $fileName.") if T(File => 3);
1702 :	parrello	1.60	}
1703 :			# Close the output file.
1704 :			close $handle;
1705 :			}
1706 :
1707 :	olson	1.1	=head3 QTrace
1708 :
1709 :			C<< my $data = QTrace($format); >>
1710 :
1711 :			Return the queued trace data in the specified format.
1712 :
1713 :			=over 4
1714 :
1715 :			=item format
1716 :
1717 :			C<html> to format the data as an HTML list, C<text> to format it as straight text.
1718 :
1719 :			=back
1720 :
1721 :			=cut
1722 :
1723 :			sub QTrace {
1724 :	parrello	1.12	# Get the parameter.
1725 :			my ($format) = @_;
1726 :			# Create the return variable.
1727 :			my $retVal = "";
1728 :	parrello	1.14	# Only proceed if there is an actual queue.
1729 :			if (@Queue) {
1730 :			# Process according to the format.
1731 :			if ($format =~ m/^HTML$/i) {
1732 :			# Convert the queue into an HTML list.
1733 :			$retVal = "<ul>\n";
1734 :			for my $line (@Queue) {
1735 :			my $escapedLine = CGI::escapeHTML($line);
1736 :			$retVal .= "<li>$escapedLine</li>\n";
1737 :			}
1738 :			$retVal .= "</ul>\n";
1739 :			} elsif ($format =~ m/^TEXT$/i) {
1740 :			# Convert the queue into a list of text lines.
1741 :			$retVal = join("\n", @Queue) . "\n";
1742 :			}
1743 :			# Clear the queue.
1744 :			@Queue = ();
1745 :	parrello	1.12	}
1746 :			# Return the formatted list.
1747 :			return $retVal;
1748 :	olson	1.1	}
1749 :
1750 :			=head3 Confess
1751 :
1752 :			C<< Confess($message); >>
1753 :
1754 :	parrello	1.22	Trace the call stack and abort the program with the specified message. When used with
1755 :	parrello	1.9	the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1756 :	parrello	1.6	So, for example
1757 :	olson	1.1
1758 :	parrello	1.6	C<< Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum."); >>
1759 :	olson	1.1
1760 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
1761 :
1762 :			=over 4
1763 :
1764 :			=item message
1765 :
1766 :			Message to include in the trace.
1767 :
1768 :			=back
1769 :
1770 :			=cut
1771 :
1772 :			sub Confess {
1773 :	parrello	1.12	# Get the parameters.
1774 :			my ($message) = @_;
1775 :			# Trace the call stack.
1776 :	parrello	1.22	Cluck($message);
1777 :	parrello	1.12	# Abort the program.
1778 :			croak(">>> $message");
1779 :	olson	1.1	}
1780 :
1781 :	parrello	1.6	=head3 Assert
1782 :
1783 :			C<< Assert($condition1, $condition2, ... $conditionN); >>
1784 :
1785 :			Return TRUE if all the conditions are true. This method can be used in conjunction with
1786 :	parrello	1.29	the OR operator and the L</Confess> method as a debugging assert.
1787 :	parrello	1.6	So, for example
1788 :
1789 :			C<< Assert($recNum >= 0) \|\| Confess("Invalid record number $recNum."); >>
1790 :
1791 :			Will abort the program with a stack trace if the value of C<$recNum> is negative.
1792 :
1793 :			=cut
1794 :			sub Assert {
1795 :			my $retVal = 1;
1796 :			LOOP: for my $condition (@_) {
1797 :			if (! $condition) {
1798 :			$retVal = 0;
1799 :			last LOOP;
1800 :			}
1801 :			}
1802 :			return $retVal;
1803 :			}
1804 :
1805 :	olson	1.1	=head3 Cluck
1806 :
1807 :			C<< Cluck($message); >>
1808 :
1809 :			Trace the call stack. Note that for best results, you should qualify the call with a
1810 :			trace condition. For example,
1811 :
1812 :			C<< Cluck("Starting record parse.") if T(3); >>
1813 :
1814 :			will only trace the stack if the trace level for the package is 3 or more.
1815 :
1816 :			=over 4
1817 :
1818 :			=item message
1819 :
1820 :			Message to include in the trace.
1821 :
1822 :			=back
1823 :
1824 :			=cut
1825 :
1826 :			sub Cluck {
1827 :	parrello	1.12	# Get the parameters.
1828 :			my ($message) = @_;
1829 :	parrello	1.5	# Trace what's happening.
1830 :			Trace("Stack trace for event: $message");
1831 :	parrello	1.12	my $confession = longmess($message);
1832 :			# Convert the confession to a series of trace messages. Note we skip any
1833 :	parrello	1.5	# messages relating to calls into Tracer.
1834 :	parrello	1.12	for my $line (split /\s*\n/, $confession) {
1835 :			Trace($line) if ($line !~ /Tracer\.pm/);
1836 :			}
1837 :	olson	1.1	}
1838 :
1839 :	parrello	1.5	=head3 Min
1840 :
1841 :			C<< my $min = Min($value1, $value2, ... $valueN); >>
1842 :
1843 :			Return the minimum argument. The arguments are treated as numbers.
1844 :
1845 :			=over 4
1846 :
1847 :			=item $value1, $value2, ... $valueN
1848 :
1849 :			List of numbers to compare.
1850 :
1851 :			=item RETURN
1852 :
1853 :			Returns the lowest number in the list.
1854 :
1855 :			=back
1856 :
1857 :			=cut
1858 :
1859 :			sub Min {
1860 :	parrello	1.12	# Get the parameters. Note that we prime the return value with the first parameter.
1861 :			my ($retVal, @values) = @_;
1862 :			# Loop through the remaining parameters, looking for the lowest.
1863 :			for my $value (@values) {
1864 :			if ($value < $retVal) {
1865 :			$retVal = $value;
1866 :			}
1867 :			}
1868 :			# Return the minimum found.
1869 :			return $retVal;
1870 :	parrello	1.5	}
1871 :
1872 :			=head3 Max
1873 :
1874 :			C<< my $max = Max($value1, $value2, ... $valueN); >>
1875 :
1876 :			Return the maximum argument. The arguments are treated as numbers.
1877 :
1878 :			=over 4
1879 :
1880 :			=item $value1, $value2, ... $valueN
1881 :
1882 :			List of numbers to compare.
1883 :
1884 :			=item RETURN
1885 :
1886 :			Returns the highest number in the list.
1887 :
1888 :			=back
1889 :
1890 :			=cut
1891 :
1892 :			sub Max {
1893 :	parrello	1.12	# Get the parameters. Note that we prime the return value with the first parameter.
1894 :			my ($retVal, @values) = @_;
1895 :			# Loop through the remaining parameters, looking for the highest.
1896 :			for my $value (@values) {
1897 :			if ($value > $retVal) {
1898 :			$retVal = $value;
1899 :			}
1900 :			}
1901 :			# Return the maximum found.
1902 :			return $retVal;
1903 :	parrello	1.5	}
1904 :
1905 :			=head3 AddToListMap
1906 :
1907 :	parrello	1.53	C<< Tracer::AddToListMap(\%hash, $key, $value1, $value2, ... valueN); >>
1908 :	parrello	1.5
1909 :			Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1910 :			is created for the key. Otherwise, the new value is pushed onto the list.
1911 :
1912 :			=over 4
1913 :
1914 :			=item hash
1915 :
1916 :			Reference to the target hash.
1917 :
1918 :			=item key
1919 :
1920 :			Key for which the value is to be added.
1921 :
1922 :	parrello	1.53	=item value1, value2, ... valueN
1923 :	parrello	1.5
1924 :	parrello	1.53	List of values to add to the key's value list.
1925 :	parrello	1.5
1926 :			=back
1927 :
1928 :			=cut
1929 :
1930 :			sub AddToListMap {
1931 :			# Get the parameters.
1932 :	parrello	1.53	my ($hash, $key, @values) = @_;
1933 :	parrello	1.5	# Process according to whether or not the key already has a value.
1934 :			if (! exists $hash->{$key}) {
1935 :	parrello	1.53	$hash->{$key} = [@values];
1936 :	parrello	1.5	} else {
1937 :	parrello	1.53	push @{$hash->{$key}}, @values;
1938 :	parrello	1.5	}
1939 :			}
1940 :	olson	1.1
1941 :	parrello	1.7	=head3 DebugMode
1942 :
1943 :			C<< if (Tracer::DebugMode) { ...code... } >>
1944 :
1945 :	parrello	1.69	Return TRUE if debug mode has been turned on, else abort.
1946 :	parrello	1.7
1947 :			Certain CGI scripts are too dangerous to exist in the production
1948 :			environment. This method provides a simple way to prevent them
1949 :	parrello	1.21	from working unless they are explicitly turned on by creating a password
1950 :			cookie via the B<SetPassword> script. If debugging mode
1951 :	parrello	1.69	is not turned on, an error will occur.
1952 :	parrello	1.7
1953 :			=cut
1954 :
1955 :			sub DebugMode {
1956 :	parrello	1.12	# Declare the return variable.
1957 :	parrello	1.21	my $retVal = 0;
1958 :	parrello	1.12	# Check the debug configuration.
1959 :	parrello	1.21	my $password = CGI::cookie("DebugMode");
1960 :			my $encrypted = Digest::MD5::md5_hex($password);
1961 :			if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1962 :	parrello	1.12	$retVal = 1;
1963 :			} else {
1964 :	parrello	1.69	# Here debug mode is off, so we generate an error.
1965 :			Confess("Cannot use this facility without logging in.");
1966 :	parrello	1.12	}
1967 :			# Return the determination indicator.
1968 :	parrello	1.18	return $retVal;
1969 :	parrello	1.9	}
1970 :
1971 :			=head3 Strip
1972 :
1973 :			C<< my $string = Tracer::Strip($line); >>
1974 :
1975 :			Strip all line terminators off a string. This is necessary when dealing with files
1976 :			that may have been transferred back and forth several times among different
1977 :			operating environments.
1978 :
1979 :			=over 4
1980 :
1981 :			=item line
1982 :
1983 :			Line of text to be stripped.
1984 :
1985 :			=item RETURN
1986 :
1987 :			The same line of text with all the line-ending characters chopped from the end.
1988 :
1989 :			=back
1990 :
1991 :			=cut
1992 :
1993 :			sub Strip {
1994 :	parrello	1.12	# Get a copy of the parameter string.
1995 :			my ($string) = @_;
1996 :	parrello	1.29	my $retVal = (defined $string ? $string : "");
1997 :	parrello	1.9	# Strip the line terminator characters.
1998 :			$retVal =~ s/(\r\|\n)+$//g;
1999 :	parrello	1.12	# Return the result.
2000 :			return $retVal;
2001 :	parrello	1.9	}
2002 :
2003 :			=head3 Pad
2004 :
2005 :			C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
2006 :
2007 :			Pad a string to a specified length. The pad character will be a
2008 :			space, and the padding will be on the right side unless specified
2009 :			in the third parameter.
2010 :
2011 :			=over 4
2012 :
2013 :			=item string
2014 :
2015 :			String to be padded.
2016 :
2017 :			=item len
2018 :
2019 :			Desired length of the padded string.
2020 :
2021 :			=item left (optional)
2022 :
2023 :			TRUE if the string is to be left-padded; otherwise it will be padded on the right.
2024 :
2025 :			=item padChar (optional)
2026 :
2027 :	parrello	1.22	Character to use for padding. The default is a space.
2028 :
2029 :	parrello	1.9	=item RETURN
2030 :
2031 :	parrello	1.22	Returns a copy of the original string with the pad character added to the
2032 :			specified end so that it achieves the desired length.
2033 :	parrello	1.9
2034 :			=back
2035 :
2036 :			=cut
2037 :
2038 :			sub Pad {
2039 :	parrello	1.12	# Get the parameters.
2040 :			my ($string, $len, $left, $padChar) = @_;
2041 :			# Compute the padding character.
2042 :			if (! defined $padChar) {
2043 :			$padChar = " ";
2044 :			}
2045 :			# Compute the number of spaces needed.
2046 :			my $needed = $len - length $string;
2047 :			# Copy the string into the return variable.
2048 :			my $retVal = $string;
2049 :			# Only proceed if padding is needed.
2050 :			if ($needed > 0) {
2051 :			# Create the pad string.
2052 :			my $pad = $padChar x $needed;
2053 :			# Affix it to the return value.
2054 :			if ($left) {
2055 :			$retVal = $pad . $retVal;
2056 :			} else {
2057 :			$retVal .= $pad;
2058 :			}
2059 :			}
2060 :			# Return the result.
2061 :			return $retVal;
2062 :	parrello	1.7	}
2063 :
2064 :	parrello	1.29	=head3 EOF
2065 :
2066 :			This is a constant that is lexically greater than any useful string.
2067 :
2068 :			=cut
2069 :
2070 :			sub EOF {
2071 :			return "\xFF\xFF\xFF\xFF\xFF";
2072 :			}
2073 :
2074 :	parrello	1.15	=head3 TICK
2075 :
2076 :			C<< my @results = TICK($commandString); >>
2077 :
2078 :			Perform a back-tick operation on a command. If this is a Windows environment, any leading
2079 :			dot-slash (C<./> will be removed. So, for example, if you were doing
2080 :
2081 :			`./protein.cgi`
2082 :
2083 :			from inside a CGI script, it would work fine in Unix, but would issue an error message
2084 :			in Windows complaining that C<'.'> is not a valid command. If instead you code
2085 :
2086 :			TICK("./protein.cgi")
2087 :
2088 :			it will work correctly in both environments.
2089 :
2090 :			=over 4
2091 :
2092 :			=item commandString
2093 :
2094 :			The command string to pass to the system.
2095 :
2096 :			=item RETURN
2097 :
2098 :			Returns the standard output from the specified command, as a list.
2099 :
2100 :			=back
2101 :
2102 :			=cut
2103 :			#: Return Type @;
2104 :			sub TICK {
2105 :			# Get the parameters.
2106 :			my ($commandString) = @_;
2107 :			# Chop off the dot-slash if this is Windows.
2108 :			if ($FIG_Config::win_mode) {
2109 :			$commandString =~ s!^\./!!;
2110 :			}
2111 :			# Activate the command and return the result.
2112 :			return `$commandString`;
2113 :			}
2114 :
2115 :	parrello	1.35	=head3 ScriptSetup
2116 :
2117 :	parrello	1.69	C<< my ($cgi, $varHash) = ScriptSetup($noTrace); >>
2118 :	parrello	1.35
2119 :			Perform standard tracing and debugging setup for scripts. The value returned is
2120 :	parrello	1.81	the CGI object followed by a pre-built variable hash. At the end of the script,
2121 :			the client should call L</ScriptFinish> to output the web page.
2122 :	parrello	1.35
2123 :	parrello	1.81	This method calls L</ETracing> to configure tracing, which allows the tracing
2124 :			to be configured via the emergency tracing form on the debugging control panel.
2125 :	parrello	1.72	Tracing will then be turned on automatically for all programs that use the L</ETracing>
2126 :			method, which includes every program that uses this method or L</StandardSetup>.
2127 :	parrello	1.69
2128 :			=over 4
2129 :
2130 :			=item noTrace (optional)
2131 :
2132 :			If specified, tracing will be suppressed. This is useful if the script wants to set up
2133 :			tracing manually.
2134 :
2135 :			=item RETURN
2136 :
2137 :			Returns a two-element list consisting of a CGI query object and a variable hash for
2138 :			the output page.
2139 :
2140 :			=back
2141 :	parrello	1.35
2142 :			=cut
2143 :
2144 :			sub ScriptSetup {
2145 :	parrello	1.69	# Get the parameters.
2146 :			my ($noTrace) = @_;
2147 :	parrello	1.35	# Get the CGI query object.
2148 :	parrello	1.69	my $cgi = CGI->new();
2149 :			# Set up tracing if it's not suppressed.
2150 :	parrello	1.72	ETracing($cgi) unless $noTrace;
2151 :	parrello	1.69	# Create the variable hash.
2152 :			my $varHash = { results => '' };
2153 :			# Return the query object and variable hash.
2154 :			return ($cgi, $varHash);
2155 :			}
2156 :
2157 :	parrello	1.72	=head3 ETracing
2158 :	parrello	1.69
2159 :	parrello	1.72	C<< ETracing($parameter); >>
2160 :	parrello	1.69
2161 :	parrello	1.72	Set up emergency tracing. Emergency tracing is tracing that is turned
2162 :			on automatically for any program that calls this method. The emergency
2163 :			tracing parameters are stored in a a file identified by a tracing key.
2164 :			If this method is called with a CGI object, then the tracing key is
2165 :			taken from a cookie. If it is called with no parameters, then the tracing
2166 :			key is taken from an environment variable. If it is called with a string,
2167 :			the tracing key is that string.
2168 :	parrello	1.69
2169 :			=over 4
2170 :
2171 :	parrello	1.72	=item parameter
2172 :	parrello	1.69
2173 :	parrello	1.72	A parameter from which the tracing key is computed. If it is a scalar,
2174 :			that scalar is used as the tracing key. If it is a CGI object, the
2175 :			tracing key is taken from the C<IP> cookie. If it is omitted, the
2176 :			tracing key is taken from the C<TRACING> environment variable. If it
2177 :			is a CGI object and emergency tracing is not on, the C<Trace> and
2178 :			C<TF> parameters will be used to determine the type of tracing.
2179 :	parrello	1.69
2180 :			=back
2181 :
2182 :			=cut
2183 :
2184 :	parrello	1.72	sub ETracing {
2185 :			# Get the parameter.
2186 :			my ($parameter) = @_;
2187 :			# Check for CGI mode.
2188 :			my $cgi = (ref $parameter eq 'CGI' ? $parameter : undef);
2189 :	parrello	1.69	# Default to no tracing except errors.
2190 :			my ($tracing, $dest) = ("0", "WARN");
2191 :			# Check for emergency tracing.
2192 :	parrello	1.72	my $tkey = EmergencyKey($parameter);
2193 :			my $emergencyFile = EmergencyFileName($tkey);
2194 :	parrello	1.69	if (-e $emergencyFile) {
2195 :			# We have the file. Read in the data.
2196 :			my @tracing = GetFile($emergencyFile);
2197 :			# Pull off the time limit.
2198 :			my $expire = shift @tracing;
2199 :			# Convert it to seconds.
2200 :			$expire *= 3600;
2201 :			# Check the file data.
2202 :			my $stat = stat($emergencyFile);
2203 :			my ($now) = gettimeofday;
2204 :			if ($now - $stat->mtime > $expire) {
2205 :			# Delete the expired file.
2206 :			unlink $emergencyFile;
2207 :			} else {
2208 :			# Emergency tracing is on. Pull off the destination and
2209 :			# the trace level;
2210 :			$dest = shift @tracing;
2211 :			my $level = shift @tracing;
2212 :			# Convert the destination to a real tracing destination.
2213 :			# temp directory.
2214 :	parrello	1.72	$dest = EmergencyTracingDest($tkey, $dest);
2215 :	parrello	1.69	# Insure Tracer is specified.
2216 :			my %moduleHash = map { $_ => 1 } @tracing;
2217 :			$moduleHash{Tracer} = 1;
2218 :			# Set the trace parameter.
2219 :			$tracing = join(" ", $level, sort keys %moduleHash);
2220 :	parrello	1.72	}
2221 :			} elsif (defined $cgi) {
2222 :			# There's no emergency tracing, but we have a CGI object, so check
2223 :			# for tracing from the form parameters.
2224 :			if ($cgi->param('Trace')) {
2225 :			# Here the user has requested tracing via a form.
2226 :			$dest = ($cgi->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
2227 :			$tracing = $cgi->param('Trace') . " Tracer";
2228 :			}
2229 :			}
2230 :	parrello	1.69	# Setup the tracing we've determined from all the stuff above.
2231 :			TSetup($tracing, $dest);
2232 :	parrello	1.72	# If we're a web script, trace the parameter and environment data.
2233 :			if (defined $cgi) {
2234 :			TraceParms($cgi);
2235 :			}
2236 :	parrello	1.69	}
2237 :
2238 :			=head3 EmergencyFileName
2239 :
2240 :	parrello	1.72	C<< my $fileName = Tracer::EmergencyFileName($tkey); >>
2241 :	parrello	1.69
2242 :			Return the emergency tracing file name. This is the file that specifies
2243 :			the tracing information.
2244 :
2245 :			=over 4
2246 :
2247 :	parrello	1.72	=item tkey
2248 :	parrello	1.69
2249 :	parrello	1.72	Tracing key for the current program.
2250 :	parrello	1.69
2251 :			=item RETURN
2252 :
2253 :			Returns the name of the file to contain the emergency tracing information.
2254 :
2255 :			=back
2256 :
2257 :			=cut
2258 :
2259 :			sub EmergencyFileName {
2260 :			# Get the parameters.
2261 :	parrello	1.72	my ($tkey) = @_;
2262 :	parrello	1.69	# Compute the emergency tracing file name.
2263 :	parrello	1.72	return "$FIG_Config::temp/Emergency$tkey.txt";
2264 :	parrello	1.69	}
2265 :
2266 :			=head3 EmergencyFileTarget
2267 :
2268 :	parrello	1.72	C<< my $fileName = Tracer::EmergencyFileTarget($tkey); >>
2269 :	parrello	1.69
2270 :			Return the emergency tracing target file name. This is the file that receives
2271 :			the tracing output for file-based tracing.
2272 :
2273 :			=over 4
2274 :
2275 :	parrello	1.72	=item tkey
2276 :	parrello	1.69
2277 :	parrello	1.72	Tracing key for the current program.
2278 :	parrello	1.69
2279 :			=item RETURN
2280 :
2281 :	parrello	1.72	Returns the name of the file to contain the trace output.
2282 :	parrello	1.69
2283 :			=back
2284 :
2285 :			=cut
2286 :
2287 :			sub EmergencyFileTarget {
2288 :			# Get the parameters.
2289 :	parrello	1.72	my ($tkey) = @_;
2290 :	parrello	1.69	# Compute the emergency tracing file name.
2291 :	parrello	1.72	return "$FIG_Config::temp/trace$tkey.log";
2292 :	parrello	1.69	}
2293 :
2294 :			=head3 EmergencyTracingDest
2295 :
2296 :	parrello	1.72	C<< my $dest = Tracer::EmergencyTracingDest($tkey, $myDest); >>
2297 :	parrello	1.69
2298 :			This method converts an emergency tracing destination to a real
2299 :			tracing destination. The main difference is that if the
2300 :			destination is C<FILE> or C<APPEND>, we convert it to file
2301 :	parrello	1.84	output. If the destination is C<DUAL>, we convert it to file
2302 :			and standard output.
2303 :	parrello	1.69
2304 :			=over 4
2305 :
2306 :	parrello	1.72	=item tkey
2307 :	parrello	1.69
2308 :	parrello	1.72	Tracing key for this environment.
2309 :	parrello	1.69
2310 :			=item myDest
2311 :
2312 :			Destination from the emergency tracing file.
2313 :
2314 :			=item RETURN
2315 :
2316 :			Returns a destination that can be passed into L</TSetup>.
2317 :
2318 :			=back
2319 :
2320 :			=cut
2321 :
2322 :			sub EmergencyTracingDest {
2323 :			# Get the parameters.
2324 :	parrello	1.72	my ($tkey, $myDest) = @_;
2325 :	parrello	1.69	# Declare the return variable.
2326 :			my $retVal;
2327 :			# Process according to the destination value.
2328 :			if ($myDest eq 'FILE') {
2329 :	parrello	1.72	$retVal = ">" . EmergencyFileTarget($tkey);
2330 :	parrello	1.69	} elsif ($myDest eq 'APPEND') {
2331 :	parrello	1.72	$retVal = ">>" . EmergencyFileTarget($tkey);
2332 :	parrello	1.84	} elsif ($myDest eq 'DUAL') {
2333 :			$retVal = "+>" . EmergencyFileTarget($tkey);
2334 :	parrello	1.35	}
2335 :	parrello	1.69	# Return the result.
2336 :			return $retVal;
2337 :			}
2338 :
2339 :			=head3 Emergency
2340 :
2341 :	parrello	1.72	C<< Emergency($key, $hours, $dest, $level, @modules); >>
2342 :	parrello	1.69
2343 :	parrello	1.84	Turn on emergency tracing. This method is normally invoked over the web from
2344 :			a debugging console, but it can also be called by the C<trace.pl> script.
2345 :			The caller specifies the duration of the emergency in hours, the desired tracing
2346 :			destination, the trace level, and a list of the trace modules to activate.
2347 :			For the length of the duration, when a program in an environment with the
2348 :			specified tracing key active invokes a Sprout CGI script, tracing will be
2349 :			turned on automatically. See L</TSetup> for more about tracing setup and
2350 :			L</ETracing> for more about emergency tracing.
2351 :	parrello	1.69
2352 :			=over 4
2353 :
2354 :	parrello	1.72	=item tkey
2355 :	parrello	1.69
2356 :	parrello	1.72	The tracing key. This is used to identify the control file and the trace file.
2357 :	parrello	1.69
2358 :			=item hours
2359 :
2360 :			Number of hours to keep emergency tracing alive.
2361 :
2362 :			=item dest
2363 :
2364 :			Tracing destination. If no path information is specified for a file
2365 :			destination, it is put in the FIG temporary directory.
2366 :
2367 :			=item level
2368 :
2369 :			Tracing level. A higher level means more trace messages.
2370 :
2371 :			=item modules
2372 :
2373 :			A list of the tracing modules to activate.
2374 :
2375 :			=back
2376 :
2377 :			=cut
2378 :
2379 :			sub Emergency {
2380 :			# Get the parameters.
2381 :	parrello	1.72	my ($tkey, $hours, $dest, $level, @modules) = @_;
2382 :	parrello	1.69	# Create the emergency file.
2383 :	parrello	1.72	my $specFile = EmergencyFileName($tkey);
2384 :	parrello	1.69	my $outHandle = Open(undef, ">$specFile");
2385 :	parrello	1.71	print $outHandle join("\n", $hours, $dest, $level, @modules, "");
2386 :	parrello	1.69	}
2387 :
2388 :	parrello	1.72	=head3 EmergencyKey
2389 :	parrello	1.69
2390 :	parrello	1.72	C<< my $tkey = EmergencyKey($parameter); >>
2391 :	parrello	1.69
2392 :	parrello	1.72	Return the Key to be used for emergency tracing. This could be an IP address,
2393 :			a session ID, or a user name, depending on the environment.
2394 :	parrello	1.69
2395 :			=over 4
2396 :
2397 :	parrello	1.72	=item parameter
2398 :	parrello	1.69
2399 :	parrello	1.72	Parameter defining the method for finding the tracing key. If it is a scalar,
2400 :			then it is presumed to be the tracing key itself. If it is a CGI object, then
2401 :			the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
2402 :			taken from the C<TRACING> environment variable.
2403 :	parrello	1.69
2404 :			=item RETURN
2405 :
2406 :	parrello	1.72	Returns the key to be used for labels in emergency tracing.
2407 :	parrello	1.69
2408 :			=back
2409 :
2410 :			=cut
2411 :
2412 :	parrello	1.72	sub EmergencyKey {
2413 :	parrello	1.69	# Get the parameters.
2414 :	parrello	1.72	my ($parameter) = @_;
2415 :			# Declare the return variable.
2416 :			my $retVal;
2417 :			# Determine the parameter type.
2418 :			if (! defined $parameter) {
2419 :			# Here we're supposed to check the environment.
2420 :			$retVal = $ENV{TRACING};
2421 :			} else {
2422 :			my $ptype = ref $parameter;
2423 :			if ($ptype eq 'CGI') {
2424 :			# Here we were invoked from a web page. Look for a cookie.
2425 :			$retVal = $parameter->cookie('IP');
2426 :			} elsif (! $ptype) {
2427 :			# Here the key was passed in.
2428 :			$retVal = $parameter;
2429 :			}
2430 :			}
2431 :			# If no luck finding a key, use the PID.
2432 :			if (! defined $retVal) {
2433 :			$retVal = $$;
2434 :			}
2435 :	parrello	1.69	# Return the result.
2436 :	parrello	1.70	return $retVal;
2437 :	parrello	1.35	}
2438 :
2439 :	parrello	1.69
2440 :	parrello	1.65	=head3 TraceParms
2441 :
2442 :	parrello	1.69	C<< Tracer::TraceParms($cgi); >>
2443 :	parrello	1.65
2444 :			Trace the CGI parameters at trace level CGI => 3 and the environment variables
2445 :			at level CGI => 4.
2446 :
2447 :			=over 4
2448 :
2449 :	parrello	1.69	=item cgi
2450 :	parrello	1.65
2451 :			CGI query object containing the parameters to trace.
2452 :
2453 :			=back
2454 :
2455 :			=cut
2456 :
2457 :			sub TraceParms {
2458 :			# Get the parameters.
2459 :	parrello	1.69	my ($cgi) = @_;
2460 :	parrello	1.65	if (T(CGI => 3)) {
2461 :			# Here we want to trace the parameter data.
2462 :	parrello	1.69	my @names = $cgi->param;
2463 :	parrello	1.65	for my $parmName (sort @names) {
2464 :	parrello	1.68	# Note we skip the Trace parameters, which are for our use only.
2465 :			if ($parmName ne 'Trace' && $parmName ne 'TF') {
2466 :	parrello	1.69	my @values = $cgi->param($parmName);
2467 :	parrello	1.65	Trace("CGI: $parmName = " . join(", ", @values));
2468 :			}
2469 :			}
2470 :	parrello	1.67	# Display the request method.
2471 :	parrello	1.69	my $method = $cgi->request_method();
2472 :	parrello	1.67	Trace("Method: $method");
2473 :	parrello	1.65	}
2474 :			if (T(CGI => 4)) {
2475 :			# Here we want the environment data too.
2476 :			for my $envName (sort keys %ENV) {
2477 :			Trace("ENV: $envName = $ENV{$envName}");
2478 :			}
2479 :			}
2480 :			}
2481 :
2482 :	parrello	1.35	=head3 ScriptFinish
2483 :
2484 :			C<< ScriptFinish($webData, $varHash); >>
2485 :
2486 :			Output a web page at the end of a script. Either the string to be output or the
2487 :			name of a template file can be specified. If the second parameter is omitted,
2488 :			it is assumed we have a string to be output; otherwise, it is assumed we have the
2489 :			name of a template file. The template should have the variable C<DebugData>
2490 :			specified in any form that invokes a standard script. If debugging mode is turned
2491 :			on, a form field will be put in that allows the user to enter tracing data.
2492 :			Trace messages will be placed immediately before the terminal C<BODY> tag in
2493 :			the output, formatted as a list.
2494 :
2495 :			A typical standard script would loook like the following.
2496 :
2497 :			BEGIN {
2498 :			# Print the HTML header.
2499 :			print "CONTENT-TYPE: text/html\n\n";
2500 :			}
2501 :			use Tracer;
2502 :			use CGI;
2503 :			use FIG;
2504 :			# ... more uses ...
2505 :	parrello	1.61
2506 :	parrello	1.69	my ($cgi, $varHash) = ScriptSetup();
2507 :	parrello	1.35	eval {
2508 :	parrello	1.69	# ... get data from $cgi, put it in $varHash ...
2509 :	parrello	1.35	};
2510 :			if ($@) {
2511 :			Trace("Script Error: $@") if T(0);
2512 :			}
2513 :			ScriptFinish("Html/MyTemplate.html", $varHash);
2514 :
2515 :			The idea here is that even if the script fails, you'll see trace messages and
2516 :			useful output.
2517 :
2518 :			=over 4
2519 :
2520 :			=item webData
2521 :
2522 :			A string containing either the full web page to be written to the output or the
2523 :			name of a template file from which the page is to be constructed. If the name
2524 :			of a template file is specified, then the second parameter must be present;
2525 :			otherwise, it must be absent.
2526 :
2527 :			=item varHash (optional)
2528 :
2529 :			If specified, then a reference to a hash mapping variable names for a template
2530 :			to their values. The template file will be read into memory, and variable markers
2531 :			will be replaced by data in this hash reference.
2532 :
2533 :	parrello	1.37	=back
2534 :
2535 :	parrello	1.35	=cut
2536 :
2537 :			sub ScriptFinish {
2538 :			# Get the parameters.
2539 :			my ($webData, $varHash) = @_;
2540 :			# Check for a template file situation.
2541 :			my $outputString;
2542 :			if (defined $varHash) {
2543 :	parrello	1.64	# Here we have a template file. We need to determine the template type.
2544 :			my $template;
2545 :			if ($FIG_Config::template_url && $webData =~ /\.php$/) {
2546 :			$template = "$FIG_Config::template_url/$webData";
2547 :			} else {
2548 :			$template = "<<$webData";
2549 :			}
2550 :			$outputString = PageBuilder::Build($template, $varHash, "Html");
2551 :	parrello	1.35	} else {
2552 :			# Here the user gave us a raw string.
2553 :			$outputString = $webData;
2554 :			}
2555 :			# Check for trace messages.
2556 :	parrello	1.68	if ($Destination ne "NONE" && $TraceLevel > 0) {
2557 :	parrello	1.35	# We have trace messages, so we want to put them at the end of the body. This
2558 :			# is either at the end of the whole string or at the beginning of the BODY
2559 :			# end-tag.
2560 :			my $pos = length $outputString;
2561 :			if ($outputString =~ m#</body>#gi) {
2562 :			$pos = (pos $outputString) - 7;
2563 :			}
2564 :	parrello	1.68	# If the trace messages were queued, we unroll them. Otherwise, we display the
2565 :			# destination.
2566 :			my $traceHtml;
2567 :			if ($Destination eq "QUEUE") {
2568 :			$traceHtml = QTrace('Html');
2569 :			} elsif ($Destination =~ /^>>(.+)$/) {
2570 :			# Here the tracing output it to a file. We code it as a hyperlink so the user
2571 :			# can copy the file name into the clipboard easily.
2572 :			my $actualDest = $1;
2573 :	parrello	1.73	$traceHtml = "<p>Tracing output to $actualDest.</p>\n";
2574 :	parrello	1.68	} else {
2575 :			# Here we have one of the special destinations.
2576 :			$traceHtml = "<P>Tracing output type is $Destination.</p>\n";
2577 :			}
2578 :			substr $outputString, $pos, 0, $traceHtml;
2579 :	parrello	1.35	}
2580 :			# Write the output string.
2581 :			print $outputString;
2582 :			}
2583 :
2584 :	parrello	1.37	=head3 Insure
2585 :
2586 :			C<< Insure($dirName); >>
2587 :
2588 :			Insure a directory is present.
2589 :
2590 :			=over 4
2591 :
2592 :			=item dirName
2593 :
2594 :			Name of the directory to check. If it does not exist, it will be created.
2595 :
2596 :			=back
2597 :
2598 :			=cut
2599 :
2600 :			sub Insure {
2601 :			my ($dirName) = @_;
2602 :			if (! -d $dirName) {
2603 :	parrello	1.77	Trace("Creating $dirName directory.") if T(File => 2);
2604 :	parrello	1.43	eval { mkpath $dirName; };
2605 :			if ($@) {
2606 :			Confess("Error creating $dirName: $@");
2607 :			}
2608 :			}
2609 :			}
2610 :
2611 :			=head3 ChDir
2612 :
2613 :			C<< ChDir($dirName); >>
2614 :
2615 :			Change to the specified directory.
2616 :
2617 :			=over 4
2618 :
2619 :			=item dirName
2620 :
2621 :			Name of the directory to which we want to change.
2622 :
2623 :			=back
2624 :
2625 :			=cut
2626 :
2627 :			sub ChDir {
2628 :			my ($dirName) = @_;
2629 :			if (! -d $dirName) {
2630 :			Confess("Cannot change to directory $dirName: no such directory.");
2631 :			} else {
2632 :	parrello	1.77	Trace("Changing to directory $dirName.") if T(File => 4);
2633 :	parrello	1.43	my $okFlag = chdir $dirName;
2634 :			if (! $okFlag) {
2635 :			Confess("Error switching to directory $dirName.");
2636 :			}
2637 :	parrello	1.37	}
2638 :			}
2639 :
2640 :	parrello	1.59	=head3 SendSMS
2641 :
2642 :			C<< my $msgID = Tracer::SendSMS($phoneNumber, $msg); >>
2643 :
2644 :			Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
2645 :			user name, password, and API ID for the relevant account in the hash reference variable
2646 :			I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
2647 :			example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
2648 :			is C<2561022>, then the FIG_Config file must contain
2649 :
2650 :			$phone = { user => 'BruceTheHumanPet',
2651 :			password => 'silly',
2652 :			api_id => '2561022' };
2653 :
2654 :			The original purpose of this method was to insure Bruce would be notified immediately when the
2655 :			Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
2656 :			when you call this method.
2657 :
2658 :			The message ID will be returned if successful, and C<undef> if an error occurs.
2659 :
2660 :			=over 4
2661 :
2662 :			=item phoneNumber
2663 :
2664 :			Phone number to receive the message, in international format. A United States phone number
2665 :			would be prefixed by "1". A British phone number would be prefixed by "44".
2666 :
2667 :			=item msg
2668 :
2669 :			Message to send to the specified phone.
2670 :
2671 :			=item RETURN
2672 :
2673 :			Returns the message ID if successful, and C<undef> if the message could not be sent.
2674 :
2675 :			=back
2676 :
2677 :			=cut
2678 :
2679 :			sub SendSMS {
2680 :			# Get the parameters.
2681 :			my ($phoneNumber, $msg) = @_;
2682 :			# Declare the return variable. If we do not change it, C<undef> will be returned.
2683 :			my $retVal;
2684 :			# Only proceed if we have phone support.
2685 :			if (! defined $FIG_Config::phone) {
2686 :			Trace("Phone support not present in FIG_Config.") if T(1);
2687 :			} else {
2688 :			# Get the phone data.
2689 :			my $parms = $FIG_Config::phone;
2690 :			# Get the Clickatell URL.
2691 :			my $url = "http://api.clickatell.com/http/";
2692 :			# Create the user agent.
2693 :			my $ua = LWP::UserAgent->new;
2694 :			# Request a Clickatell session.
2695 :			my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
2696 :			password => $parms->{password},
2697 :			api_id => $parms->{api_id},
2698 :			to => $phoneNumber,
2699 :			text => $msg});
2700 :			# Check for an error.
2701 :			if (! $resp->is_success) {
2702 :			Trace("Alert failed.") if T(1);
2703 :			} else {
2704 :			# Get the message ID.
2705 :			my $rstring = $resp->content;
2706 :			if ($rstring =~ /^ID:\s+(.*)$/) {
2707 :			$retVal = $1;
2708 :			} else {
2709 :			Trace("Phone attempt failed with $rstring") if T(1);
2710 :			}
2711 :			}
2712 :			}
2713 :			# Return the result.
2714 :			return $retVal;
2715 :			}
2716 :
2717 :	parrello	1.55	=head3 CommaFormat
2718 :
2719 :			C<< my $formatted = Tracer::CommaFormat($number); >>
2720 :
2721 :			Insert commas into a number.
2722 :
2723 :			=over 4
2724 :
2725 :			=item number
2726 :
2727 :			A sequence of digits.
2728 :
2729 :			=item RETURN
2730 :
2731 :			Returns the same digits with commas strategically inserted.
2732 :
2733 :			=back
2734 :
2735 :			=cut
2736 :
2737 :			sub CommaFormat {
2738 :			# Get the parameters.
2739 :			my ($number) = @_;
2740 :			# Pad the length up to a multiple of three.
2741 :			my $padded = "$number";
2742 :			$padded = " " . $padded while length($padded) % 3 != 0;
2743 :			# This is a fancy PERL trick. The parentheses in the SPLIT pattern
2744 :			# cause the delimiters to be included in the output stream. The
2745 :			# GREP removes the empty strings in between the delimiters.
2746 :			my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
2747 :			# Clean out the spaces.
2748 :			$retVal =~ s/ //g;
2749 :			# Return the result.
2750 :			return $retVal;
2751 :			}
2752 :	parrello	1.46	=head3 SetPermissions
2753 :
2754 :	parrello	1.49	C<< Tracer::SetPermissions($dirName, $group, $mask, %otherMasks); >>
2755 :	parrello	1.46
2756 :			Set the permissions for a directory and all the files and folders inside it.
2757 :			In addition, the group ownership will be changed to the specified value.
2758 :
2759 :			This method is more vulnerable than most to permission and compatability
2760 :			problems, so it does internal error recovery.
2761 :
2762 :			=over 4
2763 :
2764 :			=item dirName
2765 :
2766 :			Name of the directory to process.
2767 :
2768 :			=item group
2769 :
2770 :			Name of the group to be assigned.
2771 :
2772 :			=item mask
2773 :
2774 :			Permission mask. Bits that are C<1> in this mask will be ORed into the
2775 :			permission bits of any file or directory that does not already have them
2776 :			set to 1.
2777 :
2778 :	parrello	1.49	=item otherMasks
2779 :
2780 :			Map of search patterns to permission masks. If a directory name matches
2781 :			one of the patterns, that directory and all its members and subdirectories
2782 :			will be assigned the new pattern. For example, the following would
2783 :			assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2784 :
2785 :			Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2786 :
2787 :			The list is ordered, so the following would use 0777 for C<tmp1> and
2788 :			0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2789 :
2790 :			Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2791 :			'^tmp' => 0666);
2792 :
2793 :			Note that the pattern matches are all case-insensitive, and only directory
2794 :			names are matched, not file names.
2795 :
2796 :	parrello	1.46	=back
2797 :
2798 :			=cut
2799 :
2800 :			sub SetPermissions {
2801 :			# Get the parameters.
2802 :	parrello	1.49	my ($dirName, $group, $mask, @otherMasks) = @_;
2803 :	parrello	1.46	# Set up for error recovery.
2804 :			eval {
2805 :	parrello	1.49	# Switch to the specified directory.
2806 :	parrello	1.46	ChDir($dirName);
2807 :			# Get the group ID.
2808 :			my $gid = getgrnam($group);
2809 :	parrello	1.50	# Get the mask for tracing.
2810 :	parrello	1.51	my $traceMask = sprintf("%04o", $mask) . "($mask)";
2811 :	parrello	1.77	Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2812 :	parrello	1.46	my $fixCount = 0;
2813 :			my $lookCount = 0;
2814 :			# @dirs will be a stack of directories to be processed.
2815 :			my @dirs = (getcwd());
2816 :			while (scalar(@dirs) > 0) {
2817 :			# Get the current directory.
2818 :			my $dir = pop @dirs;
2819 :	parrello	1.49	# Check for a match to one of the specified directory names. To do
2820 :			# that, we need to pull the individual part of the name off of the
2821 :			# whole path.
2822 :			my $simpleName = $dir;
2823 :	parrello	1.57	if ($dir =~ m!/([^/]+)$!) {
2824 :	parrello	1.49	$simpleName = $1;
2825 :			}
2826 :	parrello	1.77	Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2827 :	parrello	1.49	# Search for a match.
2828 :			my $match = 0;
2829 :			my $i;
2830 :			for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2831 :			my $pattern = $otherMasks[$i];
2832 :			if ($simpleName =~ /$pattern/i) {
2833 :			$match = 1;
2834 :	parrello	1.46	}
2835 :	parrello	1.49	}
2836 :	parrello	1.52	# Check for a match. Note we use $i-1 because the loop added 2
2837 :			# before terminating due to the match.
2838 :			if ($match && $otherMasks[$i-1] != $mask) {
2839 :	parrello	1.49	# This directory matches one of the incoming patterns, and it's
2840 :			# a different mask, so we process it recursively with that mask.
2841 :	parrello	1.52	SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2842 :	parrello	1.49	} else {
2843 :			# Here we can process normally. Get all of the non-hidden members.
2844 :			my @submems = OpenDir($dir, 1);
2845 :			for my $submem (@submems) {
2846 :			# Get the full name.
2847 :			my $thisMem = "$dir/$submem";
2848 :			Trace("Checking member $thisMem.") if T(4);
2849 :			$lookCount++;
2850 :			if ($lookCount % 1000 == 0) {
2851 :	parrello	1.77	Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2852 :	parrello	1.49	}
2853 :			# Fix the group.
2854 :			chown -1, $gid, $thisMem;
2855 :			# Insure this member is not a symlink.
2856 :			if (! -l $thisMem) {
2857 :			# Get its info.
2858 :			my $fileInfo = stat $thisMem;
2859 :			# Only proceed if we got the info. Otherwise, it's a hard link
2860 :			# and we want to skip it anyway.
2861 :			if ($fileInfo) {
2862 :			my $fileMode = $fileInfo->mode;
2863 :	parrello	1.58	if (($fileMode & $mask) != $mask) {
2864 :	parrello	1.49	# Fix this member.
2865 :			$fileMode \|= $mask;
2866 :			chmod $fileMode, $thisMem;
2867 :			$fixCount++;
2868 :			}
2869 :			# If it's a subdirectory, stack it.
2870 :			if (-d $thisMem) {
2871 :			push @dirs, $thisMem;
2872 :			}
2873 :	parrello	1.46	}
2874 :			}
2875 :			}
2876 :			}
2877 :			}
2878 :	parrello	1.77	Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2879 :	parrello	1.46	};
2880 :			# Check for an error.
2881 :			if ($@) {
2882 :			Confess("SetPermissions error: $@");
2883 :			}
2884 :			}
2885 :
2886 :	parrello	1.62	=head3 CompareLists
2887 :
2888 :			C<< my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex); >>
2889 :
2890 :			Compare two lists of tuples, and return a hash analyzing the differences. The lists
2891 :			are presumed to be sorted alphabetically by the value in the $keyIndex column.
2892 :			The return value contains a list of items that are only in the new list
2893 :			(inserted) and only in the old list (deleted).
2894 :
2895 :			=over 4
2896 :
2897 :			=item newList
2898 :
2899 :			Reference to a list of new tuples.
2900 :
2901 :			=item oldList
2902 :
2903 :			Reference to a list of old tuples.
2904 :
2905 :			=item keyIndex (optional)
2906 :
2907 :			Index into each tuple of its key field. The default is 0.
2908 :
2909 :			=item RETURN
2910 :
2911 :			Returns a 2-tuple consisting of a reference to the list of items that are only in the new
2912 :			list (inserted) followed by a reference to the list of items that are only in the old
2913 :			list (deleted).
2914 :
2915 :			=back
2916 :
2917 :			=cut
2918 :
2919 :			sub CompareLists {
2920 :			# Get the parameters.
2921 :			my ($newList, $oldList, $keyIndex) = @_;
2922 :			if (! defined $keyIndex) {
2923 :			$keyIndex = 0;
2924 :			}
2925 :			# Declare the return variables.
2926 :			my ($inserted, $deleted) = ([], []);
2927 :			# Loop through the two lists simultaneously.
2928 :			my ($newI, $oldI) = (0, 0);
2929 :			my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
2930 :			while ($newI < $newN \|\| $oldI < $oldN) {
2931 :			# Get the current object in each list. Note that if one
2932 :			# of the lists is past the end, we'll get undef.
2933 :			my $newItem = $newList->[$newI];
2934 :			my $oldItem = $oldList->[$oldI];
2935 :	parrello	1.63	if (! defined($newItem) \|\| defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
2936 :	parrello	1.62	# The old item is not in the new list, so mark it deleted.
2937 :			push @{$deleted}, $oldItem;
2938 :			$oldI++;
2939 :			} elsif (! defined($oldItem) \|\| $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
2940 :			# The new item is not in the old list, so mark it inserted.
2941 :			push @{$inserted}, $newItem;
2942 :			$newI++;
2943 :			} else {
2944 :			# The item is in both lists, so push forward.
2945 :			$oldI++;
2946 :			$newI++;
2947 :			}
2948 :			}
2949 :			# Return the result.
2950 :			return ($inserted, $deleted);
2951 :			}
2952 :
2953 :	parrello	1.65	=head3 GetLine
2954 :
2955 :			C<< my @data = Tracer::GetLine($handle); >>
2956 :
2957 :			Read a line of data from a tab-delimited file.
2958 :
2959 :			=over 4
2960 :
2961 :			=item handle
2962 :
2963 :			Open file handle from which to read.
2964 :
2965 :			=item RETURN
2966 :
2967 :			Returns a list of the fields in the record read. The fields are presumed to be
2968 :			tab-delimited. If we are at the end of the file, then an empty list will be
2969 :			returned. If an empty line is read, a single list item consisting of a null
2970 :			string will be returned.
2971 :
2972 :			=back
2973 :
2974 :			=cut
2975 :
2976 :			sub GetLine {
2977 :			# Get the parameters.
2978 :			my ($handle) = @_;
2979 :			# Declare the return variable.
2980 :			my @retVal = ();
2981 :	parrello	1.77	Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2982 :	parrello	1.65	# Read from the file.
2983 :			my $line = <$handle>;
2984 :			# Only proceed if we found something.
2985 :			if (defined $line) {
2986 :	parrello	1.80	# Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2987 :			# upload control and have a nonstandard EOL combination.
2988 :			$line =~ s/(\r\|\n)+$//;
2989 :			# Here we do some fancy tracing to help in debugging complicated EOL marks.
2990 :			if (T(File => 4)) {
2991 :			my $escapedLine = $line;
2992 :			$escapedLine =~ s/\n/\\n/g;
2993 :			$escapedLine =~ s/\r/\\r/g;
2994 :			$escapedLine =~ s/\t/\\t/g;
2995 :			Trace("Line read: -->$escapedLine<--");
2996 :			}
2997 :	parrello	1.65	# If the line is empty, return a single empty string; otherwise, parse
2998 :			# it into fields.
2999 :			if ($line eq "") {
3000 :			push @retVal, "";
3001 :			} else {
3002 :			push @retVal, split /\t/,$line;
3003 :			}
3004 :	parrello	1.77	} else {
3005 :			# Trace the reason the read failed.
3006 :			Trace("End of file: $!") if T(File => 3);
3007 :	parrello	1.65	}
3008 :			# Return the result.
3009 :			return @retVal;
3010 :			}
3011 :
3012 :			=head3 PutLine
3013 :
3014 :	parrello	1.82	C<< Tracer::PutLine($handle, \@fields, $eol); >>
3015 :	parrello	1.65
3016 :			Write a line of data to a tab-delimited file. The specified field values will be
3017 :			output in tab-separated form, with a trailing new-line.
3018 :
3019 :			=over 4
3020 :
3021 :			=item handle
3022 :
3023 :			Output file handle.
3024 :
3025 :			=item fields
3026 :
3027 :			List of field values.
3028 :
3029 :	parrello	1.82	=item eol (optional)
3030 :
3031 :			End-of-line character (default is "\n").
3032 :
3033 :	parrello	1.65	=back
3034 :
3035 :			=cut
3036 :
3037 :			sub PutLine {
3038 :			# Get the parameters.
3039 :	parrello	1.82	my ($handle, $fields, $eol) = @_;
3040 :	parrello	1.65	# Write the data.
3041 :	parrello	1.82	print $handle join("\t", @{$fields}) . ($eol \|\| "\n");
3042 :	parrello	1.65	}
3043 :
3044 :			=head3 GenerateURL
3045 :
3046 :			C<< my $queryUrl = Tracer::GenerateURL($page, %parameters); >>
3047 :
3048 :			Generate a GET-style URL for the specified page with the specified parameter
3049 :			names and values. The values will be URL-escaped automatically. So, for
3050 :			example
3051 :
3052 :			Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3053 :
3054 :			would return
3055 :
3056 :	parrello	1.79	form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3057 :	parrello	1.65
3058 :			=over 4
3059 :
3060 :			=item page
3061 :
3062 :			Page URL.
3063 :
3064 :			=item parameters
3065 :
3066 :			Hash mapping parameter names to parameter values.
3067 :
3068 :			=item RETURN
3069 :
3070 :			Returns a GET-style URL that goes to the specified page and passes in the
3071 :			specified parameters and values.
3072 :
3073 :			=back
3074 :
3075 :			=cut
3076 :
3077 :			sub GenerateURL {
3078 :			# Get the parameters.
3079 :			my ($page, %parameters) = @_;
3080 :			# Prime the return variable with the page URL.
3081 :			my $retVal = $page;
3082 :			# Loop through the parameters, creating parameter elements in a list.
3083 :			my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3084 :			# If the list is nonempty, tack it on.
3085 :			if (@parmList) {
3086 :	parrello	1.79	$retVal .= "?" . join(";", @parmList);
3087 :	parrello	1.65	}
3088 :			# Return the result.
3089 :			return $retVal;
3090 :			}
3091 :
3092 :	parrello	1.78	=head3 ApplyURL
3093 :
3094 :			C<< Tracer::ApplyURL($table, $target, $url); >>
3095 :
3096 :			Run through a two-dimensional table (or more accurately, a list of lists), converting the
3097 :			I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3098 :			URL column will be deleted by this process and the target column will be HTML-escaped.
3099 :
3100 :			This provides a simple way to process the results of a database query into something
3101 :			displayable by combining a URL with text.
3102 :
3103 :			=over 4
3104 :
3105 :			=item table
3106 :
3107 :			Reference to a list of lists. The elements in the containing list will be updated by
3108 :			this method.
3109 :
3110 :			=item target
3111 :
3112 :			The index of the column to be converted into HTML.
3113 :
3114 :			=item url
3115 :
3116 :			The index of the column containing the URL. Note that the URL must have a recognizable
3117 :			C<http:> at the beginning.
3118 :
3119 :			=back
3120 :
3121 :			=cut
3122 :
3123 :			sub ApplyURL {
3124 :			# Get the parameters.
3125 :			my ($table, $target, $url) = @_;
3126 :			# Loop through the table.
3127 :			for my $row (@{$table}) {
3128 :			# Apply the URL to the target cell.
3129 :			$row->[$target] = CombineURL($row->[$target], $row->[$url]);
3130 :			# Delete the URL from the row.
3131 :			delete $row->[$url];
3132 :			}
3133 :			}
3134 :
3135 :			=head3 CombineURL
3136 :
3137 :			C<< my $combinedHtml = Tracer::CombineURL($text, $url); >>
3138 :
3139 :			This method will convert the specified text into HTML hyperlinked to the specified
3140 :			URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3141 :			is defined and begins with an C<http:> header.
3142 :
3143 :			=over 4
3144 :
3145 :			=item text
3146 :
3147 :			Text to return. This will be HTML-escaped automatically.
3148 :
3149 :			=item url
3150 :
3151 :			A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3152 :			will be returned without any hyperlinking.
3153 :
3154 :			=item RETURN
3155 :
3156 :			Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3157 :			doesn't look right, the HTML-escaped text will be returned without any further
3158 :			modification.
3159 :
3160 :			=back
3161 :
3162 :			=cut
3163 :
3164 :			sub CombineURL {
3165 :			# Get the parameters.
3166 :			my ($text, $url) = @_;
3167 :			# Declare the return variable.
3168 :			my $retVal = CGI::escapeHTML($text);
3169 :			# Verify the URL.
3170 :			if (defined($url) && $url =~ m!http://!i) {
3171 :			# It's good, so we apply it to the text.
3172 :			$retVal = "<a href=\"$url\">$retVal</a>";
3173 :			}
3174 :			# Return the result.
3175 :			return $retVal;
3176 :			}
3177 :
3178 :	parrello	1.65	1;

MCS Webmaster	ViewVC Help
Powered by ViewVC 1.0.3