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1 : gdpusch 1.95 # -*- perl -*-
2 :     ########################################################################
3 : olson 1.30 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 : parrello 1.61 #
8 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 : parrello 1.61 # Public License.
11 : olson 1.30 #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.95 ########################################################################
18 : olson 1.30
19 : olson 1.1 package Tracer;
20 :    
21 : parrello 1.12 require Exporter;
22 :     @ISA = ('Exporter');
23 : parrello 1.99 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24 : parrello 1.97 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25 : parrello 1.12 use strict;
26 : gdpusch 1.96 use Carp qw(longmess croak carp);
27 : parrello 1.12 use CGI;
28 : parrello 1.47 use Cwd;
29 : parrello 1.12 use FIG_Config;
30 : parrello 1.9 use PageBuilder;
31 : parrello 1.21 use Digest::MD5;
32 : parrello 1.36 use File::Basename;
33 : parrello 1.37 use File::Path;
34 : parrello 1.48 use File::stat;
35 : parrello 1.59 use LWP::UserAgent;
36 : parrello 1.64 use Time::HiRes 'gettimeofday';
37 : parrello 1.65 use URI::Escape;
38 : parrello 1.74 use Time::Local;
39 : parrello 1.99 use POSIX qw(strftime);
40 :     use Time::Zone;
41 : parrello 1.106 use Fcntl ':flock';
42 : parrello 1.99
43 : olson 1.1
44 :     =head1 Tracing and Debugging Helpers
45 :    
46 : parrello 1.72 =head2 Tracing
47 : olson 1.1
48 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
49 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
50 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
51 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
52 :     level is less than or equal to the setup trace level and whose category is activated will
53 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
54 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
55 :     appear.
56 : olson 1.1
57 : parrello 1.72 =head3 Putting Trace Messages in Your Code
58 :    
59 :     To generate a trace message, use the following syntax.
60 :    
61 :     Trace($message) if T(errors => 4);
62 : olson 1.1
63 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
64 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
65 : olson 1.1
66 : parrello 1.72 Trace($message) if T(main => 4);
67 : olson 1.1
68 :     will trace if the trace level is 4 or more.
69 :    
70 :     If the category name is the same as the package name, all you need is the number. So, if the
71 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
72 :     active and the trace level is 2 or more.
73 :    
74 : parrello 1.72 Trace($message) if T(2);
75 :    
76 :     In scripts, where no package name is available, the category defaults to C<main>.
77 :    
78 :     =head3 Custom Tracing
79 :    
80 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
81 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
82 :     L</Emergency Tracing> easier to understand.
83 : olson 1.1
84 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
85 :     a list of category names, and a destination. The trace level and list of category names are
86 : olson 1.1 specified as a space-delimited string. Thus
87 :    
88 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
89 : olson 1.1
90 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
91 : parrello 1.72 specifies that messages should be sent to the standard output.
92 : parrello 1.12
93 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
94 :     level 3 and writes the output to the standard error output. This sort of thing might be
95 :     useful in a CGI environment.
96 :    
97 : parrello 1.72 TSetup('3 *', 'WARN');
98 : olson 1.1
99 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
100 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
101 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
102 :     the page output, they can be gathered together and displayed at the end of the page. This makes
103 :     it easier to debug page formatting problems.
104 :    
105 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
106 :     a file at the same time. To trace to a file, specify the filename with an output character in front
107 :     of it.
108 :    
109 :     TSetup('4 SQL', ">$fileName");
110 :    
111 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
112 :     bracket.
113 :    
114 :     TSetup('3 *', "+>$fileName");
115 : parrello 1.4
116 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
117 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
118 :     Thus, debugging information is available and easily retrieved even when the application is
119 :     being used out in the field.
120 :    
121 : parrello 1.72 =head3 Trace Levels
122 :    
123 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
124 :     a suggestion.
125 :    
126 :     =over 4
127 :    
128 : parrello 1.32 =item Error 0
129 : parrello 1.10
130 :     Message indicates an error that may lead to incorrect results or that has stopped the
131 :     application entirely.
132 :    
133 : parrello 1.32 =item Warning 1
134 : parrello 1.10
135 :     Message indicates something that is unexpected but that probably did not interfere
136 :     with program execution.
137 :    
138 : parrello 1.32 =item Notice 2
139 : parrello 1.10
140 :     Message indicates the beginning or end of a major task.
141 :    
142 : parrello 1.32 =item Information 3
143 : parrello 1.10
144 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
145 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
146 :    
147 : parrello 1.32 =item Detail 4
148 : parrello 1.10
149 :     Message indicates a low-level loop iteration.
150 :    
151 :     =back
152 :    
153 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
154 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
155 :     The time stamp is between square brackets and the category name between angle brackets.
156 :     After the category name there is a colon (C<:>) followed by the message text.
157 :     If the square brackets or angle brackets are missing, then the trace management
158 :     utilities assume that they are encountering a set of pre-formatted lines.
159 :    
160 :     Note, however, that this formatting is done automatically by the tracing functions. You
161 :     only need to know about it if you want to parse a trace file.
162 :    
163 :     =head3 Emergency Tracing
164 :    
165 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
166 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
167 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
168 :     that you specify a tracing key. For command-line tools, the key is
169 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
170 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
171 :     the tracing in your environment without stepping on other users.
172 :    
173 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
174 :     generate one for you.
175 :    
176 :     You can activate and de-activate emergency tracing from the debugging control panel, as
177 :     well as display the trace file itself.
178 :    
179 :     To enable emergency tracing in your code, call
180 :    
181 :     ETracing($cgi)
182 :    
183 :     from a web script and
184 :    
185 :     ETracing()
186 :    
187 :     from a command-line script.
188 :    
189 :     The web script will look for the tracing key in the cookies, and the command-line
190 :     script will look for it in the C<TRACING> environment variable. If you are
191 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
192 : parrello 1.72 will be configured automatically.
193 :    
194 : olson 1.1 =cut
195 : parrello 1.2
196 : olson 1.1 # Declare the configuration variables.
197 :    
198 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
199 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
200 :     # standard output
201 : parrello 1.3 my %Categories = ( main => 1 );
202 : parrello 1.12 # hash of active category names
203 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
204 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
205 :     # messages
206 :     my @Queue = (); # queued list of trace messages.
207 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
208 : parrello 1.97 my $LastLevel = 0; # level of the last test call
209 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
210 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
211 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
212 : parrello 1.104 my $CommandLine; # Command line passed to StandardSetup
213 : parrello 1.99 umask 2; # Fix the damn umask so everything is group-writable.
214 : olson 1.1
215 : parrello 1.93 =head2 Tracing Methods
216 :    
217 :     =head3 Setups
218 :    
219 :     my $count = Tracer::Setups();
220 :    
221 :     Return the number of times L</TSetup> has been called.
222 :    
223 :     This method allows for the creation of conditional tracing setups where, for example, we
224 :     may want to set up tracing if nobody else has done it before us.
225 :    
226 :     =cut
227 :    
228 :     sub Setups {
229 :     return $SetupCount;
230 :     }
231 : olson 1.1
232 :     =head3 TSetup
233 :    
234 : parrello 1.92 TSetup($categoryList, $target);
235 : olson 1.1
236 :     This method is used to specify the trace options. The options are stored as package data
237 :     and interrogated by the L</Trace> and L</T> methods.
238 :    
239 :     =over 4
240 :    
241 :     =item categoryList
242 :    
243 :     A string specifying the trace level and the categories to be traced, separated by spaces.
244 :     The trace level must come first.
245 :    
246 :     =item target
247 :    
248 :     The destination for the trace output. To send the trace output to a file, specify the file
249 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
250 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
251 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
252 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
253 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
254 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
255 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
256 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
257 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
258 : parrello 1.6 cause tracing to be suppressed.
259 : olson 1.1
260 :     =back
261 :    
262 :     =cut
263 :    
264 :     sub TSetup {
265 : parrello 1.12 # Get the parameters.
266 :     my ($categoryList, $target) = @_;
267 :     # Parse the category list.
268 :     my @categoryData = split /\s+/, $categoryList;
269 :     # Extract the trace level.
270 :     $TraceLevel = shift @categoryData;
271 :     # Presume category-based tracing until we learn otherwise.
272 :     $AllTrace = 0;
273 :     # Build the category hash. Note that if we find a "*", we turn on non-category
274 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
275 : parrello 1.34 %Categories = ( main => 1 );
276 : parrello 1.12 for my $category (@categoryData) {
277 :     if ($category eq '*') {
278 :     $AllTrace = 1;
279 :     } else {
280 : parrello 1.13 $Categories{lc $category} = 1;
281 : parrello 1.12 }
282 :     }
283 :     # Now we need to process the destination information. The most important special
284 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
285 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
286 :     # the standard output (tee mode).
287 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
288 :     if ($target =~ m/^\+/) {
289 :     $TeeFlag = 1;
290 :     $target = substr($target, 1);
291 :     }
292 :     if ($target =~ m/^>[^>]/) {
293 : parrello 1.98 # We need to initialize the file (which clears it).
294 : parrello 1.12 open TRACEFILE, $target;
295 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
296 : parrello 1.12 close TRACEFILE;
297 : parrello 1.98 # Set to append mode now that the file has been cleared.
298 : parrello 1.12 $Destination = ">$target";
299 :     } else {
300 :     $Destination = $target;
301 :     }
302 :     } else {
303 :     $Destination = uc($target);
304 :     }
305 :     # Increment the setup counter.
306 :     $SetupCount++;
307 : parrello 1.11 }
308 :    
309 : parrello 1.93 =head3 SetLevel
310 : parrello 1.31
311 : parrello 1.93 Tracer::SetLevel($newLevel);
312 : parrello 1.31
313 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
314 : parrello 1.31
315 : parrello 1.93 =over 4
316 : parrello 1.31
317 : parrello 1.93 =item newLevel
318 : parrello 1.31
319 : parrello 1.93 Proposed new trace level.
320 : parrello 1.31
321 : parrello 1.93 =back
322 : parrello 1.31
323 : parrello 1.93 =cut
324 : parrello 1.31
325 : parrello 1.93 sub SetLevel {
326 :     $TraceLevel = $_[0];
327 :     }
328 : parrello 1.31
329 : parrello 1.97 =head3 ParseDate
330 :    
331 :     my $time = Tracer::ParseDate($dateString);
332 :    
333 :     Convert a date into a PERL time number. This method expects a date-like string
334 :     and parses it into a number. The string must be vaguely date-like or it will
335 :     return an undefined value. Our requirement is that a month and day be
336 :     present and that three pieces of the date string (time of day, month and day,
337 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
338 :    
339 :     If a time of day is present, it must be in military time with two digits for
340 :     everything but the hour.
341 : parrello 1.31
342 : parrello 1.97 The year must be exactly four digits.
343 : parrello 1.31
344 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
345 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
346 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
347 :    
348 :     It should be guaranteed that this method will parse the output of the L</Now> function.
349 :    
350 :     The parameters are as follows.
351 : parrello 1.31
352 : parrello 1.93 =over 4
353 : parrello 1.31
354 : parrello 1.93 =item dateString
355 : parrello 1.31
356 : parrello 1.97 The date string to convert.
357 : parrello 1.31
358 : parrello 1.93 =item RETURN
359 : parrello 1.31
360 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
361 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
362 : parrello 1.31
363 : parrello 1.93 =back
364 : parrello 1.38
365 : parrello 1.93 =cut
366 : parrello 1.38
367 : parrello 1.97 # Universal month conversion table.
368 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
369 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
370 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
371 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
372 :     May => 4, May => 4, '05' => 4, '5' => 4,
373 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
374 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
375 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
376 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
377 :     Oct => 9, October => 9, '10' => 9,
378 :     Nov => 10, November => 10, '11' => 10,
379 :     Dec => 11, December => 11, '12' => 11
380 :     };
381 :    
382 :     sub ParseDate {
383 : parrello 1.93 # Get the parameters.
384 :     my ($dateString) = @_;
385 :     # Declare the return variable.
386 :     my $retVal;
387 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
388 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
389 :     # won't be fooled into thinking the month is Sunday.
390 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
391 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
392 :     # Insist that the month and day are valid.
393 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
394 :     # Find the time.
395 :     my ($hour, $min, $sec) = (0, 0, 0);
396 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
397 :     ($hour, $min, $sec) = ($1, $2, $3);
398 :     }
399 :     # Find the year.
400 :     my $year;
401 :     if ($dateString =~ /\b(\d{4})\b/) {
402 :     $year = $1;
403 :     } else {
404 :     # Get the default year, which is this one. Note we must convert it to
405 :     # the four-digit value expected by "timelocal".
406 :     (undef, undef, undef, undef, undef, $year) = localtime();
407 :     $year += 1900;
408 :     }
409 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
410 :     }
411 : parrello 1.93 }
412 :     # Return the result.
413 :     return $retVal;
414 :     }
415 : parrello 1.31
416 : parrello 1.93 =head3 LogErrors
417 : parrello 1.42
418 : parrello 1.93 Tracer::LogErrors($fileName);
419 : parrello 1.31
420 : parrello 1.93 Route the standard error output to a log file.
421 : parrello 1.31
422 : parrello 1.93 =over 4
423 : parrello 1.31
424 : parrello 1.93 =item fileName
425 : parrello 1.31
426 : parrello 1.93 Name of the file to receive the error output.
427 : parrello 1.31
428 : parrello 1.93 =back
429 : parrello 1.31
430 : parrello 1.93 =cut
431 : parrello 1.84
432 : parrello 1.93 sub LogErrors {
433 :     # Get the file name.
434 :     my ($fileName) = @_;
435 :     # Open the file as the standard error output.
436 :     open STDERR, '>', $fileName;
437 :     }
438 : parrello 1.84
439 : parrello 1.93 =head3 Trace
440 : parrello 1.31
441 : parrello 1.93 Trace($message);
442 : parrello 1.31
443 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
444 :     any prior call to B<TSetup>.
445 : parrello 1.31
446 : parrello 1.93 =over 4
447 : parrello 1.42
448 : parrello 1.93 =item message
449 : parrello 1.42
450 : parrello 1.93 Message to write.
451 : parrello 1.42
452 : parrello 1.93 =back
453 : parrello 1.72
454 : parrello 1.93 =cut
455 : parrello 1.36
456 : parrello 1.93 sub Trace {
457 :     # Get the parameters.
458 :     my ($message) = @_;
459 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
460 :     # new-line stuff ourselves.
461 :     my $stripped = Strip($message);
462 :     # Compute the caller information.
463 :     my ($callPackage, $callFile, $callLine) = caller();
464 :     my $callFileTitle = basename($callFile);
465 :     # Check the caller.
466 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
467 : parrello 1.93 # Get the timestamp.
468 :     my $timeStamp = Now();
469 : parrello 1.97 # Build the prefix.
470 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
471 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
472 : parrello 1.97 # Format the message.
473 :     my $formatted = "$prefix $stripped";
474 : parrello 1.93 # Process according to the destination.
475 :     if ($Destination eq "TEXT") {
476 :     # Write the message to the standard output.
477 :     print "$formatted\n";
478 :     } elsif ($Destination eq "ERROR") {
479 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
480 : parrello 1.93 print STDERR "$formatted\n";
481 : parrello 1.97 } elsif ($Destination eq "WARN") {
482 :     # Emit the message to the standard error output. It is presumed that the
483 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
484 :     # the caller info.
485 :     print STDERR "$callerInfo$stripped\n";
486 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
487 :     # Push the message into the queue.
488 :     push @Queue, "$formatted";
489 :     } elsif ($Destination eq "HTML") {
490 :     # Convert the message to HTML and write it to the standard output.
491 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
492 :     print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
493 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
494 :     # Write the trace message to an output file.
495 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
496 : parrello 1.93 print TRACING "$formatted\n";
497 :     close TRACING;
498 :     # If the Tee flag is on, echo it to the standard output.
499 :     if ($TeeFlag) {
500 :     print "$formatted\n";
501 :     }
502 :     }
503 :     }
504 : parrello 1.36
505 : parrello 1.93 =head3 T
506 : parrello 1.36
507 : parrello 1.93 my $switch = T($category, $traceLevel);
508 : parrello 1.36
509 : parrello 1.93 or
510 : parrello 1.44
511 : parrello 1.93 my $switch = T($traceLevel);
512 : parrello 1.44
513 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
514 :     is active, else FALSE. If no category is specified, the caller's package name is used.
515 : parrello 1.44
516 : parrello 1.93 =over 4
517 : parrello 1.44
518 : parrello 1.93 =item category
519 : parrello 1.44
520 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
521 :     used.
522 : parrello 1.31
523 : parrello 1.93 =item traceLevel
524 : parrello 1.31
525 : parrello 1.93 Relevant tracing level.
526 : parrello 1.31
527 : parrello 1.93 =item RETURN
528 : parrello 1.31
529 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
530 : parrello 1.31
531 : parrello 1.93 =back
532 : parrello 1.36
533 : parrello 1.93 =cut
534 :    
535 :     sub T {
536 :     # Declare the return variable.
537 :     my $retVal = 0;
538 :     # Only proceed if tracing is turned on.
539 :     if ($Destination ne "NONE") {
540 :     # Get the parameters.
541 :     my ($category, $traceLevel) = @_;
542 :     if (!defined $traceLevel) {
543 :     # Here we have no category, so we need to get the calling package.
544 :     # The calling package is normally the first parameter. If it is
545 :     # omitted, the first parameter will be the tracelevel. So, the
546 :     # first thing we do is shift the so-called category into the
547 :     # $traceLevel variable where it belongs.
548 :     $traceLevel = $category;
549 :     my ($package, $fileName, $line) = caller;
550 :     # If there is no calling package, we default to "main".
551 :     if (!$package) {
552 :     $category = "main";
553 :     } else {
554 :     my @cats = split /::/, $package;
555 :     $category = $cats[$#cats];
556 :     }
557 :     }
558 : parrello 1.97 # Save the category name and level.
559 : parrello 1.93 $LastCategory = $category;
560 : parrello 1.97 $LastLevel = $traceLevel;
561 : parrello 1.93 # Convert it to lower case before we hash it.
562 :     $category = lc $category;
563 : parrello 1.100 # Validate the trace level.
564 : parrello 1.93 if (ref $traceLevel) {
565 :     Confess("Bad trace level.");
566 :     } elsif (ref $TraceLevel) {
567 :     Confess("Bad trace config.");
568 :     }
569 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
570 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
571 : parrello 1.93 }
572 :     # Return the computed result.
573 :     return $retVal;
574 :     }
575 :    
576 :     =head3 QTrace
577 :    
578 :     my $data = QTrace($format);
579 :    
580 :     Return the queued trace data in the specified format.
581 :    
582 :     =over 4
583 :    
584 :     =item format
585 :    
586 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
587 :    
588 :     =back
589 :    
590 :     =cut
591 :    
592 :     sub QTrace {
593 :     # Get the parameter.
594 :     my ($format) = @_;
595 :     # Create the return variable.
596 :     my $retVal = "";
597 :     # Only proceed if there is an actual queue.
598 :     if (@Queue) {
599 :     # Process according to the format.
600 :     if ($format =~ m/^HTML$/i) {
601 :     # Convert the queue into an HTML list.
602 :     $retVal = "<ul>\n";
603 :     for my $line (@Queue) {
604 :     my $escapedLine = CGI::escapeHTML($line);
605 :     $retVal .= "<li>$escapedLine</li>\n";
606 :     }
607 :     $retVal .= "</ul>\n";
608 :     } elsif ($format =~ m/^TEXT$/i) {
609 :     # Convert the queue into a list of text lines.
610 :     $retVal = join("\n", @Queue) . "\n";
611 :     }
612 :     # Clear the queue.
613 :     @Queue = ();
614 :     }
615 :     # Return the formatted list.
616 :     return $retVal;
617 :     }
618 :    
619 :     =head3 Confess
620 :    
621 :     Confess($message);
622 :    
623 :     Trace the call stack and abort the program with the specified message. When used with
624 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
625 :     So, for example
626 :    
627 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
628 :    
629 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
630 :    
631 :     =over 4
632 :    
633 :     =item message
634 :    
635 :     Message to include in the trace.
636 :    
637 :     =back
638 :    
639 :     =cut
640 :    
641 :     sub Confess {
642 :     # Get the parameters.
643 :     my ($message) = @_;
644 : parrello 1.97 # Set up the category and level.
645 :     $LastCategory = "(confess)";
646 :     $LastLevel = 0;
647 : parrello 1.93 if (! defined($FIG_Config::no_tool_hdr)) {
648 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
649 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
650 :     # Only proceed if the tool header file is actually present.
651 :     if (-f $toolHeaderFile) {
652 : parrello 1.97 my $fh;
653 :     if (open $fh, "<$toolHeaderFile") {
654 :     my @lines = <$fh>;
655 :     Trace("Tool header has " . scalar(@lines) . " lines.");
656 :     }
657 : parrello 1.93 }
658 :     }
659 :     # Trace the call stack.
660 :     Cluck($message);
661 :     # Abort the program.
662 :     croak(">>> $message");
663 :     }
664 :    
665 : parrello 1.106 =head3 SaveCGI
666 :    
667 :     Tracer::SaveCGI($cgi);
668 :    
669 :     This method saves the CGI object but does not activate emergency tracing.
670 :     It is used to allow L</Warn> to work in situations where emergency
671 :     tracing is contra-indicated (e.g. the wiki).
672 :    
673 :     =over 4
674 :    
675 :     =item cgi
676 :    
677 :     Active CGI query object.
678 :    
679 :     =back
680 :    
681 :     =cut
682 :    
683 :     sub SaveCGI {
684 :     $SavedCGI = $_[0];
685 :     }
686 :    
687 : parrello 1.99 =head3 Warn
688 :    
689 : parrello 1.106 Warn($message, @options);
690 : parrello 1.99
691 :     This method traces an important message. If an RSS feed is configured
692 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
693 :     then the message will be echoed to the feed. In general, a tracing
694 :     destination of C<WARN> indicates that the caller is running as a web
695 :     service in a production environment; however, this is not a requirement.
696 :    
697 : parrello 1.103 To force warnings into the RSS feed even when the tracing destination
698 :     is not C<WARN>, simply specify the C<Feed> tracing module. This can be
699 :     configured automatically when L</StandardSetup> is used.
700 :    
701 : parrello 1.99 The L</Cluck> method calls this one for its final message. Since
702 :     L</Confess> calls L</Cluck>, this means that any error which is caught
703 :     and confessed will put something in the feed. This insures that someone
704 :     will be alerted relatively quickly when a failure occurs.
705 :    
706 :     =over 4
707 :    
708 :     =item message
709 :    
710 :     Message to be traced.
711 :    
712 : parrello 1.106 =item options
713 :    
714 :     A list containing zero or more options.
715 :    
716 :     =back
717 :    
718 :     The permissible options are as follows.
719 :    
720 :     =over 4
721 :    
722 :     =item noStack
723 :    
724 :     If specified, then the stack trace is not included in the output.
725 :    
726 : parrello 1.99 =back
727 :    
728 :     =cut
729 :    
730 :     sub Warn {
731 :     # Get the parameters.
732 : parrello 1.106 my $message = shift @_;
733 :     my %options = map { $_ => 1 } @_;
734 : parrello 1.107 # Save $@;
735 :     my $savedError = $@;
736 : parrello 1.99 # Trace the message.
737 :     Trace($message);
738 : parrello 1.106 # This will contain the lock handle. If it's defined, it means we need to unlock.
739 :     my $lock;
740 : parrello 1.103 # Check for feed forcing.
741 :     my $forceFeed = exists $Categories{feed};
742 : parrello 1.106 # An error here would be disastrous. Note that if debug mode is specified,
743 :     # we do this stuff even in a test environment.
744 : parrello 1.99 eval {
745 :     # Do we need to put this in the RSS feed?
746 : parrello 1.103 if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
747 : parrello 1.99 # Yes. We now need to compute the date, the link, and the title.
748 :     # First, the date, in a very specific format.
749 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
750 :     (tz_local_offset() / 30);
751 : parrello 1.102 # Environment data goes in here. We start with the date.
752 :     my $environment = "$date. ";
753 :     # If we need to recap the message (because it's too long to be a title), we'll
754 :     # put it in here.
755 :     my $recap;
756 :     # Copy the message and remove excess space.
757 :     my $title = $message;
758 : parrello 1.101 $title =~ s/\s+/ /gs;
759 : parrello 1.102 # If it's too long, we have to split it up.
760 : parrello 1.101 if (length $title > 60) {
761 : parrello 1.102 # Put the full message in the environment string.
762 :     $recap = $title;
763 :     # Excerpt it as the title.
764 : parrello 1.101 $title = substr($title, 0, 50) . "...";
765 :     }
766 : parrello 1.99 # If we have a CGI object, then this is a web error. Otherwise, it's
767 :     # command-line.
768 :     if (defined $SavedCGI) {
769 : parrello 1.101 # We're in a web service. The environment is the user's IP, and the link
770 : parrello 1.99 # is the URL that got us here.
771 :     my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
772 : parrello 1.106 $environment .= "Event Reported at IP address $key process $$.";
773 :     my $url = $SavedCGI->self_url();
774 : parrello 1.100 # We need the user agent string and (if available) the referrer.
775 : parrello 1.102 # The referrer will be the link.
776 : parrello 1.106 $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
777 : parrello 1.100 if ($ENV{HTTP_REFERER}) {
778 : parrello 1.102 my $link = $ENV{HTTP_REFERER};
779 :     $environment .= " referred from <a href=\"$link\">$link</a>.";
780 :     } else {
781 :     $environment .= " referrer unknown.";
782 : parrello 1.100 }
783 : parrello 1.102 # Close off the sentence with the original link.
784 : parrello 1.106 $environment .= " URL of event is <a href=\"$url\">$url</a>.";
785 : parrello 1.99 } else {
786 :     # No CGI object, so we're a command-line tool. Use the tracing
787 : parrello 1.101 # key and the PID as the user identifier, and add the command.
788 : parrello 1.99 my $key = EmergencyKey();
789 : parrello 1.106 $environment .= "Event Reported by $key process $$.";
790 : parrello 1.104 if ($CommandLine) {
791 :     # We're in a StandardSetup script, so we have the real command line.
792 :     $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
793 :     } elsif ($ENV{_}) {
794 :     # We're in a BASH script, so the command has been stored in the _ variable.
795 :     $environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
796 :     }
797 : parrello 1.99 }
798 :     # Build a GUID. We use the current time, the title, and the process ID,
799 :     # then digest the result.
800 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
801 :     # Finally, the description. This is a stack trace plus various environmental stuff.
802 : parrello 1.106 # The trace is optional.
803 :     my $stackTrace;
804 :     if ($options{noStack}) {
805 :     $stackTrace = "";
806 :     } else {
807 :     my @trace = LongMess();
808 :     # Only proceed if we got something back.
809 :     if (scalar(@trace) > 0) {
810 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
811 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
812 :     }
813 : parrello 1.101 }
814 : parrello 1.102 # We got the stack trace. Now it's time to put it all together.
815 :     # We have a goofy thing here in that we need to HTML-escape some sections of the description
816 :     # twice. They will be escaped once here, and then once when written by XML::Simple. They are
817 :     # unescaped once when processed by the RSS reader, and stuff in the description is treated as
818 :     # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
819 :     # our <br>s and <pre>s are used to format the description.
820 :     $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
821 :     my $description = "$recap$environment $stackTrace";
822 : parrello 1.99 # Okay, we have all the pieces. Create a hash of the new event.
823 :     my $newItem = { title => $title,
824 : parrello 1.102 description => $description,
825 : parrello 1.99 category => $LastCategory,
826 :     pubDate => $date,
827 :     guid => $guid,
828 : parrello 1.106 };
829 : parrello 1.99 # We need XML capability for this.
830 :     require XML::Simple;
831 :     # The RSS document goes in here.
832 :     my $rss;
833 :     # Get the name of the RSS file. It's in the FIG temporary directory.
834 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
835 : parrello 1.106 # Open the config file and lock it.
836 :     $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
837 :     flock $lock, LOCK_EX;
838 : parrello 1.99 # Does it exist?
839 :     if (-s $fileName) {
840 :     # Slurp it in.
841 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
842 :     } else {
843 :     my $size = -s $fileName;
844 :     # Create an empty channel.
845 :     $rss = {
846 :     channel => {
847 :     title => 'NMPDR Warning Feed',
848 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
849 :     description => "Important messages regarding the status of the NMPDR.",
850 :     generator => "NMPDR Trace Facility",
851 :     docs => "http://blogs.law.harvard.edu/tech/rss",
852 :     item => []
853 :     },
854 :     };
855 :     }
856 :     # Get the channel object.
857 :     my $channel = $rss->{channel};
858 :     # Update the last-build date.
859 :     $channel->{lastBuildDate} = $date;
860 :     # Get the item array.
861 :     my $items = $channel->{item};
862 :     # Insure it has only 100 entries.
863 :     while (scalar @{$items} > 100) {
864 :     pop @{$items};
865 :     }
866 :     # Add our new item at the front.
867 :     unshift @{$items}, $newItem;
868 : parrello 1.102 # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
869 :     # the requirements for those.
870 : parrello 1.106 my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
871 : parrello 1.102 # Here we put in the root and declaration. The problem is that the root has to have the version attribute
872 :     # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
873 :     $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
874 : parrello 1.99 # We don't use Open here because we can't afford an error.
875 :     if (open XMLOUT, ">$fileName") {
876 :     print XMLOUT $xml;
877 :     close XMLOUT;
878 :     }
879 :     }
880 :     };
881 : parrello 1.103 if ($@) {
882 :     # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
883 :     # (which is a good thing).
884 : parrello 1.102 my $error = $@;
885 : parrello 1.103 Trace("Feed Error: $error") if T(Feed => 0);
886 : parrello 1.102 }
887 : parrello 1.106 # Be sure to unlock.
888 :     if ($lock) {
889 :     flock $lock, LOCK_UN;
890 :     undef $lock;
891 :     }
892 : parrello 1.107 # Restore the error message.
893 :     $@ = $savedError;
894 : parrello 1.99 }
895 :    
896 : parrello 1.106
897 :    
898 :    
899 : parrello 1.93 =head3 Assert
900 :    
901 :     Assert($condition1, $condition2, ... $conditionN);
902 :    
903 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
904 :     the OR operator and the L</Confess> method as a debugging assert.
905 :     So, for example
906 :    
907 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
908 :    
909 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
910 :    
911 :     =cut
912 :     sub Assert {
913 :     my $retVal = 1;
914 :     LOOP: for my $condition (@_) {
915 :     if (! $condition) {
916 :     $retVal = 0;
917 :     last LOOP;
918 :     }
919 :     }
920 :     return $retVal;
921 :     }
922 :    
923 :     =head3 Cluck
924 :    
925 :     Cluck($message);
926 :    
927 :     Trace the call stack. Note that for best results, you should qualify the call with a
928 :     trace condition. For example,
929 :    
930 :     Cluck("Starting record parse.") if T(3);
931 :    
932 :     will only trace the stack if the trace level for the package is 3 or more.
933 :    
934 :     =over 4
935 :    
936 :     =item message
937 :    
938 :     Message to include in the trace.
939 :    
940 :     =back
941 :    
942 :     =cut
943 :    
944 :     sub Cluck {
945 :     # Get the parameters.
946 :     my ($message) = @_;
947 :     # Trace what's happening.
948 :     Trace("Stack trace for event: $message");
949 : parrello 1.99 # Get the stack trace.
950 :     my @trace = LongMess();
951 :     # Convert the trace to a series of messages.
952 :     for my $line (@trace) {
953 :     # Replace the tab at the beginning with spaces.
954 :     $line =~ s/^\t/ /;
955 :     # Trace the line.
956 :     Trace($line);
957 :     }
958 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
959 :     Warn($message);
960 :     }
961 :    
962 :     =head3 LongMess
963 :    
964 :     my @lines = Tracer::LongMess();
965 :    
966 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
967 :     of message strings.
968 :    
969 :     =cut
970 :    
971 :     sub LongMess {
972 :     # Declare the return variable.
973 :     my @retVal = ();
974 :     my $confession = longmess("");
975 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
976 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
977 :     # Here we have a line worth keeping. Push it onto the result list.
978 :     push @retVal, $line;
979 : parrello 1.97 }
980 : parrello 1.93 }
981 : parrello 1.99 # Return the result.
982 :     return @retVal;
983 : parrello 1.93 }
984 :    
985 :     =head3 ETracing
986 :    
987 :     ETracing($parameter);
988 :    
989 :     Set up emergency tracing. Emergency tracing is tracing that is turned
990 :     on automatically for any program that calls this method. The emergency
991 :     tracing parameters are stored in a a file identified by a tracing key.
992 :     If this method is called with a CGI object, then the tracing key is
993 :     taken from a cookie. If it is called with no parameters, then the tracing
994 :     key is taken from an environment variable. If it is called with a string,
995 :     the tracing key is that string.
996 :    
997 :     =over 4
998 :    
999 :     =item parameter
1000 :    
1001 :     A parameter from which the tracing key is computed. If it is a scalar,
1002 :     that scalar is used as the tracing key. If it is a CGI object, the
1003 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
1004 :     tracing key is taken from the C<TRACING> environment variable. If it
1005 :     is a CGI object and emergency tracing is not on, the C<Trace> and
1006 :     C<TF> parameters will be used to determine the type of tracing.
1007 :    
1008 :     =back
1009 :    
1010 :     =cut
1011 :    
1012 :     sub ETracing {
1013 :     # Get the parameter.
1014 :     my ($parameter) = @_;
1015 :     # Check for CGI mode.
1016 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
1017 :     $SavedCGI = $parameter;
1018 :     } else {
1019 :     $SavedCGI = undef;
1020 :     }
1021 : parrello 1.93 # Default to no tracing except errors.
1022 :     my ($tracing, $dest) = ("0", "WARN");
1023 :     # Check for emergency tracing.
1024 :     my $tkey = EmergencyKey($parameter);
1025 :     my $emergencyFile = EmergencyFileName($tkey);
1026 :     if (-e $emergencyFile) {
1027 :     # We have the file. Read in the data.
1028 :     my @tracing = GetFile($emergencyFile);
1029 :     # Pull off the time limit.
1030 :     my $expire = shift @tracing;
1031 :     # Convert it to seconds.
1032 :     $expire *= 3600;
1033 :     # Check the file data.
1034 :     my $stat = stat($emergencyFile);
1035 :     my ($now) = gettimeofday;
1036 :     if ($now - $stat->mtime > $expire) {
1037 :     # Delete the expired file.
1038 :     unlink $emergencyFile;
1039 : parrello 1.44 } else {
1040 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
1041 :     # the trace level;
1042 :     $dest = shift @tracing;
1043 :     my $level = shift @tracing;
1044 :     # Convert the destination to a real tracing destination.
1045 :     # temp directory.
1046 :     $dest = EmergencyTracingDest($tkey, $dest);
1047 :     # Insure Tracer is specified.
1048 :     my %moduleHash = map { $_ => 1 } @tracing;
1049 :     $moduleHash{Tracer} = 1;
1050 :     # Set the trace parameter.
1051 :     $tracing = join(" ", $level, sort keys %moduleHash);
1052 : parrello 1.44 }
1053 : parrello 1.99 } elsif (defined $SavedCGI) {
1054 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1055 :     # for tracing from the form parameters.
1056 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1057 : parrello 1.93 # Here the user has requested tracing via a form.
1058 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1059 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1060 : parrello 1.36 }
1061 :     }
1062 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1063 :     TSetup($tracing, $dest);
1064 : parrello 1.94 # Check to see if we're a web script.
1065 : parrello 1.99 if (defined $SavedCGI) {
1066 : parrello 1.94 # Yes we are. Trace the form and environment data.
1067 : parrello 1.99 TraceParms($SavedCGI);
1068 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1069 :     # emitted by the script in its raw form.
1070 :     if (T(Raw => 3)) {
1071 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1072 :     }
1073 : parrello 1.83 }
1074 : parrello 1.31 }
1075 :    
1076 : parrello 1.93 =head3 EmergencyFileName
1077 :    
1078 :     my $fileName = Tracer::EmergencyFileName($tkey);
1079 :    
1080 :     Return the emergency tracing file name. This is the file that specifies
1081 :     the tracing information.
1082 :    
1083 :     =over 4
1084 :    
1085 :     =item tkey
1086 :    
1087 :     Tracing key for the current program.
1088 : parrello 1.11
1089 : parrello 1.93 =item RETURN
1090 : parrello 1.11
1091 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1092 : parrello 1.11
1093 : parrello 1.93 =back
1094 : parrello 1.11
1095 :     =cut
1096 :    
1097 : parrello 1.93 sub EmergencyFileName {
1098 :     # Get the parameters.
1099 :     my ($tkey) = @_;
1100 :     # Compute the emergency tracing file name.
1101 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1102 : olson 1.1 }
1103 :    
1104 : parrello 1.93 =head3 EmergencyFileTarget
1105 : parrello 1.10
1106 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1107 : parrello 1.10
1108 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1109 :     the tracing output for file-based tracing.
1110 : parrello 1.10
1111 : parrello 1.93 =over 4
1112 : parrello 1.10
1113 : parrello 1.93 =item tkey
1114 : parrello 1.10
1115 : parrello 1.93 Tracing key for the current program.
1116 : parrello 1.10
1117 : parrello 1.93 =item RETURN
1118 : parrello 1.10
1119 : parrello 1.93 Returns the name of the file to contain the trace output.
1120 : parrello 1.10
1121 : parrello 1.93 =back
1122 : parrello 1.10
1123 : parrello 1.93 =cut
1124 : parrello 1.10
1125 : parrello 1.93 sub EmergencyFileTarget {
1126 :     # Get the parameters.
1127 :     my ($tkey) = @_;
1128 :     # Compute the emergency tracing file name.
1129 :     return "$FIG_Config::temp/trace$tkey.log";
1130 :     }
1131 : parrello 1.10
1132 : parrello 1.93 =head3 EmergencyTracingDest
1133 : parrello 1.10
1134 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1135 : parrello 1.10
1136 : parrello 1.93 This method converts an emergency tracing destination to a real
1137 :     tracing destination. The main difference is that if the
1138 :     destination is C<FILE> or C<APPEND>, we convert it to file
1139 :     output. If the destination is C<DUAL>, we convert it to file
1140 :     and standard output.
1141 : parrello 1.10
1142 :     =over 4
1143 :    
1144 : parrello 1.93 =item tkey
1145 : parrello 1.10
1146 : parrello 1.93 Tracing key for this environment.
1147 : parrello 1.10
1148 : parrello 1.93 =item myDest
1149 : parrello 1.10
1150 : parrello 1.93 Destination from the emergency tracing file.
1151 : parrello 1.10
1152 :     =item RETURN
1153 :    
1154 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1155 : parrello 1.10
1156 :     =back
1157 :    
1158 :     =cut
1159 :    
1160 : parrello 1.93 sub EmergencyTracingDest {
1161 : parrello 1.12 # Get the parameters.
1162 : parrello 1.93 my ($tkey, $myDest) = @_;
1163 :     # Declare the return variable.
1164 :     my $retVal = $myDest;
1165 :     # Process according to the destination value.
1166 :     if ($myDest eq 'FILE') {
1167 :     $retVal = ">" . EmergencyFileTarget($tkey);
1168 :     } elsif ($myDest eq 'APPEND') {
1169 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1170 :     } elsif ($myDest eq 'DUAL') {
1171 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1172 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1173 :     $retVal = "WARN";
1174 : parrello 1.12 }
1175 : parrello 1.93 # Return the result.
1176 :     return $retVal;
1177 : parrello 1.10 }
1178 :    
1179 : parrello 1.93 =head3 Emergency
1180 :    
1181 :     Emergency($key, $hours, $dest, $level, @modules);
1182 :    
1183 :     Turn on emergency tracing. This method is normally invoked over the web from
1184 :     a debugging console, but it can also be called by the C<trace.pl> script.
1185 :     The caller specifies the duration of the emergency in hours, the desired tracing
1186 :     destination, the trace level, and a list of the trace modules to activate.
1187 :     For the length of the duration, when a program in an environment with the
1188 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1189 :     turned on automatically. See L</TSetup> for more about tracing setup and
1190 :     L</ETracing> for more about emergency tracing.
1191 :    
1192 :     =over 4
1193 : parrello 1.11
1194 : parrello 1.93 =item tkey
1195 : parrello 1.11
1196 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1197 : parrello 1.11
1198 : parrello 1.93 =item hours
1199 : parrello 1.11
1200 : parrello 1.93 Number of hours to keep emergency tracing alive.
1201 : parrello 1.11
1202 : parrello 1.93 =item dest
1203 : parrello 1.11
1204 : parrello 1.93 Tracing destination. If no path information is specified for a file
1205 :     destination, it is put in the FIG temporary directory.
1206 : parrello 1.11
1207 : parrello 1.93 =item level
1208 : parrello 1.11
1209 : parrello 1.93 Tracing level. A higher level means more trace messages.
1210 : parrello 1.11
1211 : parrello 1.93 =item modules
1212 : parrello 1.11
1213 : parrello 1.93 A list of the tracing modules to activate.
1214 : parrello 1.11
1215 :     =back
1216 :    
1217 :     =cut
1218 : parrello 1.93
1219 :     sub Emergency {
1220 : parrello 1.11 # Get the parameters.
1221 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1222 :     # Create the emergency file.
1223 :     my $specFile = EmergencyFileName($tkey);
1224 :     my $outHandle = Open(undef, ">$specFile");
1225 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1226 : parrello 1.11 }
1227 :    
1228 : parrello 1.93 =head3 EmergencyKey
1229 :    
1230 :     my $tkey = EmergencyKey($parameter);
1231 :    
1232 :     Return the Key to be used for emergency tracing. This could be an IP address,
1233 :     a session ID, or a user name, depending on the environment.
1234 : parrello 1.11
1235 : parrello 1.93 =over 4
1236 : parrello 1.11
1237 : parrello 1.93 =item parameter
1238 : parrello 1.11
1239 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1240 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1241 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1242 :     taken from the C<TRACING> environment variable.
1243 : parrello 1.29
1244 : parrello 1.93 =item RETURN
1245 : parrello 1.11
1246 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1247 : parrello 1.11
1248 : parrello 1.93 =back
1249 : parrello 1.11
1250 : parrello 1.93 =cut
1251 : parrello 1.29
1252 : parrello 1.93 sub EmergencyKey {
1253 :     # Get the parameters.
1254 :     my ($parameter) = @_;
1255 :     # Declare the return variable.
1256 :     my $retVal;
1257 :     # Determine the parameter type.
1258 :     if (! defined $parameter) {
1259 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1260 :     # get the effective login ID.
1261 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1262 : parrello 1.93 } else {
1263 :     my $ptype = ref $parameter;
1264 :     if ($ptype eq 'CGI') {
1265 :     # Here we were invoked from a web page. Look for a cookie.
1266 :     $retVal = $parameter->cookie('IP');
1267 :     } elsif (! $ptype) {
1268 :     # Here the key was passed in.
1269 :     $retVal = $parameter;
1270 :     }
1271 :     }
1272 :     # If no luck finding a key, use the PID.
1273 :     if (! defined $retVal) {
1274 :     $retVal = $$;
1275 :     }
1276 :     # Return the result.
1277 :     return $retVal;
1278 :     }
1279 : parrello 1.11
1280 :    
1281 : parrello 1.93 =head3 TraceParms
1282 : parrello 1.11
1283 : parrello 1.93 Tracer::TraceParms($cgi);
1284 : parrello 1.11
1285 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1286 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1287 : parrello 1.11
1288 : parrello 1.93 =over 4
1289 : parrello 1.11
1290 : parrello 1.93 =item cgi
1291 : parrello 1.31
1292 : parrello 1.93 CGI query object containing the parameters to trace.
1293 : parrello 1.31
1294 : parrello 1.11 =back
1295 :    
1296 :     =cut
1297 : parrello 1.93
1298 :     sub TraceParms {
1299 : parrello 1.11 # Get the parameters.
1300 : parrello 1.93 my ($cgi) = @_;
1301 : parrello 1.94 if (T(CGI => 2)) {
1302 :     # Here we trace the GET-style URL for the script.
1303 : parrello 1.97 Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1304 : parrello 1.94 }
1305 : parrello 1.93 if (T(CGI => 3)) {
1306 :     # Here we want to trace the parameter data.
1307 :     my @names = $cgi->param;
1308 :     for my $parmName (sort @names) {
1309 :     # Note we skip the Trace parameters, which are for our use only.
1310 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1311 :     my @values = $cgi->param($parmName);
1312 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1313 : parrello 1.93 }
1314 :     }
1315 :     # Display the request method.
1316 :     my $method = $cgi->request_method();
1317 :     Trace("Method: $method");
1318 :     }
1319 :     if (T(CGI => 4)) {
1320 :     # Here we want the environment data too.
1321 :     for my $envName (sort keys %ENV) {
1322 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1323 : parrello 1.12 }
1324 :     }
1325 : parrello 1.11 }
1326 :    
1327 : parrello 1.94 =head3 TraceImages
1328 :    
1329 :     Tracer::TraceImages($htmlString);
1330 :    
1331 :     Trace information about all of an html document's images. The tracing
1332 :     will be for type "IMG" at level 3. The image's source string
1333 :     will be displayed. This is generally either the URL of the image or
1334 :     raw data for the image itself. If the source is too long, only the first 300
1335 :     characters will be shown at trace level 3. The entire source will be shown,
1336 :     however, at trace level 4. This method is not very smart, and might catch
1337 :     Javascript code, but it is still useful when debugging the arcane
1338 :     behavior of images in multiple browser environments.
1339 :    
1340 :     =over 4
1341 :    
1342 :     =item htmlString
1343 :    
1344 :     HTML text for an outgoing web page.
1345 :    
1346 :     =back
1347 :    
1348 :     =cut
1349 :    
1350 :     sub TraceImages {
1351 :     # Only proceed if we're at the proper trace level.
1352 :     if (T(IMG => 3)) {
1353 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1354 :     # into a variable called "$htmlString". This is because we expect html strings to be
1355 :     # long, and don't want to copy them any more than we have to.
1356 :     Trace(length($_[0]) . " characters in web page.");
1357 :     # Loop through the HTML, culling image tags.
1358 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1359 :     # Extract the source string and determine whether or not it's too long.
1360 :     my $srcString = $1;
1361 :     my $pos = pos($_[0]) - length($srcString);
1362 :     my $excess = length($srcString) - 300;
1363 :     # We'll put the display string in here.
1364 :     my $srcDisplay = $srcString;
1365 :     # If it's a data string, split it at the comma.
1366 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1367 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1368 :     # a long string, however, we only show the first 300 characters.
1369 :     if ($excess > 0 && ! T(IMG => 4)) {
1370 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1371 :     }
1372 :     # Output the trace message.
1373 :     Trace("Image tag at position $pos:\n$srcDisplay");
1374 :     }
1375 :     }
1376 :     }
1377 :    
1378 : parrello 1.93 =head2 Command-Line Utility Methods
1379 : olson 1.1
1380 : parrello 1.93 =head3 SendSMS
1381 : olson 1.1
1382 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1383 : olson 1.1
1384 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1385 :     user name, password, and API ID for the relevant account in the hash reference variable
1386 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1387 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1388 :     is C<2561022>, then the FIG_Config file must contain
1389 : olson 1.1
1390 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1391 :     password => 'silly',
1392 :     api_id => '2561022' };
1393 : olson 1.1
1394 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1395 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1396 :     when you call this method.
1397 : olson 1.1
1398 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1399 : parrello 1.74
1400 : parrello 1.93 =over 4
1401 : parrello 1.74
1402 : parrello 1.93 =item phoneNumber
1403 : parrello 1.74
1404 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1405 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1406 : parrello 1.74
1407 : parrello 1.93 =item msg
1408 : parrello 1.74
1409 : parrello 1.93 Message to send to the specified phone.
1410 : parrello 1.74
1411 :     =item RETURN
1412 :    
1413 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1414 : parrello 1.74
1415 : parrello 1.78 =back
1416 :    
1417 : parrello 1.74 =cut
1418 :    
1419 : parrello 1.93 sub SendSMS {
1420 : parrello 1.74 # Get the parameters.
1421 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1422 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1423 : parrello 1.74 my $retVal;
1424 : parrello 1.93 # Only proceed if we have phone support.
1425 :     if (! defined $FIG_Config::phone) {
1426 :     Trace("Phone support not present in FIG_Config.") if T(1);
1427 :     } else {
1428 :     # Get the phone data.
1429 :     my $parms = $FIG_Config::phone;
1430 :     # Get the Clickatell URL.
1431 :     my $url = "http://api.clickatell.com/http/";
1432 :     # Create the user agent.
1433 :     my $ua = LWP::UserAgent->new;
1434 :     # Request a Clickatell session.
1435 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1436 :     password => $parms->{password},
1437 :     api_id => $parms->{api_id},
1438 :     to => $phoneNumber,
1439 :     text => $msg});
1440 :     # Check for an error.
1441 :     if (! $resp->is_success) {
1442 :     Trace("Alert failed.") if T(1);
1443 :     } else {
1444 :     # Get the message ID.
1445 :     my $rstring = $resp->content;
1446 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1447 :     $retVal = $1;
1448 :     } else {
1449 :     Trace("Phone attempt failed with $rstring") if T(1);
1450 :     }
1451 :     }
1452 : parrello 1.74 }
1453 :     # Return the result.
1454 :     return $retVal;
1455 :     }
1456 :    
1457 : parrello 1.93 =head3 StandardSetup
1458 : olson 1.1
1459 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1460 : olson 1.1
1461 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1462 :     values are a hash of the command-line options and a list of the positional
1463 :     parameters. Tracing is automatically set up and the command-line options are
1464 :     validated.
1465 : olson 1.1
1466 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1467 :     be more easily understood, however, once they are examined individually.
1468 : olson 1.1
1469 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1470 :     special-purpose tracing categories. Most tracing categories are PERL package
1471 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1472 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1473 : olson 1.1
1474 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1475 : olson 1.1
1476 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1477 :     the output. There are two special tracing categories that are automatically
1478 :     handled by this method. In other words, if you used L</TSetup> you would need
1479 :     to include these categories manually, but if you use this method they are turned
1480 :     on automatically.
1481 : parrello 1.5
1482 :     =over 4
1483 :    
1484 : parrello 1.93 =item SQL
1485 : parrello 1.5
1486 : parrello 1.93 Traces SQL commands and activity.
1487 : parrello 1.5
1488 : parrello 1.93 =item Tracer
1489 : parrello 1.5
1490 : parrello 1.93 Traces error messages and call stacks.
1491 : parrello 1.5
1492 :     =back
1493 :    
1494 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1495 :     The trace level is specified using the C<-trace> command-line option. For example,
1496 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1497 :     all tracing at level 3.
1498 : parrello 1.5
1499 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1500 : parrello 1.5
1501 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1502 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1503 :     process ID. You can also specify the C<user> parameter to put a user ID
1504 :     instead of a process ID in the trace file name. So, for example
1505 : olson 1.1
1506 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1507 :     For a genome-by-genome update, use 3.
1508 : olson 1.1
1509 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1510 : olson 1.1
1511 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1512 : olson 1.1
1513 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1514 :     options, their default values, and an explanation of what they mean. Command-line
1515 :     options may be in the form of switches or keywords. In the case of a switch, the
1516 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1517 :     of a keyword, the value is separated from the option name by an equal sign. You
1518 :     can see this last in the command-line example above.
1519 : olson 1.1
1520 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1521 :     prior to calling this method.
1522 : olson 1.1
1523 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1524 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1525 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1526 :     the following code.
1527 : olson 1.1
1528 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1529 :     { safe => [0, "use database transactions"],
1530 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1531 :     start => [' ', "start with this genome"],
1532 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1533 :     "<command> <transactionDirectory> <IDfile>",
1534 :     @ARGV);
1535 : olson 1.1
1536 :    
1537 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1538 :     stores the actual options in a hash that is returned as C<$options>. The
1539 :     positional parameters are returned in C<@parameters>.
1540 : olson 1.1
1541 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1542 : olson 1.1
1543 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1544 : olson 1.1
1545 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1546 :     above command as
1547 : olson 1.1
1548 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1549 : olson 1.1
1550 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1551 :     parameters, and would find themselves in I<@parameters> after executing the
1552 :     above code fragment. The tracing would be set to level 2, and the categories
1553 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1554 :     and C<DocUtils> was included because it came in within the first parameter
1555 :     to this method. The I<$options> hash would be
1556 : olson 1.1
1557 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1558 :     noAlias => 1, start => ' ', tblFiles => 0 }
1559 : olson 1.1
1560 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1561 :     standard tracing setup and command-line parsing. Note that the caller is
1562 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1563 :     are used by this method to control the tracing. If additional tracing features
1564 :     need to be added in the future, they can be processed by this method without
1565 :     upsetting the command-line utilities.
1566 : olson 1.1
1567 : parrello 1.93 If the C<background> option is specified on the command line, then the
1568 :     standard and error outputs will be directed to files in the temporary
1569 :     directory, using the same suffix as the trace file. So, if the command
1570 :     line specified
1571 : olson 1.1
1572 : parrello 1.93 -user=Bruce -background
1573 : olson 1.1
1574 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1575 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1576 :     simplify starting a command in the background.
1577 : olson 1.1
1578 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1579 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1580 :     be used instead of custom tracing. If the user name is not specified,
1581 :     the tracing key is taken from the C<Tracing> environment variable. If there
1582 : parrello 1.103 is no value for that variable, the tracing key will be computed from the active
1583 :     login ID.
1584 :    
1585 :     Since the default situation in StandardSetup is to trace to the standard
1586 :     output, errors that occur in command-line scripts will not generate
1587 :     RSS events. To force the events, use the C<warn> option.
1588 :    
1589 :     TransactFeatures -background -warn register ../xacts IDs.tbl
1590 : olson 1.1
1591 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1592 :     names will be traced at level 0 and the program will exit without processing.
1593 :     This provides a limited help capability. For example, if the user enters
1594 : olson 1.1
1595 : parrello 1.93 TransactFeatures -help
1596 : olson 1.1
1597 : parrello 1.93 he would see the following output.
1598 : olson 1.1
1599 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1600 :     -trace tracing level (default E)
1601 :     -sql trace SQL commands
1602 :     -safe use database transactions
1603 :     -noAlias do not expect aliases in CHANGE transactions
1604 :     -start start with this genome
1605 :     -tblFiles output TBL files containing the corrected IDs
1606 : olson 1.1
1607 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1608 :     for C<trace> in the incoming options hash. The default value can be overridden,
1609 :     or the tracing to the standard output can be turned off by suffixing a minus
1610 :     sign to the trace level. So, for example,
1611 : olson 1.1
1612 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1613 :     ...
1614 : olson 1.1
1615 : parrello 1.93 would set the default trace level to 0 instead of E, while
1616 : olson 1.1
1617 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1618 :     ...
1619 : olson 1.1
1620 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1621 :     standard output.
1622 : olson 1.1
1623 : parrello 1.93 The parameters to this method are as follows.
1624 : olson 1.1
1625 : parrello 1.93 =over 4
1626 : olson 1.1
1627 : parrello 1.93 =item categories
1628 : parrello 1.2
1629 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1630 :     packages whose internal workings will need to be debugged to get the
1631 :     command working.
1632 : olson 1.1
1633 : parrello 1.93 =item options
1634 : olson 1.1
1635 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1636 :     to their default values and descriptions. The user can override the defaults
1637 :     by specifying the options as command-line switches prefixed by a hyphen.
1638 :     Tracing-related options may be added to this hash. If the C<-h> option is
1639 :     specified on the command line, the option descriptions will be used to
1640 :     explain the options. To turn off tracing to the standard output, add a
1641 :     minus sign to the value for C<trace> (see above).
1642 : olson 1.1
1643 : parrello 1.93 =item parmHelp
1644 : olson 1.1
1645 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1646 :     if the user specifies the C<-h> option.
1647 : olson 1.1
1648 : parrello 1.93 =item argv
1649 : olson 1.1
1650 : parrello 1.93 List of command line parameters, including the option switches, which must
1651 :     precede the positional parameters and be prefixed by a hyphen.
1652 : olson 1.1
1653 :     =item RETURN
1654 :    
1655 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1656 :     maps the command-line option switches to their values. These will either be the
1657 :     default values or overrides specified on the command line. The remaining
1658 :     elements of the list are the position parameters, in order.
1659 : olson 1.1
1660 :     =back
1661 :    
1662 :     =cut
1663 :    
1664 : parrello 1.93 sub StandardSetup {
1665 :     # Get the parameters.
1666 :     my ($categories, $options, $parmHelp, @argv) = @_;
1667 :     # Get the default tracing key.
1668 :     my $tkey = EmergencyKey();
1669 : parrello 1.104 # Save the command line.
1670 :     $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1671 : parrello 1.93 # Add the tracing options.
1672 :     if (! exists $options->{trace}) {
1673 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1674 :     }
1675 :     $options->{sql} = [0, "turn on SQL tracing"];
1676 :     $options->{help} = [0, "display command-line options"];
1677 :     $options->{user} = [$tkey, "tracing key"];
1678 :     $options->{background} = [0, "spool standard and error output"];
1679 : parrello 1.103 $options->{warn} = [0, "send errors to RSS feed"];
1680 : parrello 1.93 # Create a parsing hash from the options hash. The parsing hash
1681 :     # contains the default values rather than the default value
1682 :     # and the description. While we're at it, we'll memorize the
1683 :     # length of the longest option name.
1684 :     my $longestName = 0;
1685 :     my %parseOptions = ();
1686 :     for my $key (keys %{$options}) {
1687 :     if (length $key > $longestName) {
1688 :     $longestName = length $key;
1689 :     }
1690 :     $parseOptions{$key} = $options->{$key}->[0];
1691 :     }
1692 :     # Parse the command line.
1693 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1694 :     # Get the logfile suffix.
1695 :     my $suffix = $retOptions->{user};
1696 :     # Check for background mode.
1697 :     if ($retOptions->{background}) {
1698 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
1699 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
1700 :     open STDOUT, ">$outFileName";
1701 :     open STDERR, ">$errFileName";
1702 :     # Check for phone support. If we have phone support and a phone number,
1703 :     # we want to turn it on.
1704 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1705 :     $retOptions->{phone} = $ENV{PHONE};
1706 :     }
1707 :     }
1708 :     # Now we want to set up tracing. First, we need to know if the user
1709 :     # wants emergency tracing.
1710 :     if ($retOptions->{trace} eq 'E') {
1711 :     ETracing($retOptions->{user});
1712 :     } else {
1713 :     # Here the tracing is controlled from the command line.
1714 :     my @cats = @{$categories};
1715 :     if ($retOptions->{sql}) {
1716 :     push @cats, "SQL";
1717 :     }
1718 : parrello 1.103 if ($retOptions->{warn}) {
1719 :     push @cats, "Feed";
1720 :     }
1721 : parrello 1.93 # Add the default categories.
1722 :     push @cats, "Tracer";
1723 :     # Next, we create the category string by joining the categories.
1724 :     my $cats = join(" ", @cats);
1725 :     # Check to determine whether or not the caller wants to turn off tracing
1726 :     # to the standard output.
1727 :     my $traceLevel = $retOptions->{trace};
1728 :     my $textOKFlag = 1;
1729 :     if ($traceLevel =~ /^(.)-/) {
1730 :     $traceLevel = $1;
1731 :     $textOKFlag = 0;
1732 :     }
1733 :     # Now we set up the trace mode.
1734 :     my $traceMode;
1735 :     # Verify that we can open a file in the FIG temporary directory.
1736 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1737 :     if (open TESTTRACE, ">$traceFileName") {
1738 :     # Here we can trace to a file.
1739 :     $traceMode = ">$traceFileName";
1740 :     if ($textOKFlag) {
1741 :     # Echo to standard output if the text-OK flag is set.
1742 :     $traceMode = "+$traceMode";
1743 :     }
1744 :     # Close the test file.
1745 :     close TESTTRACE;
1746 :     } else {
1747 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1748 :     warn "Could not open trace file $traceFileName: $!\n";
1749 :     # We trace to the standard output if it's
1750 :     # okay, and the error log otherwise.
1751 : parrello 1.93 if ($textOKFlag) {
1752 :     $traceMode = "TEXT";
1753 : parrello 1.12 } else {
1754 : parrello 1.93 $traceMode = "WARN";
1755 : parrello 1.12 }
1756 :     }
1757 : parrello 1.93 # Now set up the tracing.
1758 :     TSetup("$traceLevel $cats", $traceMode);
1759 :     }
1760 :     # Check for the "help" option. If it is specified, dump the command-line
1761 :     # options and exit the program.
1762 :     if ($retOptions->{help}) {
1763 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1764 :     print "$1 [options] $parmHelp\n";
1765 :     for my $key (sort keys %{$options}) {
1766 :     my $name = Pad($key, $longestName, 0, ' ');
1767 :     my $desc = $options->{$key}->[1];
1768 :     if ($options->{$key}->[0]) {
1769 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1770 :     }
1771 :     print " $name $desc\n";
1772 : parrello 1.36 }
1773 : parrello 1.93 exit(0);
1774 :     }
1775 :     # Trace the options, if applicable.
1776 :     if (T(3)) {
1777 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1778 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1779 : parrello 1.3 }
1780 : parrello 1.93 # Return the parsed parameters.
1781 :     return ($retOptions, @retParameters);
1782 : olson 1.1 }
1783 :    
1784 : parrello 1.93 =head3 ReadOptions
1785 : olson 1.1
1786 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1787 : olson 1.1
1788 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1789 :     format
1790 : olson 1.1
1791 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1792 : olson 1.1
1793 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1794 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1795 :     character is a semi-colon will be ignored. The return hash will map each option name to
1796 :     the corresponding option value.
1797 : olson 1.1
1798 :     =over 4
1799 :    
1800 : parrello 1.93 =item fileName
1801 : olson 1.1
1802 : parrello 1.93 Name of the file containing the option data.
1803 : olson 1.1
1804 :     =item RETURN
1805 :    
1806 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1807 :     value.
1808 : olson 1.1
1809 :     =back
1810 :    
1811 :     =cut
1812 :    
1813 : parrello 1.93 sub ReadOptions {
1814 : parrello 1.12 # Get the parameters.
1815 : parrello 1.93 my ($fileName) = @_;
1816 :     # Open the file.
1817 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1818 :     # Count the number of records read.
1819 :     my ($records, $comments) = 0;
1820 :     # Create the return hash.
1821 :     my %retVal = ();
1822 :     # Loop through the file, accumulating key-value pairs.
1823 :     while (my $line = <CONFIGFILE>) {
1824 :     # Denote we've read a line.
1825 :     $records++;
1826 :     # Determine the line type.
1827 :     if ($line =~ /^\s*[\n\r]/) {
1828 :     # A blank line is a comment.
1829 :     $comments++;
1830 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1831 :     # Here we have an option assignment.
1832 :     retVal{$1} = $2;
1833 :     } elsif ($line =~ /^\s*;/) {
1834 :     # Here we have a text comment.
1835 :     $comments++;
1836 : parrello 1.12 } else {
1837 : parrello 1.93 # Here we have an invalid line.
1838 :     Trace("Invalid option statement in record $records.") if T(0);
1839 : parrello 1.12 }
1840 :     }
1841 : parrello 1.93 # Return the hash created.
1842 :     return %retVal;
1843 : olson 1.1 }
1844 :    
1845 : parrello 1.93 =head3 GetOptions
1846 : parrello 1.9
1847 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1848 : parrello 1.9
1849 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1850 :     as input and uses the data from the second to update the first. If the second does not exist,
1851 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1852 :     exist in the first.
1853 : parrello 1.9
1854 : parrello 1.93 Consider the following example.
1855 : parrello 1.9
1856 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1857 : parrello 1.9
1858 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1859 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1860 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1861 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1862 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1863 : parrello 1.9
1864 : parrello 1.93 {databaseType => 'Oracle'}
1865 : parrello 1.9
1866 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1867 : parrello 1.9
1868 : parrello 1.93 =over 4
1869 : parrello 1.9
1870 : parrello 1.93 =item defaults
1871 : parrello 1.9
1872 : parrello 1.93 Table of default option values.
1873 : parrello 1.9
1874 : parrello 1.93 =item options
1875 : olson 1.1
1876 : parrello 1.93 Table of overrides, if any.
1877 : olson 1.1
1878 :     =item RETURN
1879 :    
1880 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1881 : olson 1.1
1882 :     =back
1883 :    
1884 :     =cut
1885 :    
1886 : parrello 1.93 sub GetOptions {
1887 :     # Get the parameters.
1888 :     my ($defaults, $options) = @_;
1889 :     # Check for overrides.
1890 :     if ($options) {
1891 :     # Loop through the overrides.
1892 :     while (my ($option, $setting) = each %{$options}) {
1893 :     # Insure this override exists.
1894 :     if (!exists $defaults->{$option}) {
1895 :     croak "Unrecognized option $option encountered.";
1896 : parrello 1.12 } else {
1897 : parrello 1.93 # Apply the override.
1898 :     $defaults->{$option} = $setting;
1899 : parrello 1.12 }
1900 :     }
1901 :     }
1902 : parrello 1.93 # Return the merged table.
1903 :     return $defaults;
1904 : olson 1.1 }
1905 :    
1906 : parrello 1.93 =head3 MergeOptions
1907 : olson 1.1
1908 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1909 : olson 1.1
1910 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1911 :     second (default) hash, and if a matching key is not found in the first hash, the default
1912 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1913 :     checking and no return value.
1914 : olson 1.1
1915 :     =over 4
1916 :    
1917 : parrello 1.93 =item table
1918 : olson 1.1
1919 : parrello 1.93 Hash table to be updated with the default values.
1920 : olson 1.1
1921 : parrello 1.93 =item defaults
1922 : olson 1.1
1923 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1924 : olson 1.1
1925 :     =back
1926 :    
1927 :     =cut
1928 :    
1929 : parrello 1.93 sub MergeOptions {
1930 :     # Get the parameters.
1931 :     my ($table, $defaults) = @_;
1932 :     # Loop through the defaults.
1933 :     while (my ($key, $value) = each %{$defaults}) {
1934 :     if (!exists $table->{$key}) {
1935 :     $table->{$key} = $value;
1936 :     }
1937 : parrello 1.12 }
1938 : olson 1.1 }
1939 :    
1940 : parrello 1.93 =head3 ParseCommand
1941 : olson 1.1
1942 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1943 : olson 1.1
1944 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
1945 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1946 :     off and merged into a table of default options. The remainder of the command line is
1947 :     returned as a list of positional arguments. For example, consider the following invocation.
1948 : olson 1.1
1949 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1950 : olson 1.1
1951 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
1952 :     B<errors> and B<logFile>. If @words has the following format
1953 : olson 1.1
1954 : parrello 1.93 -logFile=error.log apple orange rutabaga
1955 : olson 1.1
1956 : parrello 1.93 then at the end of the invocation, C<$options> will be
1957 : olson 1.1
1958 : parrello 1.93 { errors => 0, logFile => 'error.log' }
1959 : olson 1.1
1960 : parrello 1.93 and C<@arguments> will contain
1961 : olson 1.1
1962 : parrello 1.93 apple orange rutabaga
1963 : olson 1.1
1964 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1965 :     support for quote characters. Options can be specified with single or double hyphens.
1966 : parrello 1.54
1967 :     =over 4
1968 :    
1969 : parrello 1.93 =item optionTable
1970 : parrello 1.54
1971 : parrello 1.93 Table of default options.
1972 : parrello 1.54
1973 : parrello 1.93 =item inputList
1974 : parrello 1.54
1975 : parrello 1.93 List of words on the command line.
1976 : parrello 1.54
1977 :     =item RETURN
1978 :    
1979 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
1980 : parrello 1.54
1981 :     =back
1982 :    
1983 :     =cut
1984 :    
1985 : parrello 1.93 sub ParseCommand {
1986 : parrello 1.54 # Get the parameters.
1987 : parrello 1.93 my ($optionTable, @inputList) = @_;
1988 :     # Process any options in the input list.
1989 :     my %overrides = ();
1990 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
1991 :     # Get the current option.
1992 :     my $arg = shift @inputList;
1993 :     # Pull out the option name.
1994 :     $arg =~ /^--?([^=]*)/g;
1995 :     my $name = $1;
1996 :     # Check for an option value.
1997 :     if ($arg =~ /\G=(.*)$/g) {
1998 :     # Here we have a value for the option.
1999 :     $overrides{$name} = UnEscape($1);
2000 :     } else {
2001 :     # Here there is no value, so we use 1.
2002 :     $overrides{$name} = 1;
2003 :     }
2004 :     }
2005 :     # Merge the options into the defaults.
2006 :     GetOptions($optionTable, \%overrides);
2007 :     # Translate the remaining parameters.
2008 :     my @retVal = ();
2009 :     for my $inputParm (@inputList) {
2010 :     push @retVal, UnEscape($inputParm);
2011 : parrello 1.54 }
2012 : parrello 1.93 # Return the results.
2013 :     return ($optionTable, @retVal);
2014 : parrello 1.54 }
2015 :    
2016 : parrello 1.93
2017 :     =head2 File Utility Methods
2018 :    
2019 : olson 1.1 =head3 GetFile
2020 :    
2021 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2022 : olson 1.1
2023 : parrello 1.35 or
2024 :    
2025 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2026 : parrello 1.35
2027 :     Return the entire contents of a file. In list context, line-ends are removed and
2028 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2029 : olson 1.1
2030 :     =over 4
2031 :    
2032 :     =item fileName
2033 :    
2034 :     Name of the file to read.
2035 :    
2036 :     =item RETURN
2037 :    
2038 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2039 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2040 :     the file, an empty list will be returned.
2041 : olson 1.1
2042 :     =back
2043 :    
2044 :     =cut
2045 :    
2046 :     sub GetFile {
2047 : parrello 1.12 # Get the parameters.
2048 :     my ($fileName) = @_;
2049 :     # Declare the return variable.
2050 :     my @retVal = ();
2051 :     # Open the file for input.
2052 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2053 :     # Read the whole file into the return variable, stripping off any terminator
2054 :     # characters.
2055 :     my $lineCount = 0;
2056 :     while (my $line = <$handle>) {
2057 :     $lineCount++;
2058 :     $line = Strip($line);
2059 :     push @retVal, $line;
2060 :     }
2061 :     # Close it.
2062 :     close $handle;
2063 :     my $actualLines = @retVal;
2064 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2065 : parrello 1.12 # Return the file's contents in the desired format.
2066 : parrello 1.9 if (wantarray) {
2067 : parrello 1.12 return @retVal;
2068 : parrello 1.6 } else {
2069 :     return join "\n", @retVal;
2070 :     }
2071 : olson 1.1 }
2072 :    
2073 : parrello 1.60 =head3 PutFile
2074 :    
2075 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2076 : parrello 1.60
2077 :     Write out a file from a list of lines of text.
2078 :    
2079 :     =over 4
2080 :    
2081 :     =item fileName
2082 :    
2083 :     Name of the output file.
2084 :    
2085 :     =item lines
2086 :    
2087 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2088 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2089 :     modification.
2090 : parrello 1.60
2091 :     =back
2092 :    
2093 :     =cut
2094 :    
2095 :     sub PutFile {
2096 :     # Get the parameters.
2097 :     my ($fileName, $lines) = @_;
2098 :     # Open the output file.
2099 :     my $handle = Open(undef, ">$fileName");
2100 : parrello 1.77 # Count the lines written.
2101 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2102 :     # Here we have a scalar, so we write it raw.
2103 :     print $handle $lines;
2104 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2105 : parrello 1.66 } else {
2106 :     # Write the lines one at a time.
2107 : parrello 1.77 my $count = 0;
2108 : parrello 1.66 for my $line (@{$lines}) {
2109 :     print $handle "$line\n";
2110 : parrello 1.77 $count++;
2111 : parrello 1.66 }
2112 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2113 : parrello 1.60 }
2114 :     # Close the output file.
2115 :     close $handle;
2116 :     }
2117 :    
2118 : parrello 1.93 =head3 ParseRecord
2119 : olson 1.1
2120 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2121 : olson 1.1
2122 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2123 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2124 :     These will automatically be converted.
2125 : olson 1.1
2126 :     =over 4
2127 :    
2128 : parrello 1.93 =item line
2129 :    
2130 :     Line of data containing the tab-delimited fields.
2131 :    
2132 :     =item RETURN
2133 : olson 1.1
2134 : parrello 1.93 Returns a list of the fields found in the data line.
2135 : olson 1.1
2136 :     =back
2137 :    
2138 :     =cut
2139 :    
2140 : parrello 1.93 sub ParseRecord {
2141 : parrello 1.12 # Get the parameter.
2142 : parrello 1.93 my ($line) = @_;
2143 :     # Remove the trailing new-line, if any.
2144 :     chomp $line;
2145 :     # Split the line read into pieces using the tab character.
2146 :     my @retVal = split /\t/, $line;
2147 :     # Trim and fix the escapes in each piece.
2148 :     for my $value (@retVal) {
2149 :     # Trim leading whitespace.
2150 :     $value =~ s/^\s+//;
2151 :     # Trim trailing whitespace.
2152 :     $value =~ s/\s+$//;
2153 :     # Delete the carriage returns.
2154 :     $value =~ s/\r//g;
2155 :     # Convert the escapes into their real values.
2156 :     $value =~ s/\\t/"\t"/ge;
2157 :     $value =~ s/\\n/"\n"/ge;
2158 :     }
2159 :     # Return the result.
2160 :     return @retVal;
2161 :     }
2162 :    
2163 :     =head3 Merge
2164 :    
2165 :     my @mergedList = Tracer::Merge(@inputList);
2166 :    
2167 :     Sort a list of strings and remove duplicates.
2168 :    
2169 :     =over 4
2170 :    
2171 :     =item inputList
2172 :    
2173 :     List of scalars to sort and merge.
2174 :    
2175 :     =item RETURN
2176 :    
2177 :     Returns a list containing the same elements sorted in ascending order with duplicates
2178 :     removed.
2179 :    
2180 :     =back
2181 :    
2182 :     =cut
2183 :    
2184 :     sub Merge {
2185 :     # Get the input list in sort order.
2186 :     my @inputList = sort @_;
2187 :     # Only proceed if the list has at least two elements.
2188 :     if (@inputList > 1) {
2189 :     # Now we want to move through the list splicing out duplicates.
2190 :     my $i = 0;
2191 :     while ($i < @inputList) {
2192 :     # Get the current entry.
2193 :     my $thisEntry = $inputList[$i];
2194 :     # Find out how many elements duplicate the current entry.
2195 :     my $j = $i + 1;
2196 :     my $dup1 = $i + 1;
2197 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2198 :     # If the number is nonzero, splice out the duplicates found.
2199 :     if ($j > $dup1) {
2200 :     splice @inputList, $dup1, $j - $dup1;
2201 : parrello 1.14 }
2202 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2203 :     # at position $i. We push $i forward one position and start again.
2204 :     $i++;
2205 : parrello 1.14 }
2206 : parrello 1.12 }
2207 : parrello 1.93 # Return the merged list.
2208 :     return @inputList;
2209 : olson 1.1 }
2210 :    
2211 : parrello 1.93 =head3 Open
2212 : olson 1.1
2213 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2214 : olson 1.1
2215 : parrello 1.93 Open a file.
2216 : olson 1.1
2217 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2218 :     function. The mode is specified using Unix-like shell information. So, for
2219 :     example,
2220 : olson 1.1
2221 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2222 : olson 1.1
2223 : parrello 1.93 would open for output appended to the specified file, and
2224 : olson 1.1
2225 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2226 : olson 1.1
2227 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2228 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2229 :     code as follows.
2230 : olson 1.1
2231 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2232 : olson 1.1
2233 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2234 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2235 :     failed open will throw an exception and the third parameter will be used to construct
2236 :     an error message. If the parameter is omitted, a standard message is constructed
2237 :     using the file spec.
2238 : olson 1.1
2239 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2240 : olson 1.1
2241 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2242 :     The actual error message from the file system will be captured and appended to the
2243 :     message in any case.
2244 : parrello 1.6
2245 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2246 : parrello 1.6
2247 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2248 :     corresponds to the C++ C<errno> value.
2249 : parrello 1.6
2250 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2251 : parrello 1.6
2252 : parrello 1.93 =over 4
2253 : parrello 1.6
2254 : parrello 1.93 =item fileHandle
2255 : parrello 1.6
2256 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2257 :     and returned as the value of this method.
2258 : olson 1.1
2259 : parrello 1.93 =item fileSpec
2260 : olson 1.1
2261 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2262 : olson 1.1
2263 : parrello 1.93 =item message (optional)
2264 : olson 1.1
2265 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2266 :     will be generated. In either case, the error information from the file system
2267 :     is appended to the message. To specify a conditional open that does not throw
2268 :     an error if it fails, use C<0>.
2269 : olson 1.1
2270 : parrello 1.93 =item RETURN
2271 : olson 1.1
2272 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2273 :     open failed.
2274 : olson 1.1
2275 :     =back
2276 :    
2277 :     =cut
2278 :    
2279 : parrello 1.93 sub Open {
2280 : parrello 1.12 # Get the parameters.
2281 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2282 :     # Attempt to open the file.
2283 :     my $rv = open $fileHandle, $fileSpec;
2284 :     # If the open failed, generate an error message.
2285 :     if (! $rv) {
2286 :     # Save the system error message.
2287 :     my $sysMessage = $!;
2288 :     # See if we need a default message.
2289 :     if (!$message) {
2290 :     # Clean any obvious mode characters and leading spaces from the
2291 :     # filename.
2292 :     my ($fileName) = FindNamePart($fileSpec);
2293 :     $message = "Could not open \"$fileName\"";
2294 :     }
2295 :     # Terminate with an error using the supplied message and the
2296 :     # error message from the file system.
2297 :     Confess("$message: $!");
2298 : parrello 1.12 }
2299 : parrello 1.93 # Return the file handle.
2300 :     return $fileHandle;
2301 : olson 1.1 }
2302 :    
2303 : parrello 1.93 =head3 FindNamePart
2304 :    
2305 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2306 :    
2307 :     Extract the portion of a file specification that contains the file name.
2308 :    
2309 :     A file specification is the string passed to an C<open> call. It specifies the file
2310 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2311 :     method assumes that the file name is whatever follows the first angle bracket
2312 :     sequence. So, for example, in the following strings the file name is
2313 :     C</usr/fig/myfile.txt>.
2314 : parrello 1.5
2315 : parrello 1.93 >>/usr/fig/myfile.txt
2316 :     </usr/fig/myfile.txt
2317 :     | sort -u > /usr/fig/myfile.txt
2318 : parrello 1.5
2319 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2320 :     whole incoming string.
2321 : parrello 1.5
2322 :     =over 4
2323 :    
2324 : parrello 1.93 =item fileSpec
2325 : parrello 1.5
2326 : parrello 1.93 File specification string from which the file name is to be extracted.
2327 : parrello 1.5
2328 :     =item RETURN
2329 :    
2330 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2331 :     the specified string, or the whole string if a file name cannot be found via normal
2332 :     methods. The second element contains the start position of the file name portion and
2333 :     the third element contains the length.
2334 : parrello 1.5
2335 :     =back
2336 :    
2337 :     =cut
2338 : parrello 1.93 #: Return Type $;
2339 :     sub FindNamePart {
2340 :     # Get the parameters.
2341 :     my ($fileSpec) = @_;
2342 :     # Default to the whole input string.
2343 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2344 :     # Parse out the file name if we can.
2345 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2346 :     $retVal = $2;
2347 :     $len = length $retVal;
2348 :     $pos = (length $fileSpec) - (length $3) - $len;
2349 : parrello 1.12 }
2350 : parrello 1.93 # Return the result.
2351 :     return ($retVal, $pos, $len);
2352 : parrello 1.5 }
2353 :    
2354 : parrello 1.93 =head3 OpenDir
2355 : parrello 1.5
2356 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2357 : parrello 1.5
2358 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2359 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2360 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2361 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2362 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2363 :     set, an exception is thrown. So, for example,
2364 : parrello 1.5
2365 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2366 : parrello 1.5
2367 : parrello 1.93 is effectively the same as
2368 : parrello 1.5
2369 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2370 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2371 : parrello 1.5
2372 : parrello 1.93 Similarly, the following code
2373 : parrello 1.5
2374 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2375 : parrello 1.5
2376 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2377 :     automatically returns an empty list if the directory fails to open.
2378 : parrello 1.5
2379 : parrello 1.93 =over 4
2380 : parrello 1.5
2381 : parrello 1.93 =item dirName
2382 : parrello 1.5
2383 : parrello 1.93 Name of the directory to open.
2384 : parrello 1.5
2385 : parrello 1.93 =item filtered
2386 : parrello 1.5
2387 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2388 :     from the list, else FALSE.
2389 : parrello 1.5
2390 : parrello 1.93 =item flag
2391 : parrello 1.5
2392 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2393 : parrello 1.5
2394 : parrello 1.93 =back
2395 : parrello 1.5
2396 : parrello 1.93 =cut
2397 :     #: Return Type @;
2398 :     sub OpenDir {
2399 :     # Get the parameters.
2400 :     my ($dirName, $filtered, $flag) = @_;
2401 :     # Declare the return variable.
2402 :     my @retVal = ();
2403 :     # Open the directory.
2404 :     if (opendir(my $dirHandle, $dirName)) {
2405 :     # The directory opened successfully. Get the appropriate list according to the
2406 :     # strictures of the filter parameter.
2407 :     if ($filtered) {
2408 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2409 :     } else {
2410 :     @retVal = readdir $dirHandle;
2411 :     }
2412 :     } elsif (! $flag) {
2413 :     # Here the directory would not open and it's considered an error.
2414 :     Confess("Could not open directory $dirName.");
2415 :     }
2416 :     # Return the result.
2417 :     return @retVal;
2418 :     }
2419 : parrello 1.5
2420 :    
2421 : parrello 1.93 =head3 Insure
2422 : parrello 1.5
2423 : parrello 1.93 Insure($dirName, $chmod);
2424 : parrello 1.5
2425 : parrello 1.93 Insure a directory is present.
2426 : parrello 1.5
2427 : parrello 1.93 =over 4
2428 : parrello 1.5
2429 : parrello 1.93 =item dirName
2430 : olson 1.1
2431 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2432 : parrello 1.7
2433 : parrello 1.93 =item chmod (optional)
2434 : parrello 1.7
2435 : parrello 1.93 Security privileges to be given to the directory if it is created.
2436 : parrello 1.7
2437 : parrello 1.93 =back
2438 : parrello 1.7
2439 :     =cut
2440 :    
2441 : parrello 1.93 sub Insure {
2442 :     my ($dirName, $chmod) = @_;
2443 :     if (! -d $dirName) {
2444 :     Trace("Creating $dirName directory.") if T(2);
2445 :     eval {
2446 :     mkpath $dirName;
2447 :     # If we have permissions specified, set them here.
2448 :     if (defined($chmod)) {
2449 :     chmod $chmod, $dirName;
2450 :     }
2451 :     };
2452 :     if ($@) {
2453 :     Confess("Error creating $dirName: $@");
2454 :     }
2455 : parrello 1.12 }
2456 : parrello 1.9 }
2457 :    
2458 : parrello 1.93 =head3 ChDir
2459 : parrello 1.9
2460 : parrello 1.93 ChDir($dirName);
2461 : parrello 1.9
2462 : parrello 1.93 Change to the specified directory.
2463 : parrello 1.9
2464 :     =over 4
2465 :    
2466 : parrello 1.93 =item dirName
2467 : parrello 1.9
2468 : parrello 1.93 Name of the directory to which we want to change.
2469 : parrello 1.9
2470 :     =back
2471 :    
2472 :     =cut
2473 :    
2474 : parrello 1.93 sub ChDir {
2475 :     my ($dirName) = @_;
2476 :     if (! -d $dirName) {
2477 :     Confess("Cannot change to directory $dirName: no such directory.");
2478 :     } else {
2479 :     Trace("Changing to directory $dirName.") if T(File => 4);
2480 :     my $okFlag = chdir $dirName;
2481 :     if (! $okFlag) {
2482 :     Confess("Error switching to directory $dirName.");
2483 :     }
2484 :     }
2485 : parrello 1.9 }
2486 :    
2487 : parrello 1.93 =head3 SetPermissions
2488 :    
2489 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2490 : parrello 1.9
2491 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2492 :     In addition, the group ownership will be changed to the specified value.
2493 : parrello 1.9
2494 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2495 :     problems, so it does internal error recovery.
2496 : parrello 1.9
2497 :     =over 4
2498 :    
2499 : parrello 1.93 =item dirName
2500 :    
2501 :     Name of the directory to process.
2502 :    
2503 :     =item group
2504 : parrello 1.9
2505 : parrello 1.93 Name of the group to be assigned.
2506 : parrello 1.9
2507 : parrello 1.93 =item mask
2508 : parrello 1.9
2509 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2510 :     permission bits of any file or directory that does not already have them
2511 :     set to 1.
2512 : parrello 1.9
2513 : parrello 1.93 =item otherMasks
2514 : parrello 1.9
2515 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2516 :     one of the patterns, that directory and all its members and subdirectories
2517 :     will be assigned the new pattern. For example, the following would
2518 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2519 : parrello 1.9
2520 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2521 : parrello 1.9
2522 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2523 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2524 : parrello 1.22
2525 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2526 :     '^tmp' => 0666);
2527 : parrello 1.9
2528 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2529 :     names are matched, not file names.
2530 : parrello 1.9
2531 :     =back
2532 :    
2533 :     =cut
2534 :    
2535 : parrello 1.93 sub SetPermissions {
2536 : parrello 1.12 # Get the parameters.
2537 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2538 :     # Set up for error recovery.
2539 :     eval {
2540 :     # Switch to the specified directory.
2541 :     ChDir($dirName);
2542 :     # Get the group ID.
2543 :     my $gid = getgrnam($group);
2544 :     # Get the mask for tracing.
2545 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2546 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2547 :     my $fixCount = 0;
2548 :     my $lookCount = 0;
2549 :     # @dirs will be a stack of directories to be processed.
2550 :     my @dirs = (getcwd());
2551 :     while (scalar(@dirs) > 0) {
2552 :     # Get the current directory.
2553 :     my $dir = pop @dirs;
2554 :     # Check for a match to one of the specified directory names. To do
2555 :     # that, we need to pull the individual part of the name off of the
2556 :     # whole path.
2557 :     my $simpleName = $dir;
2558 :     if ($dir =~ m!/([^/]+)$!) {
2559 :     $simpleName = $1;
2560 :     }
2561 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2562 :     # Search for a match.
2563 :     my $match = 0;
2564 :     my $i;
2565 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2566 :     my $pattern = $otherMasks[$i];
2567 :     if ($simpleName =~ /$pattern/i) {
2568 :     $match = 1;
2569 :     }
2570 :     }
2571 :     # Check for a match. Note we use $i-1 because the loop added 2
2572 :     # before terminating due to the match.
2573 :     if ($match && $otherMasks[$i-1] != $mask) {
2574 :     # This directory matches one of the incoming patterns, and it's
2575 :     # a different mask, so we process it recursively with that mask.
2576 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2577 :     } else {
2578 :     # Here we can process normally. Get all of the non-hidden members.
2579 :     my @submems = OpenDir($dir, 1);
2580 :     for my $submem (@submems) {
2581 :     # Get the full name.
2582 :     my $thisMem = "$dir/$submem";
2583 :     Trace("Checking member $thisMem.") if T(4);
2584 :     $lookCount++;
2585 :     if ($lookCount % 1000 == 0) {
2586 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2587 :     }
2588 :     # Fix the group.
2589 :     chown -1, $gid, $thisMem;
2590 :     # Insure this member is not a symlink.
2591 :     if (! -l $thisMem) {
2592 :     # Get its info.
2593 :     my $fileInfo = stat $thisMem;
2594 :     # Only proceed if we got the info. Otherwise, it's a hard link
2595 :     # and we want to skip it anyway.
2596 :     if ($fileInfo) {
2597 :     my $fileMode = $fileInfo->mode;
2598 :     if (($fileMode & $mask) != $mask) {
2599 :     # Fix this member.
2600 :     $fileMode |= $mask;
2601 :     chmod $fileMode, $thisMem;
2602 :     $fixCount++;
2603 :     }
2604 :     # If it's a subdirectory, stack it.
2605 :     if (-d $thisMem) {
2606 :     push @dirs, $thisMem;
2607 :     }
2608 :     }
2609 :     }
2610 :     }
2611 :     }
2612 : parrello 1.12 }
2613 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2614 :     };
2615 :     # Check for an error.
2616 :     if ($@) {
2617 :     Confess("SetPermissions error: $@");
2618 : parrello 1.12 }
2619 : parrello 1.7 }
2620 :    
2621 : parrello 1.93 =head3 GetLine
2622 : parrello 1.29
2623 : parrello 1.93 my @data = Tracer::GetLine($handle);
2624 : parrello 1.15
2625 : parrello 1.93 Read a line of data from a tab-delimited file.
2626 : parrello 1.15
2627 :     =over 4
2628 :    
2629 : parrello 1.93 =item handle
2630 : parrello 1.15
2631 : parrello 1.93 Open file handle from which to read.
2632 : parrello 1.15
2633 :     =item RETURN
2634 :    
2635 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2636 :     tab-delimited. If we are at the end of the file, then an empty list will be
2637 :     returned. If an empty line is read, a single list item consisting of a null
2638 :     string will be returned.
2639 : parrello 1.15
2640 :     =back
2641 :    
2642 :     =cut
2643 : parrello 1.93
2644 :     sub GetLine {
2645 : parrello 1.15 # Get the parameters.
2646 : parrello 1.93 my ($handle) = @_;
2647 :     # Declare the return variable.
2648 :     my @retVal = ();
2649 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2650 :     # Read from the file.
2651 :     my $line = <$handle>;
2652 :     # Only proceed if we found something.
2653 :     if (defined $line) {
2654 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2655 :     # upload control and have a nonstandard EOL combination.
2656 :     $line =~ s/(\r|\n)+$//;
2657 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2658 :     if (T(File => 4)) {
2659 :     my $escapedLine = $line;
2660 :     $escapedLine =~ s/\n/\\n/g;
2661 :     $escapedLine =~ s/\r/\\r/g;
2662 :     $escapedLine =~ s/\t/\\t/g;
2663 :     Trace("Line read: -->$escapedLine<--");
2664 :     }
2665 :     # If the line is empty, return a single empty string; otherwise, parse
2666 :     # it into fields.
2667 :     if ($line eq "") {
2668 :     push @retVal, "";
2669 :     } else {
2670 :     push @retVal, split /\t/,$line;
2671 :     }
2672 :     } else {
2673 :     # Trace the reason the read failed.
2674 :     Trace("End of file: $!") if T(File => 3);
2675 : parrello 1.15 }
2676 : parrello 1.93 # Return the result.
2677 :     return @retVal;
2678 : parrello 1.15 }
2679 :    
2680 : parrello 1.93 =head3 PutLine
2681 :    
2682 :     Tracer::PutLine($handle, \@fields, $eol);
2683 : parrello 1.35
2684 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2685 :     output in tab-separated form, with a trailing new-line.
2686 : parrello 1.35
2687 : parrello 1.93 =over 4
2688 : parrello 1.35
2689 : parrello 1.93 =item handle
2690 : parrello 1.69
2691 : parrello 1.93 Output file handle.
2692 : parrello 1.69
2693 : parrello 1.93 =item fields
2694 : parrello 1.69
2695 : parrello 1.93 List of field values.
2696 : parrello 1.69
2697 : parrello 1.93 =item eol (optional)
2698 : parrello 1.69
2699 : parrello 1.93 End-of-line character (default is "\n").
2700 : parrello 1.69
2701 :     =back
2702 : parrello 1.35
2703 :     =cut
2704 :    
2705 : parrello 1.93 sub PutLine {
2706 : parrello 1.69 # Get the parameters.
2707 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2708 :     # Write the data.
2709 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2710 : parrello 1.69 }
2711 :    
2712 :    
2713 : parrello 1.97 =head3 PrintLine
2714 :    
2715 :     Tracer::PrintLine($line);
2716 :    
2717 :     Print a line of text with a trailing new-line.
2718 :    
2719 :     =over 4
2720 :    
2721 :     =item line
2722 :    
2723 :     Line of text to print.
2724 :    
2725 :     =back
2726 :    
2727 :     =cut
2728 :    
2729 :     sub PrintLine {
2730 :     # Get the parameters.
2731 :     my ($line) = @_;
2732 :     # Print the line.
2733 :     print "$line\n";
2734 :     }
2735 :    
2736 : parrello 1.69
2737 : parrello 1.93 =head2 Other Useful Methods
2738 :    
2739 :     =head3 ParseParm
2740 :    
2741 :     my $listValue = Tracer::ParseParm($string);
2742 :    
2743 :     Convert a parameter into a list reference. If the parameter is undefined,
2744 :     an undefined value will be returned. Otherwise, it will be parsed as a
2745 :     comma-separated list of values.
2746 : parrello 1.69
2747 :     =over 4
2748 :    
2749 : parrello 1.93 =item string
2750 :    
2751 :     Incoming string.
2752 :    
2753 :     =item RETURN
2754 : parrello 1.69
2755 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2756 :     was undefined.
2757 : parrello 1.69
2758 :     =back
2759 :    
2760 :     =cut
2761 :    
2762 : parrello 1.93 sub ParseParm {
2763 :     # Get the parameters.
2764 :     my ($string) = @_;
2765 :     # Declare the return variable.
2766 :     my $retVal;
2767 :     # Check for data.
2768 :     if (defined $string) {
2769 :     # We have some, so split it into a list.
2770 :     $retVal = [ split /\s*,\s*/, $string];
2771 : parrello 1.72 }
2772 : parrello 1.93 # Return the result.
2773 :     return $retVal;
2774 : parrello 1.69 }
2775 :    
2776 : parrello 1.97 =head3 Now
2777 :    
2778 :     my $string = Tracer::Now();
2779 :    
2780 :     Return a displayable time stamp containing the local time. Whatever format this
2781 :     method produces must be parseable by L</ParseDate>.
2782 :    
2783 :     =cut
2784 :    
2785 :     sub Now {
2786 :     return DisplayTime(time);
2787 :     }
2788 :    
2789 :     =head3 DisplayTime
2790 :    
2791 :     my $string = Tracer::DisplayTime($time);
2792 : parrello 1.69
2793 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
2794 :     method produces must be parseable by L</ParseDate>.
2795 :    
2796 :     =over 4
2797 : parrello 1.69
2798 : parrello 1.97 =item time
2799 : parrello 1.69
2800 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2801 :    
2802 :     =item RETURN
2803 : parrello 1.69
2804 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2805 : parrello 1.69
2806 : parrello 1.97 =back
2807 : parrello 1.69
2808 : parrello 1.93 =cut
2809 : parrello 1.69
2810 : parrello 1.97 sub DisplayTime {
2811 :     my ($time) = @_;
2812 :     my $retVal = "(n/a)";
2813 :     if (defined $time) {
2814 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2815 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2816 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2817 :     }
2818 : parrello 1.93 return $retVal;
2819 :     }
2820 : parrello 1.69
2821 : parrello 1.93 # Pad a number to 2 digits.
2822 :     sub _p2 {
2823 :     my ($value) = @_;
2824 :     $value = "0$value" if ($value < 10);
2825 :     return $value;
2826 : parrello 1.69 }
2827 :    
2828 : parrello 1.93 =head3 Escape
2829 : parrello 1.69
2830 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2831 : parrello 1.69
2832 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2833 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2834 :     result is to reverse the effect of L</UnEscape>.
2835 : parrello 1.69
2836 :     =over 4
2837 :    
2838 : parrello 1.93 =item realString
2839 : parrello 1.69
2840 : parrello 1.93 String to escape.
2841 : parrello 1.69
2842 :     =item RETURN
2843 :    
2844 : parrello 1.93 Escaped equivalent of the real string.
2845 :    
2846 :     =back
2847 :    
2848 :     =cut
2849 :    
2850 :     sub Escape {
2851 :     # Get the parameter.
2852 :     my ($realString) = @_;
2853 :     # Initialize the return variable.
2854 :     my $retVal = "";
2855 :     # Loop through the parameter string, looking for sequences to escape.
2856 :     while (length $realString > 0) {
2857 :     # Look for the first sequence to escape.
2858 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2859 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2860 :     # itself is in $2. First, move the clear text to the return variable.
2861 :     $retVal .= $1;
2862 :     # Strip the processed section off the real string.
2863 :     $realString = substr $realString, (length $2) + (length $1);
2864 :     # Get the matched character.
2865 :     my $char = $2;
2866 :     # If we have a CR, we are done.
2867 :     if ($char ne "\r") {
2868 :     # It's not a CR, so encode the escape sequence.
2869 :     $char =~ tr/\t\n/tn/;
2870 :     $retVal .= "\\" . $char;
2871 :     }
2872 :     } else {
2873 :     # Here there are no more escape sequences. The rest of the string is
2874 :     # transferred unmodified.
2875 :     $retVal .= $realString;
2876 :     $realString = "";
2877 :     }
2878 :     }
2879 :     # Return the result.
2880 :     return $retVal;
2881 : parrello 1.69 }
2882 :    
2883 : parrello 1.93 =head3 UnEscape
2884 : parrello 1.69
2885 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2886 : parrello 1.69
2887 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2888 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2889 :     be deleted.
2890 : parrello 1.69
2891 :     =over 4
2892 :    
2893 : parrello 1.93 =item codedString
2894 : parrello 1.69
2895 : parrello 1.93 String to un-escape.
2896 : parrello 1.69
2897 :     =item RETURN
2898 :    
2899 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2900 :     values.
2901 : parrello 1.69
2902 :     =back
2903 :    
2904 :     =cut
2905 :    
2906 : parrello 1.93 sub UnEscape {
2907 :     # Get the parameter.
2908 :     my ($codedString) = @_;
2909 :     # Initialize the return variable.
2910 :     my $retVal = "";
2911 :     # Only proceed if the incoming string is nonempty.
2912 :     if (defined $codedString) {
2913 :     # Loop through the parameter string, looking for escape sequences. We can't do
2914 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
2915 :     # "\<tab>" no matter what we do.)
2916 :     while (length $codedString > 0) {
2917 :     # Look for the first escape sequence.
2918 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2919 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2920 :     # itself is in $2. First, move the clear text to the return variable.
2921 :     $retVal .= $1;
2922 :     $codedString = substr $codedString, (2 + length $1);
2923 :     # Get the escape value.
2924 :     my $char = $2;
2925 :     # If we have a "\r", we are done.
2926 :     if ($char ne 'r') {
2927 :     # Here it's not an 'r', so we convert it.
2928 :     $char =~ tr/\\tn/\\\t\n/;
2929 :     $retVal .= $char;
2930 :     }
2931 :     } else {
2932 :     # Here there are no more escape sequences. The rest of the string is
2933 :     # transferred unmodified.
2934 :     $retVal .= $codedString;
2935 :     $codedString = "";
2936 :     }
2937 :     }
2938 : parrello 1.35 }
2939 : parrello 1.69 # Return the result.
2940 :     return $retVal;
2941 :     }
2942 :    
2943 : parrello 1.93 =head3 Percent
2944 : parrello 1.69
2945 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
2946 : parrello 1.69
2947 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
2948 :     is zero, returns zero.
2949 : parrello 1.69
2950 :     =over 4
2951 :    
2952 : parrello 1.93 =item number
2953 : parrello 1.69
2954 : parrello 1.93 Percent numerator.
2955 : parrello 1.69
2956 : parrello 1.93 =item base
2957 : parrello 1.69
2958 : parrello 1.93 Percent base.
2959 : parrello 1.69
2960 : parrello 1.93 =item RETURN
2961 : parrello 1.69
2962 : parrello 1.93 Returns the percentage of the base represented by the numerator.
2963 : parrello 1.69
2964 :     =back
2965 :    
2966 :     =cut
2967 :    
2968 : parrello 1.93 sub Percent {
2969 : parrello 1.69 # Get the parameters.
2970 : parrello 1.93 my ($number, $base) = @_;
2971 :     # Declare the return variable.
2972 :     my $retVal = 0;
2973 :     # Compute the percent.
2974 :     if ($base != 0) {
2975 :     $retVal = $number * 100 / $base;
2976 :     }
2977 :     # Return the result.
2978 :     return $retVal;
2979 : parrello 1.69 }
2980 :    
2981 : parrello 1.97 =head3 Constrain
2982 :    
2983 :     my $constrained = Constrain($value, $min, $max);
2984 :    
2985 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
2986 :    
2987 :     =over 4
2988 :    
2989 :     =item value
2990 :    
2991 :     Value to constrain.
2992 :    
2993 :     =item min (optional)
2994 :    
2995 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
2996 :    
2997 :     =item max (optional)
2998 :    
2999 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3000 :    
3001 :     =item RETURN
3002 :    
3003 :     Returns the incoming value, constrained according to the other parameters.
3004 :    
3005 :     =back
3006 :    
3007 :     =cut
3008 :    
3009 :     sub Constrain {
3010 :     # Get the parameters.
3011 :     my ($value, $min, $max) = @_;
3012 :     # Declare the return variable.
3013 :     my $retVal = $value;
3014 :     # Apply the minimum constraint.
3015 :     if (defined $min && $retVal < $min) {
3016 :     $retVal = $min;
3017 :     }
3018 :     # Apply the maximum constraint.
3019 :     if (defined $max && $retVal > $max) {
3020 :     $retVal = $max;
3021 :     }
3022 :     # Return the result.
3023 :     return $retVal;
3024 :     }
3025 :    
3026 : parrello 1.93 =head3 Min
3027 : parrello 1.69
3028 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3029 : parrello 1.69
3030 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3031 : parrello 1.69
3032 :     =over 4
3033 :    
3034 : parrello 1.93 =item $value1, $value2, ... $valueN
3035 : parrello 1.69
3036 : parrello 1.93 List of numbers to compare.
3037 : parrello 1.69
3038 :     =item RETURN
3039 :    
3040 : parrello 1.93 Returns the lowest number in the list.
3041 : parrello 1.69
3042 :     =back
3043 :    
3044 :     =cut
3045 :    
3046 : parrello 1.93 sub Min {
3047 :     # Get the parameters. Note that we prime the return value with the first parameter.
3048 :     my ($retVal, @values) = @_;
3049 :     # Loop through the remaining parameters, looking for the lowest.
3050 :     for my $value (@values) {
3051 :     if ($value < $retVal) {
3052 :     $retVal = $value;
3053 : parrello 1.72 }
3054 :     }
3055 : parrello 1.93 # Return the minimum found.
3056 : parrello 1.70 return $retVal;
3057 : parrello 1.35 }
3058 :    
3059 : parrello 1.93 =head3 Max
3060 :    
3061 :     my $max = Max($value1, $value2, ... $valueN);
3062 : parrello 1.69
3063 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3064 : parrello 1.65
3065 : parrello 1.93 =over 4
3066 : parrello 1.65
3067 : parrello 1.93 =item $value1, $value2, ... $valueN
3068 : parrello 1.65
3069 : parrello 1.93 List of numbers to compare.
3070 : parrello 1.65
3071 : parrello 1.93 =item RETURN
3072 : parrello 1.65
3073 : parrello 1.93 Returns the highest number in the list.
3074 : parrello 1.65
3075 :     =back
3076 :    
3077 :     =cut
3078 :    
3079 : parrello 1.93 sub Max {
3080 :     # Get the parameters. Note that we prime the return value with the first parameter.
3081 :     my ($retVal, @values) = @_;
3082 :     # Loop through the remaining parameters, looking for the highest.
3083 :     for my $value (@values) {
3084 :     if ($value > $retVal) {
3085 :     $retVal = $value;
3086 : parrello 1.65 }
3087 :     }
3088 : parrello 1.93 # Return the maximum found.
3089 :     return $retVal;
3090 : parrello 1.65 }
3091 :    
3092 : parrello 1.93 =head3 Strip
3093 : parrello 1.37
3094 : parrello 1.93 my $string = Tracer::Strip($line);
3095 : parrello 1.37
3096 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3097 :     that may have been transferred back and forth several times among different
3098 :     operating environments.
3099 : parrello 1.37
3100 :     =over 4
3101 :    
3102 : parrello 1.93 =item line
3103 : parrello 1.37
3104 : parrello 1.93 Line of text to be stripped.
3105 : parrello 1.37
3106 : parrello 1.93 =item RETURN
3107 : parrello 1.91
3108 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3109 : parrello 1.91
3110 : parrello 1.37 =back
3111 :    
3112 :     =cut
3113 :    
3114 : parrello 1.93 sub Strip {
3115 :     # Get a copy of the parameter string.
3116 :     my ($string) = @_;
3117 :     my $retVal = (defined $string ? $string : "");
3118 :     # Strip the line terminator characters.
3119 :     $retVal =~ s/(\r|\n)+$//g;
3120 :     # Return the result.
3121 :     return $retVal;
3122 : parrello 1.43 }
3123 :    
3124 : parrello 1.93 =head3 Pad
3125 : parrello 1.43
3126 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3127 : parrello 1.43
3128 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3129 :     space, and the padding will be on the right side unless specified
3130 :     in the third parameter.
3131 : parrello 1.43
3132 :     =over 4
3133 :    
3134 : parrello 1.93 =item string
3135 :    
3136 :     String to be padded.
3137 :    
3138 :     =item len
3139 :    
3140 :     Desired length of the padded string.
3141 :    
3142 :     =item left (optional)
3143 :    
3144 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3145 :    
3146 :     =item padChar (optional)
3147 :    
3148 :     Character to use for padding. The default is a space.
3149 :    
3150 :     =item RETURN
3151 : parrello 1.43
3152 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3153 :     specified end so that it achieves the desired length.
3154 : parrello 1.43
3155 :     =back
3156 :    
3157 :     =cut
3158 :    
3159 : parrello 1.93 sub Pad {
3160 :     # Get the parameters.
3161 :     my ($string, $len, $left, $padChar) = @_;
3162 :     # Compute the padding character.
3163 :     if (! defined $padChar) {
3164 :     $padChar = " ";
3165 :     }
3166 :     # Compute the number of spaces needed.
3167 :     my $needed = $len - length $string;
3168 :     # Copy the string into the return variable.
3169 :     my $retVal = $string;
3170 :     # Only proceed if padding is needed.
3171 :     if ($needed > 0) {
3172 :     # Create the pad string.
3173 :     my $pad = $padChar x $needed;
3174 :     # Affix it to the return value.
3175 :     if ($left) {
3176 :     $retVal = $pad . $retVal;
3177 :     } else {
3178 :     $retVal .= $pad;
3179 : parrello 1.43 }
3180 : parrello 1.37 }
3181 : parrello 1.93 # Return the result.
3182 :     return $retVal;
3183 : parrello 1.37 }
3184 :    
3185 : parrello 1.93 =head3 EOF
3186 :    
3187 :     This is a constant that is lexically greater than any useful string.
3188 :    
3189 :     =cut
3190 :    
3191 :     sub EOF {
3192 :     return "\xFF\xFF\xFF\xFF\xFF";
3193 :     }
3194 : parrello 1.59
3195 : parrello 1.93 =head3 TICK
3196 : parrello 1.59
3197 : parrello 1.93 my @results = TICK($commandString);
3198 : parrello 1.59
3199 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3200 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3201 : parrello 1.59
3202 : parrello 1.93 `./protein.cgi`
3203 : parrello 1.59
3204 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3205 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3206 : parrello 1.59
3207 : parrello 1.93 TICK("./protein.cgi")
3208 : parrello 1.59
3209 : parrello 1.93 it will work correctly in both environments.
3210 : parrello 1.59
3211 : parrello 1.93 =over 4
3212 : parrello 1.59
3213 : parrello 1.93 =item commandString
3214 : parrello 1.59
3215 : parrello 1.93 The command string to pass to the system.
3216 : parrello 1.59
3217 :     =item RETURN
3218 :    
3219 : parrello 1.93 Returns the standard output from the specified command, as a list.
3220 : parrello 1.59
3221 :     =back
3222 :    
3223 :     =cut
3224 : parrello 1.93 #: Return Type @;
3225 :     sub TICK {
3226 : parrello 1.59 # Get the parameters.
3227 : parrello 1.93 my ($commandString) = @_;
3228 :     # Chop off the dot-slash if this is Windows.
3229 :     if ($FIG_Config::win_mode) {
3230 :     $commandString =~ s!^\./!!;
3231 : parrello 1.59 }
3232 : parrello 1.93 # Activate the command and return the result.
3233 :     return `$commandString`;
3234 : parrello 1.59 }
3235 :    
3236 : parrello 1.93
3237 : parrello 1.55 =head3 CommaFormat
3238 :    
3239 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3240 : parrello 1.55
3241 :     Insert commas into a number.
3242 :    
3243 :     =over 4
3244 :    
3245 :     =item number
3246 :    
3247 :     A sequence of digits.
3248 :    
3249 :     =item RETURN
3250 :    
3251 :     Returns the same digits with commas strategically inserted.
3252 :    
3253 :     =back
3254 :    
3255 :     =cut
3256 :    
3257 :     sub CommaFormat {
3258 :     # Get the parameters.
3259 :     my ($number) = @_;
3260 :     # Pad the length up to a multiple of three.
3261 :     my $padded = "$number";
3262 :     $padded = " " . $padded while length($padded) % 3 != 0;
3263 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3264 :     # cause the delimiters to be included in the output stream. The
3265 :     # GREP removes the empty strings in between the delimiters.
3266 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3267 :     # Clean out the spaces.
3268 :     $retVal =~ s/ //g;
3269 :     # Return the result.
3270 :     return $retVal;
3271 :     }
3272 : parrello 1.46
3273 :    
3274 : parrello 1.62 =head3 CompareLists
3275 :    
3276 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3277 : parrello 1.62
3278 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3279 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3280 :     The return value contains a list of items that are only in the new list
3281 :     (inserted) and only in the old list (deleted).
3282 :    
3283 :     =over 4
3284 :    
3285 :     =item newList
3286 :    
3287 :     Reference to a list of new tuples.
3288 :    
3289 :     =item oldList
3290 :    
3291 :     Reference to a list of old tuples.
3292 :    
3293 :     =item keyIndex (optional)
3294 :    
3295 :     Index into each tuple of its key field. The default is 0.
3296 :    
3297 :     =item RETURN
3298 :    
3299 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3300 :     list (inserted) followed by a reference to the list of items that are only in the old
3301 :     list (deleted).
3302 :    
3303 :     =back
3304 :    
3305 :     =cut
3306 :    
3307 :     sub CompareLists {
3308 :     # Get the parameters.
3309 :     my ($newList, $oldList, $keyIndex) = @_;
3310 :     if (! defined $keyIndex) {
3311 :     $keyIndex = 0;
3312 :     }
3313 :     # Declare the return variables.
3314 :     my ($inserted, $deleted) = ([], []);
3315 :     # Loop through the two lists simultaneously.
3316 :     my ($newI, $oldI) = (0, 0);
3317 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3318 :     while ($newI < $newN || $oldI < $oldN) {
3319 :     # Get the current object in each list. Note that if one
3320 :     # of the lists is past the end, we'll get undef.
3321 :     my $newItem = $newList->[$newI];
3322 :     my $oldItem = $oldList->[$oldI];
3323 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3324 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3325 :     push @{$deleted}, $oldItem;
3326 :     $oldI++;
3327 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3328 :     # The new item is not in the old list, so mark it inserted.
3329 :     push @{$inserted}, $newItem;
3330 :     $newI++;
3331 :     } else {
3332 :     # The item is in both lists, so push forward.
3333 :     $oldI++;
3334 :     $newI++;
3335 :     }
3336 :     }
3337 :     # Return the result.
3338 :     return ($inserted, $deleted);
3339 :     }
3340 :    
3341 : parrello 1.105 =head3 Cmp
3342 :    
3343 :     my $cmp = Tracer::Cmp($a, $b);
3344 :    
3345 :     This method performs a universal sort comparison. Each value coming in is
3346 :     separated into a leading text part and a trailing number part. The text
3347 :     part is string compared, and if both parts are equal, then the number
3348 :     parts are compared numerically. A stream of just numbers or a stream of
3349 :     just strings will sort correctly, and a mixed stream will sort with the
3350 :     numbers first. Strings with a label and a number will sort in the
3351 :     expected manner instead of lexically.
3352 :    
3353 :     =over 4
3354 :    
3355 :     =item a
3356 :    
3357 :     First item to compare.
3358 :    
3359 :     =item b
3360 :    
3361 :     Second item to compare.
3362 :    
3363 :     =item RETURN
3364 :    
3365 :     Returns a negative number if the first item should sort first (is less), a positive
3366 :     number if the first item should sort second (is greater), and a zero if the items are
3367 :     equal.
3368 :    
3369 :     =back
3370 :    
3371 :     =cut
3372 :    
3373 :     sub Cmp {
3374 :     # Get the parameters.
3375 :     my ($a, $b) = @_;
3376 :     # Declare the return value.
3377 :     my $retVal;
3378 :     # Check for nulls.
3379 :     if (! defined($a)) {
3380 :     $retVal = (! defined($b) ? 0 : -1);
3381 :     } elsif (! defined($b)) {
3382 :     $retVal = 1;
3383 :     } else {
3384 :     # Here we have two real values. Parse the two strings.
3385 :     $a =~ /^(\D*)(\d*)$/;
3386 :     my $aParsed = [$1, $2];
3387 :     $b =~ /^(\D*)(\d*)$/;
3388 :     my $bParsed = [$1, $2];
3389 :     # Compare the string parts.
3390 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3391 :     if (! $retVal) {
3392 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3393 :     }
3394 :     }
3395 :     # Return the result.
3396 :     return $retVal;
3397 :     }
3398 :    
3399 : parrello 1.108 =head3 ListEQ
3400 :    
3401 :     my $flag = Tracer::ListEQ(\@a, \@b);
3402 :    
3403 :     Return TRUE if the specified lists contain the same strings in the same
3404 :     order, else FALSE.
3405 :    
3406 :     =over 4
3407 :    
3408 :     =item a
3409 :    
3410 :     Reference to the first list.
3411 :    
3412 :     =item b
3413 :    
3414 :     Reference to the second list.
3415 :    
3416 :     =item RETURN
3417 :    
3418 :     Returns TRUE if the two parameters are identical string lists, else FALSE.
3419 :    
3420 :     =back
3421 :    
3422 :     =cut
3423 :    
3424 :     sub ListEQ {
3425 :     # Get the parameters.
3426 :     my ($a, $b) = @_;
3427 :     # Declare the return variable. Start by checking the lengths.
3428 :     my $n = scalar(@$a);
3429 :     my $retVal = ($n == scalar(@$b));
3430 :     # Now compare the list elements.
3431 :     for (my $i = 0; $retVal && $i < $n; $i++) {
3432 :     $retVal = ($a->[$i] eq $b->[$i]);
3433 :     }
3434 :     # Return the result.
3435 :     return $retVal;
3436 :     }
3437 :    
3438 : parrello 1.105 =head2 CGI Script Utilities
3439 :    
3440 :     =head3 ScriptSetup (deprecated)
3441 :    
3442 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
3443 :    
3444 :     Perform standard tracing and debugging setup for scripts. The value returned is
3445 :     the CGI object followed by a pre-built variable hash. At the end of the script,
3446 :     the client should call L</ScriptFinish> to output the web page.
3447 :    
3448 :     This method calls L</ETracing> to configure tracing, which allows the tracing
3449 :     to be configured via the emergency tracing form on the debugging control panel.
3450 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
3451 :     method, which includes every program that uses this method or L</StandardSetup>.
3452 :    
3453 :     =over 4
3454 :    
3455 :     =item noTrace (optional)
3456 :    
3457 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
3458 :     tracing manually.
3459 :    
3460 :     =item RETURN
3461 :    
3462 :     Returns a two-element list consisting of a CGI query object and a variable hash for
3463 :     the output page.
3464 :    
3465 :     =back
3466 :    
3467 :     =cut
3468 :    
3469 :     sub ScriptSetup {
3470 :     # Get the parameters.
3471 :     my ($noTrace) = @_;
3472 :     # Get the CGI query object.
3473 :     my $cgi = CGI->new();
3474 :     # Set up tracing if it's not suppressed.
3475 :     ETracing($cgi) unless $noTrace;
3476 :     # Create the variable hash.
3477 :     my $varHash = { results => '' };
3478 :     # Return the query object and variable hash.
3479 :     return ($cgi, $varHash);
3480 :     }
3481 :    
3482 :     =head3 ScriptFinish (deprecated)
3483 :    
3484 :     ScriptFinish($webData, $varHash);
3485 :    
3486 :     Output a web page at the end of a script. Either the string to be output or the
3487 :     name of a template file can be specified. If the second parameter is omitted,
3488 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
3489 :     name of a template file. The template should have the variable C<DebugData>
3490 :     specified in any form that invokes a standard script. If debugging mode is turned
3491 :     on, a form field will be put in that allows the user to enter tracing data.
3492 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
3493 :     the output, formatted as a list.
3494 :    
3495 :     A typical standard script would loook like the following.
3496 :    
3497 :     BEGIN {
3498 :     # Print the HTML header.
3499 :     print "CONTENT-TYPE: text/html\n\n";
3500 :     }
3501 :     use Tracer;
3502 :     use CGI;
3503 :     use FIG;
3504 :     # ... more uses ...
3505 :    
3506 :     my ($cgi, $varHash) = ScriptSetup();
3507 :     eval {
3508 :     # ... get data from $cgi, put it in $varHash ...
3509 :     };
3510 :     if ($@) {
3511 :     Trace("Script Error: $@") if T(0);
3512 :     }
3513 :     ScriptFinish("Html/MyTemplate.html", $varHash);
3514 :    
3515 :     The idea here is that even if the script fails, you'll see trace messages and
3516 :     useful output.
3517 :    
3518 :     =over 4
3519 :    
3520 :     =item webData
3521 :    
3522 :     A string containing either the full web page to be written to the output or the
3523 :     name of a template file from which the page is to be constructed. If the name
3524 :     of a template file is specified, then the second parameter must be present;
3525 :     otherwise, it must be absent.
3526 :    
3527 :     =item varHash (optional)
3528 :    
3529 :     If specified, then a reference to a hash mapping variable names for a template
3530 :     to their values. The template file will be read into memory, and variable markers
3531 :     will be replaced by data in this hash reference.
3532 :    
3533 :     =back
3534 :    
3535 :     =cut
3536 :    
3537 :     sub ScriptFinish {
3538 :     # Get the parameters.
3539 :     my ($webData, $varHash) = @_;
3540 :     # Check for a template file situation.
3541 :     my $outputString;
3542 :     if (defined $varHash) {
3543 :     # Here we have a template file. We need to determine the template type.
3544 :     my $template;
3545 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3546 :     $template = "$FIG_Config::template_url/$webData";
3547 :     } else {
3548 :     $template = "<<$webData";
3549 :     }
3550 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
3551 :     } else {
3552 :     # Here the user gave us a raw string.
3553 :     $outputString = $webData;
3554 :     }
3555 :     # Check for trace messages.
3556 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
3557 :     # We have trace messages, so we want to put them at the end of the body. This
3558 :     # is either at the end of the whole string or at the beginning of the BODY
3559 :     # end-tag.
3560 :     my $pos = length $outputString;
3561 :     if ($outputString =~ m#</body>#gi) {
3562 :     $pos = (pos $outputString) - 7;
3563 :     }
3564 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
3565 :     # destination.
3566 :     my $traceHtml;
3567 :     if ($Destination eq "QUEUE") {
3568 :     $traceHtml = QTrace('Html');
3569 :     } elsif ($Destination =~ /^>>(.+)$/) {
3570 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
3571 :     # can copy the file name into the clipboard easily.
3572 :     my $actualDest = $1;
3573 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3574 :     } else {
3575 :     # Here we have one of the special destinations.
3576 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3577 :     }
3578 :     substr $outputString, $pos, 0, $traceHtml;
3579 :     }
3580 :     # Write the output string.
3581 :     print $outputString;
3582 :     }
3583 :    
3584 : parrello 1.65 =head3 GenerateURL
3585 :    
3586 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3587 : parrello 1.65
3588 :     Generate a GET-style URL for the specified page with the specified parameter
3589 :     names and values. The values will be URL-escaped automatically. So, for
3590 :     example
3591 :    
3592 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3593 :    
3594 :     would return
3595 :    
3596 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3597 : parrello 1.65
3598 :     =over 4
3599 :    
3600 :     =item page
3601 :    
3602 :     Page URL.
3603 :    
3604 :     =item parameters
3605 :    
3606 :     Hash mapping parameter names to parameter values.
3607 :    
3608 :     =item RETURN
3609 :    
3610 :     Returns a GET-style URL that goes to the specified page and passes in the
3611 :     specified parameters and values.
3612 :    
3613 :     =back
3614 :    
3615 :     =cut
3616 :    
3617 :     sub GenerateURL {
3618 :     # Get the parameters.
3619 :     my ($page, %parameters) = @_;
3620 :     # Prime the return variable with the page URL.
3621 :     my $retVal = $page;
3622 :     # Loop through the parameters, creating parameter elements in a list.
3623 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3624 :     # If the list is nonempty, tack it on.
3625 :     if (@parmList) {
3626 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3627 : parrello 1.65 }
3628 :     # Return the result.
3629 :     return $retVal;
3630 :     }
3631 :    
3632 : parrello 1.78 =head3 ApplyURL
3633 :    
3634 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3635 : parrello 1.78
3636 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3637 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3638 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3639 :    
3640 :     This provides a simple way to process the results of a database query into something
3641 :     displayable by combining a URL with text.
3642 :    
3643 :     =over 4
3644 :    
3645 :     =item table
3646 :    
3647 :     Reference to a list of lists. The elements in the containing list will be updated by
3648 :     this method.
3649 :    
3650 :     =item target
3651 :    
3652 :     The index of the column to be converted into HTML.
3653 :    
3654 :     =item url
3655 :    
3656 :     The index of the column containing the URL. Note that the URL must have a recognizable
3657 :     C<http:> at the beginning.
3658 :    
3659 :     =back
3660 :    
3661 :     =cut
3662 :    
3663 :     sub ApplyURL {
3664 :     # Get the parameters.
3665 :     my ($table, $target, $url) = @_;
3666 :     # Loop through the table.
3667 :     for my $row (@{$table}) {
3668 :     # Apply the URL to the target cell.
3669 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3670 :     # Delete the URL from the row.
3671 :     delete $row->[$url];
3672 :     }
3673 :     }
3674 :    
3675 :     =head3 CombineURL
3676 :    
3677 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3678 : parrello 1.78
3679 :     This method will convert the specified text into HTML hyperlinked to the specified
3680 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3681 :     is defined and begins with an C<http:> header.
3682 :    
3683 :     =over 4
3684 :    
3685 :     =item text
3686 :    
3687 :     Text to return. This will be HTML-escaped automatically.
3688 :    
3689 :     =item url
3690 :    
3691 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3692 :     will be returned without any hyperlinking.
3693 :    
3694 :     =item RETURN
3695 :    
3696 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3697 :     doesn't look right, the HTML-escaped text will be returned without any further
3698 :     modification.
3699 :    
3700 :     =back
3701 :    
3702 :     =cut
3703 :    
3704 :     sub CombineURL {
3705 :     # Get the parameters.
3706 :     my ($text, $url) = @_;
3707 :     # Declare the return variable.
3708 :     my $retVal = CGI::escapeHTML($text);
3709 :     # Verify the URL.
3710 :     if (defined($url) && $url =~ m!http://!i) {
3711 :     # It's good, so we apply it to the text.
3712 :     $retVal = "<a href=\"$url\">$retVal</a>";
3713 :     }
3714 :     # Return the result.
3715 :     return $retVal;
3716 :     }
3717 :    
3718 : parrello 1.97 =head3 TrackingCode
3719 :    
3720 :     my $html = Tracer::TrackingCode();
3721 :    
3722 :     Returns the HTML code for doing web page traffic monitoring. If the
3723 :     current environment is a test system, then it returns a null string;
3724 :     otherwise, it returns a bunch of javascript containing code for turning
3725 :     on SiteMeter and Google Analytics.
3726 :    
3727 :     =cut
3728 :    
3729 :     sub TrackingCode {
3730 :     # Declare the return variable.
3731 :     my $retVal = "<!-- tracking off -->";
3732 :     # Determine if we're in production.
3733 :     if ($FIG_Config::site_meter) {
3734 :     $retVal = <<END_HTML
3735 :     <!-- Site Meter -->
3736 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3737 :     </script>
3738 :     <noscript>
3739 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3740 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3741 :     </noscript>
3742 :     <!-- Copyright (c)2006 Site Meter -->
3743 :     END_HTML
3744 :     }
3745 :     return $retVal;
3746 :     }
3747 :    
3748 : parrello 1.105 =head3 Clean
3749 :    
3750 :     my $cleaned = Tracer::Clean($string);
3751 :    
3752 :     Clean up a string for HTML display. This not only converts special
3753 :     characters to HTML entity names, it also removes control characters.
3754 :    
3755 :     =over 4
3756 :    
3757 :     =item string
3758 :    
3759 :     String to convert.
3760 :    
3761 :     =item RETURN
3762 :    
3763 :     Returns the input string with anything that might disrupt an HTML literal removed. An
3764 :     undefined value will be converted to an empty string.
3765 :    
3766 :     =back
3767 :    
3768 :     =cut
3769 :    
3770 :     sub Clean {
3771 :     # Get the parameters.
3772 :     my ($string) = @_;
3773 :     # Declare the return variable.
3774 :     my $retVal = "";
3775 :     # Only proceed if the value exists.
3776 :     if (defined $string) {
3777 :     # Get the string.
3778 :     $retVal = $string;
3779 :     # Clean the control characters.
3780 :     $retVal =~ tr/\x00-\x1F/?/;
3781 :     # Escape the rest.
3782 :     $retVal = CGI::escapeHTML($retVal);
3783 :     }
3784 :     # Return the result.
3785 :     return $retVal;
3786 :     }
3787 :    
3788 :    
3789 :    
3790 : parrello 1.97
3791 : olson 1.88 1;

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