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1 : gdpusch 1.95 # -*- perl -*-
2 :     ########################################################################
3 : olson 1.30 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 : parrello 1.61 #
8 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 : parrello 1.61 # Public License.
11 : olson 1.30 #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.95 ########################################################################
18 : olson 1.30
19 : olson 1.1 package Tracer;
20 :    
21 : parrello 1.115 use strict;
22 :     use base qw(Exporter);
23 :     use vars qw(@EXPORT @EXPORT_OK);
24 :     @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25 : parrello 1.97 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26 : gdpusch 1.96 use Carp qw(longmess croak carp);
27 : parrello 1.12 use CGI;
28 : parrello 1.47 use Cwd;
29 : parrello 1.12 use FIG_Config;
30 : parrello 1.9 use PageBuilder;
31 : parrello 1.21 use Digest::MD5;
32 : parrello 1.36 use File::Basename;
33 : parrello 1.37 use File::Path;
34 : parrello 1.48 use File::stat;
35 : parrello 1.59 use LWP::UserAgent;
36 : parrello 1.64 use Time::HiRes 'gettimeofday';
37 : parrello 1.65 use URI::Escape;
38 : parrello 1.74 use Time::Local;
39 : parrello 1.99 use POSIX qw(strftime);
40 :     use Time::Zone;
41 : parrello 1.115 use Fcntl qw(:DEFAULT :flock);
42 :     use Data::Dumper;
43 : parrello 1.99
44 : olson 1.1
45 :     =head1 Tracing and Debugging Helpers
46 :    
47 : parrello 1.72 =head2 Tracing
48 : olson 1.1
49 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
50 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
51 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
52 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
53 :     level is less than or equal to the setup trace level and whose category is activated will
54 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
55 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
56 :     appear.
57 : olson 1.1
58 : parrello 1.72 =head3 Putting Trace Messages in Your Code
59 :    
60 :     To generate a trace message, use the following syntax.
61 :    
62 :     Trace($message) if T(errors => 4);
63 : olson 1.1
64 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
65 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
66 : olson 1.1
67 : parrello 1.72 Trace($message) if T(main => 4);
68 : olson 1.1
69 :     will trace if the trace level is 4 or more.
70 :    
71 :     If the category name is the same as the package name, all you need is the number. So, if the
72 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
73 :     active and the trace level is 2 or more.
74 :    
75 : parrello 1.72 Trace($message) if T(2);
76 :    
77 :     In scripts, where no package name is available, the category defaults to C<main>.
78 :    
79 :     =head3 Custom Tracing
80 :    
81 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
83 :     L</Emergency Tracing> easier to understand.
84 : olson 1.1
85 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86 :     a list of category names, and a destination. The trace level and list of category names are
87 : olson 1.1 specified as a space-delimited string. Thus
88 :    
89 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
90 : olson 1.1
91 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
92 : parrello 1.72 specifies that messages should be sent to the standard output.
93 : parrello 1.12
94 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95 :     level 3 and writes the output to the standard error output. This sort of thing might be
96 :     useful in a CGI environment.
97 :    
98 : parrello 1.72 TSetup('3 *', 'WARN');
99 : olson 1.1
100 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
101 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
102 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
103 :     the page output, they can be gathered together and displayed at the end of the page. This makes
104 :     it easier to debug page formatting problems.
105 :    
106 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
107 :     a file at the same time. To trace to a file, specify the filename with an output character in front
108 :     of it.
109 :    
110 :     TSetup('4 SQL', ">$fileName");
111 :    
112 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113 :     bracket.
114 :    
115 :     TSetup('3 *', "+>$fileName");
116 : parrello 1.4
117 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
118 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
119 :     Thus, debugging information is available and easily retrieved even when the application is
120 :     being used out in the field.
121 :    
122 : parrello 1.72 =head3 Trace Levels
123 :    
124 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
125 :     a suggestion.
126 :    
127 :     =over 4
128 :    
129 : parrello 1.32 =item Error 0
130 : parrello 1.10
131 :     Message indicates an error that may lead to incorrect results or that has stopped the
132 :     application entirely.
133 :    
134 : parrello 1.32 =item Warning 1
135 : parrello 1.10
136 :     Message indicates something that is unexpected but that probably did not interfere
137 :     with program execution.
138 :    
139 : parrello 1.32 =item Notice 2
140 : parrello 1.10
141 :     Message indicates the beginning or end of a major task.
142 :    
143 : parrello 1.32 =item Information 3
144 : parrello 1.10
145 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
146 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
147 :    
148 : parrello 1.32 =item Detail 4
149 : parrello 1.10
150 :     Message indicates a low-level loop iteration.
151 :    
152 :     =back
153 :    
154 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
155 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
156 :     The time stamp is between square brackets and the category name between angle brackets.
157 :     After the category name there is a colon (C<:>) followed by the message text.
158 :     If the square brackets or angle brackets are missing, then the trace management
159 :     utilities assume that they are encountering a set of pre-formatted lines.
160 :    
161 :     Note, however, that this formatting is done automatically by the tracing functions. You
162 :     only need to know about it if you want to parse a trace file.
163 :    
164 :     =head3 Emergency Tracing
165 :    
166 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
167 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169 :     that you specify a tracing key. For command-line tools, the key is
170 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
171 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
172 :     the tracing in your environment without stepping on other users.
173 :    
174 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175 :     generate one for you.
176 :    
177 :     You can activate and de-activate emergency tracing from the debugging control panel, as
178 :     well as display the trace file itself.
179 :    
180 :     To enable emergency tracing in your code, call
181 :    
182 :     ETracing($cgi)
183 :    
184 :     from a web script and
185 :    
186 :     ETracing()
187 :    
188 :     from a command-line script.
189 :    
190 :     The web script will look for the tracing key in the cookies, and the command-line
191 :     script will look for it in the C<TRACING> environment variable. If you are
192 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193 : parrello 1.72 will be configured automatically.
194 :    
195 : olson 1.1 =cut
196 : parrello 1.2
197 : olson 1.1 # Declare the configuration variables.
198 :    
199 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
200 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
201 :     # standard output
202 : parrello 1.3 my %Categories = ( main => 1 );
203 : parrello 1.12 # hash of active category names
204 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
205 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
206 :     # messages
207 :     my @Queue = (); # queued list of trace messages.
208 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
209 : parrello 1.97 my $LastLevel = 0; # level of the last test call
210 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
211 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
212 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
213 : parrello 1.104 my $CommandLine; # Command line passed to StandardSetup
214 : parrello 1.99 umask 2; # Fix the damn umask so everything is group-writable.
215 : olson 1.1
216 : parrello 1.93 =head2 Tracing Methods
217 :    
218 :     =head3 Setups
219 :    
220 :     my $count = Tracer::Setups();
221 :    
222 :     Return the number of times L</TSetup> has been called.
223 :    
224 :     This method allows for the creation of conditional tracing setups where, for example, we
225 :     may want to set up tracing if nobody else has done it before us.
226 :    
227 :     =cut
228 :    
229 :     sub Setups {
230 :     return $SetupCount;
231 :     }
232 : olson 1.1
233 :     =head3 TSetup
234 :    
235 : parrello 1.92 TSetup($categoryList, $target);
236 : olson 1.1
237 :     This method is used to specify the trace options. The options are stored as package data
238 :     and interrogated by the L</Trace> and L</T> methods.
239 :    
240 :     =over 4
241 :    
242 :     =item categoryList
243 :    
244 :     A string specifying the trace level and the categories to be traced, separated by spaces.
245 :     The trace level must come first.
246 :    
247 :     =item target
248 :    
249 :     The destination for the trace output. To send the trace output to a file, specify the file
250 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
251 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
252 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
253 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
254 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
255 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
256 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
257 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
258 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
259 : parrello 1.6 cause tracing to be suppressed.
260 : olson 1.1
261 :     =back
262 :    
263 :     =cut
264 :    
265 :     sub TSetup {
266 : parrello 1.12 # Get the parameters.
267 :     my ($categoryList, $target) = @_;
268 :     # Parse the category list.
269 :     my @categoryData = split /\s+/, $categoryList;
270 :     # Extract the trace level.
271 :     $TraceLevel = shift @categoryData;
272 :     # Presume category-based tracing until we learn otherwise.
273 :     $AllTrace = 0;
274 :     # Build the category hash. Note that if we find a "*", we turn on non-category
275 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
276 : parrello 1.34 %Categories = ( main => 1 );
277 : parrello 1.12 for my $category (@categoryData) {
278 :     if ($category eq '*') {
279 :     $AllTrace = 1;
280 :     } else {
281 : parrello 1.13 $Categories{lc $category} = 1;
282 : parrello 1.12 }
283 :     }
284 :     # Now we need to process the destination information. The most important special
285 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
287 :     # the standard output (tee mode).
288 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
289 :     if ($target =~ m/^\+/) {
290 :     $TeeFlag = 1;
291 :     $target = substr($target, 1);
292 :     }
293 :     if ($target =~ m/^>[^>]/) {
294 : parrello 1.98 # We need to initialize the file (which clears it).
295 : parrello 1.12 open TRACEFILE, $target;
296 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297 : parrello 1.12 close TRACEFILE;
298 : parrello 1.98 # Set to append mode now that the file has been cleared.
299 : parrello 1.12 $Destination = ">$target";
300 :     } else {
301 :     $Destination = $target;
302 :     }
303 :     } else {
304 :     $Destination = uc($target);
305 :     }
306 :     # Increment the setup counter.
307 :     $SetupCount++;
308 : parrello 1.11 }
309 :    
310 : parrello 1.93 =head3 SetLevel
311 : parrello 1.31
312 : parrello 1.93 Tracer::SetLevel($newLevel);
313 : parrello 1.31
314 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
315 : parrello 1.31
316 : parrello 1.93 =over 4
317 : parrello 1.31
318 : parrello 1.93 =item newLevel
319 : parrello 1.31
320 : parrello 1.93 Proposed new trace level.
321 : parrello 1.31
322 : parrello 1.93 =back
323 : parrello 1.31
324 : parrello 1.93 =cut
325 : parrello 1.31
326 : parrello 1.93 sub SetLevel {
327 :     $TraceLevel = $_[0];
328 :     }
329 : parrello 1.31
330 : parrello 1.97 =head3 ParseDate
331 :    
332 :     my $time = Tracer::ParseDate($dateString);
333 :    
334 :     Convert a date into a PERL time number. This method expects a date-like string
335 :     and parses it into a number. The string must be vaguely date-like or it will
336 :     return an undefined value. Our requirement is that a month and day be
337 :     present and that three pieces of the date string (time of day, month and day,
338 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
339 :    
340 :     If a time of day is present, it must be in military time with two digits for
341 :     everything but the hour.
342 : parrello 1.31
343 : parrello 1.97 The year must be exactly four digits.
344 : parrello 1.31
345 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
346 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
347 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
348 :    
349 :     It should be guaranteed that this method will parse the output of the L</Now> function.
350 :    
351 :     The parameters are as follows.
352 : parrello 1.31
353 : parrello 1.93 =over 4
354 : parrello 1.31
355 : parrello 1.93 =item dateString
356 : parrello 1.31
357 : parrello 1.97 The date string to convert.
358 : parrello 1.31
359 : parrello 1.93 =item RETURN
360 : parrello 1.31
361 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
363 : parrello 1.31
364 : parrello 1.93 =back
365 : parrello 1.38
366 : parrello 1.93 =cut
367 : parrello 1.38
368 : parrello 1.97 # Universal month conversion table.
369 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
370 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
371 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
372 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
373 :     May => 4, May => 4, '05' => 4, '5' => 4,
374 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
375 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
376 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
377 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
378 :     Oct => 9, October => 9, '10' => 9,
379 :     Nov => 10, November => 10, '11' => 10,
380 :     Dec => 11, December => 11, '12' => 11
381 :     };
382 :    
383 :     sub ParseDate {
384 : parrello 1.93 # Get the parameters.
385 :     my ($dateString) = @_;
386 :     # Declare the return variable.
387 :     my $retVal;
388 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
389 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390 :     # won't be fooled into thinking the month is Sunday.
391 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
393 :     # Insist that the month and day are valid.
394 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
395 :     # Find the time.
396 :     my ($hour, $min, $sec) = (0, 0, 0);
397 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398 :     ($hour, $min, $sec) = ($1, $2, $3);
399 :     }
400 :     # Find the year.
401 :     my $year;
402 :     if ($dateString =~ /\b(\d{4})\b/) {
403 :     $year = $1;
404 :     } else {
405 :     # Get the default year, which is this one. Note we must convert it to
406 :     # the four-digit value expected by "timelocal".
407 :     (undef, undef, undef, undef, undef, $year) = localtime();
408 :     $year += 1900;
409 :     }
410 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411 :     }
412 : parrello 1.93 }
413 :     # Return the result.
414 :     return $retVal;
415 :     }
416 : parrello 1.31
417 : parrello 1.93 =head3 LogErrors
418 : parrello 1.42
419 : parrello 1.93 Tracer::LogErrors($fileName);
420 : parrello 1.31
421 : parrello 1.93 Route the standard error output to a log file.
422 : parrello 1.31
423 : parrello 1.93 =over 4
424 : parrello 1.31
425 : parrello 1.93 =item fileName
426 : parrello 1.31
427 : parrello 1.93 Name of the file to receive the error output.
428 : parrello 1.31
429 : parrello 1.93 =back
430 : parrello 1.31
431 : parrello 1.93 =cut
432 : parrello 1.84
433 : parrello 1.93 sub LogErrors {
434 :     # Get the file name.
435 :     my ($fileName) = @_;
436 :     # Open the file as the standard error output.
437 :     open STDERR, '>', $fileName;
438 :     }
439 : parrello 1.84
440 : parrello 1.93 =head3 Trace
441 : parrello 1.31
442 : parrello 1.93 Trace($message);
443 : parrello 1.31
444 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
445 :     any prior call to B<TSetup>.
446 : parrello 1.31
447 : parrello 1.93 =over 4
448 : parrello 1.42
449 : parrello 1.93 =item message
450 : parrello 1.42
451 : parrello 1.93 Message to write.
452 : parrello 1.42
453 : parrello 1.93 =back
454 : parrello 1.72
455 : parrello 1.93 =cut
456 : parrello 1.36
457 : parrello 1.93 sub Trace {
458 :     # Get the parameters.
459 :     my ($message) = @_;
460 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
461 :     # new-line stuff ourselves.
462 :     my $stripped = Strip($message);
463 :     # Compute the caller information.
464 :     my ($callPackage, $callFile, $callLine) = caller();
465 :     my $callFileTitle = basename($callFile);
466 :     # Check the caller.
467 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468 : parrello 1.93 # Get the timestamp.
469 :     my $timeStamp = Now();
470 : parrello 1.97 # Build the prefix.
471 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473 : parrello 1.97 # Format the message.
474 :     my $formatted = "$prefix $stripped";
475 : parrello 1.93 # Process according to the destination.
476 :     if ($Destination eq "TEXT") {
477 :     # Write the message to the standard output.
478 :     print "$formatted\n";
479 :     } elsif ($Destination eq "ERROR") {
480 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
481 : parrello 1.93 print STDERR "$formatted\n";
482 : parrello 1.97 } elsif ($Destination eq "WARN") {
483 :     # Emit the message to the standard error output. It is presumed that the
484 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
485 :     # the caller info.
486 :     print STDERR "$callerInfo$stripped\n";
487 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
488 :     # Push the message into the queue.
489 :     push @Queue, "$formatted";
490 :     } elsif ($Destination eq "HTML") {
491 : parrello 1.116 # Convert the message to HTML.
492 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
493 : parrello 1.116 # The stuff after the first line feed should be pre-formatted.
494 :     my @lines = split /\s*\n/, $escapedMessage;
495 :     # Get the normal portion.
496 :     my $line1 = shift @lines;
497 :     print "<p>$timeStamp $LastCategory $LastLevel: $line1</p>\n";
498 :     if (@lines) {
499 :     print "<pre>" . join("\n", @lines, "<pre>");
500 :     }
501 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
502 :     # Write the trace message to an output file.
503 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
504 : parrello 1.111 # Lock the file.
505 :     flock TRACING, LOCK_EX;
506 : parrello 1.93 print TRACING "$formatted\n";
507 :     close TRACING;
508 :     # If the Tee flag is on, echo it to the standard output.
509 :     if ($TeeFlag) {
510 :     print "$formatted\n";
511 :     }
512 :     }
513 :     }
514 : parrello 1.36
515 : parrello 1.115 =head3 TraceDump
516 :    
517 :     TraceDump($title, $object);
518 :    
519 :     Dump an object to the trace log. This method simply calls the C<Dumper>
520 :     function, but routes the output to the trace log instead of returning it
521 :     as a string. The output is arranged so that it comes out monospaced when
522 :     it appears in an HTML trace dump.
523 :    
524 :     =over 4
525 :    
526 :     =item title
527 :    
528 :     Title to give to the object being dumped.
529 :    
530 :     =item object
531 :    
532 :     Reference to a list, hash, or object to dump.
533 :    
534 :     =back
535 :    
536 :     =cut
537 :    
538 :     sub TraceDump {
539 :     # Get the parameters.
540 :     my ($title, $object) = @_;
541 :     # Trace the object.
542 :     Trace("Object dump for $title:\n" . Dumper($object));
543 :     }
544 :    
545 : parrello 1.93 =head3 T
546 : parrello 1.36
547 : parrello 1.93 my $switch = T($category, $traceLevel);
548 : parrello 1.36
549 : parrello 1.93 or
550 : parrello 1.44
551 : parrello 1.93 my $switch = T($traceLevel);
552 : parrello 1.44
553 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
554 :     is active, else FALSE. If no category is specified, the caller's package name is used.
555 : parrello 1.44
556 : parrello 1.93 =over 4
557 : parrello 1.44
558 : parrello 1.93 =item category
559 : parrello 1.44
560 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
561 :     used.
562 : parrello 1.31
563 : parrello 1.93 =item traceLevel
564 : parrello 1.31
565 : parrello 1.93 Relevant tracing level.
566 : parrello 1.31
567 : parrello 1.93 =item RETURN
568 : parrello 1.31
569 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
570 : parrello 1.31
571 : parrello 1.93 =back
572 : parrello 1.36
573 : parrello 1.93 =cut
574 :    
575 :     sub T {
576 :     # Declare the return variable.
577 :     my $retVal = 0;
578 :     # Only proceed if tracing is turned on.
579 :     if ($Destination ne "NONE") {
580 :     # Get the parameters.
581 :     my ($category, $traceLevel) = @_;
582 :     if (!defined $traceLevel) {
583 :     # Here we have no category, so we need to get the calling package.
584 :     # The calling package is normally the first parameter. If it is
585 :     # omitted, the first parameter will be the tracelevel. So, the
586 :     # first thing we do is shift the so-called category into the
587 :     # $traceLevel variable where it belongs.
588 :     $traceLevel = $category;
589 :     my ($package, $fileName, $line) = caller;
590 :     # If there is no calling package, we default to "main".
591 :     if (!$package) {
592 :     $category = "main";
593 :     } else {
594 :     my @cats = split /::/, $package;
595 :     $category = $cats[$#cats];
596 :     }
597 :     }
598 : parrello 1.97 # Save the category name and level.
599 : parrello 1.93 $LastCategory = $category;
600 : parrello 1.97 $LastLevel = $traceLevel;
601 : parrello 1.93 # Convert it to lower case before we hash it.
602 :     $category = lc $category;
603 : parrello 1.100 # Validate the trace level.
604 : parrello 1.93 if (ref $traceLevel) {
605 :     Confess("Bad trace level.");
606 :     } elsif (ref $TraceLevel) {
607 :     Confess("Bad trace config.");
608 :     }
609 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
610 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
611 : parrello 1.93 }
612 :     # Return the computed result.
613 :     return $retVal;
614 :     }
615 :    
616 :     =head3 QTrace
617 :    
618 :     my $data = QTrace($format);
619 :    
620 :     Return the queued trace data in the specified format.
621 :    
622 :     =over 4
623 :    
624 :     =item format
625 :    
626 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
627 :    
628 :     =back
629 :    
630 :     =cut
631 :    
632 :     sub QTrace {
633 :     # Get the parameter.
634 :     my ($format) = @_;
635 :     # Create the return variable.
636 :     my $retVal = "";
637 :     # Only proceed if there is an actual queue.
638 :     if (@Queue) {
639 :     # Process according to the format.
640 :     if ($format =~ m/^HTML$/i) {
641 :     # Convert the queue into an HTML list.
642 :     $retVal = "<ul>\n";
643 :     for my $line (@Queue) {
644 :     my $escapedLine = CGI::escapeHTML($line);
645 :     $retVal .= "<li>$escapedLine</li>\n";
646 :     }
647 :     $retVal .= "</ul>\n";
648 :     } elsif ($format =~ m/^TEXT$/i) {
649 :     # Convert the queue into a list of text lines.
650 :     $retVal = join("\n", @Queue) . "\n";
651 :     }
652 :     # Clear the queue.
653 :     @Queue = ();
654 :     }
655 :     # Return the formatted list.
656 :     return $retVal;
657 :     }
658 :    
659 :     =head3 Confess
660 :    
661 :     Confess($message);
662 :    
663 :     Trace the call stack and abort the program with the specified message. When used with
664 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
665 :     So, for example
666 :    
667 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
668 :    
669 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
670 :    
671 :     =over 4
672 :    
673 :     =item message
674 :    
675 :     Message to include in the trace.
676 :    
677 :     =back
678 :    
679 :     =cut
680 :    
681 :     sub Confess {
682 :     # Get the parameters.
683 :     my ($message) = @_;
684 : parrello 1.97 # Set up the category and level.
685 :     $LastCategory = "(confess)";
686 :     $LastLevel = 0;
687 : parrello 1.93 # Trace the call stack.
688 :     Cluck($message);
689 :     # Abort the program.
690 :     croak(">>> $message");
691 :     }
692 :    
693 : parrello 1.106 =head3 SaveCGI
694 :    
695 :     Tracer::SaveCGI($cgi);
696 :    
697 :     This method saves the CGI object but does not activate emergency tracing.
698 :     It is used to allow L</Warn> to work in situations where emergency
699 :     tracing is contra-indicated (e.g. the wiki).
700 :    
701 :     =over 4
702 :    
703 :     =item cgi
704 :    
705 :     Active CGI query object.
706 :    
707 :     =back
708 :    
709 :     =cut
710 :    
711 :     sub SaveCGI {
712 :     $SavedCGI = $_[0];
713 :     }
714 :    
715 : parrello 1.99 =head3 Warn
716 :    
717 : parrello 1.106 Warn($message, @options);
718 : parrello 1.99
719 :     This method traces an important message. If an RSS feed is configured
720 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
721 :     then the message will be echoed to the feed. In general, a tracing
722 :     destination of C<WARN> indicates that the caller is running as a web
723 :     service in a production environment; however, this is not a requirement.
724 :    
725 : parrello 1.103 To force warnings into the RSS feed even when the tracing destination
726 :     is not C<WARN>, simply specify the C<Feed> tracing module. This can be
727 :     configured automatically when L</StandardSetup> is used.
728 :    
729 : parrello 1.99 The L</Cluck> method calls this one for its final message. Since
730 :     L</Confess> calls L</Cluck>, this means that any error which is caught
731 :     and confessed will put something in the feed. This insures that someone
732 :     will be alerted relatively quickly when a failure occurs.
733 :    
734 :     =over 4
735 :    
736 :     =item message
737 :    
738 :     Message to be traced.
739 :    
740 : parrello 1.106 =item options
741 :    
742 :     A list containing zero or more options.
743 :    
744 :     =back
745 :    
746 :     The permissible options are as follows.
747 :    
748 :     =over 4
749 :    
750 :     =item noStack
751 :    
752 :     If specified, then the stack trace is not included in the output.
753 :    
754 : parrello 1.99 =back
755 :    
756 :     =cut
757 :    
758 :     sub Warn {
759 :     # Get the parameters.
760 : parrello 1.106 my $message = shift @_;
761 :     my %options = map { $_ => 1 } @_;
762 : parrello 1.107 # Save $@;
763 :     my $savedError = $@;
764 : parrello 1.99 # Trace the message.
765 :     Trace($message);
766 : parrello 1.106 # This will contain the lock handle. If it's defined, it means we need to unlock.
767 :     my $lock;
768 : parrello 1.103 # Check for feed forcing.
769 :     my $forceFeed = exists $Categories{feed};
770 : parrello 1.106 # An error here would be disastrous. Note that if debug mode is specified,
771 :     # we do this stuff even in a test environment.
772 : parrello 1.99 eval {
773 :     # Do we need to put this in the RSS feed?
774 : parrello 1.103 if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
775 : parrello 1.109 # Probably. We need to check first, however, to see if it's from an
776 :     # ignored IP. For non-CGI situations, we default the IP to the self-referent.
777 :     my $key = "127.0.0.1";
778 :     if (defined $SavedCGI) {
779 :     # Get the IP address.
780 :     $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
781 : parrello 1.101 }
782 : parrello 1.109 # Is the IP address in the ignore list?
783 :     my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
784 :     if (! $found) {
785 :     # No. We're good. We now need to compute the date, the link, and the title.
786 :     # First, the date, in a very specific format.
787 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
788 :     (tz_local_offset() / 30);
789 :     # Environment data goes in here. We start with the date.
790 :     my $environment = "$date. ";
791 :     # If we need to recap the message (because it's too long to be a title), we'll
792 :     # put it in here.
793 :     my $recap;
794 :     # Copy the message and remove excess space.
795 :     my $title = $message;
796 :     $title =~ s/\s+/ /gs;
797 :     # If it's too long, we have to split it up.
798 :     if (length $title > 60) {
799 :     # Put the full message in the environment string.
800 :     $recap = $title;
801 :     # Excerpt it as the title.
802 :     $title = substr($title, 0, 50) . "...";
803 :     }
804 :     # If we have a CGI object, then this is a web error. Otherwise, it's
805 :     # command-line.
806 :     if (defined $SavedCGI) {
807 :     # We're in a web service. The environment is the user's IP, and the link
808 :     # is the URL that got us here.
809 :     $environment .= "Event Reported at IP address $key process $$.";
810 :     my $url = $SavedCGI->self_url();
811 :     # We need the user agent string and (if available) the referrer.
812 :     # The referrer will be the link.
813 :     $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
814 :     if ($ENV{HTTP_REFERER}) {
815 :     my $link = $ENV{HTTP_REFERER};
816 :     $environment .= " referred from <a href=\"$link\">$link</a>.";
817 :     } else {
818 :     $environment .= " referrer unknown.";
819 :     }
820 :     # Close off the sentence with the original link.
821 :     $environment .= " URL of event is <a href=\"$url\">$url</a>.";
822 :     } else {
823 :     # No CGI object, so we're a command-line tool. Use the tracing
824 :     # key and the PID as the user identifier, and add the command.
825 :     my $key = EmergencyKey();
826 :     $environment .= "Event Reported by $key process $$.";
827 :     if ($CommandLine) {
828 :     # We're in a StandardSetup script, so we have the real command line.
829 :     $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
830 :     } elsif ($ENV{_}) {
831 :     # We're in a BASH script, so the command has been stored in the _ variable.
832 :     $environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
833 :     }
834 :     }
835 :     # Build a GUID. We use the current time, the title, and the process ID,
836 :     # then digest the result.
837 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
838 :     # Finally, the description. This is a stack trace plus various environmental stuff.
839 :     # The trace is optional.
840 :     my $stackTrace;
841 :     if ($options{noStack}) {
842 :     $stackTrace = "";
843 :     } else {
844 :     my @trace = LongMess();
845 :     # Only proceed if we got something back.
846 :     if (scalar(@trace) > 0) {
847 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
848 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
849 :     }
850 :     }
851 :     # We got the stack trace. Now it's time to put it all together.
852 :     # We have a goofy thing here in that we need to HTML-escape some sections of the description
853 :     # twice. They will be escaped once here, and then once when written by XML::Simple. They are
854 :     # unescaped once when processed by the RSS reader, and stuff in the description is treated as
855 :     # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
856 :     # our <br>s and <pre>s are used to format the description.
857 :     $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
858 :     my $description = "$recap$environment $stackTrace";
859 :     # Okay, we have all the pieces. Create a hash of the new event.
860 :     my $newItem = { title => $title,
861 :     description => $description,
862 :     category => $LastCategory,
863 :     pubDate => $date,
864 :     guid => $guid,
865 :     };
866 :     # We need XML capability for this.
867 :     require XML::Simple;
868 :     # The RSS document goes in here.
869 :     my $rss;
870 :     # Get the name of the RSS file. It's in the FIG temporary directory.
871 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
872 :     # Open the config file and lock it.
873 :     $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
874 :     flock $lock, LOCK_EX;
875 :     # Does it exist?
876 :     if (-s $fileName) {
877 :     # Slurp it in.
878 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
879 : parrello 1.102 } else {
880 : parrello 1.109 my $size = -s $fileName;
881 :     # Create an empty channel.
882 :     $rss = {
883 :     channel => {
884 :     title => 'NMPDR Warning Feed',
885 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
886 :     description => "Important messages regarding the status of the NMPDR.",
887 :     generator => "NMPDR Trace Facility",
888 :     docs => "http://blogs.law.harvard.edu/tech/rss",
889 :     item => []
890 :     },
891 :     };
892 : parrello 1.100 }
893 : parrello 1.109 # Get the channel object.
894 :     my $channel = $rss->{channel};
895 :     # Update the last-build date.
896 :     $channel->{lastBuildDate} = $date;
897 :     # Get the item array.
898 :     my $items = $channel->{item};
899 :     # Insure it has only 100 entries.
900 :     while (scalar @{$items} > 100) {
901 :     pop @{$items};
902 : parrello 1.104 }
903 : parrello 1.109 # Add our new item at the front.
904 :     unshift @{$items}, $newItem;
905 :     # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
906 :     # the requirements for those.
907 :     my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
908 :     # Here we put in the root and declaration. The problem is that the root has to have the version attribute
909 :     # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
910 :     $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
911 :     # We don't use Open here because we can't afford an error.
912 :     if (open XMLOUT, ">$fileName") {
913 :     print XMLOUT $xml;
914 :     close XMLOUT;
915 : parrello 1.106 }
916 : parrello 1.101 }
917 : parrello 1.99 }
918 :     };
919 : parrello 1.103 if ($@) {
920 :     # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
921 :     # (which is a good thing).
922 : parrello 1.102 my $error = $@;
923 : parrello 1.103 Trace("Feed Error: $error") if T(Feed => 0);
924 : parrello 1.102 }
925 : parrello 1.106 # Be sure to unlock.
926 :     if ($lock) {
927 :     flock $lock, LOCK_UN;
928 :     undef $lock;
929 :     }
930 : parrello 1.107 # Restore the error message.
931 :     $@ = $savedError;
932 : parrello 1.99 }
933 :    
934 : parrello 1.106
935 :    
936 :    
937 : parrello 1.93 =head3 Assert
938 :    
939 :     Assert($condition1, $condition2, ... $conditionN);
940 :    
941 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
942 :     the OR operator and the L</Confess> method as a debugging assert.
943 :     So, for example
944 :    
945 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
946 :    
947 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
948 :    
949 :     =cut
950 :     sub Assert {
951 :     my $retVal = 1;
952 :     LOOP: for my $condition (@_) {
953 :     if (! $condition) {
954 :     $retVal = 0;
955 :     last LOOP;
956 :     }
957 :     }
958 :     return $retVal;
959 :     }
960 :    
961 :     =head3 Cluck
962 :    
963 :     Cluck($message);
964 :    
965 :     Trace the call stack. Note that for best results, you should qualify the call with a
966 :     trace condition. For example,
967 :    
968 :     Cluck("Starting record parse.") if T(3);
969 :    
970 :     will only trace the stack if the trace level for the package is 3 or more.
971 :    
972 :     =over 4
973 :    
974 :     =item message
975 :    
976 :     Message to include in the trace.
977 :    
978 :     =back
979 :    
980 :     =cut
981 :    
982 :     sub Cluck {
983 :     # Get the parameters.
984 :     my ($message) = @_;
985 :     # Trace what's happening.
986 :     Trace("Stack trace for event: $message");
987 : parrello 1.99 # Get the stack trace.
988 :     my @trace = LongMess();
989 :     # Convert the trace to a series of messages.
990 :     for my $line (@trace) {
991 :     # Replace the tab at the beginning with spaces.
992 :     $line =~ s/^\t/ /;
993 :     # Trace the line.
994 :     Trace($line);
995 :     }
996 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
997 :     Warn($message);
998 :     }
999 :    
1000 :     =head3 LongMess
1001 :    
1002 :     my @lines = Tracer::LongMess();
1003 :    
1004 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
1005 :     of message strings.
1006 :    
1007 :     =cut
1008 :    
1009 :     sub LongMess {
1010 :     # Declare the return variable.
1011 :     my @retVal = ();
1012 :     my $confession = longmess("");
1013 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
1014 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
1015 :     # Here we have a line worth keeping. Push it onto the result list.
1016 :     push @retVal, $line;
1017 : parrello 1.97 }
1018 : parrello 1.93 }
1019 : parrello 1.99 # Return the result.
1020 :     return @retVal;
1021 : parrello 1.93 }
1022 :    
1023 :     =head3 ETracing
1024 :    
1025 :     ETracing($parameter);
1026 :    
1027 :     Set up emergency tracing. Emergency tracing is tracing that is turned
1028 :     on automatically for any program that calls this method. The emergency
1029 :     tracing parameters are stored in a a file identified by a tracing key.
1030 :     If this method is called with a CGI object, then the tracing key is
1031 :     taken from a cookie. If it is called with no parameters, then the tracing
1032 :     key is taken from an environment variable. If it is called with a string,
1033 :     the tracing key is that string.
1034 :    
1035 :     =over 4
1036 :    
1037 :     =item parameter
1038 :    
1039 :     A parameter from which the tracing key is computed. If it is a scalar,
1040 :     that scalar is used as the tracing key. If it is a CGI object, the
1041 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
1042 :     tracing key is taken from the C<TRACING> environment variable. If it
1043 :     is a CGI object and emergency tracing is not on, the C<Trace> and
1044 :     C<TF> parameters will be used to determine the type of tracing.
1045 :    
1046 :     =back
1047 :    
1048 :     =cut
1049 :    
1050 :     sub ETracing {
1051 :     # Get the parameter.
1052 :     my ($parameter) = @_;
1053 :     # Check for CGI mode.
1054 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
1055 :     $SavedCGI = $parameter;
1056 :     } else {
1057 :     $SavedCGI = undef;
1058 :     }
1059 : parrello 1.93 # Default to no tracing except errors.
1060 :     my ($tracing, $dest) = ("0", "WARN");
1061 :     # Check for emergency tracing.
1062 :     my $tkey = EmergencyKey($parameter);
1063 :     my $emergencyFile = EmergencyFileName($tkey);
1064 :     if (-e $emergencyFile) {
1065 :     # We have the file. Read in the data.
1066 :     my @tracing = GetFile($emergencyFile);
1067 :     # Pull off the time limit.
1068 :     my $expire = shift @tracing;
1069 :     # Convert it to seconds.
1070 :     $expire *= 3600;
1071 :     # Check the file data.
1072 :     my $stat = stat($emergencyFile);
1073 :     my ($now) = gettimeofday;
1074 :     if ($now - $stat->mtime > $expire) {
1075 :     # Delete the expired file.
1076 :     unlink $emergencyFile;
1077 : parrello 1.44 } else {
1078 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
1079 :     # the trace level;
1080 :     $dest = shift @tracing;
1081 :     my $level = shift @tracing;
1082 :     # Convert the destination to a real tracing destination.
1083 :     # temp directory.
1084 :     $dest = EmergencyTracingDest($tkey, $dest);
1085 :     # Insure Tracer is specified.
1086 :     my %moduleHash = map { $_ => 1 } @tracing;
1087 :     $moduleHash{Tracer} = 1;
1088 :     # Set the trace parameter.
1089 :     $tracing = join(" ", $level, sort keys %moduleHash);
1090 : parrello 1.44 }
1091 : parrello 1.99 } elsif (defined $SavedCGI) {
1092 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1093 :     # for tracing from the form parameters.
1094 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1095 : parrello 1.93 # Here the user has requested tracing via a form.
1096 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1097 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1098 : parrello 1.36 }
1099 :     }
1100 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1101 :     TSetup($tracing, $dest);
1102 : parrello 1.94 # Check to see if we're a web script.
1103 : parrello 1.99 if (defined $SavedCGI) {
1104 : parrello 1.94 # Yes we are. Trace the form and environment data.
1105 : parrello 1.99 TraceParms($SavedCGI);
1106 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1107 :     # emitted by the script in its raw form.
1108 :     if (T(Raw => 3)) {
1109 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1110 :     }
1111 : parrello 1.83 }
1112 : parrello 1.31 }
1113 :    
1114 : parrello 1.93 =head3 EmergencyFileName
1115 :    
1116 :     my $fileName = Tracer::EmergencyFileName($tkey);
1117 :    
1118 :     Return the emergency tracing file name. This is the file that specifies
1119 :     the tracing information.
1120 :    
1121 :     =over 4
1122 :    
1123 :     =item tkey
1124 :    
1125 :     Tracing key for the current program.
1126 : parrello 1.11
1127 : parrello 1.93 =item RETURN
1128 : parrello 1.11
1129 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1130 : parrello 1.11
1131 : parrello 1.93 =back
1132 : parrello 1.11
1133 :     =cut
1134 :    
1135 : parrello 1.93 sub EmergencyFileName {
1136 :     # Get the parameters.
1137 :     my ($tkey) = @_;
1138 :     # Compute the emergency tracing file name.
1139 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1140 : olson 1.1 }
1141 :    
1142 : parrello 1.93 =head3 EmergencyFileTarget
1143 : parrello 1.10
1144 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1145 : parrello 1.10
1146 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1147 :     the tracing output for file-based tracing.
1148 : parrello 1.10
1149 : parrello 1.93 =over 4
1150 : parrello 1.10
1151 : parrello 1.93 =item tkey
1152 : parrello 1.10
1153 : parrello 1.93 Tracing key for the current program.
1154 : parrello 1.10
1155 : parrello 1.93 =item RETURN
1156 : parrello 1.10
1157 : parrello 1.93 Returns the name of the file to contain the trace output.
1158 : parrello 1.10
1159 : parrello 1.93 =back
1160 : parrello 1.10
1161 : parrello 1.93 =cut
1162 : parrello 1.10
1163 : parrello 1.93 sub EmergencyFileTarget {
1164 :     # Get the parameters.
1165 :     my ($tkey) = @_;
1166 :     # Compute the emergency tracing file name.
1167 :     return "$FIG_Config::temp/trace$tkey.log";
1168 :     }
1169 : parrello 1.10
1170 : parrello 1.93 =head3 EmergencyTracingDest
1171 : parrello 1.10
1172 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1173 : parrello 1.10
1174 : parrello 1.93 This method converts an emergency tracing destination to a real
1175 :     tracing destination. The main difference is that if the
1176 :     destination is C<FILE> or C<APPEND>, we convert it to file
1177 :     output. If the destination is C<DUAL>, we convert it to file
1178 :     and standard output.
1179 : parrello 1.10
1180 :     =over 4
1181 :    
1182 : parrello 1.93 =item tkey
1183 : parrello 1.10
1184 : parrello 1.93 Tracing key for this environment.
1185 : parrello 1.10
1186 : parrello 1.93 =item myDest
1187 : parrello 1.10
1188 : parrello 1.93 Destination from the emergency tracing file.
1189 : parrello 1.10
1190 :     =item RETURN
1191 :    
1192 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1193 : parrello 1.10
1194 :     =back
1195 :    
1196 :     =cut
1197 :    
1198 : parrello 1.93 sub EmergencyTracingDest {
1199 : parrello 1.12 # Get the parameters.
1200 : parrello 1.93 my ($tkey, $myDest) = @_;
1201 :     # Declare the return variable.
1202 :     my $retVal = $myDest;
1203 :     # Process according to the destination value.
1204 :     if ($myDest eq 'FILE') {
1205 :     $retVal = ">" . EmergencyFileTarget($tkey);
1206 :     } elsif ($myDest eq 'APPEND') {
1207 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1208 :     } elsif ($myDest eq 'DUAL') {
1209 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1210 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1211 :     $retVal = "WARN";
1212 : parrello 1.12 }
1213 : parrello 1.93 # Return the result.
1214 :     return $retVal;
1215 : parrello 1.10 }
1216 :    
1217 : parrello 1.93 =head3 Emergency
1218 :    
1219 :     Emergency($key, $hours, $dest, $level, @modules);
1220 :    
1221 :     Turn on emergency tracing. This method is normally invoked over the web from
1222 :     a debugging console, but it can also be called by the C<trace.pl> script.
1223 :     The caller specifies the duration of the emergency in hours, the desired tracing
1224 :     destination, the trace level, and a list of the trace modules to activate.
1225 :     For the length of the duration, when a program in an environment with the
1226 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1227 :     turned on automatically. See L</TSetup> for more about tracing setup and
1228 :     L</ETracing> for more about emergency tracing.
1229 :    
1230 :     =over 4
1231 : parrello 1.11
1232 : parrello 1.93 =item tkey
1233 : parrello 1.11
1234 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1235 : parrello 1.11
1236 : parrello 1.93 =item hours
1237 : parrello 1.11
1238 : parrello 1.93 Number of hours to keep emergency tracing alive.
1239 : parrello 1.11
1240 : parrello 1.93 =item dest
1241 : parrello 1.11
1242 : parrello 1.93 Tracing destination. If no path information is specified for a file
1243 :     destination, it is put in the FIG temporary directory.
1244 : parrello 1.11
1245 : parrello 1.93 =item level
1246 : parrello 1.11
1247 : parrello 1.93 Tracing level. A higher level means more trace messages.
1248 : parrello 1.11
1249 : parrello 1.93 =item modules
1250 : parrello 1.11
1251 : parrello 1.93 A list of the tracing modules to activate.
1252 : parrello 1.11
1253 :     =back
1254 :    
1255 :     =cut
1256 : parrello 1.93
1257 :     sub Emergency {
1258 : parrello 1.11 # Get the parameters.
1259 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1260 :     # Create the emergency file.
1261 :     my $specFile = EmergencyFileName($tkey);
1262 :     my $outHandle = Open(undef, ">$specFile");
1263 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1264 : parrello 1.11 }
1265 :    
1266 : parrello 1.93 =head3 EmergencyKey
1267 :    
1268 :     my $tkey = EmergencyKey($parameter);
1269 :    
1270 :     Return the Key to be used for emergency tracing. This could be an IP address,
1271 :     a session ID, or a user name, depending on the environment.
1272 : parrello 1.11
1273 : parrello 1.93 =over 4
1274 : parrello 1.11
1275 : parrello 1.93 =item parameter
1276 : parrello 1.11
1277 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1278 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1279 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1280 :     taken from the C<TRACING> environment variable.
1281 : parrello 1.29
1282 : parrello 1.93 =item RETURN
1283 : parrello 1.11
1284 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1285 : parrello 1.11
1286 : parrello 1.93 =back
1287 : parrello 1.11
1288 : parrello 1.93 =cut
1289 : parrello 1.29
1290 : parrello 1.93 sub EmergencyKey {
1291 :     # Get the parameters.
1292 :     my ($parameter) = @_;
1293 :     # Declare the return variable.
1294 :     my $retVal;
1295 :     # Determine the parameter type.
1296 : olson 1.114 if (! defined $parameter || defined($ENV{TRACING})) {
1297 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1298 :     # get the effective login ID.
1299 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1300 : parrello 1.93 } else {
1301 :     my $ptype = ref $parameter;
1302 :     if ($ptype eq 'CGI') {
1303 :     # Here we were invoked from a web page. Look for a cookie.
1304 :     $retVal = $parameter->cookie('IP');
1305 :     } elsif (! $ptype) {
1306 :     # Here the key was passed in.
1307 :     $retVal = $parameter;
1308 :     }
1309 :     }
1310 :     # If no luck finding a key, use the PID.
1311 :     if (! defined $retVal) {
1312 :     $retVal = $$;
1313 :     }
1314 :     # Return the result.
1315 :     return $retVal;
1316 :     }
1317 : parrello 1.11
1318 :    
1319 : parrello 1.93 =head3 TraceParms
1320 : parrello 1.11
1321 : parrello 1.93 Tracer::TraceParms($cgi);
1322 : parrello 1.11
1323 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1324 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1325 : parrello 1.11
1326 : parrello 1.93 =over 4
1327 : parrello 1.11
1328 : parrello 1.93 =item cgi
1329 : parrello 1.31
1330 : parrello 1.93 CGI query object containing the parameters to trace.
1331 : parrello 1.31
1332 : parrello 1.11 =back
1333 :    
1334 :     =cut
1335 : parrello 1.93
1336 :     sub TraceParms {
1337 : parrello 1.11 # Get the parameters.
1338 : parrello 1.93 my ($cgi) = @_;
1339 : parrello 1.94 if (T(CGI => 2)) {
1340 : parrello 1.115 # Here we trace the GET-style URL for the script, but only if it's
1341 :     # relatively small.
1342 :     my $url = $cgi->url(-relative => 1, -query => 1);
1343 :     my $len = length($url);
1344 :     if ($len < 500) {
1345 :     Trace("[URL] $url");
1346 :     } elsif ($len > 2048) {
1347 :     Trace("[URL] URL is too long to use with GET ($len characters).");
1348 :     } else {
1349 :     Trace("[URL] URL length is $len characters.");
1350 :     }
1351 : parrello 1.94 }
1352 : parrello 1.93 if (T(CGI => 3)) {
1353 :     # Here we want to trace the parameter data.
1354 :     my @names = $cgi->param;
1355 :     for my $parmName (sort @names) {
1356 :     # Note we skip the Trace parameters, which are for our use only.
1357 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1358 :     my @values = $cgi->param($parmName);
1359 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1360 : parrello 1.93 }
1361 :     }
1362 :     # Display the request method.
1363 :     my $method = $cgi->request_method();
1364 :     Trace("Method: $method");
1365 :     }
1366 :     if (T(CGI => 4)) {
1367 :     # Here we want the environment data too.
1368 :     for my $envName (sort keys %ENV) {
1369 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1370 : parrello 1.12 }
1371 :     }
1372 : parrello 1.11 }
1373 :    
1374 : parrello 1.94 =head3 TraceImages
1375 :    
1376 :     Tracer::TraceImages($htmlString);
1377 :    
1378 :     Trace information about all of an html document's images. The tracing
1379 :     will be for type "IMG" at level 3. The image's source string
1380 :     will be displayed. This is generally either the URL of the image or
1381 :     raw data for the image itself. If the source is too long, only the first 300
1382 :     characters will be shown at trace level 3. The entire source will be shown,
1383 :     however, at trace level 4. This method is not very smart, and might catch
1384 :     Javascript code, but it is still useful when debugging the arcane
1385 :     behavior of images in multiple browser environments.
1386 :    
1387 :     =over 4
1388 :    
1389 :     =item htmlString
1390 :    
1391 :     HTML text for an outgoing web page.
1392 :    
1393 :     =back
1394 :    
1395 :     =cut
1396 :    
1397 :     sub TraceImages {
1398 :     # Only proceed if we're at the proper trace level.
1399 :     if (T(IMG => 3)) {
1400 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1401 :     # into a variable called "$htmlString". This is because we expect html strings to be
1402 :     # long, and don't want to copy them any more than we have to.
1403 :     Trace(length($_[0]) . " characters in web page.");
1404 :     # Loop through the HTML, culling image tags.
1405 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1406 :     # Extract the source string and determine whether or not it's too long.
1407 :     my $srcString = $1;
1408 :     my $pos = pos($_[0]) - length($srcString);
1409 :     my $excess = length($srcString) - 300;
1410 :     # We'll put the display string in here.
1411 :     my $srcDisplay = $srcString;
1412 :     # If it's a data string, split it at the comma.
1413 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1414 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1415 :     # a long string, however, we only show the first 300 characters.
1416 :     if ($excess > 0 && ! T(IMG => 4)) {
1417 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1418 :     }
1419 :     # Output the trace message.
1420 :     Trace("Image tag at position $pos:\n$srcDisplay");
1421 :     }
1422 :     }
1423 :     }
1424 :    
1425 : parrello 1.93 =head2 Command-Line Utility Methods
1426 : olson 1.1
1427 : parrello 1.93 =head3 SendSMS
1428 : olson 1.1
1429 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430 : olson 1.1
1431 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432 :     user name, password, and API ID for the relevant account in the hash reference variable
1433 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435 :     is C<2561022>, then the FIG_Config file must contain
1436 : olson 1.1
1437 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1438 :     password => 'silly',
1439 :     api_id => '2561022' };
1440 : olson 1.1
1441 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1442 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443 :     when you call this method.
1444 : olson 1.1
1445 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1446 : parrello 1.74
1447 : parrello 1.93 =over 4
1448 : parrello 1.74
1449 : parrello 1.93 =item phoneNumber
1450 : parrello 1.74
1451 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1452 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1453 : parrello 1.74
1454 : parrello 1.93 =item msg
1455 : parrello 1.74
1456 : parrello 1.93 Message to send to the specified phone.
1457 : parrello 1.74
1458 :     =item RETURN
1459 :    
1460 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1461 : parrello 1.74
1462 : parrello 1.78 =back
1463 :    
1464 : parrello 1.74 =cut
1465 :    
1466 : parrello 1.93 sub SendSMS {
1467 : parrello 1.74 # Get the parameters.
1468 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1469 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1470 : parrello 1.74 my $retVal;
1471 : parrello 1.93 # Only proceed if we have phone support.
1472 :     if (! defined $FIG_Config::phone) {
1473 :     Trace("Phone support not present in FIG_Config.") if T(1);
1474 :     } else {
1475 :     # Get the phone data.
1476 :     my $parms = $FIG_Config::phone;
1477 :     # Get the Clickatell URL.
1478 :     my $url = "http://api.clickatell.com/http/";
1479 :     # Create the user agent.
1480 :     my $ua = LWP::UserAgent->new;
1481 :     # Request a Clickatell session.
1482 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483 :     password => $parms->{password},
1484 :     api_id => $parms->{api_id},
1485 :     to => $phoneNumber,
1486 :     text => $msg});
1487 :     # Check for an error.
1488 :     if (! $resp->is_success) {
1489 :     Trace("Alert failed.") if T(1);
1490 :     } else {
1491 :     # Get the message ID.
1492 :     my $rstring = $resp->content;
1493 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1494 :     $retVal = $1;
1495 :     } else {
1496 :     Trace("Phone attempt failed with $rstring") if T(1);
1497 :     }
1498 :     }
1499 : parrello 1.74 }
1500 :     # Return the result.
1501 :     return $retVal;
1502 :     }
1503 :    
1504 : parrello 1.93 =head3 StandardSetup
1505 : olson 1.1
1506 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507 : olson 1.1
1508 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1509 :     values are a hash of the command-line options and a list of the positional
1510 :     parameters. Tracing is automatically set up and the command-line options are
1511 :     validated.
1512 : olson 1.1
1513 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1514 :     be more easily understood, however, once they are examined individually.
1515 : olson 1.1
1516 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1517 :     special-purpose tracing categories. Most tracing categories are PERL package
1518 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520 : olson 1.1
1521 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1522 : olson 1.1
1523 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1524 :     the output. There are two special tracing categories that are automatically
1525 :     handled by this method. In other words, if you used L</TSetup> you would need
1526 :     to include these categories manually, but if you use this method they are turned
1527 :     on automatically.
1528 : parrello 1.5
1529 :     =over 4
1530 :    
1531 : parrello 1.93 =item SQL
1532 : parrello 1.5
1533 : parrello 1.93 Traces SQL commands and activity.
1534 : parrello 1.5
1535 : parrello 1.93 =item Tracer
1536 : parrello 1.5
1537 : parrello 1.93 Traces error messages and call stacks.
1538 : parrello 1.5
1539 :     =back
1540 :    
1541 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542 :     The trace level is specified using the C<-trace> command-line option. For example,
1543 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544 :     all tracing at level 3.
1545 : parrello 1.5
1546 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547 : parrello 1.5
1548 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1549 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550 :     process ID. You can also specify the C<user> parameter to put a user ID
1551 :     instead of a process ID in the trace file name. So, for example
1552 : olson 1.1
1553 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1554 :     For a genome-by-genome update, use 3.
1555 : olson 1.1
1556 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557 : olson 1.1
1558 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1559 : olson 1.1
1560 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1561 :     options, their default values, and an explanation of what they mean. Command-line
1562 :     options may be in the form of switches or keywords. In the case of a switch, the
1563 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1564 :     of a keyword, the value is separated from the option name by an equal sign. You
1565 :     can see this last in the command-line example above.
1566 : olson 1.1
1567 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1568 :     prior to calling this method.
1569 : olson 1.1
1570 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1571 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573 :     the following code.
1574 : olson 1.1
1575 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576 :     { safe => [0, "use database transactions"],
1577 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578 :     start => [' ', "start with this genome"],
1579 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580 :     "<command> <transactionDirectory> <IDfile>",
1581 :     @ARGV);
1582 : olson 1.1
1583 :    
1584 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1585 :     stores the actual options in a hash that is returned as C<$options>. The
1586 :     positional parameters are returned in C<@parameters>.
1587 : olson 1.1
1588 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1589 : olson 1.1
1590 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591 : olson 1.1
1592 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1593 :     above command as
1594 : olson 1.1
1595 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596 : olson 1.1
1597 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598 :     parameters, and would find themselves in I<@parameters> after executing the
1599 :     above code fragment. The tracing would be set to level 2, and the categories
1600 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601 :     and C<DocUtils> was included because it came in within the first parameter
1602 :     to this method. The I<$options> hash would be
1603 : olson 1.1
1604 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1605 :     noAlias => 1, start => ' ', tblFiles => 0 }
1606 : olson 1.1
1607 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1608 :     standard tracing setup and command-line parsing. Note that the caller is
1609 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1610 :     are used by this method to control the tracing. If additional tracing features
1611 :     need to be added in the future, they can be processed by this method without
1612 :     upsetting the command-line utilities.
1613 : olson 1.1
1614 : parrello 1.93 If the C<background> option is specified on the command line, then the
1615 :     standard and error outputs will be directed to files in the temporary
1616 :     directory, using the same suffix as the trace file. So, if the command
1617 :     line specified
1618 : olson 1.1
1619 : parrello 1.93 -user=Bruce -background
1620 : olson 1.1
1621 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1622 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623 :     simplify starting a command in the background.
1624 : olson 1.1
1625 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1626 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1627 :     be used instead of custom tracing. If the user name is not specified,
1628 :     the tracing key is taken from the C<Tracing> environment variable. If there
1629 : parrello 1.103 is no value for that variable, the tracing key will be computed from the active
1630 :     login ID.
1631 :    
1632 :     Since the default situation in StandardSetup is to trace to the standard
1633 :     output, errors that occur in command-line scripts will not generate
1634 :     RSS events. To force the events, use the C<warn> option.
1635 :    
1636 :     TransactFeatures -background -warn register ../xacts IDs.tbl
1637 : olson 1.1
1638 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1639 :     names will be traced at level 0 and the program will exit without processing.
1640 :     This provides a limited help capability. For example, if the user enters
1641 : olson 1.1
1642 : parrello 1.93 TransactFeatures -help
1643 : olson 1.1
1644 : parrello 1.93 he would see the following output.
1645 : olson 1.1
1646 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1647 :     -trace tracing level (default E)
1648 :     -sql trace SQL commands
1649 :     -safe use database transactions
1650 :     -noAlias do not expect aliases in CHANGE transactions
1651 :     -start start with this genome
1652 :     -tblFiles output TBL files containing the corrected IDs
1653 : parrello 1.111 -forked do not erase the trace file before tracing
1654 : olson 1.1
1655 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1656 :     for C<trace> in the incoming options hash. The default value can be overridden,
1657 :     or the tracing to the standard output can be turned off by suffixing a minus
1658 :     sign to the trace level. So, for example,
1659 : olson 1.1
1660 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1661 :     ...
1662 : olson 1.1
1663 : parrello 1.93 would set the default trace level to 0 instead of E, while
1664 : olson 1.1
1665 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1666 :     ...
1667 : olson 1.1
1668 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1669 :     standard output.
1670 : olson 1.1
1671 : parrello 1.93 The parameters to this method are as follows.
1672 : olson 1.1
1673 : parrello 1.93 =over 4
1674 : olson 1.1
1675 : parrello 1.93 =item categories
1676 : parrello 1.2
1677 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1678 :     packages whose internal workings will need to be debugged to get the
1679 :     command working.
1680 : olson 1.1
1681 : parrello 1.93 =item options
1682 : olson 1.1
1683 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1684 :     to their default values and descriptions. The user can override the defaults
1685 :     by specifying the options as command-line switches prefixed by a hyphen.
1686 :     Tracing-related options may be added to this hash. If the C<-h> option is
1687 :     specified on the command line, the option descriptions will be used to
1688 :     explain the options. To turn off tracing to the standard output, add a
1689 :     minus sign to the value for C<trace> (see above).
1690 : olson 1.1
1691 : parrello 1.93 =item parmHelp
1692 : olson 1.1
1693 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1694 :     if the user specifies the C<-h> option.
1695 : olson 1.1
1696 : parrello 1.93 =item argv
1697 : olson 1.1
1698 : parrello 1.93 List of command line parameters, including the option switches, which must
1699 :     precede the positional parameters and be prefixed by a hyphen.
1700 : olson 1.1
1701 :     =item RETURN
1702 :    
1703 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1704 :     maps the command-line option switches to their values. These will either be the
1705 :     default values or overrides specified on the command line. The remaining
1706 :     elements of the list are the position parameters, in order.
1707 : olson 1.1
1708 :     =back
1709 :    
1710 :     =cut
1711 :    
1712 : parrello 1.93 sub StandardSetup {
1713 :     # Get the parameters.
1714 :     my ($categories, $options, $parmHelp, @argv) = @_;
1715 :     # Get the default tracing key.
1716 :     my $tkey = EmergencyKey();
1717 : parrello 1.104 # Save the command line.
1718 :     $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1719 : parrello 1.93 # Add the tracing options.
1720 :     if (! exists $options->{trace}) {
1721 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1722 :     }
1723 : parrello 1.112 if (! exists $options->{forked}) {
1724 :     $options->{forked} = [0, "keep old trace file"];
1725 :     }
1726 : parrello 1.93 $options->{sql} = [0, "turn on SQL tracing"];
1727 :     $options->{help} = [0, "display command-line options"];
1728 :     $options->{user} = [$tkey, "tracing key"];
1729 :     $options->{background} = [0, "spool standard and error output"];
1730 : parrello 1.103 $options->{warn} = [0, "send errors to RSS feed"];
1731 : parrello 1.113 $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1732 : parrello 1.93 # Create a parsing hash from the options hash. The parsing hash
1733 :     # contains the default values rather than the default value
1734 :     # and the description. While we're at it, we'll memorize the
1735 :     # length of the longest option name.
1736 :     my $longestName = 0;
1737 :     my %parseOptions = ();
1738 :     for my $key (keys %{$options}) {
1739 :     if (length $key > $longestName) {
1740 :     $longestName = length $key;
1741 :     }
1742 :     $parseOptions{$key} = $options->{$key}->[0];
1743 :     }
1744 :     # Parse the command line.
1745 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1746 :     # Get the logfile suffix.
1747 :     my $suffix = $retOptions->{user};
1748 : parrello 1.113 # We'll put the trace file name in here. We need it later if background
1749 :     # mode is on.
1750 :     my $traceFileName;
1751 : parrello 1.93 # Now we want to set up tracing. First, we need to know if the user
1752 :     # wants emergency tracing.
1753 :     if ($retOptions->{trace} eq 'E') {
1754 :     ETracing($retOptions->{user});
1755 :     } else {
1756 :     # Here the tracing is controlled from the command line.
1757 :     my @cats = @{$categories};
1758 :     if ($retOptions->{sql}) {
1759 :     push @cats, "SQL";
1760 :     }
1761 : parrello 1.103 if ($retOptions->{warn}) {
1762 :     push @cats, "Feed";
1763 :     }
1764 : parrello 1.93 # Add the default categories.
1765 :     push @cats, "Tracer";
1766 : parrello 1.113 # Check for more tracing groups.
1767 :     if ($retOptions->{moreTracing}) {
1768 :     push @cats, split /,/, $retOptions->{moreTracing};
1769 :     }
1770 : parrello 1.93 # Next, we create the category string by joining the categories.
1771 :     my $cats = join(" ", @cats);
1772 :     # Check to determine whether or not the caller wants to turn off tracing
1773 :     # to the standard output.
1774 :     my $traceLevel = $retOptions->{trace};
1775 :     my $textOKFlag = 1;
1776 :     if ($traceLevel =~ /^(.)-/) {
1777 :     $traceLevel = $1;
1778 :     $textOKFlag = 0;
1779 :     }
1780 :     # Now we set up the trace mode.
1781 :     my $traceMode;
1782 :     # Verify that we can open a file in the FIG temporary directory.
1783 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1784 : parrello 1.111 my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1785 :     if (open TESTTRACE, "$traceFileSpec") {
1786 : parrello 1.93 # Here we can trace to a file.
1787 : parrello 1.111 $traceMode = ">>$traceFileName";
1788 : parrello 1.93 if ($textOKFlag) {
1789 :     # Echo to standard output if the text-OK flag is set.
1790 :     $traceMode = "+$traceMode";
1791 :     }
1792 :     # Close the test file.
1793 :     close TESTTRACE;
1794 :     } else {
1795 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1796 :     warn "Could not open trace file $traceFileName: $!\n";
1797 :     # We trace to the standard output if it's
1798 :     # okay, and the error log otherwise.
1799 : parrello 1.93 if ($textOKFlag) {
1800 :     $traceMode = "TEXT";
1801 : parrello 1.12 } else {
1802 : parrello 1.93 $traceMode = "WARN";
1803 : parrello 1.12 }
1804 :     }
1805 : parrello 1.93 # Now set up the tracing.
1806 :     TSetup("$traceLevel $cats", $traceMode);
1807 :     }
1808 : parrello 1.113 # Check for background mode.
1809 :     if ($retOptions->{background}) {
1810 :     my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1811 :     my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1812 :     # Spool the output.
1813 :     open STDOUT, ">$outFileName";
1814 :     # If we have a trace file, trace the errors to the log. Otherwise,
1815 :     # spool the errors.
1816 :     if (defined $traceFileName) {
1817 :     open STDERR, "| Tracer $traceFileName";
1818 :     } else {
1819 :     open STDERR, ">$errFileName";
1820 :     }
1821 :     # Check for phone support. If we have phone support and a phone number,
1822 :     # we want to turn it on.
1823 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1824 :     $retOptions->{phone} = $ENV{PHONE};
1825 :     }
1826 :     }
1827 : parrello 1.93 # Check for the "help" option. If it is specified, dump the command-line
1828 :     # options and exit the program.
1829 :     if ($retOptions->{help}) {
1830 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1831 :     print "$1 [options] $parmHelp\n";
1832 :     for my $key (sort keys %{$options}) {
1833 :     my $name = Pad($key, $longestName, 0, ' ');
1834 :     my $desc = $options->{$key}->[1];
1835 :     if ($options->{$key}->[0]) {
1836 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1837 :     }
1838 :     print " $name $desc\n";
1839 : parrello 1.36 }
1840 : parrello 1.93 exit(0);
1841 :     }
1842 :     # Trace the options, if applicable.
1843 :     if (T(3)) {
1844 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1845 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1846 : parrello 1.3 }
1847 : parrello 1.93 # Return the parsed parameters.
1848 :     return ($retOptions, @retParameters);
1849 : olson 1.1 }
1850 :    
1851 : parrello 1.93 =head3 ReadOptions
1852 : olson 1.1
1853 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1854 : olson 1.1
1855 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1856 :     format
1857 : olson 1.1
1858 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1859 : olson 1.1
1860 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1861 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1862 :     character is a semi-colon will be ignored. The return hash will map each option name to
1863 :     the corresponding option value.
1864 : olson 1.1
1865 :     =over 4
1866 :    
1867 : parrello 1.93 =item fileName
1868 : olson 1.1
1869 : parrello 1.93 Name of the file containing the option data.
1870 : olson 1.1
1871 :     =item RETURN
1872 :    
1873 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1874 :     value.
1875 : olson 1.1
1876 :     =back
1877 :    
1878 :     =cut
1879 :    
1880 : parrello 1.93 sub ReadOptions {
1881 : parrello 1.12 # Get the parameters.
1882 : parrello 1.93 my ($fileName) = @_;
1883 :     # Open the file.
1884 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1885 :     # Count the number of records read.
1886 :     my ($records, $comments) = 0;
1887 :     # Create the return hash.
1888 :     my %retVal = ();
1889 :     # Loop through the file, accumulating key-value pairs.
1890 :     while (my $line = <CONFIGFILE>) {
1891 :     # Denote we've read a line.
1892 :     $records++;
1893 :     # Determine the line type.
1894 :     if ($line =~ /^\s*[\n\r]/) {
1895 :     # A blank line is a comment.
1896 :     $comments++;
1897 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1898 :     # Here we have an option assignment.
1899 :     retVal{$1} = $2;
1900 :     } elsif ($line =~ /^\s*;/) {
1901 :     # Here we have a text comment.
1902 :     $comments++;
1903 : parrello 1.12 } else {
1904 : parrello 1.93 # Here we have an invalid line.
1905 :     Trace("Invalid option statement in record $records.") if T(0);
1906 : parrello 1.12 }
1907 :     }
1908 : parrello 1.93 # Return the hash created.
1909 :     return %retVal;
1910 : olson 1.1 }
1911 :    
1912 : parrello 1.93 =head3 GetOptions
1913 : parrello 1.9
1914 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1915 : parrello 1.9
1916 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1917 :     as input and uses the data from the second to update the first. If the second does not exist,
1918 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1919 :     exist in the first.
1920 : parrello 1.9
1921 : parrello 1.93 Consider the following example.
1922 : parrello 1.9
1923 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1924 : parrello 1.9
1925 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1926 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1927 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1928 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1929 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1930 : parrello 1.9
1931 : parrello 1.93 {databaseType => 'Oracle'}
1932 : parrello 1.9
1933 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1934 : parrello 1.9
1935 : parrello 1.93 =over 4
1936 : parrello 1.9
1937 : parrello 1.93 =item defaults
1938 : parrello 1.9
1939 : parrello 1.93 Table of default option values.
1940 : parrello 1.9
1941 : parrello 1.93 =item options
1942 : olson 1.1
1943 : parrello 1.93 Table of overrides, if any.
1944 : olson 1.1
1945 :     =item RETURN
1946 :    
1947 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1948 : olson 1.1
1949 :     =back
1950 :    
1951 :     =cut
1952 :    
1953 : parrello 1.93 sub GetOptions {
1954 :     # Get the parameters.
1955 :     my ($defaults, $options) = @_;
1956 :     # Check for overrides.
1957 :     if ($options) {
1958 :     # Loop through the overrides.
1959 :     while (my ($option, $setting) = each %{$options}) {
1960 :     # Insure this override exists.
1961 :     if (!exists $defaults->{$option}) {
1962 :     croak "Unrecognized option $option encountered.";
1963 : parrello 1.12 } else {
1964 : parrello 1.93 # Apply the override.
1965 :     $defaults->{$option} = $setting;
1966 : parrello 1.12 }
1967 :     }
1968 :     }
1969 : parrello 1.93 # Return the merged table.
1970 :     return $defaults;
1971 : olson 1.1 }
1972 :    
1973 : parrello 1.93 =head3 MergeOptions
1974 : olson 1.1
1975 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1976 : olson 1.1
1977 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1978 :     second (default) hash, and if a matching key is not found in the first hash, the default
1979 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1980 :     checking and no return value.
1981 : olson 1.1
1982 :     =over 4
1983 :    
1984 : parrello 1.93 =item table
1985 : olson 1.1
1986 : parrello 1.93 Hash table to be updated with the default values.
1987 : olson 1.1
1988 : parrello 1.93 =item defaults
1989 : olson 1.1
1990 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1991 : olson 1.1
1992 :     =back
1993 :    
1994 :     =cut
1995 :    
1996 : parrello 1.93 sub MergeOptions {
1997 :     # Get the parameters.
1998 :     my ($table, $defaults) = @_;
1999 :     # Loop through the defaults.
2000 :     while (my ($key, $value) = each %{$defaults}) {
2001 :     if (!exists $table->{$key}) {
2002 :     $table->{$key} = $value;
2003 :     }
2004 : parrello 1.12 }
2005 : olson 1.1 }
2006 :    
2007 : parrello 1.111 =head3 UnparseOptions
2008 :    
2009 :     my $optionString = Tracer::UnparseOptions(\%options);
2010 :    
2011 :     Convert an option hash into a command-line string. This will not
2012 :     necessarily be the same text that came in, but it will nonetheless
2013 :     produce the same ultimate result when parsed by L</StandardSetup>.
2014 :    
2015 :     =over 4
2016 :    
2017 :     =item options
2018 :    
2019 :     Reference to a hash of options to convert into an option string.
2020 :    
2021 :     =item RETURN
2022 :    
2023 :     Returns a string that will parse to the same set of options when
2024 :     parsed by L</StandardSetup>.
2025 :    
2026 :     =back
2027 :    
2028 :     =cut
2029 :    
2030 :     sub UnparseOptions {
2031 :     # Get the parameters.
2032 :     my ($options) = @_;
2033 :     # The option segments will be put in here.
2034 :     my @retVal = ();
2035 :     # Loop through the options.
2036 :     for my $key (keys %$options) {
2037 :     # Get the option value.
2038 :     my $value = $options->{$key};
2039 :     # Only use it if it's nonempty.
2040 :     if (defined $value && $value ne "") {
2041 :     my $segment = "--$key=$value";
2042 :     # Quote it if necessary.
2043 :     if ($segment =~ /[ |<>*]/) {
2044 :     $segment = '"' . $segment . '"';
2045 :     }
2046 :     # Add it to the return list.
2047 :     push @retVal, $segment;
2048 :     }
2049 :     }
2050 :     # Return the result.
2051 :     return join(" ", @retVal);
2052 :     }
2053 :    
2054 : parrello 1.93 =head3 ParseCommand
2055 : olson 1.1
2056 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2057 : olson 1.1
2058 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
2059 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2060 :     off and merged into a table of default options. The remainder of the command line is
2061 :     returned as a list of positional arguments. For example, consider the following invocation.
2062 : olson 1.1
2063 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2064 : olson 1.1
2065 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
2066 :     B<errors> and B<logFile>. If @words has the following format
2067 : olson 1.1
2068 : parrello 1.93 -logFile=error.log apple orange rutabaga
2069 : olson 1.1
2070 : parrello 1.93 then at the end of the invocation, C<$options> will be
2071 : olson 1.1
2072 : parrello 1.93 { errors => 0, logFile => 'error.log' }
2073 : olson 1.1
2074 : parrello 1.93 and C<@arguments> will contain
2075 : olson 1.1
2076 : parrello 1.93 apple orange rutabaga
2077 : olson 1.1
2078 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2079 :     support for quote characters. Options can be specified with single or double hyphens.
2080 : parrello 1.54
2081 :     =over 4
2082 :    
2083 : parrello 1.93 =item optionTable
2084 : parrello 1.54
2085 : parrello 1.93 Table of default options.
2086 : parrello 1.54
2087 : parrello 1.93 =item inputList
2088 : parrello 1.54
2089 : parrello 1.93 List of words on the command line.
2090 : parrello 1.54
2091 :     =item RETURN
2092 :    
2093 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2094 : parrello 1.54
2095 :     =back
2096 :    
2097 :     =cut
2098 :    
2099 : parrello 1.93 sub ParseCommand {
2100 : parrello 1.54 # Get the parameters.
2101 : parrello 1.93 my ($optionTable, @inputList) = @_;
2102 :     # Process any options in the input list.
2103 :     my %overrides = ();
2104 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2105 :     # Get the current option.
2106 :     my $arg = shift @inputList;
2107 :     # Pull out the option name.
2108 :     $arg =~ /^--?([^=]*)/g;
2109 :     my $name = $1;
2110 :     # Check for an option value.
2111 :     if ($arg =~ /\G=(.*)$/g) {
2112 :     # Here we have a value for the option.
2113 :     $overrides{$name} = UnEscape($1);
2114 :     } else {
2115 :     # Here there is no value, so we use 1.
2116 :     $overrides{$name} = 1;
2117 :     }
2118 :     }
2119 :     # Merge the options into the defaults.
2120 :     GetOptions($optionTable, \%overrides);
2121 :     # Translate the remaining parameters.
2122 :     my @retVal = ();
2123 :     for my $inputParm (@inputList) {
2124 :     push @retVal, UnEscape($inputParm);
2125 : parrello 1.54 }
2126 : parrello 1.93 # Return the results.
2127 :     return ($optionTable, @retVal);
2128 : parrello 1.54 }
2129 :    
2130 : parrello 1.93
2131 :     =head2 File Utility Methods
2132 :    
2133 : olson 1.1 =head3 GetFile
2134 :    
2135 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2136 : olson 1.1
2137 : parrello 1.35 or
2138 :    
2139 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2140 : parrello 1.35
2141 :     Return the entire contents of a file. In list context, line-ends are removed and
2142 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2143 : olson 1.1
2144 :     =over 4
2145 :    
2146 :     =item fileName
2147 :    
2148 :     Name of the file to read.
2149 :    
2150 :     =item RETURN
2151 :    
2152 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2153 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2154 :     the file, an empty list will be returned.
2155 : olson 1.1
2156 :     =back
2157 :    
2158 :     =cut
2159 :    
2160 :     sub GetFile {
2161 : parrello 1.12 # Get the parameters.
2162 :     my ($fileName) = @_;
2163 :     # Declare the return variable.
2164 :     my @retVal = ();
2165 :     # Open the file for input.
2166 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2167 :     # Read the whole file into the return variable, stripping off any terminator
2168 :     # characters.
2169 :     my $lineCount = 0;
2170 :     while (my $line = <$handle>) {
2171 :     $lineCount++;
2172 :     $line = Strip($line);
2173 :     push @retVal, $line;
2174 :     }
2175 :     # Close it.
2176 :     close $handle;
2177 :     my $actualLines = @retVal;
2178 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2179 : parrello 1.12 # Return the file's contents in the desired format.
2180 : parrello 1.9 if (wantarray) {
2181 : parrello 1.12 return @retVal;
2182 : parrello 1.6 } else {
2183 :     return join "\n", @retVal;
2184 :     }
2185 : olson 1.1 }
2186 :    
2187 : parrello 1.60 =head3 PutFile
2188 :    
2189 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2190 : parrello 1.60
2191 :     Write out a file from a list of lines of text.
2192 :    
2193 :     =over 4
2194 :    
2195 :     =item fileName
2196 :    
2197 :     Name of the output file.
2198 :    
2199 :     =item lines
2200 :    
2201 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2202 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2203 :     modification.
2204 : parrello 1.60
2205 :     =back
2206 :    
2207 :     =cut
2208 :    
2209 :     sub PutFile {
2210 :     # Get the parameters.
2211 :     my ($fileName, $lines) = @_;
2212 :     # Open the output file.
2213 :     my $handle = Open(undef, ">$fileName");
2214 : parrello 1.77 # Count the lines written.
2215 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2216 :     # Here we have a scalar, so we write it raw.
2217 :     print $handle $lines;
2218 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2219 : parrello 1.66 } else {
2220 :     # Write the lines one at a time.
2221 : parrello 1.77 my $count = 0;
2222 : parrello 1.66 for my $line (@{$lines}) {
2223 :     print $handle "$line\n";
2224 : parrello 1.77 $count++;
2225 : parrello 1.66 }
2226 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2227 : parrello 1.60 }
2228 :     # Close the output file.
2229 :     close $handle;
2230 :     }
2231 :    
2232 : parrello 1.93 =head3 ParseRecord
2233 : olson 1.1
2234 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2235 : olson 1.1
2236 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2237 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2238 :     These will automatically be converted.
2239 : olson 1.1
2240 :     =over 4
2241 :    
2242 : parrello 1.93 =item line
2243 :    
2244 :     Line of data containing the tab-delimited fields.
2245 :    
2246 :     =item RETURN
2247 : olson 1.1
2248 : parrello 1.93 Returns a list of the fields found in the data line.
2249 : olson 1.1
2250 :     =back
2251 :    
2252 :     =cut
2253 :    
2254 : parrello 1.93 sub ParseRecord {
2255 : parrello 1.12 # Get the parameter.
2256 : parrello 1.93 my ($line) = @_;
2257 :     # Remove the trailing new-line, if any.
2258 :     chomp $line;
2259 :     # Split the line read into pieces using the tab character.
2260 :     my @retVal = split /\t/, $line;
2261 :     # Trim and fix the escapes in each piece.
2262 :     for my $value (@retVal) {
2263 :     # Trim leading whitespace.
2264 :     $value =~ s/^\s+//;
2265 :     # Trim trailing whitespace.
2266 :     $value =~ s/\s+$//;
2267 :     # Delete the carriage returns.
2268 :     $value =~ s/\r//g;
2269 :     # Convert the escapes into their real values.
2270 :     $value =~ s/\\t/"\t"/ge;
2271 :     $value =~ s/\\n/"\n"/ge;
2272 :     }
2273 :     # Return the result.
2274 :     return @retVal;
2275 :     }
2276 :    
2277 :     =head3 Merge
2278 :    
2279 :     my @mergedList = Tracer::Merge(@inputList);
2280 :    
2281 :     Sort a list of strings and remove duplicates.
2282 :    
2283 :     =over 4
2284 :    
2285 :     =item inputList
2286 :    
2287 :     List of scalars to sort and merge.
2288 :    
2289 :     =item RETURN
2290 :    
2291 :     Returns a list containing the same elements sorted in ascending order with duplicates
2292 :     removed.
2293 :    
2294 :     =back
2295 :    
2296 :     =cut
2297 :    
2298 :     sub Merge {
2299 :     # Get the input list in sort order.
2300 :     my @inputList = sort @_;
2301 :     # Only proceed if the list has at least two elements.
2302 :     if (@inputList > 1) {
2303 :     # Now we want to move through the list splicing out duplicates.
2304 :     my $i = 0;
2305 :     while ($i < @inputList) {
2306 :     # Get the current entry.
2307 :     my $thisEntry = $inputList[$i];
2308 :     # Find out how many elements duplicate the current entry.
2309 :     my $j = $i + 1;
2310 :     my $dup1 = $i + 1;
2311 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2312 :     # If the number is nonzero, splice out the duplicates found.
2313 :     if ($j > $dup1) {
2314 :     splice @inputList, $dup1, $j - $dup1;
2315 : parrello 1.14 }
2316 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2317 :     # at position $i. We push $i forward one position and start again.
2318 :     $i++;
2319 : parrello 1.14 }
2320 : parrello 1.12 }
2321 : parrello 1.93 # Return the merged list.
2322 :     return @inputList;
2323 : olson 1.1 }
2324 :    
2325 : parrello 1.93 =head3 Open
2326 : olson 1.1
2327 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2328 : olson 1.1
2329 : parrello 1.93 Open a file.
2330 : olson 1.1
2331 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2332 :     function. The mode is specified using Unix-like shell information. So, for
2333 :     example,
2334 : olson 1.1
2335 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2336 : olson 1.1
2337 : parrello 1.93 would open for output appended to the specified file, and
2338 : olson 1.1
2339 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2340 : olson 1.1
2341 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2342 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2343 :     code as follows.
2344 : olson 1.1
2345 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2346 : olson 1.1
2347 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2348 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2349 :     failed open will throw an exception and the third parameter will be used to construct
2350 :     an error message. If the parameter is omitted, a standard message is constructed
2351 :     using the file spec.
2352 : olson 1.1
2353 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2354 : olson 1.1
2355 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2356 :     The actual error message from the file system will be captured and appended to the
2357 :     message in any case.
2358 : parrello 1.6
2359 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2360 : parrello 1.6
2361 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2362 :     corresponds to the C++ C<errno> value.
2363 : parrello 1.6
2364 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2365 : parrello 1.6
2366 : parrello 1.93 =over 4
2367 : parrello 1.6
2368 : parrello 1.93 =item fileHandle
2369 : parrello 1.6
2370 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2371 :     and returned as the value of this method.
2372 : olson 1.1
2373 : parrello 1.93 =item fileSpec
2374 : olson 1.1
2375 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2376 : olson 1.1
2377 : parrello 1.93 =item message (optional)
2378 : olson 1.1
2379 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2380 :     will be generated. In either case, the error information from the file system
2381 :     is appended to the message. To specify a conditional open that does not throw
2382 :     an error if it fails, use C<0>.
2383 : olson 1.1
2384 : parrello 1.93 =item RETURN
2385 : olson 1.1
2386 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2387 :     open failed.
2388 : olson 1.1
2389 :     =back
2390 :    
2391 :     =cut
2392 :    
2393 : parrello 1.93 sub Open {
2394 : parrello 1.12 # Get the parameters.
2395 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2396 :     # Attempt to open the file.
2397 :     my $rv = open $fileHandle, $fileSpec;
2398 :     # If the open failed, generate an error message.
2399 :     if (! $rv) {
2400 :     # Save the system error message.
2401 :     my $sysMessage = $!;
2402 :     # See if we need a default message.
2403 :     if (!$message) {
2404 :     # Clean any obvious mode characters and leading spaces from the
2405 :     # filename.
2406 :     my ($fileName) = FindNamePart($fileSpec);
2407 :     $message = "Could not open \"$fileName\"";
2408 :     }
2409 :     # Terminate with an error using the supplied message and the
2410 :     # error message from the file system.
2411 :     Confess("$message: $!");
2412 : parrello 1.12 }
2413 : parrello 1.93 # Return the file handle.
2414 :     return $fileHandle;
2415 : olson 1.1 }
2416 :    
2417 : parrello 1.93 =head3 FindNamePart
2418 :    
2419 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2420 :    
2421 :     Extract the portion of a file specification that contains the file name.
2422 :    
2423 :     A file specification is the string passed to an C<open> call. It specifies the file
2424 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2425 :     method assumes that the file name is whatever follows the first angle bracket
2426 :     sequence. So, for example, in the following strings the file name is
2427 :     C</usr/fig/myfile.txt>.
2428 : parrello 1.5
2429 : parrello 1.93 >>/usr/fig/myfile.txt
2430 :     </usr/fig/myfile.txt
2431 :     | sort -u > /usr/fig/myfile.txt
2432 : parrello 1.5
2433 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2434 :     whole incoming string.
2435 : parrello 1.5
2436 :     =over 4
2437 :    
2438 : parrello 1.93 =item fileSpec
2439 : parrello 1.5
2440 : parrello 1.93 File specification string from which the file name is to be extracted.
2441 : parrello 1.5
2442 :     =item RETURN
2443 :    
2444 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2445 :     the specified string, or the whole string if a file name cannot be found via normal
2446 :     methods. The second element contains the start position of the file name portion and
2447 :     the third element contains the length.
2448 : parrello 1.5
2449 :     =back
2450 :    
2451 :     =cut
2452 : parrello 1.93 #: Return Type $;
2453 :     sub FindNamePart {
2454 :     # Get the parameters.
2455 :     my ($fileSpec) = @_;
2456 :     # Default to the whole input string.
2457 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2458 :     # Parse out the file name if we can.
2459 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2460 :     $retVal = $2;
2461 :     $len = length $retVal;
2462 :     $pos = (length $fileSpec) - (length $3) - $len;
2463 : parrello 1.12 }
2464 : parrello 1.93 # Return the result.
2465 :     return ($retVal, $pos, $len);
2466 : parrello 1.5 }
2467 :    
2468 : parrello 1.93 =head3 OpenDir
2469 : parrello 1.5
2470 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2471 : parrello 1.5
2472 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2473 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2474 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2475 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2476 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2477 :     set, an exception is thrown. So, for example,
2478 : parrello 1.5
2479 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2480 : parrello 1.5
2481 : parrello 1.93 is effectively the same as
2482 : parrello 1.5
2483 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2484 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2485 : parrello 1.5
2486 : parrello 1.93 Similarly, the following code
2487 : parrello 1.5
2488 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2489 : parrello 1.5
2490 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2491 :     automatically returns an empty list if the directory fails to open.
2492 : parrello 1.5
2493 : parrello 1.93 =over 4
2494 : parrello 1.5
2495 : parrello 1.93 =item dirName
2496 : parrello 1.5
2497 : parrello 1.93 Name of the directory to open.
2498 : parrello 1.5
2499 : parrello 1.93 =item filtered
2500 : parrello 1.5
2501 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2502 :     from the list, else FALSE.
2503 : parrello 1.5
2504 : parrello 1.93 =item flag
2505 : parrello 1.5
2506 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2507 : parrello 1.5
2508 : parrello 1.93 =back
2509 : parrello 1.5
2510 : parrello 1.93 =cut
2511 :     #: Return Type @;
2512 :     sub OpenDir {
2513 :     # Get the parameters.
2514 :     my ($dirName, $filtered, $flag) = @_;
2515 :     # Declare the return variable.
2516 :     my @retVal = ();
2517 :     # Open the directory.
2518 :     if (opendir(my $dirHandle, $dirName)) {
2519 :     # The directory opened successfully. Get the appropriate list according to the
2520 :     # strictures of the filter parameter.
2521 :     if ($filtered) {
2522 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2523 :     } else {
2524 :     @retVal = readdir $dirHandle;
2525 :     }
2526 :     } elsif (! $flag) {
2527 :     # Here the directory would not open and it's considered an error.
2528 :     Confess("Could not open directory $dirName.");
2529 :     }
2530 :     # Return the result.
2531 :     return @retVal;
2532 :     }
2533 : parrello 1.5
2534 :    
2535 : parrello 1.93 =head3 Insure
2536 : parrello 1.5
2537 : parrello 1.93 Insure($dirName, $chmod);
2538 : parrello 1.5
2539 : parrello 1.93 Insure a directory is present.
2540 : parrello 1.5
2541 : parrello 1.93 =over 4
2542 : parrello 1.5
2543 : parrello 1.93 =item dirName
2544 : olson 1.1
2545 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2546 : parrello 1.7
2547 : parrello 1.93 =item chmod (optional)
2548 : parrello 1.7
2549 : parrello 1.93 Security privileges to be given to the directory if it is created.
2550 : parrello 1.7
2551 : parrello 1.93 =back
2552 : parrello 1.7
2553 :     =cut
2554 :    
2555 : parrello 1.93 sub Insure {
2556 :     my ($dirName, $chmod) = @_;
2557 :     if (! -d $dirName) {
2558 :     Trace("Creating $dirName directory.") if T(2);
2559 :     eval {
2560 :     mkpath $dirName;
2561 :     # If we have permissions specified, set them here.
2562 :     if (defined($chmod)) {
2563 :     chmod $chmod, $dirName;
2564 :     }
2565 :     };
2566 :     if ($@) {
2567 :     Confess("Error creating $dirName: $@");
2568 :     }
2569 : parrello 1.12 }
2570 : parrello 1.9 }
2571 :    
2572 : parrello 1.93 =head3 ChDir
2573 : parrello 1.9
2574 : parrello 1.93 ChDir($dirName);
2575 : parrello 1.9
2576 : parrello 1.93 Change to the specified directory.
2577 : parrello 1.9
2578 :     =over 4
2579 :    
2580 : parrello 1.93 =item dirName
2581 : parrello 1.9
2582 : parrello 1.93 Name of the directory to which we want to change.
2583 : parrello 1.9
2584 :     =back
2585 :    
2586 :     =cut
2587 :    
2588 : parrello 1.93 sub ChDir {
2589 :     my ($dirName) = @_;
2590 :     if (! -d $dirName) {
2591 :     Confess("Cannot change to directory $dirName: no such directory.");
2592 :     } else {
2593 :     Trace("Changing to directory $dirName.") if T(File => 4);
2594 :     my $okFlag = chdir $dirName;
2595 :     if (! $okFlag) {
2596 :     Confess("Error switching to directory $dirName.");
2597 :     }
2598 :     }
2599 : parrello 1.9 }
2600 :    
2601 : parrello 1.93 =head3 SetPermissions
2602 :    
2603 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2604 : parrello 1.9
2605 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2606 :     In addition, the group ownership will be changed to the specified value.
2607 : parrello 1.9
2608 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2609 :     problems, so it does internal error recovery.
2610 : parrello 1.9
2611 :     =over 4
2612 :    
2613 : parrello 1.93 =item dirName
2614 :    
2615 :     Name of the directory to process.
2616 :    
2617 :     =item group
2618 : parrello 1.9
2619 : parrello 1.93 Name of the group to be assigned.
2620 : parrello 1.9
2621 : parrello 1.93 =item mask
2622 : parrello 1.9
2623 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2624 :     permission bits of any file or directory that does not already have them
2625 :     set to 1.
2626 : parrello 1.9
2627 : parrello 1.93 =item otherMasks
2628 : parrello 1.9
2629 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2630 :     one of the patterns, that directory and all its members and subdirectories
2631 :     will be assigned the new pattern. For example, the following would
2632 : parrello 1.110 assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2633 : parrello 1.9
2634 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2635 : parrello 1.9
2636 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2637 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2638 : parrello 1.22
2639 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2640 :     '^tmp' => 0666);
2641 : parrello 1.9
2642 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2643 :     names are matched, not file names.
2644 : parrello 1.9
2645 :     =back
2646 :    
2647 :     =cut
2648 :    
2649 : parrello 1.93 sub SetPermissions {
2650 : parrello 1.12 # Get the parameters.
2651 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2652 :     # Set up for error recovery.
2653 :     eval {
2654 :     # Switch to the specified directory.
2655 :     ChDir($dirName);
2656 :     # Get the group ID.
2657 :     my $gid = getgrnam($group);
2658 :     # Get the mask for tracing.
2659 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2660 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2661 :     my $fixCount = 0;
2662 :     my $lookCount = 0;
2663 :     # @dirs will be a stack of directories to be processed.
2664 :     my @dirs = (getcwd());
2665 :     while (scalar(@dirs) > 0) {
2666 :     # Get the current directory.
2667 :     my $dir = pop @dirs;
2668 :     # Check for a match to one of the specified directory names. To do
2669 :     # that, we need to pull the individual part of the name off of the
2670 :     # whole path.
2671 :     my $simpleName = $dir;
2672 :     if ($dir =~ m!/([^/]+)$!) {
2673 :     $simpleName = $1;
2674 :     }
2675 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2676 :     # Search for a match.
2677 :     my $match = 0;
2678 :     my $i;
2679 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2680 :     my $pattern = $otherMasks[$i];
2681 :     if ($simpleName =~ /$pattern/i) {
2682 :     $match = 1;
2683 :     }
2684 :     }
2685 : parrello 1.110 # Find out if we have a match. Note we use $i-1 because the loop added 2
2686 : parrello 1.93 # before terminating due to the match.
2687 :     if ($match && $otherMasks[$i-1] != $mask) {
2688 :     # This directory matches one of the incoming patterns, and it's
2689 :     # a different mask, so we process it recursively with that mask.
2690 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2691 :     } else {
2692 :     # Here we can process normally. Get all of the non-hidden members.
2693 :     my @submems = OpenDir($dir, 1);
2694 :     for my $submem (@submems) {
2695 :     # Get the full name.
2696 :     my $thisMem = "$dir/$submem";
2697 :     Trace("Checking member $thisMem.") if T(4);
2698 :     $lookCount++;
2699 :     if ($lookCount % 1000 == 0) {
2700 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2701 :     }
2702 :     # Fix the group.
2703 :     chown -1, $gid, $thisMem;
2704 :     # Insure this member is not a symlink.
2705 :     if (! -l $thisMem) {
2706 :     # Get its info.
2707 :     my $fileInfo = stat $thisMem;
2708 :     # Only proceed if we got the info. Otherwise, it's a hard link
2709 :     # and we want to skip it anyway.
2710 :     if ($fileInfo) {
2711 :     my $fileMode = $fileInfo->mode;
2712 :     if (($fileMode & $mask) != $mask) {
2713 :     # Fix this member.
2714 :     $fileMode |= $mask;
2715 :     chmod $fileMode, $thisMem;
2716 :     $fixCount++;
2717 :     }
2718 :     # If it's a subdirectory, stack it.
2719 :     if (-d $thisMem) {
2720 :     push @dirs, $thisMem;
2721 :     }
2722 :     }
2723 :     }
2724 :     }
2725 :     }
2726 : parrello 1.12 }
2727 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2728 :     };
2729 :     # Check for an error.
2730 :     if ($@) {
2731 :     Confess("SetPermissions error: $@");
2732 : parrello 1.12 }
2733 : parrello 1.7 }
2734 :    
2735 : parrello 1.93 =head3 GetLine
2736 : parrello 1.29
2737 : parrello 1.93 my @data = Tracer::GetLine($handle);
2738 : parrello 1.15
2739 : parrello 1.93 Read a line of data from a tab-delimited file.
2740 : parrello 1.15
2741 :     =over 4
2742 :    
2743 : parrello 1.93 =item handle
2744 : parrello 1.15
2745 : parrello 1.93 Open file handle from which to read.
2746 : parrello 1.15
2747 :     =item RETURN
2748 :    
2749 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2750 :     tab-delimited. If we are at the end of the file, then an empty list will be
2751 :     returned. If an empty line is read, a single list item consisting of a null
2752 :     string will be returned.
2753 : parrello 1.15
2754 :     =back
2755 :    
2756 :     =cut
2757 : parrello 1.93
2758 :     sub GetLine {
2759 : parrello 1.15 # Get the parameters.
2760 : parrello 1.93 my ($handle) = @_;
2761 :     # Declare the return variable.
2762 :     my @retVal = ();
2763 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2764 :     # Read from the file.
2765 :     my $line = <$handle>;
2766 :     # Only proceed if we found something.
2767 :     if (defined $line) {
2768 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2769 :     # upload control and have a nonstandard EOL combination.
2770 :     $line =~ s/(\r|\n)+$//;
2771 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2772 :     if (T(File => 4)) {
2773 :     my $escapedLine = $line;
2774 :     $escapedLine =~ s/\n/\\n/g;
2775 :     $escapedLine =~ s/\r/\\r/g;
2776 :     $escapedLine =~ s/\t/\\t/g;
2777 :     Trace("Line read: -->$escapedLine<--");
2778 :     }
2779 :     # If the line is empty, return a single empty string; otherwise, parse
2780 :     # it into fields.
2781 :     if ($line eq "") {
2782 :     push @retVal, "";
2783 :     } else {
2784 :     push @retVal, split /\t/,$line;
2785 :     }
2786 :     } else {
2787 :     # Trace the reason the read failed.
2788 :     Trace("End of file: $!") if T(File => 3);
2789 : parrello 1.15 }
2790 : parrello 1.93 # Return the result.
2791 :     return @retVal;
2792 : parrello 1.15 }
2793 :    
2794 : parrello 1.93 =head3 PutLine
2795 :    
2796 :     Tracer::PutLine($handle, \@fields, $eol);
2797 : parrello 1.35
2798 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2799 :     output in tab-separated form, with a trailing new-line.
2800 : parrello 1.35
2801 : parrello 1.93 =over 4
2802 : parrello 1.35
2803 : parrello 1.93 =item handle
2804 : parrello 1.69
2805 : parrello 1.93 Output file handle.
2806 : parrello 1.69
2807 : parrello 1.93 =item fields
2808 : parrello 1.69
2809 : parrello 1.93 List of field values.
2810 : parrello 1.69
2811 : parrello 1.93 =item eol (optional)
2812 : parrello 1.69
2813 : parrello 1.93 End-of-line character (default is "\n").
2814 : parrello 1.69
2815 :     =back
2816 : parrello 1.35
2817 :     =cut
2818 :    
2819 : parrello 1.93 sub PutLine {
2820 : parrello 1.69 # Get the parameters.
2821 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2822 :     # Write the data.
2823 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2824 : parrello 1.69 }
2825 :    
2826 :    
2827 : parrello 1.97 =head3 PrintLine
2828 :    
2829 :     Tracer::PrintLine($line);
2830 :    
2831 :     Print a line of text with a trailing new-line.
2832 :    
2833 :     =over 4
2834 :    
2835 :     =item line
2836 :    
2837 :     Line of text to print.
2838 :    
2839 :     =back
2840 :    
2841 :     =cut
2842 :    
2843 :     sub PrintLine {
2844 :     # Get the parameters.
2845 :     my ($line) = @_;
2846 :     # Print the line.
2847 :     print "$line\n";
2848 :     }
2849 :    
2850 : parrello 1.69
2851 : parrello 1.93 =head2 Other Useful Methods
2852 :    
2853 : parrello 1.115 =head3 IDHASH
2854 :    
2855 :     my $hash = SHTargetSearch::IDHASH(@keys);
2856 :    
2857 :     This is a dinky little method that converts a list of values to a reference
2858 :     to hash of values to labels. The values and labels are the same.
2859 :    
2860 :     =cut
2861 :    
2862 :     sub IDHASH {
2863 :     my %retVal = map { $_ => $_ } @_;
2864 :     return \%retVal;
2865 :     }
2866 :    
2867 :     =head3 Pluralize
2868 :    
2869 :     my $plural = Tracer::Pluralize($word);
2870 :    
2871 :     This is a very simple pluralization utility. It adds an C<s> at the end
2872 :     of the input word unless it already ends in an C<s>, in which case it
2873 :     adds C<es>.
2874 :    
2875 :     =over 4
2876 :    
2877 :     =item word
2878 :    
2879 :     Singular word to pluralize.
2880 :    
2881 :     =item RETURN
2882 :    
2883 :     Returns the probable plural form of the word.
2884 :    
2885 :     =back
2886 :    
2887 :     =cut
2888 :    
2889 :     sub Pluralize {
2890 :     # Get the parameters.
2891 :     my ($word) = @_;
2892 :     # Declare the return variable.
2893 :     my $retVal;
2894 :     if ($word =~ /s$/) {
2895 :     $retVal = $word . 'es';
2896 :     } else {
2897 :     $retVal = $word . 's';
2898 :     }
2899 :     # Return the result.
2900 :     return $retVal;
2901 :     }
2902 :    
2903 :     =head3 Numeric
2904 :    
2905 :     my $okFlag = Tracer::Numeric($string);
2906 :    
2907 :     Return the value of the specified string if it is numeric, or an undefined value
2908 :     if it is not numeric.
2909 :    
2910 :     =over 4
2911 :    
2912 :     =item string
2913 :    
2914 :     String to check.
2915 :    
2916 :     =item RETURN
2917 :    
2918 :     Returns the numeric value of the string if successful, or C<undef> if the string
2919 :     is not numeric.
2920 :    
2921 :     =back
2922 :    
2923 :     =cut
2924 :    
2925 :     sub Numeric {
2926 :     # Get the parameters.
2927 :     my ($string) = @_;
2928 :     # We'll put the value in here if we succeed.
2929 :     my $retVal;
2930 :     # Get a working copy of the string.
2931 :     my $copy = $string;
2932 :     # Trim leading and trailing spaces.
2933 :     $copy =~ s/^\s+//;
2934 :     $copy =~ s/\s+$//;
2935 :     # Check the result.
2936 :     if ($copy =~ /^[+-]?\d+$/) {
2937 :     $retVal = $copy;
2938 :     } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2939 :     $retVal = $copy;
2940 :     } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2941 :     $retVal = $copy;
2942 :     }
2943 :     # Return the result.
2944 :     return $retVal;
2945 :     }
2946 :    
2947 :    
2948 : parrello 1.93 =head3 ParseParm
2949 :    
2950 :     my $listValue = Tracer::ParseParm($string);
2951 :    
2952 :     Convert a parameter into a list reference. If the parameter is undefined,
2953 :     an undefined value will be returned. Otherwise, it will be parsed as a
2954 :     comma-separated list of values.
2955 : parrello 1.69
2956 :     =over 4
2957 :    
2958 : parrello 1.93 =item string
2959 :    
2960 :     Incoming string.
2961 :    
2962 :     =item RETURN
2963 : parrello 1.69
2964 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2965 :     was undefined.
2966 : parrello 1.69
2967 :     =back
2968 :    
2969 :     =cut
2970 :    
2971 : parrello 1.93 sub ParseParm {
2972 :     # Get the parameters.
2973 :     my ($string) = @_;
2974 :     # Declare the return variable.
2975 :     my $retVal;
2976 :     # Check for data.
2977 :     if (defined $string) {
2978 :     # We have some, so split it into a list.
2979 :     $retVal = [ split /\s*,\s*/, $string];
2980 : parrello 1.72 }
2981 : parrello 1.93 # Return the result.
2982 :     return $retVal;
2983 : parrello 1.69 }
2984 :    
2985 : parrello 1.97 =head3 Now
2986 :    
2987 :     my $string = Tracer::Now();
2988 :    
2989 :     Return a displayable time stamp containing the local time. Whatever format this
2990 :     method produces must be parseable by L</ParseDate>.
2991 :    
2992 :     =cut
2993 :    
2994 :     sub Now {
2995 :     return DisplayTime(time);
2996 :     }
2997 :    
2998 :     =head3 DisplayTime
2999 :    
3000 :     my $string = Tracer::DisplayTime($time);
3001 : parrello 1.69
3002 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
3003 :     method produces must be parseable by L</ParseDate>.
3004 :    
3005 :     =over 4
3006 : parrello 1.69
3007 : parrello 1.97 =item time
3008 : parrello 1.69
3009 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3010 :    
3011 :     =item RETURN
3012 : parrello 1.69
3013 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3014 : parrello 1.69
3015 : parrello 1.97 =back
3016 : parrello 1.69
3017 : parrello 1.93 =cut
3018 : parrello 1.69
3019 : parrello 1.97 sub DisplayTime {
3020 :     my ($time) = @_;
3021 :     my $retVal = "(n/a)";
3022 :     if (defined $time) {
3023 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3024 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3025 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3026 :     }
3027 : parrello 1.93 return $retVal;
3028 :     }
3029 : parrello 1.69
3030 : parrello 1.93 # Pad a number to 2 digits.
3031 :     sub _p2 {
3032 :     my ($value) = @_;
3033 :     $value = "0$value" if ($value < 10);
3034 :     return $value;
3035 : parrello 1.69 }
3036 :    
3037 : parrello 1.93 =head3 Escape
3038 : parrello 1.69
3039 : parrello 1.93 my $codedString = Tracer::Escape($realString);
3040 : parrello 1.69
3041 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3042 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3043 :     result is to reverse the effect of L</UnEscape>.
3044 : parrello 1.69
3045 :     =over 4
3046 :    
3047 : parrello 1.93 =item realString
3048 : parrello 1.69
3049 : parrello 1.93 String to escape.
3050 : parrello 1.69
3051 :     =item RETURN
3052 :    
3053 : parrello 1.93 Escaped equivalent of the real string.
3054 :    
3055 :     =back
3056 :    
3057 :     =cut
3058 :    
3059 :     sub Escape {
3060 :     # Get the parameter.
3061 :     my ($realString) = @_;
3062 :     # Initialize the return variable.
3063 :     my $retVal = "";
3064 :     # Loop through the parameter string, looking for sequences to escape.
3065 :     while (length $realString > 0) {
3066 :     # Look for the first sequence to escape.
3067 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3068 :     # Here we found it. The text preceding the sequence is in $1. The sequence
3069 :     # itself is in $2. First, move the clear text to the return variable.
3070 :     $retVal .= $1;
3071 :     # Strip the processed section off the real string.
3072 :     $realString = substr $realString, (length $2) + (length $1);
3073 :     # Get the matched character.
3074 :     my $char = $2;
3075 :     # If we have a CR, we are done.
3076 :     if ($char ne "\r") {
3077 :     # It's not a CR, so encode the escape sequence.
3078 :     $char =~ tr/\t\n/tn/;
3079 :     $retVal .= "\\" . $char;
3080 :     }
3081 :     } else {
3082 :     # Here there are no more escape sequences. The rest of the string is
3083 :     # transferred unmodified.
3084 :     $retVal .= $realString;
3085 :     $realString = "";
3086 :     }
3087 :     }
3088 :     # Return the result.
3089 :     return $retVal;
3090 : parrello 1.69 }
3091 :    
3092 : parrello 1.93 =head3 UnEscape
3093 : parrello 1.69
3094 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
3095 : parrello 1.69
3096 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3097 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3098 :     be deleted.
3099 : parrello 1.69
3100 :     =over 4
3101 :    
3102 : parrello 1.93 =item codedString
3103 : parrello 1.69
3104 : parrello 1.93 String to un-escape.
3105 : parrello 1.69
3106 :     =item RETURN
3107 :    
3108 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
3109 :     values.
3110 : parrello 1.69
3111 :     =back
3112 :    
3113 :     =cut
3114 :    
3115 : parrello 1.93 sub UnEscape {
3116 :     # Get the parameter.
3117 :     my ($codedString) = @_;
3118 :     # Initialize the return variable.
3119 :     my $retVal = "";
3120 :     # Only proceed if the incoming string is nonempty.
3121 :     if (defined $codedString) {
3122 :     # Loop through the parameter string, looking for escape sequences. We can't do
3123 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
3124 :     # "\<tab>" no matter what we do.)
3125 :     while (length $codedString > 0) {
3126 :     # Look for the first escape sequence.
3127 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3128 :     # Here we found it. The text preceding the sequence is in $1. The sequence
3129 :     # itself is in $2. First, move the clear text to the return variable.
3130 :     $retVal .= $1;
3131 :     $codedString = substr $codedString, (2 + length $1);
3132 :     # Get the escape value.
3133 :     my $char = $2;
3134 :     # If we have a "\r", we are done.
3135 :     if ($char ne 'r') {
3136 :     # Here it's not an 'r', so we convert it.
3137 :     $char =~ tr/\\tn/\\\t\n/;
3138 :     $retVal .= $char;
3139 :     }
3140 :     } else {
3141 :     # Here there are no more escape sequences. The rest of the string is
3142 :     # transferred unmodified.
3143 :     $retVal .= $codedString;
3144 :     $codedString = "";
3145 :     }
3146 :     }
3147 : parrello 1.35 }
3148 : parrello 1.69 # Return the result.
3149 :     return $retVal;
3150 :     }
3151 :    
3152 : parrello 1.93 =head3 Percent
3153 : parrello 1.69
3154 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
3155 : parrello 1.69
3156 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
3157 :     is zero, returns zero.
3158 : parrello 1.69
3159 :     =over 4
3160 :    
3161 : parrello 1.93 =item number
3162 : parrello 1.69
3163 : parrello 1.93 Percent numerator.
3164 : parrello 1.69
3165 : parrello 1.93 =item base
3166 : parrello 1.69
3167 : parrello 1.93 Percent base.
3168 : parrello 1.69
3169 : parrello 1.93 =item RETURN
3170 : parrello 1.69
3171 : parrello 1.93 Returns the percentage of the base represented by the numerator.
3172 : parrello 1.69
3173 :     =back
3174 :    
3175 :     =cut
3176 :    
3177 : parrello 1.93 sub Percent {
3178 : parrello 1.69 # Get the parameters.
3179 : parrello 1.93 my ($number, $base) = @_;
3180 :     # Declare the return variable.
3181 :     my $retVal = 0;
3182 :     # Compute the percent.
3183 :     if ($base != 0) {
3184 :     $retVal = $number * 100 / $base;
3185 :     }
3186 :     # Return the result.
3187 :     return $retVal;
3188 : parrello 1.69 }
3189 :    
3190 : parrello 1.115 =head3 In
3191 :    
3192 :     my $flag = Tracer::In($value, $min, $max);
3193 :    
3194 :     Return TRUE if the value is between the minimum and the maximum, else FALSE.
3195 :    
3196 :     =cut
3197 :    
3198 :     sub In {
3199 :     return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3200 :     }
3201 :    
3202 :    
3203 : parrello 1.97 =head3 Constrain
3204 :    
3205 :     my $constrained = Constrain($value, $min, $max);
3206 :    
3207 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3208 :    
3209 :     =over 4
3210 :    
3211 :     =item value
3212 :    
3213 :     Value to constrain.
3214 :    
3215 :     =item min (optional)
3216 :    
3217 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3218 :    
3219 :     =item max (optional)
3220 :    
3221 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3222 :    
3223 :     =item RETURN
3224 :    
3225 :     Returns the incoming value, constrained according to the other parameters.
3226 :    
3227 :     =back
3228 :    
3229 :     =cut
3230 :    
3231 :     sub Constrain {
3232 :     # Get the parameters.
3233 :     my ($value, $min, $max) = @_;
3234 :     # Declare the return variable.
3235 :     my $retVal = $value;
3236 :     # Apply the minimum constraint.
3237 :     if (defined $min && $retVal < $min) {
3238 :     $retVal = $min;
3239 :     }
3240 :     # Apply the maximum constraint.
3241 :     if (defined $max && $retVal > $max) {
3242 :     $retVal = $max;
3243 :     }
3244 :     # Return the result.
3245 :     return $retVal;
3246 :     }
3247 :    
3248 : parrello 1.93 =head3 Min
3249 : parrello 1.69
3250 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3251 : parrello 1.69
3252 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3253 : parrello 1.69
3254 :     =over 4
3255 :    
3256 : parrello 1.93 =item $value1, $value2, ... $valueN
3257 : parrello 1.69
3258 : parrello 1.93 List of numbers to compare.
3259 : parrello 1.69
3260 :     =item RETURN
3261 :    
3262 : parrello 1.93 Returns the lowest number in the list.
3263 : parrello 1.69
3264 :     =back
3265 :    
3266 :     =cut
3267 :    
3268 : parrello 1.93 sub Min {
3269 :     # Get the parameters. Note that we prime the return value with the first parameter.
3270 :     my ($retVal, @values) = @_;
3271 :     # Loop through the remaining parameters, looking for the lowest.
3272 :     for my $value (@values) {
3273 :     if ($value < $retVal) {
3274 :     $retVal = $value;
3275 : parrello 1.72 }
3276 :     }
3277 : parrello 1.93 # Return the minimum found.
3278 : parrello 1.70 return $retVal;
3279 : parrello 1.35 }
3280 :    
3281 : parrello 1.93 =head3 Max
3282 :    
3283 :     my $max = Max($value1, $value2, ... $valueN);
3284 : parrello 1.69
3285 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3286 : parrello 1.65
3287 : parrello 1.93 =over 4
3288 : parrello 1.65
3289 : parrello 1.93 =item $value1, $value2, ... $valueN
3290 : parrello 1.65
3291 : parrello 1.93 List of numbers to compare.
3292 : parrello 1.65
3293 : parrello 1.93 =item RETURN
3294 : parrello 1.65
3295 : parrello 1.93 Returns the highest number in the list.
3296 : parrello 1.65
3297 :     =back
3298 :    
3299 :     =cut
3300 :    
3301 : parrello 1.93 sub Max {
3302 :     # Get the parameters. Note that we prime the return value with the first parameter.
3303 :     my ($retVal, @values) = @_;
3304 :     # Loop through the remaining parameters, looking for the highest.
3305 :     for my $value (@values) {
3306 :     if ($value > $retVal) {
3307 :     $retVal = $value;
3308 : parrello 1.65 }
3309 :     }
3310 : parrello 1.93 # Return the maximum found.
3311 :     return $retVal;
3312 : parrello 1.65 }
3313 :    
3314 : parrello 1.93 =head3 Strip
3315 : parrello 1.37
3316 : parrello 1.93 my $string = Tracer::Strip($line);
3317 : parrello 1.37
3318 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3319 :     that may have been transferred back and forth several times among different
3320 :     operating environments.
3321 : parrello 1.37
3322 :     =over 4
3323 :    
3324 : parrello 1.93 =item line
3325 : parrello 1.37
3326 : parrello 1.93 Line of text to be stripped.
3327 : parrello 1.37
3328 : parrello 1.93 =item RETURN
3329 : parrello 1.91
3330 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3331 : parrello 1.91
3332 : parrello 1.37 =back
3333 :    
3334 :     =cut
3335 :    
3336 : parrello 1.93 sub Strip {
3337 :     # Get a copy of the parameter string.
3338 :     my ($string) = @_;
3339 :     my $retVal = (defined $string ? $string : "");
3340 :     # Strip the line terminator characters.
3341 :     $retVal =~ s/(\r|\n)+$//g;
3342 :     # Return the result.
3343 :     return $retVal;
3344 : parrello 1.43 }
3345 :    
3346 : parrello 1.115 =head3 Trim
3347 :    
3348 :     my $string = Tracer::Trim($line);
3349 :    
3350 :     Trim all spaces from the beginning and ending of a string.
3351 :    
3352 :     =over 4
3353 :    
3354 :     =item line
3355 :    
3356 :     Line of text to be trimmed.
3357 :    
3358 :     =item RETURN
3359 :    
3360 :     The same line of text with all whitespace chopped off either end.
3361 :    
3362 :     =back
3363 :    
3364 :     =cut
3365 :    
3366 :     sub Trim {
3367 :     # Get a copy of the parameter string.
3368 :     my ($string) = @_;
3369 :     my $retVal = (defined $string ? $string : "");
3370 :     # Strip the front spaces.
3371 :     $retVal =~ s/^\s+//;
3372 :     # Strip the back spaces.
3373 :     $retVal =~ s/\s+$//;
3374 :     # Return the result.
3375 :     return $retVal;
3376 :     }
3377 :    
3378 : parrello 1.93 =head3 Pad
3379 : parrello 1.43
3380 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3381 : parrello 1.43
3382 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3383 :     space, and the padding will be on the right side unless specified
3384 :     in the third parameter.
3385 : parrello 1.43
3386 :     =over 4
3387 :    
3388 : parrello 1.93 =item string
3389 :    
3390 :     String to be padded.
3391 :    
3392 :     =item len
3393 :    
3394 :     Desired length of the padded string.
3395 :    
3396 :     =item left (optional)
3397 :    
3398 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3399 :    
3400 :     =item padChar (optional)
3401 :    
3402 :     Character to use for padding. The default is a space.
3403 :    
3404 :     =item RETURN
3405 : parrello 1.43
3406 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3407 :     specified end so that it achieves the desired length.
3408 : parrello 1.43
3409 :     =back
3410 :    
3411 :     =cut
3412 :    
3413 : parrello 1.93 sub Pad {
3414 :     # Get the parameters.
3415 :     my ($string, $len, $left, $padChar) = @_;
3416 :     # Compute the padding character.
3417 :     if (! defined $padChar) {
3418 :     $padChar = " ";
3419 :     }
3420 :     # Compute the number of spaces needed.
3421 :     my $needed = $len - length $string;
3422 :     # Copy the string into the return variable.
3423 :     my $retVal = $string;
3424 :     # Only proceed if padding is needed.
3425 :     if ($needed > 0) {
3426 :     # Create the pad string.
3427 :     my $pad = $padChar x $needed;
3428 :     # Affix it to the return value.
3429 :     if ($left) {
3430 :     $retVal = $pad . $retVal;
3431 :     } else {
3432 :     $retVal .= $pad;
3433 : parrello 1.43 }
3434 : parrello 1.37 }
3435 : parrello 1.93 # Return the result.
3436 :     return $retVal;
3437 : parrello 1.37 }
3438 :    
3439 : parrello 1.93 =head3 EOF
3440 :    
3441 :     This is a constant that is lexically greater than any useful string.
3442 :    
3443 :     =cut
3444 :    
3445 :     sub EOF {
3446 :     return "\xFF\xFF\xFF\xFF\xFF";
3447 :     }
3448 : parrello 1.59
3449 : parrello 1.93 =head3 TICK
3450 : parrello 1.59
3451 : parrello 1.93 my @results = TICK($commandString);
3452 : parrello 1.59
3453 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3454 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3455 : parrello 1.59
3456 : parrello 1.93 `./protein.cgi`
3457 : parrello 1.59
3458 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3459 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3460 : parrello 1.59
3461 : parrello 1.93 TICK("./protein.cgi")
3462 : parrello 1.59
3463 : parrello 1.93 it will work correctly in both environments.
3464 : parrello 1.59
3465 : parrello 1.93 =over 4
3466 : parrello 1.59
3467 : parrello 1.93 =item commandString
3468 : parrello 1.59
3469 : parrello 1.93 The command string to pass to the system.
3470 : parrello 1.59
3471 :     =item RETURN
3472 :    
3473 : parrello 1.93 Returns the standard output from the specified command, as a list.
3474 : parrello 1.59
3475 :     =back
3476 :    
3477 :     =cut
3478 : parrello 1.93 #: Return Type @;
3479 :     sub TICK {
3480 : parrello 1.59 # Get the parameters.
3481 : parrello 1.93 my ($commandString) = @_;
3482 :     # Chop off the dot-slash if this is Windows.
3483 :     if ($FIG_Config::win_mode) {
3484 :     $commandString =~ s!^\./!!;
3485 : parrello 1.59 }
3486 : parrello 1.93 # Activate the command and return the result.
3487 :     return `$commandString`;
3488 : parrello 1.59 }
3489 :    
3490 : parrello 1.93
3491 : parrello 1.55 =head3 CommaFormat
3492 :    
3493 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3494 : parrello 1.55
3495 :     Insert commas into a number.
3496 :    
3497 :     =over 4
3498 :    
3499 :     =item number
3500 :    
3501 :     A sequence of digits.
3502 :    
3503 :     =item RETURN
3504 :    
3505 :     Returns the same digits with commas strategically inserted.
3506 :    
3507 :     =back
3508 :    
3509 :     =cut
3510 :    
3511 :     sub CommaFormat {
3512 :     # Get the parameters.
3513 :     my ($number) = @_;
3514 :     # Pad the length up to a multiple of three.
3515 :     my $padded = "$number";
3516 :     $padded = " " . $padded while length($padded) % 3 != 0;
3517 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3518 :     # cause the delimiters to be included in the output stream. The
3519 :     # GREP removes the empty strings in between the delimiters.
3520 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3521 :     # Clean out the spaces.
3522 :     $retVal =~ s/ //g;
3523 :     # Return the result.
3524 :     return $retVal;
3525 :     }
3526 : parrello 1.46
3527 :    
3528 : parrello 1.62 =head3 CompareLists
3529 :    
3530 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3531 : parrello 1.62
3532 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3533 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3534 :     The return value contains a list of items that are only in the new list
3535 :     (inserted) and only in the old list (deleted).
3536 :    
3537 :     =over 4
3538 :    
3539 :     =item newList
3540 :    
3541 :     Reference to a list of new tuples.
3542 :    
3543 :     =item oldList
3544 :    
3545 :     Reference to a list of old tuples.
3546 :    
3547 :     =item keyIndex (optional)
3548 :    
3549 :     Index into each tuple of its key field. The default is 0.
3550 :    
3551 :     =item RETURN
3552 :    
3553 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3554 :     list (inserted) followed by a reference to the list of items that are only in the old
3555 :     list (deleted).
3556 :    
3557 :     =back
3558 :    
3559 :     =cut
3560 :    
3561 :     sub CompareLists {
3562 :     # Get the parameters.
3563 :     my ($newList, $oldList, $keyIndex) = @_;
3564 :     if (! defined $keyIndex) {
3565 :     $keyIndex = 0;
3566 :     }
3567 :     # Declare the return variables.
3568 :     my ($inserted, $deleted) = ([], []);
3569 :     # Loop through the two lists simultaneously.
3570 :     my ($newI, $oldI) = (0, 0);
3571 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3572 :     while ($newI < $newN || $oldI < $oldN) {
3573 :     # Get the current object in each list. Note that if one
3574 :     # of the lists is past the end, we'll get undef.
3575 :     my $newItem = $newList->[$newI];
3576 :     my $oldItem = $oldList->[$oldI];
3577 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3578 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3579 :     push @{$deleted}, $oldItem;
3580 :     $oldI++;
3581 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3582 :     # The new item is not in the old list, so mark it inserted.
3583 :     push @{$inserted}, $newItem;
3584 :     $newI++;
3585 :     } else {
3586 :     # The item is in both lists, so push forward.
3587 :     $oldI++;
3588 :     $newI++;
3589 :     }
3590 :     }
3591 :     # Return the result.
3592 :     return ($inserted, $deleted);
3593 :     }
3594 :    
3595 : parrello 1.105 =head3 Cmp
3596 :    
3597 :     my $cmp = Tracer::Cmp($a, $b);
3598 :    
3599 :     This method performs a universal sort comparison. Each value coming in is
3600 :     separated into a leading text part and a trailing number part. The text
3601 :     part is string compared, and if both parts are equal, then the number
3602 :     parts are compared numerically. A stream of just numbers or a stream of
3603 :     just strings will sort correctly, and a mixed stream will sort with the
3604 :     numbers first. Strings with a label and a number will sort in the
3605 :     expected manner instead of lexically.
3606 :    
3607 :     =over 4
3608 :    
3609 :     =item a
3610 :    
3611 :     First item to compare.
3612 :    
3613 :     =item b
3614 :    
3615 :     Second item to compare.
3616 :    
3617 :     =item RETURN
3618 :    
3619 :     Returns a negative number if the first item should sort first (is less), a positive
3620 :     number if the first item should sort second (is greater), and a zero if the items are
3621 :     equal.
3622 :    
3623 :     =back
3624 :    
3625 :     =cut
3626 :    
3627 :     sub Cmp {
3628 :     # Get the parameters.
3629 :     my ($a, $b) = @_;
3630 :     # Declare the return value.
3631 :     my $retVal;
3632 :     # Check for nulls.
3633 :     if (! defined($a)) {
3634 :     $retVal = (! defined($b) ? 0 : -1);
3635 :     } elsif (! defined($b)) {
3636 :     $retVal = 1;
3637 :     } else {
3638 :     # Here we have two real values. Parse the two strings.
3639 : parrello 1.115 my $aParsed = _Parse($a);
3640 :     my $bParsed = _Parse($b);
3641 :     # Compare the string parts insensitively.
3642 :     $retVal = (lc $aParsed->[0] cmp lc $bParsed->[0]);
3643 :     # If they're equal, compare them sensitively.
3644 :     if (! $retVal) {
3645 :     $retVal = ($aParsed->[0] cmp $bParsed->[0]);
3646 :     }
3647 :     # If they're STILL equal, compare the number parts.
3648 : parrello 1.105 if (! $retVal) {
3649 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3650 :     }
3651 :     }
3652 :     # Return the result.
3653 :     return $retVal;
3654 :     }
3655 :    
3656 : parrello 1.115 # This method parses an input string into a string part and a number part.
3657 :     sub _Parse {
3658 :     my ($string) = @_;
3659 :     my ($alpha, $num);
3660 :     if ($string =~ /^(.*?)(\d+(?:\.\d+)?)$/) {
3661 :     $alpha = $1;
3662 :     $num = $2;
3663 :     } else {
3664 :     $alpha = $string;
3665 :     $num = 0;
3666 :     }
3667 :     return [$alpha, $num];
3668 :     }
3669 :    
3670 : parrello 1.108 =head3 ListEQ
3671 :    
3672 :     my $flag = Tracer::ListEQ(\@a, \@b);
3673 :    
3674 :     Return TRUE if the specified lists contain the same strings in the same
3675 :     order, else FALSE.
3676 :    
3677 :     =over 4
3678 :    
3679 :     =item a
3680 :    
3681 :     Reference to the first list.
3682 :    
3683 :     =item b
3684 :    
3685 :     Reference to the second list.
3686 :    
3687 :     =item RETURN
3688 :    
3689 :     Returns TRUE if the two parameters are identical string lists, else FALSE.
3690 :    
3691 :     =back
3692 :    
3693 :     =cut
3694 :    
3695 :     sub ListEQ {
3696 :     # Get the parameters.
3697 :     my ($a, $b) = @_;
3698 :     # Declare the return variable. Start by checking the lengths.
3699 :     my $n = scalar(@$a);
3700 :     my $retVal = ($n == scalar(@$b));
3701 :     # Now compare the list elements.
3702 :     for (my $i = 0; $retVal && $i < $n; $i++) {
3703 :     $retVal = ($a->[$i] eq $b->[$i]);
3704 :     }
3705 :     # Return the result.
3706 :     return $retVal;
3707 :     }
3708 :    
3709 : parrello 1.105 =head2 CGI Script Utilities
3710 :    
3711 :     =head3 ScriptSetup (deprecated)
3712 :    
3713 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
3714 :    
3715 :     Perform standard tracing and debugging setup for scripts. The value returned is
3716 :     the CGI object followed by a pre-built variable hash. At the end of the script,
3717 :     the client should call L</ScriptFinish> to output the web page.
3718 :    
3719 :     This method calls L</ETracing> to configure tracing, which allows the tracing
3720 :     to be configured via the emergency tracing form on the debugging control panel.
3721 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
3722 :     method, which includes every program that uses this method or L</StandardSetup>.
3723 :    
3724 :     =over 4
3725 :    
3726 :     =item noTrace (optional)
3727 :    
3728 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
3729 :     tracing manually.
3730 :    
3731 :     =item RETURN
3732 :    
3733 :     Returns a two-element list consisting of a CGI query object and a variable hash for
3734 :     the output page.
3735 :    
3736 :     =back
3737 :    
3738 :     =cut
3739 :    
3740 :     sub ScriptSetup {
3741 :     # Get the parameters.
3742 :     my ($noTrace) = @_;
3743 :     # Get the CGI query object.
3744 :     my $cgi = CGI->new();
3745 :     # Set up tracing if it's not suppressed.
3746 :     ETracing($cgi) unless $noTrace;
3747 :     # Create the variable hash.
3748 :     my $varHash = { results => '' };
3749 :     # Return the query object and variable hash.
3750 :     return ($cgi, $varHash);
3751 :     }
3752 :    
3753 :     =head3 ScriptFinish (deprecated)
3754 :    
3755 :     ScriptFinish($webData, $varHash);
3756 :    
3757 :     Output a web page at the end of a script. Either the string to be output or the
3758 :     name of a template file can be specified. If the second parameter is omitted,
3759 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
3760 :     name of a template file. The template should have the variable C<DebugData>
3761 :     specified in any form that invokes a standard script. If debugging mode is turned
3762 :     on, a form field will be put in that allows the user to enter tracing data.
3763 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
3764 :     the output, formatted as a list.
3765 :    
3766 :     A typical standard script would loook like the following.
3767 :    
3768 :     BEGIN {
3769 :     # Print the HTML header.
3770 :     print "CONTENT-TYPE: text/html\n\n";
3771 :     }
3772 :     use Tracer;
3773 :     use CGI;
3774 :     use FIG;
3775 :     # ... more uses ...
3776 :    
3777 :     my ($cgi, $varHash) = ScriptSetup();
3778 :     eval {
3779 :     # ... get data from $cgi, put it in $varHash ...
3780 :     };
3781 :     if ($@) {
3782 :     Trace("Script Error: $@") if T(0);
3783 :     }
3784 :     ScriptFinish("Html/MyTemplate.html", $varHash);
3785 :    
3786 :     The idea here is that even if the script fails, you'll see trace messages and
3787 :     useful output.
3788 :    
3789 :     =over 4
3790 :    
3791 :     =item webData
3792 :    
3793 :     A string containing either the full web page to be written to the output or the
3794 :     name of a template file from which the page is to be constructed. If the name
3795 :     of a template file is specified, then the second parameter must be present;
3796 :     otherwise, it must be absent.
3797 :    
3798 :     =item varHash (optional)
3799 :    
3800 :     If specified, then a reference to a hash mapping variable names for a template
3801 :     to their values. The template file will be read into memory, and variable markers
3802 :     will be replaced by data in this hash reference.
3803 :    
3804 :     =back
3805 :    
3806 :     =cut
3807 :    
3808 :     sub ScriptFinish {
3809 :     # Get the parameters.
3810 :     my ($webData, $varHash) = @_;
3811 :     # Check for a template file situation.
3812 :     my $outputString;
3813 :     if (defined $varHash) {
3814 :     # Here we have a template file. We need to determine the template type.
3815 :     my $template;
3816 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3817 :     $template = "$FIG_Config::template_url/$webData";
3818 :     } else {
3819 :     $template = "<<$webData";
3820 :     }
3821 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
3822 :     } else {
3823 :     # Here the user gave us a raw string.
3824 :     $outputString = $webData;
3825 :     }
3826 :     # Check for trace messages.
3827 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
3828 :     # We have trace messages, so we want to put them at the end of the body. This
3829 :     # is either at the end of the whole string or at the beginning of the BODY
3830 :     # end-tag.
3831 :     my $pos = length $outputString;
3832 :     if ($outputString =~ m#</body>#gi) {
3833 :     $pos = (pos $outputString) - 7;
3834 :     }
3835 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
3836 :     # destination.
3837 :     my $traceHtml;
3838 :     if ($Destination eq "QUEUE") {
3839 :     $traceHtml = QTrace('Html');
3840 :     } elsif ($Destination =~ /^>>(.+)$/) {
3841 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
3842 :     # can copy the file name into the clipboard easily.
3843 :     my $actualDest = $1;
3844 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3845 :     } else {
3846 :     # Here we have one of the special destinations.
3847 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3848 :     }
3849 :     substr $outputString, $pos, 0, $traceHtml;
3850 :     }
3851 :     # Write the output string.
3852 :     print $outputString;
3853 :     }
3854 :    
3855 : parrello 1.65 =head3 GenerateURL
3856 :    
3857 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3858 : parrello 1.65
3859 :     Generate a GET-style URL for the specified page with the specified parameter
3860 :     names and values. The values will be URL-escaped automatically. So, for
3861 :     example
3862 :    
3863 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3864 :    
3865 :     would return
3866 :    
3867 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3868 : parrello 1.65
3869 :     =over 4
3870 :    
3871 :     =item page
3872 :    
3873 :     Page URL.
3874 :    
3875 :     =item parameters
3876 :    
3877 :     Hash mapping parameter names to parameter values.
3878 :    
3879 :     =item RETURN
3880 :    
3881 :     Returns a GET-style URL that goes to the specified page and passes in the
3882 :     specified parameters and values.
3883 :    
3884 :     =back
3885 :    
3886 :     =cut
3887 :    
3888 :     sub GenerateURL {
3889 :     # Get the parameters.
3890 :     my ($page, %parameters) = @_;
3891 :     # Prime the return variable with the page URL.
3892 :     my $retVal = $page;
3893 :     # Loop through the parameters, creating parameter elements in a list.
3894 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3895 :     # If the list is nonempty, tack it on.
3896 :     if (@parmList) {
3897 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3898 : parrello 1.65 }
3899 :     # Return the result.
3900 :     return $retVal;
3901 :     }
3902 :    
3903 : parrello 1.78 =head3 ApplyURL
3904 :    
3905 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3906 : parrello 1.78
3907 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3908 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3909 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3910 :    
3911 :     This provides a simple way to process the results of a database query into something
3912 :     displayable by combining a URL with text.
3913 :    
3914 :     =over 4
3915 :    
3916 :     =item table
3917 :    
3918 :     Reference to a list of lists. The elements in the containing list will be updated by
3919 :     this method.
3920 :    
3921 :     =item target
3922 :    
3923 :     The index of the column to be converted into HTML.
3924 :    
3925 :     =item url
3926 :    
3927 :     The index of the column containing the URL. Note that the URL must have a recognizable
3928 :     C<http:> at the beginning.
3929 :    
3930 :     =back
3931 :    
3932 :     =cut
3933 :    
3934 :     sub ApplyURL {
3935 :     # Get the parameters.
3936 :     my ($table, $target, $url) = @_;
3937 :     # Loop through the table.
3938 :     for my $row (@{$table}) {
3939 :     # Apply the URL to the target cell.
3940 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3941 :     # Delete the URL from the row.
3942 :     delete $row->[$url];
3943 :     }
3944 :     }
3945 :    
3946 :     =head3 CombineURL
3947 :    
3948 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3949 : parrello 1.78
3950 :     This method will convert the specified text into HTML hyperlinked to the specified
3951 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3952 :     is defined and begins with an C<http:> header.
3953 :    
3954 :     =over 4
3955 :    
3956 :     =item text
3957 :    
3958 :     Text to return. This will be HTML-escaped automatically.
3959 :    
3960 :     =item url
3961 :    
3962 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3963 :     will be returned without any hyperlinking.
3964 :    
3965 :     =item RETURN
3966 :    
3967 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3968 :     doesn't look right, the HTML-escaped text will be returned without any further
3969 :     modification.
3970 :    
3971 :     =back
3972 :    
3973 :     =cut
3974 :    
3975 :     sub CombineURL {
3976 :     # Get the parameters.
3977 :     my ($text, $url) = @_;
3978 :     # Declare the return variable.
3979 :     my $retVal = CGI::escapeHTML($text);
3980 :     # Verify the URL.
3981 :     if (defined($url) && $url =~ m!http://!i) {
3982 :     # It's good, so we apply it to the text.
3983 :     $retVal = "<a href=\"$url\">$retVal</a>";
3984 :     }
3985 :     # Return the result.
3986 :     return $retVal;
3987 :     }
3988 :    
3989 : parrello 1.97 =head3 TrackingCode
3990 :    
3991 :     my $html = Tracer::TrackingCode();
3992 :    
3993 :     Returns the HTML code for doing web page traffic monitoring. If the
3994 :     current environment is a test system, then it returns a null string;
3995 :     otherwise, it returns a bunch of javascript containing code for turning
3996 :     on SiteMeter and Google Analytics.
3997 :    
3998 :     =cut
3999 :    
4000 :     sub TrackingCode {
4001 :     # Declare the return variable.
4002 :     my $retVal = "<!-- tracking off -->";
4003 :     # Determine if we're in production.
4004 :     if ($FIG_Config::site_meter) {
4005 :     $retVal = <<END_HTML
4006 :     <!-- Site Meter -->
4007 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
4008 :     </script>
4009 :     <noscript>
4010 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
4011 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
4012 :     </noscript>
4013 :     <!-- Copyright (c)2006 Site Meter -->
4014 :     END_HTML
4015 :     }
4016 :     return $retVal;
4017 :     }
4018 :    
4019 : parrello 1.105 =head3 Clean
4020 :    
4021 :     my $cleaned = Tracer::Clean($string);
4022 :    
4023 :     Clean up a string for HTML display. This not only converts special
4024 :     characters to HTML entity names, it also removes control characters.
4025 :    
4026 :     =over 4
4027 :    
4028 :     =item string
4029 :    
4030 :     String to convert.
4031 :    
4032 :     =item RETURN
4033 :    
4034 :     Returns the input string with anything that might disrupt an HTML literal removed. An
4035 :     undefined value will be converted to an empty string.
4036 :    
4037 :     =back
4038 :    
4039 :     =cut
4040 :    
4041 :     sub Clean {
4042 :     # Get the parameters.
4043 :     my ($string) = @_;
4044 :     # Declare the return variable.
4045 :     my $retVal = "";
4046 :     # Only proceed if the value exists.
4047 :     if (defined $string) {
4048 :     # Get the string.
4049 :     $retVal = $string;
4050 :     # Clean the control characters.
4051 :     $retVal =~ tr/\x00-\x1F/?/;
4052 :     # Escape the rest.
4053 :     $retVal = CGI::escapeHTML($retVal);
4054 :     }
4055 :     # Return the result.
4056 :     return $retVal;
4057 :     }
4058 :    
4059 : parrello 1.115 =head3 SortByValue
4060 :    
4061 :     my @keys = Tracer::SortByValue(\%hash);
4062 :    
4063 :     Get a list of hash table keys sorted by hash table values.
4064 :    
4065 :     =over 4
4066 :    
4067 :     =item hash
4068 :    
4069 :     Hash reference whose keys are to be extracted.
4070 :    
4071 :     =item RETURN
4072 :    
4073 :     Returns a list of the hash keys, ordered so that the corresponding hash values
4074 :     are in alphabetical sequence.
4075 :    
4076 :     =back
4077 :    
4078 :     =cut
4079 :    
4080 :     sub SortByValue {
4081 :     # Get the parameters.
4082 :     my ($hash) = @_;
4083 :     # Sort the hash's keys using the values.
4084 :     my @retVal = sort { Cmp($hash->{$a}, $hash->{$b}) } keys %$hash;
4085 :     # Return the result.
4086 :     return @retVal;
4087 :     }
4088 :    
4089 :     =head3 GetSet
4090 :    
4091 :     my $value = Tracer::GetSet($object, $name => $newValue);
4092 : parrello 1.105
4093 : parrello 1.115 Get or set the value of an object field. The object is treated as an
4094 :     ordinary hash reference. If a new value is specified, it is stored in the
4095 :     hash under the specified name and then returned. If no new value is
4096 :     specified, the current value is returned.
4097 : parrello 1.105
4098 : parrello 1.115 =over 4
4099 :    
4100 :     =item object
4101 :    
4102 :     Reference to the hash that is to be interrogated or updated.
4103 :    
4104 :     =item name
4105 :    
4106 :     Name of the field. This is the hash key.
4107 :    
4108 :     =item newValue (optional)
4109 :    
4110 :     New value to be stored in the field. If no new value is specified, the current
4111 :     value of the field is returned.
4112 :    
4113 :     =item RETURN
4114 :    
4115 :     Returns the value of the named field in the specified hash.
4116 :    
4117 :     =back
4118 :    
4119 :     =cut