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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 :    
42 : olson 1.1
43 :     =head1 Tracing and Debugging Helpers
44 :    
45 : parrello 1.72 =head2 Tracing
46 : olson 1.1
47 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51 :     level is less than or equal to the setup trace level and whose category is activated will
52 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
53 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
54 :     appear.
55 : olson 1.1
56 : parrello 1.72 =head3 Putting Trace Messages in Your Code
57 :    
58 :     To generate a trace message, use the following syntax.
59 :    
60 :     Trace($message) if T(errors => 4);
61 : olson 1.1
62 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
64 : olson 1.1
65 : parrello 1.72 Trace($message) if T(main => 4);
66 : olson 1.1
67 :     will trace if the trace level is 4 or more.
68 :    
69 :     If the category name is the same as the package name, all you need is the number. So, if the
70 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71 :     active and the trace level is 2 or more.
72 :    
73 : parrello 1.72 Trace($message) if T(2);
74 :    
75 :     In scripts, where no package name is available, the category defaults to C<main>.
76 :    
77 :     =head3 Custom Tracing
78 :    
79 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
81 :     L</Emergency Tracing> easier to understand.
82 : olson 1.1
83 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84 :     a list of category names, and a destination. The trace level and list of category names are
85 : olson 1.1 specified as a space-delimited string. Thus
86 :    
87 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
88 : olson 1.1
89 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90 : parrello 1.72 specifies that messages should be sent to the standard output.
91 : parrello 1.12
92 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93 :     level 3 and writes the output to the standard error output. This sort of thing might be
94 :     useful in a CGI environment.
95 :    
96 : parrello 1.72 TSetup('3 *', 'WARN');
97 : olson 1.1
98 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
99 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
100 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
101 :     the page output, they can be gathered together and displayed at the end of the page. This makes
102 :     it easier to debug page formatting problems.
103 :    
104 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105 :     a file at the same time. To trace to a file, specify the filename with an output character in front
106 :     of it.
107 :    
108 :     TSetup('4 SQL', ">$fileName");
109 :    
110 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111 :     bracket.
112 :    
113 :     TSetup('3 *', "+>$fileName");
114 : parrello 1.4
115 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117 :     Thus, debugging information is available and easily retrieved even when the application is
118 :     being used out in the field.
119 :    
120 : parrello 1.72 =head3 Trace Levels
121 :    
122 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
123 :     a suggestion.
124 :    
125 :     =over 4
126 :    
127 : parrello 1.32 =item Error 0
128 : parrello 1.10
129 :     Message indicates an error that may lead to incorrect results or that has stopped the
130 :     application entirely.
131 :    
132 : parrello 1.32 =item Warning 1
133 : parrello 1.10
134 :     Message indicates something that is unexpected but that probably did not interfere
135 :     with program execution.
136 :    
137 : parrello 1.32 =item Notice 2
138 : parrello 1.10
139 :     Message indicates the beginning or end of a major task.
140 :    
141 : parrello 1.32 =item Information 3
142 : parrello 1.10
143 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
144 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
145 :    
146 : parrello 1.32 =item Detail 4
147 : parrello 1.10
148 :     Message indicates a low-level loop iteration.
149 :    
150 :     =back
151 :    
152 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
153 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
154 :     The time stamp is between square brackets and the category name between angle brackets.
155 :     After the category name there is a colon (C<:>) followed by the message text.
156 :     If the square brackets or angle brackets are missing, then the trace management
157 :     utilities assume that they are encountering a set of pre-formatted lines.
158 :    
159 :     Note, however, that this formatting is done automatically by the tracing functions. You
160 :     only need to know about it if you want to parse a trace file.
161 :    
162 :     =head3 Emergency Tracing
163 :    
164 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
165 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167 :     that you specify a tracing key. For command-line tools, the key is
168 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
169 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
170 :     the tracing in your environment without stepping on other users.
171 :    
172 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173 :     generate one for you.
174 :    
175 :     You can activate and de-activate emergency tracing from the debugging control panel, as
176 :     well as display the trace file itself.
177 :    
178 :     To enable emergency tracing in your code, call
179 :    
180 :     ETracing($cgi)
181 :    
182 :     from a web script and
183 :    
184 :     ETracing()
185 :    
186 :     from a command-line script.
187 :    
188 :     The web script will look for the tracing key in the cookies, and the command-line
189 :     script will look for it in the C<TRACING> environment variable. If you are
190 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191 : parrello 1.72 will be configured automatically.
192 :    
193 : olson 1.1 =cut
194 : parrello 1.2
195 : olson 1.1 # Declare the configuration variables.
196 :    
197 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
198 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
199 :     # standard output
200 : parrello 1.3 my %Categories = ( main => 1 );
201 : parrello 1.12 # hash of active category names
202 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
203 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
204 :     # messages
205 :     my @Queue = (); # queued list of trace messages.
206 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
207 : parrello 1.97 my $LastLevel = 0; # level of the last test call
208 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
209 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
210 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
211 :     umask 2; # Fix the damn umask so everything is group-writable.
212 : olson 1.1
213 : parrello 1.93 =head2 Tracing Methods
214 :    
215 :     =head3 Setups
216 :    
217 :     my $count = Tracer::Setups();
218 :    
219 :     Return the number of times L</TSetup> has been called.
220 :    
221 :     This method allows for the creation of conditional tracing setups where, for example, we
222 :     may want to set up tracing if nobody else has done it before us.
223 :    
224 :     =cut
225 :    
226 :     sub Setups {
227 :     return $SetupCount;
228 :     }
229 : olson 1.1
230 :     =head3 TSetup
231 :    
232 : parrello 1.92 TSetup($categoryList, $target);
233 : olson 1.1
234 :     This method is used to specify the trace options. The options are stored as package data
235 :     and interrogated by the L</Trace> and L</T> methods.
236 :    
237 :     =over 4
238 :    
239 :     =item categoryList
240 :    
241 :     A string specifying the trace level and the categories to be traced, separated by spaces.
242 :     The trace level must come first.
243 :    
244 :     =item target
245 :    
246 :     The destination for the trace output. To send the trace output to a file, specify the file
247 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
248 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
249 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
250 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
251 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
252 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
253 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
254 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
255 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
256 : parrello 1.6 cause tracing to be suppressed.
257 : olson 1.1
258 :     =back
259 :    
260 :     =cut
261 :    
262 :     sub TSetup {
263 : parrello 1.12 # Get the parameters.
264 :     my ($categoryList, $target) = @_;
265 :     # Parse the category list.
266 :     my @categoryData = split /\s+/, $categoryList;
267 :     # Extract the trace level.
268 :     $TraceLevel = shift @categoryData;
269 :     # Presume category-based tracing until we learn otherwise.
270 :     $AllTrace = 0;
271 :     # Build the category hash. Note that if we find a "*", we turn on non-category
272 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
273 : parrello 1.34 %Categories = ( main => 1 );
274 : parrello 1.12 for my $category (@categoryData) {
275 :     if ($category eq '*') {
276 :     $AllTrace = 1;
277 :     } else {
278 : parrello 1.13 $Categories{lc $category} = 1;
279 : parrello 1.12 }
280 :     }
281 :     # Now we need to process the destination information. The most important special
282 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
284 :     # the standard output (tee mode).
285 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
286 :     if ($target =~ m/^\+/) {
287 :     $TeeFlag = 1;
288 :     $target = substr($target, 1);
289 :     }
290 :     if ($target =~ m/^>[^>]/) {
291 : parrello 1.98 # We need to initialize the file (which clears it).
292 : parrello 1.12 open TRACEFILE, $target;
293 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294 : parrello 1.12 close TRACEFILE;
295 : parrello 1.98 # Set to append mode now that the file has been cleared.
296 : parrello 1.12 $Destination = ">$target";
297 :     } else {
298 :     $Destination = $target;
299 :     }
300 :     } else {
301 :     $Destination = uc($target);
302 :     }
303 :     # Increment the setup counter.
304 :     $SetupCount++;
305 : parrello 1.11 }
306 :    
307 : parrello 1.93 =head3 SetLevel
308 : parrello 1.31
309 : parrello 1.93 Tracer::SetLevel($newLevel);
310 : parrello 1.31
311 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
312 : parrello 1.31
313 : parrello 1.93 =over 4
314 : parrello 1.31
315 : parrello 1.93 =item newLevel
316 : parrello 1.31
317 : parrello 1.93 Proposed new trace level.
318 : parrello 1.31
319 : parrello 1.93 =back
320 : parrello 1.31
321 : parrello 1.93 =cut
322 : parrello 1.31
323 : parrello 1.93 sub SetLevel {
324 :     $TraceLevel = $_[0];
325 :     }
326 : parrello 1.31
327 : parrello 1.97 =head3 ParseDate
328 :    
329 :     my $time = Tracer::ParseDate($dateString);
330 :    
331 :     Convert a date into a PERL time number. This method expects a date-like string
332 :     and parses it into a number. The string must be vaguely date-like or it will
333 :     return an undefined value. Our requirement is that a month and day be
334 :     present and that three pieces of the date string (time of day, month and day,
335 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
336 :    
337 :     If a time of day is present, it must be in military time with two digits for
338 :     everything but the hour.
339 : parrello 1.31
340 : parrello 1.97 The year must be exactly four digits.
341 : parrello 1.31
342 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
343 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
344 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
345 :    
346 :     It should be guaranteed that this method will parse the output of the L</Now> function.
347 :    
348 :     The parameters are as follows.
349 : parrello 1.31
350 : parrello 1.93 =over 4
351 : parrello 1.31
352 : parrello 1.93 =item dateString
353 : parrello 1.31
354 : parrello 1.97 The date string to convert.
355 : parrello 1.31
356 : parrello 1.93 =item RETURN
357 : parrello 1.31
358 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
360 : parrello 1.31
361 : parrello 1.93 =back
362 : parrello 1.38
363 : parrello 1.93 =cut
364 : parrello 1.38
365 : parrello 1.97 # Universal month conversion table.
366 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
367 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
368 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
369 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
370 :     May => 4, May => 4, '05' => 4, '5' => 4,
371 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
372 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
373 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
374 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
375 :     Oct => 9, October => 9, '10' => 9,
376 :     Nov => 10, November => 10, '11' => 10,
377 :     Dec => 11, December => 11, '12' => 11
378 :     };
379 :    
380 :     sub ParseDate {
381 : parrello 1.93 # Get the parameters.
382 :     my ($dateString) = @_;
383 :     # Declare the return variable.
384 :     my $retVal;
385 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
386 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387 :     # won't be fooled into thinking the month is Sunday.
388 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
390 :     # Insist that the month and day are valid.
391 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
392 :     # Find the time.
393 :     my ($hour, $min, $sec) = (0, 0, 0);
394 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395 :     ($hour, $min, $sec) = ($1, $2, $3);
396 :     }
397 :     # Find the year.
398 :     my $year;
399 :     if ($dateString =~ /\b(\d{4})\b/) {
400 :     $year = $1;
401 :     } else {
402 :     # Get the default year, which is this one. Note we must convert it to
403 :     # the four-digit value expected by "timelocal".
404 :     (undef, undef, undef, undef, undef, $year) = localtime();
405 :     $year += 1900;
406 :     }
407 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408 :     }
409 : parrello 1.93 }
410 :     # Return the result.
411 :     return $retVal;
412 :     }
413 : parrello 1.31
414 : parrello 1.93 =head3 LogErrors
415 : parrello 1.42
416 : parrello 1.93 Tracer::LogErrors($fileName);
417 : parrello 1.31
418 : parrello 1.93 Route the standard error output to a log file.
419 : parrello 1.31
420 : parrello 1.93 =over 4
421 : parrello 1.31
422 : parrello 1.93 =item fileName
423 : parrello 1.31
424 : parrello 1.93 Name of the file to receive the error output.
425 : parrello 1.31
426 : parrello 1.93 =back
427 : parrello 1.31
428 : parrello 1.93 =cut
429 : parrello 1.84
430 : parrello 1.93 sub LogErrors {
431 :     # Get the file name.
432 :     my ($fileName) = @_;
433 :     # Open the file as the standard error output.
434 :     open STDERR, '>', $fileName;
435 :     }
436 : parrello 1.84
437 : parrello 1.93 =head3 Trace
438 : parrello 1.31
439 : parrello 1.93 Trace($message);
440 : parrello 1.31
441 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
442 :     any prior call to B<TSetup>.
443 : parrello 1.31
444 : parrello 1.93 =over 4
445 : parrello 1.42
446 : parrello 1.93 =item message
447 : parrello 1.42
448 : parrello 1.93 Message to write.
449 : parrello 1.42
450 : parrello 1.93 =back
451 : parrello 1.72
452 : parrello 1.93 =cut
453 : parrello 1.36
454 : parrello 1.93 sub Trace {
455 :     # Get the parameters.
456 :     my ($message) = @_;
457 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
458 :     # new-line stuff ourselves.
459 :     my $stripped = Strip($message);
460 :     # Compute the caller information.
461 :     my ($callPackage, $callFile, $callLine) = caller();
462 :     my $callFileTitle = basename($callFile);
463 :     # Check the caller.
464 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465 : parrello 1.93 # Get the timestamp.
466 :     my $timeStamp = Now();
467 : parrello 1.97 # Build the prefix.
468 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470 : parrello 1.97 # Format the message.
471 :     my $formatted = "$prefix $stripped";
472 : parrello 1.93 # Process according to the destination.
473 :     if ($Destination eq "TEXT") {
474 :     # Write the message to the standard output.
475 :     print "$formatted\n";
476 :     } elsif ($Destination eq "ERROR") {
477 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
478 : parrello 1.93 print STDERR "$formatted\n";
479 : parrello 1.97 } elsif ($Destination eq "WARN") {
480 :     # Emit the message to the standard error output. It is presumed that the
481 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
482 :     # the caller info.
483 :     print STDERR "$callerInfo$stripped\n";
484 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
485 :     # Push the message into the queue.
486 :     push @Queue, "$formatted";
487 :     } elsif ($Destination eq "HTML") {
488 :     # Convert the message to HTML and write it to the standard output.
489 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
490 :     print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
492 :     # Write the trace message to an output file.
493 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494 : parrello 1.93 print TRACING "$formatted\n";
495 :     close TRACING;
496 :     # If the Tee flag is on, echo it to the standard output.
497 :     if ($TeeFlag) {
498 :     print "$formatted\n";
499 :     }
500 :     }
501 :     }
502 : parrello 1.36
503 : parrello 1.93 =head3 T
504 : parrello 1.36
505 : parrello 1.93 my $switch = T($category, $traceLevel);
506 : parrello 1.36
507 : parrello 1.93 or
508 : parrello 1.44
509 : parrello 1.93 my $switch = T($traceLevel);
510 : parrello 1.44
511 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
512 :     is active, else FALSE. If no category is specified, the caller's package name is used.
513 : parrello 1.44
514 : parrello 1.93 =over 4
515 : parrello 1.44
516 : parrello 1.93 =item category
517 : parrello 1.44
518 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
519 :     used.
520 : parrello 1.31
521 : parrello 1.93 =item traceLevel
522 : parrello 1.31
523 : parrello 1.93 Relevant tracing level.
524 : parrello 1.31
525 : parrello 1.93 =item RETURN
526 : parrello 1.31
527 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
528 : parrello 1.31
529 : parrello 1.93 =back
530 : parrello 1.36
531 : parrello 1.93 =cut
532 :    
533 :     sub T {
534 :     # Declare the return variable.
535 :     my $retVal = 0;
536 :     # Only proceed if tracing is turned on.
537 :     if ($Destination ne "NONE") {
538 :     # Get the parameters.
539 :     my ($category, $traceLevel) = @_;
540 :     if (!defined $traceLevel) {
541 :     # Here we have no category, so we need to get the calling package.
542 :     # The calling package is normally the first parameter. If it is
543 :     # omitted, the first parameter will be the tracelevel. So, the
544 :     # first thing we do is shift the so-called category into the
545 :     # $traceLevel variable where it belongs.
546 :     $traceLevel = $category;
547 :     my ($package, $fileName, $line) = caller;
548 :     # If there is no calling package, we default to "main".
549 :     if (!$package) {
550 :     $category = "main";
551 :     } else {
552 :     my @cats = split /::/, $package;
553 :     $category = $cats[$#cats];
554 :     }
555 :     }
556 : parrello 1.97 # Save the category name and level.
557 : parrello 1.93 $LastCategory = $category;
558 : parrello 1.97 $LastLevel = $traceLevel;
559 : parrello 1.93 # Convert it to lower case before we hash it.
560 :     $category = lc $category;
561 : parrello 1.100 # Validate the trace level.
562 : parrello 1.93 if (ref $traceLevel) {
563 :     Confess("Bad trace level.");
564 :     } elsif (ref $TraceLevel) {
565 :     Confess("Bad trace config.");
566 :     }
567 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
568 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569 : parrello 1.93 }
570 :     # Return the computed result.
571 :     return $retVal;
572 :     }
573 :    
574 :     =head3 QTrace
575 :    
576 :     my $data = QTrace($format);
577 :    
578 :     Return the queued trace data in the specified format.
579 :    
580 :     =over 4
581 :    
582 :     =item format
583 :    
584 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
585 :    
586 :     =back
587 :    
588 :     =cut
589 :    
590 :     sub QTrace {
591 :     # Get the parameter.
592 :     my ($format) = @_;
593 :     # Create the return variable.
594 :     my $retVal = "";
595 :     # Only proceed if there is an actual queue.
596 :     if (@Queue) {
597 :     # Process according to the format.
598 :     if ($format =~ m/^HTML$/i) {
599 :     # Convert the queue into an HTML list.
600 :     $retVal = "<ul>\n";
601 :     for my $line (@Queue) {
602 :     my $escapedLine = CGI::escapeHTML($line);
603 :     $retVal .= "<li>$escapedLine</li>\n";
604 :     }
605 :     $retVal .= "</ul>\n";
606 :     } elsif ($format =~ m/^TEXT$/i) {
607 :     # Convert the queue into a list of text lines.
608 :     $retVal = join("\n", @Queue) . "\n";
609 :     }
610 :     # Clear the queue.
611 :     @Queue = ();
612 :     }
613 :     # Return the formatted list.
614 :     return $retVal;
615 :     }
616 :    
617 :     =head3 Confess
618 :    
619 :     Confess($message);
620 :    
621 :     Trace the call stack and abort the program with the specified message. When used with
622 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623 :     So, for example
624 :    
625 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626 :    
627 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
628 :    
629 :     =over 4
630 :    
631 :     =item message
632 :    
633 :     Message to include in the trace.
634 :    
635 :     =back
636 :    
637 :     =cut
638 :    
639 :     sub Confess {
640 :     # Get the parameters.
641 :     my ($message) = @_;
642 : parrello 1.97 # Set up the category and level.
643 :     $LastCategory = "(confess)";
644 :     $LastLevel = 0;
645 : parrello 1.93 if (! defined($FIG_Config::no_tool_hdr)) {
646 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648 :     # Only proceed if the tool header file is actually present.
649 :     if (-f $toolHeaderFile) {
650 : parrello 1.97 my $fh;
651 :     if (open $fh, "<$toolHeaderFile") {
652 :     my @lines = <$fh>;
653 :     Trace("Tool header has " . scalar(@lines) . " lines.");
654 :     }
655 : parrello 1.93 }
656 :     }
657 :     # Trace the call stack.
658 :     Cluck($message);
659 :     # Abort the program.
660 :     croak(">>> $message");
661 :     }
662 :    
663 : parrello 1.99 =head3 Warn
664 :    
665 :     Warn($message);
666 :    
667 :     This method traces an important message. If an RSS feed is configured
668 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669 :     then the message will be echoed to the feed. In general, a tracing
670 :     destination of C<WARN> indicates that the caller is running as a web
671 :     service in a production environment; however, this is not a requirement.
672 :    
673 :     The L</Cluck> method calls this one for its final message. Since
674 :     L</Confess> calls L</Cluck>, this means that any error which is caught
675 :     and confessed will put something in the feed. This insures that someone
676 :     will be alerted relatively quickly when a failure occurs.
677 :    
678 :     =over 4
679 :    
680 :     =item message
681 :    
682 :     Message to be traced.
683 :    
684 :     =back
685 :    
686 :     =cut
687 :    
688 :     sub Warn {
689 :     # Get the parameters.
690 :     my ($message) = @_;
691 :     # Trace the message.
692 :     Trace($message);
693 :     # An error here would be disastrous. Note, however, that we aren't too worried
694 :     # about losing events. The error log is always available for the occasions where
695 :     # we mess up.
696 :     eval {
697 :     # Do we need to put this in the RSS feed?
698 :     if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699 :     # Yes. We now need to compute the date, the link, and the title.
700 :     # First, the date, in a very specific format.
701 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702 :     (tz_local_offset() / 30);
703 :     # We'll put the link and title in here.
704 :     my ($link, $title);
705 :     # Environment data goes in here.
706 :     my $environment;
707 :     # HTML-escape the message.
708 :     my $escaped = CGI::escapeHTML($message);
709 :     # If we have a CGI object, then this is a web error. Otherwise, it's
710 :     # command-line.
711 :     if (defined $SavedCGI) {
712 :     # We're in a web service. The title is the user's IP, and the link
713 :     # is the URL that got us here.
714 :     my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
715 :     $title = "Event Reported at IP address $key: $escaped";
716 :     $link = $SavedCGI->url(-full => 1, -query => 1);
717 : parrello 1.100 # We need the user agent string and (if available) the referrer.
718 :     $environment = "User Agent $ENV{HTTP_USER_AGENT}";
719 :     if ($ENV{HTTP_REFERER}) {
720 :     $environment .= " referred from $ENV{HTTP_REFERER}"
721 :     }
722 :     # Close off the sentence.
723 :     $environment .= ". ";
724 : parrello 1.99 } else {
725 :     # No CGI object, so we're a command-line tool. Use the tracing
726 :     # key and the PID as the user identifier.
727 :     my $key = EmergencyKey();
728 :     $title = "Event Reported by $key Process $$: $escaped";
729 :     # Set the link to the development NMPDR. There is really no good
730 :     # choice here.
731 :     $link = "http://$FIG_Config::dev_server";
732 :     # We need the command
733 :     $environment = "Command $ENV{_}.";
734 :     }
735 :     # Build a GUID. We use the current time, the title, and the process ID,
736 :     # then digest the result.
737 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
738 :     # Finally, the description. This is a stack trace plus various environmental stuff.
739 :     my @trace = LongMess();
740 :     my $trace = join "; ", @trace;
741 :     my $description = CGI::escapeHTML("$environment Stack trace: $trace");
742 :     # Okay, we have all the pieces. Create a hash of the new event.
743 :     my $newItem = { title => $title,
744 :     description => $description,
745 :     link => $link,
746 :     category => $LastCategory,
747 :     pubDate => $date,
748 :     guid => $guid,
749 :     };
750 :     # We need XML capability for this.
751 :     require XML::Simple;
752 :     # The RSS document goes in here.
753 :     my $rss;
754 :     # Get the name of the RSS file. It's in the FIG temporary directory.
755 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
756 :     # Does it exist?
757 :     if (-s $fileName) {
758 :     # Slurp it in.
759 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
760 :     } else {
761 :     my $size = -s $fileName;
762 :     # Create an empty channel.
763 :     $rss = {
764 :     channel => {
765 :     title => 'NMPDR Warning Feed',
766 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
767 :     description => "Important messages regarding the status of the NMPDR.",
768 :     generator => "NMPDR Trace Facility",
769 :     docs => "http://blogs.law.harvard.edu/tech/rss",
770 :     item => []
771 :     },
772 :     };
773 :     }
774 :     # Get the channel object.
775 :     my $channel = $rss->{channel};
776 :     # Update the last-build date.
777 :     $channel->{lastBuildDate} = $date;
778 :     # Get the item array.
779 :     my $items = $channel->{item};
780 :     # Insure it has only 100 entries.
781 :     while (scalar @{$items} > 100) {
782 :     pop @{$items};
783 :     }
784 :     # Add our new item at the front.
785 :     unshift @{$items}, $newItem;
786 :     # Replace the file.
787 :     my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
788 :     NoEscape => 1);
789 :     # We don't use Open here because we can't afford an error.
790 :     if (open XMLOUT, ">$fileName") {
791 :     print XMLOUT $xml;
792 :     close XMLOUT;
793 :     }
794 :     }
795 :     };
796 :     # There's no "if ($@)" here, because putting an error message in the log
797 :     # saying that we missed putting an error message in the feed of messages
798 :     # in the log is not going to help anybody.
799 :     }
800 :    
801 : parrello 1.93 =head3 Assert
802 :    
803 :     Assert($condition1, $condition2, ... $conditionN);
804 :    
805 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
806 :     the OR operator and the L</Confess> method as a debugging assert.
807 :     So, for example
808 :    
809 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
810 :    
811 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
812 :    
813 :     =cut
814 :     sub Assert {
815 :     my $retVal = 1;
816 :     LOOP: for my $condition (@_) {
817 :     if (! $condition) {
818 :     $retVal = 0;
819 :     last LOOP;
820 :     }
821 :     }
822 :     return $retVal;
823 :     }
824 :    
825 :     =head3 Cluck
826 :    
827 :     Cluck($message);
828 :    
829 :     Trace the call stack. Note that for best results, you should qualify the call with a
830 :     trace condition. For example,
831 :    
832 :     Cluck("Starting record parse.") if T(3);
833 :    
834 :     will only trace the stack if the trace level for the package is 3 or more.
835 :    
836 :     =over 4
837 :    
838 :     =item message
839 :    
840 :     Message to include in the trace.
841 :    
842 :     =back
843 :    
844 :     =cut
845 :    
846 :     sub Cluck {
847 :     # Get the parameters.
848 :     my ($message) = @_;
849 :     # Trace what's happening.
850 :     Trace("Stack trace for event: $message");
851 : parrello 1.99 # Get the stack trace.
852 :     my @trace = LongMess();
853 :     # Convert the trace to a series of messages.
854 :     for my $line (@trace) {
855 :     # Replace the tab at the beginning with spaces.
856 :     $line =~ s/^\t/ /;
857 :     # Trace the line.
858 :     Trace($line);
859 :     }
860 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
861 :     Warn($message);
862 :     }
863 :    
864 :     =head3 LongMess
865 :    
866 :     my @lines = Tracer::LongMess();
867 :    
868 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
869 :     of message strings.
870 :    
871 :     =cut
872 :    
873 :     sub LongMess {
874 :     # Declare the return variable.
875 :     my @retVal = ();
876 :     my $confession = longmess("");
877 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
878 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
879 :     # Here we have a line worth keeping. Push it onto the result list.
880 :     push @retVal, $line;
881 : parrello 1.97 }
882 : parrello 1.93 }
883 : parrello 1.99 # Return the result.
884 :     return @retVal;
885 : parrello 1.93 }
886 :    
887 : parrello 1.97 =head3 ScriptSetup (deprecated)
888 : parrello 1.93
889 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
890 :    
891 :     Perform standard tracing and debugging setup for scripts. The value returned is
892 :     the CGI object followed by a pre-built variable hash. At the end of the script,
893 :     the client should call L</ScriptFinish> to output the web page.
894 :    
895 :     This method calls L</ETracing> to configure tracing, which allows the tracing
896 :     to be configured via the emergency tracing form on the debugging control panel.
897 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
898 :     method, which includes every program that uses this method or L</StandardSetup>.
899 : parrello 1.36
900 : parrello 1.93 =over 4
901 : parrello 1.31
902 : parrello 1.93 =item noTrace (optional)
903 : parrello 1.31
904 : parrello 1.93 If specified, tracing will be suppressed. This is useful if the script wants to set up
905 :     tracing manually.
906 : parrello 1.31
907 :     =item RETURN
908 :    
909 : parrello 1.93 Returns a two-element list consisting of a CGI query object and a variable hash for
910 :     the output page.
911 : parrello 1.31
912 :     =back
913 :    
914 :     =cut
915 :    
916 : parrello 1.93 sub ScriptSetup {
917 : parrello 1.31 # Get the parameters.
918 : parrello 1.93 my ($noTrace) = @_;
919 :     # Get the CGI query object.
920 :     my $cgi = CGI->new();
921 :     # Set up tracing if it's not suppressed.
922 :     ETracing($cgi) unless $noTrace;
923 :     # Create the variable hash.
924 :     my $varHash = { results => '' };
925 :     # Return the query object and variable hash.
926 :     return ($cgi, $varHash);
927 :     }
928 :    
929 :     =head3 ETracing
930 :    
931 :     ETracing($parameter);
932 :    
933 :     Set up emergency tracing. Emergency tracing is tracing that is turned
934 :     on automatically for any program that calls this method. The emergency
935 :     tracing parameters are stored in a a file identified by a tracing key.
936 :     If this method is called with a CGI object, then the tracing key is
937 :     taken from a cookie. If it is called with no parameters, then the tracing
938 :     key is taken from an environment variable. If it is called with a string,
939 :     the tracing key is that string.
940 :    
941 :     =over 4
942 :    
943 :     =item parameter
944 :    
945 :     A parameter from which the tracing key is computed. If it is a scalar,
946 :     that scalar is used as the tracing key. If it is a CGI object, the
947 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
948 :     tracing key is taken from the C<TRACING> environment variable. If it
949 :     is a CGI object and emergency tracing is not on, the C<Trace> and
950 :     C<TF> parameters will be used to determine the type of tracing.
951 :    
952 :     =back
953 :    
954 :     =cut
955 :    
956 :     sub ETracing {
957 :     # Get the parameter.
958 :     my ($parameter) = @_;
959 :     # Check for CGI mode.
960 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
961 :     $SavedCGI = $parameter;
962 :     } else {
963 :     $SavedCGI = undef;
964 :     }
965 : parrello 1.93 # Default to no tracing except errors.
966 :     my ($tracing, $dest) = ("0", "WARN");
967 :     # Check for emergency tracing.
968 :     my $tkey = EmergencyKey($parameter);
969 :     my $emergencyFile = EmergencyFileName($tkey);
970 :     if (-e $emergencyFile) {
971 :     # We have the file. Read in the data.
972 :     my @tracing = GetFile($emergencyFile);
973 :     # Pull off the time limit.
974 :     my $expire = shift @tracing;
975 :     # Convert it to seconds.
976 :     $expire *= 3600;
977 :     # Check the file data.
978 :     my $stat = stat($emergencyFile);
979 :     my ($now) = gettimeofday;
980 :     if ($now - $stat->mtime > $expire) {
981 :     # Delete the expired file.
982 :     unlink $emergencyFile;
983 : parrello 1.44 } else {
984 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
985 :     # the trace level;
986 :     $dest = shift @tracing;
987 :     my $level = shift @tracing;
988 :     # Convert the destination to a real tracing destination.
989 :     # temp directory.
990 :     $dest = EmergencyTracingDest($tkey, $dest);
991 :     # Insure Tracer is specified.
992 :     my %moduleHash = map { $_ => 1 } @tracing;
993 :     $moduleHash{Tracer} = 1;
994 :     # Set the trace parameter.
995 :     $tracing = join(" ", $level, sort keys %moduleHash);
996 : parrello 1.44 }
997 : parrello 1.99 } elsif (defined $SavedCGI) {
998 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
999 :     # for tracing from the form parameters.
1000 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1001 : parrello 1.93 # Here the user has requested tracing via a form.
1002 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1003 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1004 : parrello 1.36 }
1005 :     }
1006 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1007 :     TSetup($tracing, $dest);
1008 : parrello 1.94 # Check to see if we're a web script.
1009 : parrello 1.99 if (defined $SavedCGI) {
1010 : parrello 1.94 # Yes we are. Trace the form and environment data.
1011 : parrello 1.99 TraceParms($SavedCGI);
1012 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1013 :     # emitted by the script in its raw form.
1014 :     if (T(Raw => 3)) {
1015 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1016 :     }
1017 : parrello 1.83 }
1018 : parrello 1.31 }
1019 :    
1020 : parrello 1.93 =head3 EmergencyFileName
1021 :    
1022 :     my $fileName = Tracer::EmergencyFileName($tkey);
1023 :    
1024 :     Return the emergency tracing file name. This is the file that specifies
1025 :     the tracing information.
1026 :    
1027 :     =over 4
1028 :    
1029 :     =item tkey
1030 :    
1031 :     Tracing key for the current program.
1032 : parrello 1.11
1033 : parrello 1.93 =item RETURN
1034 : parrello 1.11
1035 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1036 : parrello 1.11
1037 : parrello 1.93 =back
1038 : parrello 1.11
1039 :     =cut
1040 :    
1041 : parrello 1.93 sub EmergencyFileName {
1042 :     # Get the parameters.
1043 :     my ($tkey) = @_;
1044 :     # Compute the emergency tracing file name.
1045 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1046 : olson 1.1 }
1047 :    
1048 : parrello 1.93 =head3 EmergencyFileTarget
1049 : parrello 1.10
1050 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1051 : parrello 1.10
1052 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1053 :     the tracing output for file-based tracing.
1054 : parrello 1.10
1055 : parrello 1.93 =over 4
1056 : parrello 1.10
1057 : parrello 1.93 =item tkey
1058 : parrello 1.10
1059 : parrello 1.93 Tracing key for the current program.
1060 : parrello 1.10
1061 : parrello 1.93 =item RETURN
1062 : parrello 1.10
1063 : parrello 1.93 Returns the name of the file to contain the trace output.
1064 : parrello 1.10
1065 : parrello 1.93 =back
1066 : parrello 1.10
1067 : parrello 1.93 =cut
1068 : parrello 1.10
1069 : parrello 1.93 sub EmergencyFileTarget {
1070 :     # Get the parameters.
1071 :     my ($tkey) = @_;
1072 :     # Compute the emergency tracing file name.
1073 :     return "$FIG_Config::temp/trace$tkey.log";
1074 :     }
1075 : parrello 1.10
1076 : parrello 1.93 =head3 EmergencyTracingDest
1077 : parrello 1.10
1078 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1079 : parrello 1.10
1080 : parrello 1.93 This method converts an emergency tracing destination to a real
1081 :     tracing destination. The main difference is that if the
1082 :     destination is C<FILE> or C<APPEND>, we convert it to file
1083 :     output. If the destination is C<DUAL>, we convert it to file
1084 :     and standard output.
1085 : parrello 1.10
1086 :     =over 4
1087 :    
1088 : parrello 1.93 =item tkey
1089 : parrello 1.10
1090 : parrello 1.93 Tracing key for this environment.
1091 : parrello 1.10
1092 : parrello 1.93 =item myDest
1093 : parrello 1.10
1094 : parrello 1.93 Destination from the emergency tracing file.
1095 : parrello 1.10
1096 :     =item RETURN
1097 :    
1098 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1099 : parrello 1.10
1100 :     =back
1101 :    
1102 :     =cut
1103 :    
1104 : parrello 1.93 sub EmergencyTracingDest {
1105 : parrello 1.12 # Get the parameters.
1106 : parrello 1.93 my ($tkey, $myDest) = @_;
1107 :     # Declare the return variable.
1108 :     my $retVal = $myDest;
1109 :     # Process according to the destination value.
1110 :     if ($myDest eq 'FILE') {
1111 :     $retVal = ">" . EmergencyFileTarget($tkey);
1112 :     } elsif ($myDest eq 'APPEND') {
1113 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1114 :     } elsif ($myDest eq 'DUAL') {
1115 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1116 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1117 :     $retVal = "WARN";
1118 : parrello 1.12 }
1119 : parrello 1.93 # Return the result.
1120 :     return $retVal;
1121 : parrello 1.10 }
1122 :    
1123 : parrello 1.93 =head3 Emergency
1124 :    
1125 :     Emergency($key, $hours, $dest, $level, @modules);
1126 :    
1127 :     Turn on emergency tracing. This method is normally invoked over the web from
1128 :     a debugging console, but it can also be called by the C<trace.pl> script.
1129 :     The caller specifies the duration of the emergency in hours, the desired tracing
1130 :     destination, the trace level, and a list of the trace modules to activate.
1131 :     For the length of the duration, when a program in an environment with the
1132 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1133 :     turned on automatically. See L</TSetup> for more about tracing setup and
1134 :     L</ETracing> for more about emergency tracing.
1135 :    
1136 :     =over 4
1137 : parrello 1.11
1138 : parrello 1.93 =item tkey
1139 : parrello 1.11
1140 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1141 : parrello 1.11
1142 : parrello 1.93 =item hours
1143 : parrello 1.11
1144 : parrello 1.93 Number of hours to keep emergency tracing alive.
1145 : parrello 1.11
1146 : parrello 1.93 =item dest
1147 : parrello 1.11
1148 : parrello 1.93 Tracing destination. If no path information is specified for a file
1149 :     destination, it is put in the FIG temporary directory.
1150 : parrello 1.11
1151 : parrello 1.93 =item level
1152 : parrello 1.11
1153 : parrello 1.93 Tracing level. A higher level means more trace messages.
1154 : parrello 1.11
1155 : parrello 1.93 =item modules
1156 : parrello 1.11
1157 : parrello 1.93 A list of the tracing modules to activate.
1158 : parrello 1.11
1159 :     =back
1160 :    
1161 :     =cut
1162 : parrello 1.93
1163 :     sub Emergency {
1164 : parrello 1.11 # Get the parameters.
1165 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1166 :     # Create the emergency file.
1167 :     my $specFile = EmergencyFileName($tkey);
1168 :     my $outHandle = Open(undef, ">$specFile");
1169 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1170 : parrello 1.11 }
1171 :    
1172 : parrello 1.93 =head3 EmergencyKey
1173 :    
1174 :     my $tkey = EmergencyKey($parameter);
1175 :    
1176 :     Return the Key to be used for emergency tracing. This could be an IP address,
1177 :     a session ID, or a user name, depending on the environment.
1178 : parrello 1.11
1179 : parrello 1.93 =over 4
1180 : parrello 1.11
1181 : parrello 1.93 =item parameter
1182 : parrello 1.11
1183 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1184 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1185 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1186 :     taken from the C<TRACING> environment variable.
1187 : parrello 1.29
1188 : parrello 1.93 =item RETURN
1189 : parrello 1.11
1190 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1191 : parrello 1.11
1192 : parrello 1.93 =back
1193 : parrello 1.11
1194 : parrello 1.93 =cut
1195 : parrello 1.29
1196 : parrello 1.93 sub EmergencyKey {
1197 :     # Get the parameters.
1198 :     my ($parameter) = @_;
1199 :     # Declare the return variable.
1200 :     my $retVal;
1201 :     # Determine the parameter type.
1202 :     if (! defined $parameter) {
1203 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1204 :     # get the effective login ID.
1205 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1206 : parrello 1.93 } else {
1207 :     my $ptype = ref $parameter;
1208 :     if ($ptype eq 'CGI') {
1209 :     # Here we were invoked from a web page. Look for a cookie.
1210 :     $retVal = $parameter->cookie('IP');
1211 :     } elsif (! $ptype) {
1212 :     # Here the key was passed in.
1213 :     $retVal = $parameter;
1214 :     }
1215 :     }
1216 :     # If no luck finding a key, use the PID.
1217 :     if (! defined $retVal) {
1218 :     $retVal = $$;
1219 :     }
1220 :     # Return the result.
1221 :     return $retVal;
1222 :     }
1223 : parrello 1.11
1224 :    
1225 : parrello 1.93 =head3 TraceParms
1226 : parrello 1.11
1227 : parrello 1.93 Tracer::TraceParms($cgi);
1228 : parrello 1.11
1229 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1230 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1231 : parrello 1.11
1232 : parrello 1.93 =over 4
1233 : parrello 1.11
1234 : parrello 1.93 =item cgi
1235 : parrello 1.31
1236 : parrello 1.93 CGI query object containing the parameters to trace.
1237 : parrello 1.31
1238 : parrello 1.11 =back
1239 :    
1240 :     =cut
1241 : parrello 1.93
1242 :     sub TraceParms {
1243 : parrello 1.11 # Get the parameters.
1244 : parrello 1.93 my ($cgi) = @_;
1245 : parrello 1.94 if (T(CGI => 2)) {
1246 :     # Here we trace the GET-style URL for the script.
1247 : parrello 1.97 Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1248 : parrello 1.94 }
1249 : parrello 1.93 if (T(CGI => 3)) {
1250 :     # Here we want to trace the parameter data.
1251 :     my @names = $cgi->param;
1252 :     for my $parmName (sort @names) {
1253 :     # Note we skip the Trace parameters, which are for our use only.
1254 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1255 :     my @values = $cgi->param($parmName);
1256 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1257 : parrello 1.93 }
1258 :     }
1259 :     # Display the request method.
1260 :     my $method = $cgi->request_method();
1261 :     Trace("Method: $method");
1262 :     }
1263 :     if (T(CGI => 4)) {
1264 :     # Here we want the environment data too.
1265 :     for my $envName (sort keys %ENV) {
1266 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1267 : parrello 1.12 }
1268 :     }
1269 : parrello 1.11 }
1270 :    
1271 : parrello 1.94 =head3 TraceImages
1272 :    
1273 :     Tracer::TraceImages($htmlString);
1274 :    
1275 :     Trace information about all of an html document's images. The tracing
1276 :     will be for type "IMG" at level 3. The image's source string
1277 :     will be displayed. This is generally either the URL of the image or
1278 :     raw data for the image itself. If the source is too long, only the first 300
1279 :     characters will be shown at trace level 3. The entire source will be shown,
1280 :     however, at trace level 4. This method is not very smart, and might catch
1281 :     Javascript code, but it is still useful when debugging the arcane
1282 :     behavior of images in multiple browser environments.
1283 :    
1284 :     =over 4
1285 :    
1286 :     =item htmlString
1287 :    
1288 :     HTML text for an outgoing web page.
1289 :    
1290 :     =back
1291 :    
1292 :     =cut
1293 :    
1294 :     sub TraceImages {
1295 :     # Only proceed if we're at the proper trace level.
1296 :     if (T(IMG => 3)) {
1297 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1298 :     # into a variable called "$htmlString". This is because we expect html strings to be
1299 :     # long, and don't want to copy them any more than we have to.
1300 :     Trace(length($_[0]) . " characters in web page.");
1301 :     # Loop through the HTML, culling image tags.
1302 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1303 :     # Extract the source string and determine whether or not it's too long.
1304 :     my $srcString = $1;
1305 :     my $pos = pos($_[0]) - length($srcString);
1306 :     my $excess = length($srcString) - 300;
1307 :     # We'll put the display string in here.
1308 :     my $srcDisplay = $srcString;
1309 :     # If it's a data string, split it at the comma.
1310 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1311 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1312 :     # a long string, however, we only show the first 300 characters.
1313 :     if ($excess > 0 && ! T(IMG => 4)) {
1314 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1315 :     }
1316 :     # Output the trace message.
1317 :     Trace("Image tag at position $pos:\n$srcDisplay");
1318 :     }
1319 :     }
1320 :     }
1321 :    
1322 :    
1323 : parrello 1.97 =head3 ScriptFinish (deprecated)
1324 : parrello 1.93
1325 :     ScriptFinish($webData, $varHash);
1326 :    
1327 :     Output a web page at the end of a script. Either the string to be output or the
1328 :     name of a template file can be specified. If the second parameter is omitted,
1329 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1330 :     name of a template file. The template should have the variable C<DebugData>
1331 :     specified in any form that invokes a standard script. If debugging mode is turned
1332 :     on, a form field will be put in that allows the user to enter tracing data.
1333 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1334 :     the output, formatted as a list.
1335 :    
1336 :     A typical standard script would loook like the following.
1337 :    
1338 :     BEGIN {
1339 :     # Print the HTML header.
1340 :     print "CONTENT-TYPE: text/html\n\n";
1341 :     }
1342 :     use Tracer;
1343 :     use CGI;
1344 :     use FIG;
1345 :     # ... more uses ...
1346 : parrello 1.6
1347 : parrello 1.93 my ($cgi, $varHash) = ScriptSetup();
1348 :     eval {
1349 :     # ... get data from $cgi, put it in $varHash ...
1350 :     };
1351 :     if ($@) {
1352 :     Trace("Script Error: $@") if T(0);
1353 :     }
1354 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1355 : parrello 1.6
1356 : parrello 1.93 The idea here is that even if the script fails, you'll see trace messages and
1357 :     useful output.
1358 : parrello 1.6
1359 :     =over 4
1360 :    
1361 : parrello 1.93 =item webData
1362 :    
1363 :     A string containing either the full web page to be written to the output or the
1364 :     name of a template file from which the page is to be constructed. If the name
1365 :     of a template file is specified, then the second parameter must be present;
1366 :     otherwise, it must be absent.
1367 :    
1368 :     =item varHash (optional)
1369 : parrello 1.6
1370 : parrello 1.93 If specified, then a reference to a hash mapping variable names for a template
1371 :     to their values. The template file will be read into memory, and variable markers
1372 :     will be replaced by data in this hash reference.
1373 : parrello 1.6
1374 :     =back
1375 :    
1376 :     =cut
1377 :    
1378 : parrello 1.93 sub ScriptFinish {
1379 :     # Get the parameters.
1380 :     my ($webData, $varHash) = @_;
1381 :     # Check for a template file situation.
1382 :     my $outputString;
1383 :     if (defined $varHash) {
1384 :     # Here we have a template file. We need to determine the template type.
1385 :     my $template;
1386 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1387 :     $template = "$FIG_Config::template_url/$webData";
1388 :     } else {
1389 :     $template = "<<$webData";
1390 :     }
1391 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
1392 :     } else {
1393 :     # Here the user gave us a raw string.
1394 :     $outputString = $webData;
1395 :     }
1396 :     # Check for trace messages.
1397 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
1398 :     # We have trace messages, so we want to put them at the end of the body. This
1399 :     # is either at the end of the whole string or at the beginning of the BODY
1400 :     # end-tag.
1401 :     my $pos = length $outputString;
1402 :     if ($outputString =~ m#</body>#gi) {
1403 :     $pos = (pos $outputString) - 7;
1404 :     }
1405 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
1406 :     # destination.
1407 :     my $traceHtml;
1408 :     if ($Destination eq "QUEUE") {
1409 :     $traceHtml = QTrace('Html');
1410 :     } elsif ($Destination =~ /^>>(.+)$/) {
1411 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
1412 :     # can copy the file name into the clipboard easily.
1413 :     my $actualDest = $1;
1414 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1415 :     } else {
1416 :     # Here we have one of the special destinations.
1417 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1418 :     }
1419 :     substr $outputString, $pos, 0, $traceHtml;
1420 :     }
1421 :     # Write the output string.
1422 :     print $outputString;
1423 : parrello 1.6 }
1424 :    
1425 : parrello 1.93 =head2 Command-Line Utility Methods
1426 : olson 1.1
1427 : parrello 1.93 =head3 SendSMS
1428 : olson 1.1
1429 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1430 : olson 1.1
1431 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1432 :     user name, password, and API ID for the relevant account in the hash reference variable
1433 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1434 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1435 :     is C<2561022>, then the FIG_Config file must contain
1436 : olson 1.1
1437 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1438 :     password => 'silly',
1439 :     api_id => '2561022' };
1440 : olson 1.1
1441 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1442 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1443 :     when you call this method.
1444 : olson 1.1
1445 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1446 : parrello 1.74
1447 : parrello 1.93 =over 4
1448 : parrello 1.74
1449 : parrello 1.93 =item phoneNumber
1450 : parrello 1.74
1451 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1452 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1453 : parrello 1.74
1454 : parrello 1.93 =item msg
1455 : parrello 1.74
1456 : parrello 1.93 Message to send to the specified phone.
1457 : parrello 1.74
1458 :     =item RETURN
1459 :    
1460 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1461 : parrello 1.74
1462 : parrello 1.78 =back
1463 :    
1464 : parrello 1.74 =cut
1465 :    
1466 : parrello 1.93 sub SendSMS {
1467 : parrello 1.74 # Get the parameters.
1468 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1469 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1470 : parrello 1.74 my $retVal;
1471 : parrello 1.93 # Only proceed if we have phone support.
1472 :     if (! defined $FIG_Config::phone) {
1473 :     Trace("Phone support not present in FIG_Config.") if T(1);
1474 :     } else {
1475 :     # Get the phone data.
1476 :     my $parms = $FIG_Config::phone;
1477 :     # Get the Clickatell URL.
1478 :     my $url = "http://api.clickatell.com/http/";
1479 :     # Create the user agent.
1480 :     my $ua = LWP::UserAgent->new;
1481 :     # Request a Clickatell session.
1482 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1483 :     password => $parms->{password},
1484 :     api_id => $parms->{api_id},
1485 :     to => $phoneNumber,
1486 :     text => $msg});
1487 :     # Check for an error.
1488 :     if (! $resp->is_success) {
1489 :     Trace("Alert failed.") if T(1);
1490 :     } else {
1491 :     # Get the message ID.
1492 :     my $rstring = $resp->content;
1493 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1494 :     $retVal = $1;
1495 :     } else {
1496 :     Trace("Phone attempt failed with $rstring") if T(1);
1497 :     }
1498 :     }
1499 : parrello 1.74 }
1500 :     # Return the result.
1501 :     return $retVal;
1502 :     }
1503 :    
1504 : parrello 1.93 =head3 StandardSetup
1505 : olson 1.1
1506 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1507 : olson 1.1
1508 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1509 :     values are a hash of the command-line options and a list of the positional
1510 :     parameters. Tracing is automatically set up and the command-line options are
1511 :     validated.
1512 : olson 1.1
1513 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1514 :     be more easily understood, however, once they are examined individually.
1515 : olson 1.1
1516 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1517 :     special-purpose tracing categories. Most tracing categories are PERL package
1518 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1519 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1520 : olson 1.1
1521 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1522 : olson 1.1
1523 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1524 :     the output. There are two special tracing categories that are automatically
1525 :     handled by this method. In other words, if you used L</TSetup> you would need
1526 :     to include these categories manually, but if you use this method they are turned
1527 :     on automatically.
1528 : parrello 1.5
1529 :     =over 4
1530 :    
1531 : parrello 1.93 =item SQL
1532 : parrello 1.5
1533 : parrello 1.93 Traces SQL commands and activity.
1534 : parrello 1.5
1535 : parrello 1.93 =item Tracer
1536 : parrello 1.5
1537 : parrello 1.93 Traces error messages and call stacks.
1538 : parrello 1.5
1539 :     =back
1540 :    
1541 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1542 :     The trace level is specified using the C<-trace> command-line option. For example,
1543 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1544 :     all tracing at level 3.
1545 : parrello 1.5
1546 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1547 : parrello 1.5
1548 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1549 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1550 :     process ID. You can also specify the C<user> parameter to put a user ID
1551 :     instead of a process ID in the trace file name. So, for example
1552 : olson 1.1
1553 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1554 :     For a genome-by-genome update, use 3.
1555 : olson 1.1
1556 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1557 : olson 1.1
1558 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1559 : olson 1.1
1560 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1561 :     options, their default values, and an explanation of what they mean. Command-line
1562 :     options may be in the form of switches or keywords. In the case of a switch, the
1563 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1564 :     of a keyword, the value is separated from the option name by an equal sign. You
1565 :     can see this last in the command-line example above.
1566 : olson 1.1
1567 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1568 :     prior to calling this method.
1569 : olson 1.1
1570 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1571 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1572 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1573 :     the following code.
1574 : olson 1.1
1575 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1576 :     { safe => [0, "use database transactions"],
1577 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1578 :     start => [' ', "start with this genome"],
1579 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1580 :     "<command> <transactionDirectory> <IDfile>",
1581 :     @ARGV);
1582 : olson 1.1
1583 :    
1584 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1585 :     stores the actual options in a hash that is returned as C<$options>. The
1586 :     positional parameters are returned in C<@parameters>.
1587 : olson 1.1
1588 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1589 : olson 1.1
1590 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1591 : olson 1.1
1592 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1593 :     above command as
1594 : olson 1.1
1595 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1596 : olson 1.1
1597 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1598 :     parameters, and would find themselves in I<@parameters> after executing the
1599 :     above code fragment. The tracing would be set to level 2, and the categories
1600 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1601 :     and C<DocUtils> was included because it came in within the first parameter
1602 :     to this method. The I<$options> hash would be
1603 : olson 1.1
1604 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1605 :     noAlias => 1, start => ' ', tblFiles => 0 }
1606 : olson 1.1
1607 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1608 :     standard tracing setup and command-line parsing. Note that the caller is
1609 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1610 :     are used by this method to control the tracing. If additional tracing features
1611 :     need to be added in the future, they can be processed by this method without
1612 :     upsetting the command-line utilities.
1613 : olson 1.1
1614 : parrello 1.93 If the C<background> option is specified on the command line, then the
1615 :     standard and error outputs will be directed to files in the temporary
1616 :     directory, using the same suffix as the trace file. So, if the command
1617 :     line specified
1618 : olson 1.1
1619 : parrello 1.93 -user=Bruce -background
1620 : olson 1.1
1621 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1622 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1623 :     simplify starting a command in the background.
1624 : olson 1.1
1625 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1626 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1627 :     be used instead of custom tracing. If the user name is not specified,
1628 :     the tracing key is taken from the C<Tracing> environment variable. If there
1629 :     is no value for that variable, the tracing key will be computed from the PID.
1630 : olson 1.1
1631 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1632 :     names will be traced at level 0 and the program will exit without processing.
1633 :     This provides a limited help capability. For example, if the user enters
1634 : olson 1.1
1635 : parrello 1.93 TransactFeatures -help
1636 : olson 1.1
1637 : parrello 1.93 he would see the following output.
1638 : olson 1.1
1639 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640 :     -trace tracing level (default E)
1641 :     -sql trace SQL commands
1642 :     -safe use database transactions
1643 :     -noAlias do not expect aliases in CHANGE transactions
1644 :     -start start with this genome
1645 :     -tblFiles output TBL files containing the corrected IDs
1646 : olson 1.1
1647 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1648 :     for C<trace> in the incoming options hash. The default value can be overridden,
1649 :     or the tracing to the standard output can be turned off by suffixing a minus
1650 :     sign to the trace level. So, for example,
1651 : olson 1.1
1652 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1653 :     ...
1654 : olson 1.1
1655 : parrello 1.93 would set the default trace level to 0 instead of E, while
1656 : olson 1.1
1657 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1658 :     ...
1659 : olson 1.1
1660 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1661 :     standard output.
1662 : olson 1.1
1663 : parrello 1.93 The parameters to this method are as follows.
1664 : olson 1.1
1665 : parrello 1.93 =over 4
1666 : olson 1.1
1667 : parrello 1.93 =item categories
1668 : parrello 1.2
1669 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1670 :     packages whose internal workings will need to be debugged to get the
1671 :     command working.
1672 : olson 1.1
1673 : parrello 1.93 =item options
1674 : olson 1.1
1675 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1676 :     to their default values and descriptions. The user can override the defaults
1677 :     by specifying the options as command-line switches prefixed by a hyphen.
1678 :     Tracing-related options may be added to this hash. If the C<-h> option is
1679 :     specified on the command line, the option descriptions will be used to
1680 :     explain the options. To turn off tracing to the standard output, add a
1681 :     minus sign to the value for C<trace> (see above).
1682 : olson 1.1
1683 : parrello 1.93 =item parmHelp
1684 : olson 1.1
1685 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1686 :     if the user specifies the C<-h> option.
1687 : olson 1.1
1688 : parrello 1.93 =item argv
1689 : olson 1.1
1690 : parrello 1.93 List of command line parameters, including the option switches, which must
1691 :     precede the positional parameters and be prefixed by a hyphen.
1692 : olson 1.1
1693 :     =item RETURN
1694 :    
1695 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1696 :     maps the command-line option switches to their values. These will either be the
1697 :     default values or overrides specified on the command line. The remaining
1698 :     elements of the list are the position parameters, in order.
1699 : olson 1.1
1700 :     =back
1701 :    
1702 :     =cut
1703 :    
1704 : parrello 1.93 sub StandardSetup {
1705 :     # Get the parameters.
1706 :     my ($categories, $options, $parmHelp, @argv) = @_;
1707 :     # Get the default tracing key.
1708 :     my $tkey = EmergencyKey();
1709 :     # Add the tracing options.
1710 :     if (! exists $options->{trace}) {
1711 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1712 :     }
1713 :     $options->{sql} = [0, "turn on SQL tracing"];
1714 :     $options->{help} = [0, "display command-line options"];
1715 :     $options->{user} = [$tkey, "tracing key"];
1716 :     $options->{background} = [0, "spool standard and error output"];
1717 :     # Create a parsing hash from the options hash. The parsing hash
1718 :     # contains the default values rather than the default value
1719 :     # and the description. While we're at it, we'll memorize the
1720 :     # length of the longest option name.
1721 :     my $longestName = 0;
1722 :     my %parseOptions = ();
1723 :     for my $key (keys %{$options}) {
1724 :     if (length $key > $longestName) {
1725 :     $longestName = length $key;
1726 :     }
1727 :     $parseOptions{$key} = $options->{$key}->[0];
1728 :     }
1729 :     # Parse the command line.
1730 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1731 :     # Get the logfile suffix.
1732 :     my $suffix = $retOptions->{user};
1733 :     # Check for background mode.
1734 :     if ($retOptions->{background}) {
1735 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
1736 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
1737 :     open STDOUT, ">$outFileName";
1738 :     open STDERR, ">$errFileName";
1739 :     # Check for phone support. If we have phone support and a phone number,
1740 :     # we want to turn it on.
1741 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1742 :     $retOptions->{phone} = $ENV{PHONE};
1743 :     }
1744 :     }
1745 :     # Now we want to set up tracing. First, we need to know if the user
1746 :     # wants emergency tracing.
1747 :     if ($retOptions->{trace} eq 'E') {
1748 :     ETracing($retOptions->{user});
1749 :     } else {
1750 :     # Here the tracing is controlled from the command line.
1751 :     my @cats = @{$categories};
1752 :     if ($retOptions->{sql}) {
1753 :     push @cats, "SQL";
1754 :     }
1755 :     # Add the default categories.
1756 :     push @cats, "Tracer";
1757 :     # Next, we create the category string by joining the categories.
1758 :     my $cats = join(" ", @cats);
1759 :     # Check to determine whether or not the caller wants to turn off tracing
1760 :     # to the standard output.
1761 :     my $traceLevel = $retOptions->{trace};
1762 :     my $textOKFlag = 1;
1763 :     if ($traceLevel =~ /^(.)-/) {
1764 :     $traceLevel = $1;
1765 :     $textOKFlag = 0;
1766 :     }
1767 :     # Now we set up the trace mode.
1768 :     my $traceMode;
1769 :     # Verify that we can open a file in the FIG temporary directory.
1770 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1771 :     if (open TESTTRACE, ">$traceFileName") {
1772 :     # Here we can trace to a file.
1773 :     $traceMode = ">$traceFileName";
1774 :     if ($textOKFlag) {
1775 :     # Echo to standard output if the text-OK flag is set.
1776 :     $traceMode = "+$traceMode";
1777 :     }
1778 :     # Close the test file.
1779 :     close TESTTRACE;
1780 :     } else {
1781 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1782 :     warn "Could not open trace file $traceFileName: $!\n";
1783 :     # We trace to the standard output if it's
1784 :     # okay, and the error log otherwise.
1785 : parrello 1.93 if ($textOKFlag) {
1786 :     $traceMode = "TEXT";
1787 : parrello 1.12 } else {
1788 : parrello 1.93 $traceMode = "WARN";
1789 : parrello 1.12 }
1790 :     }
1791 : parrello 1.93 # Now set up the tracing.
1792 :     TSetup("$traceLevel $cats", $traceMode);
1793 :     }
1794 :     # Check for the "help" option. If it is specified, dump the command-line
1795 :     # options and exit the program.
1796 :     if ($retOptions->{help}) {
1797 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1798 :     print "$1 [options] $parmHelp\n";
1799 :     for my $key (sort keys %{$options}) {
1800 :     my $name = Pad($key, $longestName, 0, ' ');
1801 :     my $desc = $options->{$key}->[1];
1802 :     if ($options->{$key}->[0]) {
1803 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1804 :     }
1805 :     print " $name $desc\n";
1806 : parrello 1.36 }
1807 : parrello 1.93 exit(0);
1808 :     }
1809 :     # Trace the options, if applicable.
1810 :     if (T(3)) {
1811 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1812 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1813 : parrello 1.3 }
1814 : parrello 1.93 # Return the parsed parameters.
1815 :     return ($retOptions, @retParameters);
1816 : olson 1.1 }
1817 :    
1818 : parrello 1.93 =head3 ReadOptions
1819 : olson 1.1
1820 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1821 : olson 1.1
1822 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1823 :     format
1824 : olson 1.1
1825 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1826 : olson 1.1
1827 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1828 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1829 :     character is a semi-colon will be ignored. The return hash will map each option name to
1830 :     the corresponding option value.
1831 : olson 1.1
1832 :     =over 4
1833 :    
1834 : parrello 1.93 =item fileName
1835 : olson 1.1
1836 : parrello 1.93 Name of the file containing the option data.
1837 : olson 1.1
1838 :     =item RETURN
1839 :    
1840 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1841 :     value.
1842 : olson 1.1
1843 :     =back
1844 :    
1845 :     =cut
1846 :    
1847 : parrello 1.93 sub ReadOptions {
1848 : parrello 1.12 # Get the parameters.
1849 : parrello 1.93 my ($fileName) = @_;
1850 :     # Open the file.
1851 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1852 :     # Count the number of records read.
1853 :     my ($records, $comments) = 0;
1854 :     # Create the return hash.
1855 :     my %retVal = ();
1856 :     # Loop through the file, accumulating key-value pairs.
1857 :     while (my $line = <CONFIGFILE>) {
1858 :     # Denote we've read a line.
1859 :     $records++;
1860 :     # Determine the line type.
1861 :     if ($line =~ /^\s*[\n\r]/) {
1862 :     # A blank line is a comment.
1863 :     $comments++;
1864 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1865 :     # Here we have an option assignment.
1866 :     retVal{$1} = $2;
1867 :     } elsif ($line =~ /^\s*;/) {
1868 :     # Here we have a text comment.
1869 :     $comments++;
1870 : parrello 1.12 } else {
1871 : parrello 1.93 # Here we have an invalid line.
1872 :     Trace("Invalid option statement in record $records.") if T(0);
1873 : parrello 1.12 }
1874 :     }
1875 : parrello 1.93 # Return the hash created.
1876 :     return %retVal;
1877 : olson 1.1 }
1878 :    
1879 : parrello 1.93 =head3 GetOptions
1880 : parrello 1.9
1881 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1882 : parrello 1.9
1883 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1884 :     as input and uses the data from the second to update the first. If the second does not exist,
1885 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1886 :     exist in the first.
1887 : parrello 1.9
1888 : parrello 1.93 Consider the following example.
1889 : parrello 1.9
1890 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1891 : parrello 1.9
1892 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1893 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1894 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1895 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1896 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1897 : parrello 1.9
1898 : parrello 1.93 {databaseType => 'Oracle'}
1899 : parrello 1.9
1900 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1901 : parrello 1.9
1902 : parrello 1.93 =over 4
1903 : parrello 1.9
1904 : parrello 1.93 =item defaults
1905 : parrello 1.9
1906 : parrello 1.93 Table of default option values.
1907 : parrello 1.9
1908 : parrello 1.93 =item options
1909 : olson 1.1
1910 : parrello 1.93 Table of overrides, if any.
1911 : olson 1.1
1912 :     =item RETURN
1913 :    
1914 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1915 : olson 1.1
1916 :     =back
1917 :    
1918 :     =cut
1919 :    
1920 : parrello 1.93 sub GetOptions {
1921 :     # Get the parameters.
1922 :     my ($defaults, $options) = @_;
1923 :     # Check for overrides.
1924 :     if ($options) {
1925 :     # Loop through the overrides.
1926 :     while (my ($option, $setting) = each %{$options}) {
1927 :     # Insure this override exists.
1928 :     if (!exists $defaults->{$option}) {
1929 :     croak "Unrecognized option $option encountered.";
1930 : parrello 1.12 } else {
1931 : parrello 1.93 # Apply the override.
1932 :     $defaults->{$option} = $setting;
1933 : parrello 1.12 }
1934 :     }
1935 :     }
1936 : parrello 1.93 # Return the merged table.
1937 :     return $defaults;
1938 : olson 1.1 }
1939 :    
1940 : parrello 1.93 =head3 MergeOptions
1941 : olson 1.1
1942 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1943 : olson 1.1
1944 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1945 :     second (default) hash, and if a matching key is not found in the first hash, the default
1946 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1947 :     checking and no return value.
1948 : olson 1.1
1949 :     =over 4
1950 :    
1951 : parrello 1.93 =item table
1952 : olson 1.1
1953 : parrello 1.93 Hash table to be updated with the default values.
1954 : olson 1.1
1955 : parrello 1.93 =item defaults
1956 : olson 1.1
1957 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1958 : olson 1.1
1959 :     =back
1960 :    
1961 :     =cut
1962 :    
1963 : parrello 1.93 sub MergeOptions {
1964 :     # Get the parameters.
1965 :     my ($table, $defaults) = @_;
1966 :     # Loop through the defaults.
1967 :     while (my ($key, $value) = each %{$defaults}) {
1968 :     if (!exists $table->{$key}) {
1969 :     $table->{$key} = $value;
1970 :     }
1971 : parrello 1.12 }
1972 : olson 1.1 }
1973 :    
1974 : parrello 1.93 =head3 ParseCommand
1975 : olson 1.1
1976 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1977 : olson 1.1
1978 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
1979 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1980 :     off and merged into a table of default options. The remainder of the command line is
1981 :     returned as a list of positional arguments. For example, consider the following invocation.
1982 : olson 1.1
1983 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1984 : olson 1.1
1985 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
1986 :     B<errors> and B<logFile>. If @words has the following format
1987 : olson 1.1
1988 : parrello 1.93 -logFile=error.log apple orange rutabaga
1989 : olson 1.1
1990 : parrello 1.93 then at the end of the invocation, C<$options> will be
1991 : olson 1.1
1992 : parrello 1.93 { errors => 0, logFile => 'error.log' }
1993 : olson 1.1
1994 : parrello 1.93 and C<@arguments> will contain
1995 : olson 1.1
1996 : parrello 1.93 apple orange rutabaga
1997 : olson 1.1
1998 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1999 :     support for quote characters. Options can be specified with single or double hyphens.
2000 : parrello 1.54
2001 :     =over 4
2002 :    
2003 : parrello 1.93 =item optionTable
2004 : parrello 1.54
2005 : parrello 1.93 Table of default options.
2006 : parrello 1.54
2007 : parrello 1.93 =item inputList
2008 : parrello 1.54
2009 : parrello 1.93 List of words on the command line.
2010 : parrello 1.54
2011 :     =item RETURN
2012 :    
2013 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2014 : parrello 1.54
2015 :     =back
2016 :    
2017 :     =cut
2018 :    
2019 : parrello 1.93 sub ParseCommand {
2020 : parrello 1.54 # Get the parameters.
2021 : parrello 1.93 my ($optionTable, @inputList) = @_;
2022 :     # Process any options in the input list.
2023 :     my %overrides = ();
2024 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2025 :     # Get the current option.
2026 :     my $arg = shift @inputList;
2027 :     # Pull out the option name.
2028 :     $arg =~ /^--?([^=]*)/g;
2029 :     my $name = $1;
2030 :     # Check for an option value.
2031 :     if ($arg =~ /\G=(.*)$/g) {
2032 :     # Here we have a value for the option.
2033 :     $overrides{$name} = UnEscape($1);
2034 :     } else {
2035 :     # Here there is no value, so we use 1.
2036 :     $overrides{$name} = 1;
2037 :     }
2038 :     }
2039 :     # Merge the options into the defaults.
2040 :     GetOptions($optionTable, \%overrides);
2041 :     # Translate the remaining parameters.
2042 :     my @retVal = ();
2043 :     for my $inputParm (@inputList) {
2044 :     push @retVal, UnEscape($inputParm);
2045 : parrello 1.54 }
2046 : parrello 1.93 # Return the results.
2047 :     return ($optionTable, @retVal);
2048 : parrello 1.54 }
2049 :    
2050 : parrello 1.93
2051 :     =head2 File Utility Methods
2052 :    
2053 : olson 1.1 =head3 GetFile
2054 :    
2055 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2056 : olson 1.1
2057 : parrello 1.35 or
2058 :    
2059 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2060 : parrello 1.35
2061 :     Return the entire contents of a file. In list context, line-ends are removed and
2062 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2063 : olson 1.1
2064 :     =over 4
2065 :    
2066 :     =item fileName
2067 :    
2068 :     Name of the file to read.
2069 :    
2070 :     =item RETURN
2071 :    
2072 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2073 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2074 :     the file, an empty list will be returned.
2075 : olson 1.1
2076 :     =back
2077 :    
2078 :     =cut
2079 :    
2080 :     sub GetFile {
2081 : parrello 1.12 # Get the parameters.
2082 :     my ($fileName) = @_;
2083 :     # Declare the return variable.
2084 :     my @retVal = ();
2085 :     # Open the file for input.
2086 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2087 :     # Read the whole file into the return variable, stripping off any terminator
2088 :     # characters.
2089 :     my $lineCount = 0;
2090 :     while (my $line = <$handle>) {
2091 :     $lineCount++;
2092 :     $line = Strip($line);
2093 :     push @retVal, $line;
2094 :     }
2095 :     # Close it.
2096 :     close $handle;
2097 :     my $actualLines = @retVal;
2098 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2099 : parrello 1.12 # Return the file's contents in the desired format.
2100 : parrello 1.9 if (wantarray) {
2101 : parrello 1.12 return @retVal;
2102 : parrello 1.6 } else {
2103 :     return join "\n", @retVal;
2104 :     }
2105 : olson 1.1 }
2106 :    
2107 : parrello 1.60 =head3 PutFile
2108 :    
2109 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2110 : parrello 1.60
2111 :     Write out a file from a list of lines of text.
2112 :    
2113 :     =over 4
2114 :    
2115 :     =item fileName
2116 :    
2117 :     Name of the output file.
2118 :    
2119 :     =item lines
2120 :    
2121 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2122 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2123 :     modification.
2124 : parrello 1.60
2125 :     =back
2126 :    
2127 :     =cut
2128 :    
2129 :     sub PutFile {
2130 :     # Get the parameters.
2131 :     my ($fileName, $lines) = @_;
2132 :     # Open the output file.
2133 :     my $handle = Open(undef, ">$fileName");
2134 : parrello 1.77 # Count the lines written.
2135 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2136 :     # Here we have a scalar, so we write it raw.
2137 :     print $handle $lines;
2138 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2139 : parrello 1.66 } else {
2140 :     # Write the lines one at a time.
2141 : parrello 1.77 my $count = 0;
2142 : parrello 1.66 for my $line (@{$lines}) {
2143 :     print $handle "$line\n";
2144 : parrello 1.77 $count++;
2145 : parrello 1.66 }
2146 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2147 : parrello 1.60 }
2148 :     # Close the output file.
2149 :     close $handle;
2150 :     }
2151 :    
2152 : parrello 1.93 =head3 ParseRecord
2153 : olson 1.1
2154 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2155 : olson 1.1
2156 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2157 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2158 :     These will automatically be converted.
2159 : olson 1.1
2160 :     =over 4
2161 :    
2162 : parrello 1.93 =item line
2163 :    
2164 :     Line of data containing the tab-delimited fields.
2165 :    
2166 :     =item RETURN
2167 : olson 1.1
2168 : parrello 1.93 Returns a list of the fields found in the data line.
2169 : olson 1.1
2170 :     =back
2171 :    
2172 :     =cut
2173 :    
2174 : parrello 1.93 sub ParseRecord {
2175 : parrello 1.12 # Get the parameter.
2176 : parrello 1.93 my ($line) = @_;
2177 :     # Remove the trailing new-line, if any.
2178 :     chomp $line;
2179 :     # Split the line read into pieces using the tab character.
2180 :     my @retVal = split /\t/, $line;
2181 :     # Trim and fix the escapes in each piece.
2182 :     for my $value (@retVal) {
2183 :     # Trim leading whitespace.
2184 :     $value =~ s/^\s+//;
2185 :     # Trim trailing whitespace.
2186 :     $value =~ s/\s+$//;
2187 :     # Delete the carriage returns.
2188 :     $value =~ s/\r//g;
2189 :     # Convert the escapes into their real values.
2190 :     $value =~ s/\\t/"\t"/ge;
2191 :     $value =~ s/\\n/"\n"/ge;
2192 :     }
2193 :     # Return the result.
2194 :     return @retVal;
2195 :     }
2196 :    
2197 :     =head3 Merge
2198 :    
2199 :     my @mergedList = Tracer::Merge(@inputList);
2200 :    
2201 :     Sort a list of strings and remove duplicates.
2202 :    
2203 :     =over 4
2204 :    
2205 :     =item inputList
2206 :    
2207 :     List of scalars to sort and merge.
2208 :    
2209 :     =item RETURN
2210 :    
2211 :     Returns a list containing the same elements sorted in ascending order with duplicates
2212 :     removed.
2213 :    
2214 :     =back
2215 :    
2216 :     =cut
2217 :    
2218 :     sub Merge {
2219 :     # Get the input list in sort order.
2220 :     my @inputList = sort @_;
2221 :     # Only proceed if the list has at least two elements.
2222 :     if (@inputList > 1) {
2223 :     # Now we want to move through the list splicing out duplicates.
2224 :     my $i = 0;
2225 :     while ($i < @inputList) {
2226 :     # Get the current entry.
2227 :     my $thisEntry = $inputList[$i];
2228 :     # Find out how many elements duplicate the current entry.
2229 :     my $j = $i + 1;
2230 :     my $dup1 = $i + 1;
2231 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2232 :     # If the number is nonzero, splice out the duplicates found.
2233 :     if ($j > $dup1) {
2234 :     splice @inputList, $dup1, $j - $dup1;
2235 : parrello 1.14 }
2236 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2237 :     # at position $i. We push $i forward one position and start again.
2238 :     $i++;
2239 : parrello 1.14 }
2240 : parrello 1.12 }
2241 : parrello 1.93 # Return the merged list.
2242 :     return @inputList;
2243 : olson 1.1 }
2244 :    
2245 : parrello 1.93 =head3 Open
2246 : olson 1.1
2247 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2248 : olson 1.1
2249 : parrello 1.93 Open a file.
2250 : olson 1.1
2251 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2252 :     function. The mode is specified using Unix-like shell information. So, for
2253 :     example,
2254 : olson 1.1
2255 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2256 : olson 1.1
2257 : parrello 1.93 would open for output appended to the specified file, and
2258 : olson 1.1
2259 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2260 : olson 1.1
2261 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2262 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2263 :     code as follows.
2264 : olson 1.1
2265 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2266 : olson 1.1
2267 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2268 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2269 :     failed open will throw an exception and the third parameter will be used to construct
2270 :     an error message. If the parameter is omitted, a standard message is constructed
2271 :     using the file spec.
2272 : olson 1.1
2273 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2274 : olson 1.1
2275 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2276 :     The actual error message from the file system will be captured and appended to the
2277 :     message in any case.
2278 : parrello 1.6
2279 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2280 : parrello 1.6
2281 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2282 :     corresponds to the C++ C<errno> value.
2283 : parrello 1.6
2284 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2285 : parrello 1.6
2286 : parrello 1.93 =over 4
2287 : parrello 1.6
2288 : parrello 1.93 =item fileHandle
2289 : parrello 1.6
2290 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2291 :     and returned as the value of this method.
2292 : olson 1.1
2293 : parrello 1.93 =item fileSpec
2294 : olson 1.1
2295 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2296 : olson 1.1
2297 : parrello 1.93 =item message (optional)
2298 : olson 1.1
2299 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2300 :     will be generated. In either case, the error information from the file system
2301 :     is appended to the message. To specify a conditional open that does not throw
2302 :     an error if it fails, use C<0>.
2303 : olson 1.1
2304 : parrello 1.93 =item RETURN
2305 : olson 1.1
2306 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2307 :     open failed.
2308 : olson 1.1
2309 :     =back
2310 :    
2311 :     =cut
2312 :    
2313 : parrello 1.93 sub Open {
2314 : parrello 1.12 # Get the parameters.
2315 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2316 :     # Attempt to open the file.
2317 :     my $rv = open $fileHandle, $fileSpec;
2318 :     # If the open failed, generate an error message.
2319 :     if (! $rv) {
2320 :     # Save the system error message.
2321 :     my $sysMessage = $!;
2322 :     # See if we need a default message.
2323 :     if (!$message) {
2324 :     # Clean any obvious mode characters and leading spaces from the
2325 :     # filename.
2326 :     my ($fileName) = FindNamePart($fileSpec);
2327 :     $message = "Could not open \"$fileName\"";
2328 :     }
2329 :     # Terminate with an error using the supplied message and the
2330 :     # error message from the file system.
2331 :     Confess("$message: $!");
2332 : parrello 1.12 }
2333 : parrello 1.93 # Return the file handle.
2334 :     return $fileHandle;
2335 : olson 1.1 }
2336 :    
2337 : parrello 1.93 =head3 FindNamePart
2338 :    
2339 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2340 :    
2341 :     Extract the portion of a file specification that contains the file name.
2342 :    
2343 :     A file specification is the string passed to an C<open> call. It specifies the file
2344 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2345 :     method assumes that the file name is whatever follows the first angle bracket
2346 :     sequence. So, for example, in the following strings the file name is
2347 :     C</usr/fig/myfile.txt>.
2348 : parrello 1.5
2349 : parrello 1.93 >>/usr/fig/myfile.txt
2350 :     </usr/fig/myfile.txt
2351 :     | sort -u > /usr/fig/myfile.txt
2352 : parrello 1.5
2353 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2354 :     whole incoming string.
2355 : parrello 1.5
2356 :     =over 4
2357 :    
2358 : parrello 1.93 =item fileSpec
2359 : parrello 1.5
2360 : parrello 1.93 File specification string from which the file name is to be extracted.
2361 : parrello 1.5
2362 :     =item RETURN
2363 :    
2364 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2365 :     the specified string, or the whole string if a file name cannot be found via normal
2366 :     methods. The second element contains the start position of the file name portion and
2367 :     the third element contains the length.
2368 : parrello 1.5
2369 :     =back
2370 :    
2371 :     =cut
2372 : parrello 1.93 #: Return Type $;
2373 :     sub FindNamePart {
2374 :     # Get the parameters.
2375 :     my ($fileSpec) = @_;
2376 :     # Default to the whole input string.
2377 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2378 :     # Parse out the file name if we can.
2379 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2380 :     $retVal = $2;
2381 :     $len = length $retVal;
2382 :     $pos = (length $fileSpec) - (length $3) - $len;
2383 : parrello 1.12 }
2384 : parrello 1.93 # Return the result.
2385 :     return ($retVal, $pos, $len);
2386 : parrello 1.5 }
2387 :    
2388 : parrello 1.93 =head3 OpenDir
2389 : parrello 1.5
2390 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2391 : parrello 1.5
2392 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2393 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2394 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2395 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2396 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2397 :     set, an exception is thrown. So, for example,
2398 : parrello 1.5
2399 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2400 : parrello 1.5
2401 : parrello 1.93 is effectively the same as
2402 : parrello 1.5
2403 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2404 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2405 : parrello 1.5
2406 : parrello 1.93 Similarly, the following code
2407 : parrello 1.5
2408 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2409 : parrello 1.5
2410 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2411 :     automatically returns an empty list if the directory fails to open.
2412 : parrello 1.5
2413 : parrello 1.93 =over 4
2414 : parrello 1.5
2415 : parrello 1.93 =item dirName
2416 : parrello 1.5
2417 : parrello 1.93 Name of the directory to open.
2418 : parrello 1.5
2419 : parrello 1.93 =item filtered
2420 : parrello 1.5
2421 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2422 :     from the list, else FALSE.
2423 : parrello 1.5
2424 : parrello 1.93 =item flag
2425 : parrello 1.5
2426 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2427 : parrello 1.5
2428 : parrello 1.93 =back
2429 : parrello 1.5
2430 : parrello 1.93 =cut
2431 :     #: Return Type @;
2432 :     sub OpenDir {
2433 :     # Get the parameters.
2434 :     my ($dirName, $filtered, $flag) = @_;
2435 :     # Declare the return variable.
2436 :     my @retVal = ();
2437 :     # Open the directory.
2438 :     if (opendir(my $dirHandle, $dirName)) {
2439 :     # The directory opened successfully. Get the appropriate list according to the
2440 :     # strictures of the filter parameter.
2441 :     if ($filtered) {
2442 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2443 :     } else {
2444 :     @retVal = readdir $dirHandle;
2445 :     }
2446 :     } elsif (! $flag) {
2447 :     # Here the directory would not open and it's considered an error.
2448 :     Confess("Could not open directory $dirName.");
2449 :     }
2450 :     # Return the result.
2451 :     return @retVal;
2452 :     }
2453 : parrello 1.5
2454 :    
2455 : parrello 1.93 =head3 Insure
2456 : parrello 1.5
2457 : parrello 1.93 Insure($dirName, $chmod);
2458 : parrello 1.5
2459 : parrello 1.93 Insure a directory is present.
2460 : parrello 1.5
2461 : parrello 1.93 =over 4
2462 : parrello 1.5
2463 : parrello 1.93 =item dirName
2464 : olson 1.1
2465 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2466 : parrello 1.7
2467 : parrello 1.93 =item chmod (optional)
2468 : parrello 1.7
2469 : parrello 1.93 Security privileges to be given to the directory if it is created.
2470 : parrello 1.7
2471 : parrello 1.93 =back
2472 : parrello 1.7
2473 :     =cut
2474 :    
2475 : parrello 1.93 sub Insure {
2476 :     my ($dirName, $chmod) = @_;
2477 :     if (! -d $dirName) {
2478 :     Trace("Creating $dirName directory.") if T(2);
2479 :     eval {
2480 :     mkpath $dirName;
2481 :     # If we have permissions specified, set them here.
2482 :     if (defined($chmod)) {
2483 :     chmod $chmod, $dirName;
2484 :     }
2485 :     };
2486 :     if ($@) {
2487 :     Confess("Error creating $dirName: $@");
2488 :     }
2489 : parrello 1.12 }
2490 : parrello 1.9 }
2491 :    
2492 : parrello 1.93 =head3 ChDir
2493 : parrello 1.9
2494 : parrello 1.93 ChDir($dirName);
2495 : parrello 1.9
2496 : parrello 1.93 Change to the specified directory.
2497 : parrello 1.9
2498 :     =over 4
2499 :    
2500 : parrello 1.93 =item dirName
2501 : parrello 1.9
2502 : parrello 1.93 Name of the directory to which we want to change.
2503 : parrello 1.9
2504 :     =back
2505 :    
2506 :     =cut
2507 :    
2508 : parrello 1.93 sub ChDir {
2509 :     my ($dirName) = @_;
2510 :     if (! -d $dirName) {
2511 :     Confess("Cannot change to directory $dirName: no such directory.");
2512 :     } else {
2513 :     Trace("Changing to directory $dirName.") if T(File => 4);
2514 :     my $okFlag = chdir $dirName;
2515 :     if (! $okFlag) {
2516 :     Confess("Error switching to directory $dirName.");
2517 :     }
2518 :     }
2519 : parrello 1.9 }
2520 :    
2521 : parrello 1.93 =head3 SetPermissions
2522 :    
2523 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2524 : parrello 1.9
2525 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2526 :     In addition, the group ownership will be changed to the specified value.
2527 : parrello 1.9
2528 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2529 :     problems, so it does internal error recovery.
2530 : parrello 1.9
2531 :     =over 4
2532 :    
2533 : parrello 1.93 =item dirName
2534 :    
2535 :     Name of the directory to process.
2536 :    
2537 :     =item group
2538 : parrello 1.9
2539 : parrello 1.93 Name of the group to be assigned.
2540 : parrello 1.9
2541 : parrello 1.93 =item mask
2542 : parrello 1.9
2543 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2544 :     permission bits of any file or directory that does not already have them
2545 :     set to 1.
2546 : parrello 1.9
2547 : parrello 1.93 =item otherMasks
2548 : parrello 1.9
2549 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2550 :     one of the patterns, that directory and all its members and subdirectories
2551 :     will be assigned the new pattern. For example, the following would
2552 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2553 : parrello 1.9
2554 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2555 : parrello 1.9
2556 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2557 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2558 : parrello 1.22
2559 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2560 :     '^tmp' => 0666);
2561 : parrello 1.9
2562 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2563 :     names are matched, not file names.
2564 : parrello 1.9
2565 :     =back
2566 :    
2567 :     =cut
2568 :    
2569 : parrello 1.93 sub SetPermissions {
2570 : parrello 1.12 # Get the parameters.
2571 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2572 :     # Set up for error recovery.
2573 :     eval {
2574 :     # Switch to the specified directory.
2575 :     ChDir($dirName);
2576 :     # Get the group ID.
2577 :     my $gid = getgrnam($group);
2578 :     # Get the mask for tracing.
2579 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2580 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2581 :     my $fixCount = 0;
2582 :     my $lookCount = 0;
2583 :     # @dirs will be a stack of directories to be processed.
2584 :     my @dirs = (getcwd());
2585 :     while (scalar(@dirs) > 0) {
2586 :     # Get the current directory.
2587 :     my $dir = pop @dirs;
2588 :     # Check for a match to one of the specified directory names. To do
2589 :     # that, we need to pull the individual part of the name off of the
2590 :     # whole path.
2591 :     my $simpleName = $dir;
2592 :     if ($dir =~ m!/([^/]+)$!) {
2593 :     $simpleName = $1;
2594 :     }
2595 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2596 :     # Search for a match.
2597 :     my $match = 0;
2598 :     my $i;
2599 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2600 :     my $pattern = $otherMasks[$i];
2601 :     if ($simpleName =~ /$pattern/i) {
2602 :     $match = 1;
2603 :     }
2604 :     }
2605 :     # Check for a match. Note we use $i-1 because the loop added 2
2606 :     # before terminating due to the match.
2607 :     if ($match && $otherMasks[$i-1] != $mask) {
2608 :     # This directory matches one of the incoming patterns, and it's
2609 :     # a different mask, so we process it recursively with that mask.
2610 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2611 :     } else {
2612 :     # Here we can process normally. Get all of the non-hidden members.
2613 :     my @submems = OpenDir($dir, 1);
2614 :     for my $submem (@submems) {
2615 :     # Get the full name.
2616 :     my $thisMem = "$dir/$submem";
2617 :     Trace("Checking member $thisMem.") if T(4);
2618 :     $lookCount++;
2619 :     if ($lookCount % 1000 == 0) {
2620 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2621 :     }
2622 :     # Fix the group.
2623 :     chown -1, $gid, $thisMem;
2624 :     # Insure this member is not a symlink.
2625 :     if (! -l $thisMem) {
2626 :     # Get its info.
2627 :     my $fileInfo = stat $thisMem;
2628 :     # Only proceed if we got the info. Otherwise, it's a hard link
2629 :     # and we want to skip it anyway.
2630 :     if ($fileInfo) {
2631 :     my $fileMode = $fileInfo->mode;
2632 :     if (($fileMode & $mask) != $mask) {
2633 :     # Fix this member.
2634 :     $fileMode |= $mask;
2635 :     chmod $fileMode, $thisMem;
2636 :     $fixCount++;
2637 :     }
2638 :     # If it's a subdirectory, stack it.
2639 :     if (-d $thisMem) {
2640 :     push @dirs, $thisMem;
2641 :     }
2642 :     }
2643 :     }
2644 :     }
2645 :     }
2646 : parrello 1.12 }
2647 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2648 :     };
2649 :     # Check for an error.
2650 :     if ($@) {
2651 :     Confess("SetPermissions error: $@");
2652 : parrello 1.12 }
2653 : parrello 1.7 }
2654 :    
2655 : parrello 1.93 =head3 GetLine
2656 : parrello 1.29
2657 : parrello 1.93 my @data = Tracer::GetLine($handle);
2658 : parrello 1.15
2659 : parrello 1.93 Read a line of data from a tab-delimited file.
2660 : parrello 1.15
2661 :     =over 4
2662 :    
2663 : parrello 1.93 =item handle
2664 : parrello 1.15
2665 : parrello 1.93 Open file handle from which to read.
2666 : parrello 1.15
2667 :     =item RETURN
2668 :    
2669 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2670 :     tab-delimited. If we are at the end of the file, then an empty list will be
2671 :     returned. If an empty line is read, a single list item consisting of a null
2672 :     string will be returned.
2673 : parrello 1.15
2674 :     =back
2675 :    
2676 :     =cut
2677 : parrello 1.93
2678 :     sub GetLine {
2679 : parrello 1.15 # Get the parameters.
2680 : parrello 1.93 my ($handle) = @_;
2681 :     # Declare the return variable.
2682 :     my @retVal = ();
2683 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2684 :     # Read from the file.
2685 :     my $line = <$handle>;
2686 :     # Only proceed if we found something.
2687 :     if (defined $line) {
2688 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2689 :     # upload control and have a nonstandard EOL combination.
2690 :     $line =~ s/(\r|\n)+$//;
2691 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2692 :     if (T(File => 4)) {
2693 :     my $escapedLine = $line;
2694 :     $escapedLine =~ s/\n/\\n/g;
2695 :     $escapedLine =~ s/\r/\\r/g;
2696 :     $escapedLine =~ s/\t/\\t/g;
2697 :     Trace("Line read: -->$escapedLine<--");
2698 :     }
2699 :     # If the line is empty, return a single empty string; otherwise, parse
2700 :     # it into fields.
2701 :     if ($line eq "") {
2702 :     push @retVal, "";
2703 :     } else {
2704 :     push @retVal, split /\t/,$line;
2705 :     }
2706 :     } else {
2707 :     # Trace the reason the read failed.
2708 :     Trace("End of file: $!") if T(File => 3);
2709 : parrello 1.15 }
2710 : parrello 1.93 # Return the result.
2711 :     return @retVal;
2712 : parrello 1.15 }
2713 :    
2714 : parrello 1.93 =head3 PutLine
2715 :    
2716 :     Tracer::PutLine($handle, \@fields, $eol);
2717 : parrello 1.35
2718 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2719 :     output in tab-separated form, with a trailing new-line.
2720 : parrello 1.35
2721 : parrello 1.93 =over 4
2722 : parrello 1.35
2723 : parrello 1.93 =item handle
2724 : parrello 1.69
2725 : parrello 1.93 Output file handle.
2726 : parrello 1.69
2727 : parrello 1.93 =item fields
2728 : parrello 1.69
2729 : parrello 1.93 List of field values.
2730 : parrello 1.69
2731 : parrello 1.93 =item eol (optional)
2732 : parrello 1.69
2733 : parrello 1.93 End-of-line character (default is "\n").
2734 : parrello 1.69
2735 :     =back
2736 : parrello 1.35
2737 :     =cut
2738 :    
2739 : parrello 1.93 sub PutLine {
2740 : parrello 1.69 # Get the parameters.
2741 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2742 :     # Write the data.
2743 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2744 : parrello 1.69 }
2745 :    
2746 :    
2747 : parrello 1.97 =head3 PrintLine
2748 :    
2749 :     Tracer::PrintLine($line);
2750 :    
2751 :     Print a line of text with a trailing new-line.
2752 :    
2753 :     =over 4
2754 :    
2755 :     =item line
2756 :    
2757 :     Line of text to print.
2758 :    
2759 :     =back
2760 :    
2761 :     =cut
2762 :    
2763 :     sub PrintLine {
2764 :     # Get the parameters.
2765 :     my ($line) = @_;
2766 :     # Print the line.
2767 :     print "$line\n";
2768 :     }
2769 :    
2770 : parrello 1.69
2771 : parrello 1.93 =head2 Other Useful Methods
2772 :    
2773 :     =head3 ParseParm
2774 :    
2775 :     my $listValue = Tracer::ParseParm($string);
2776 :    
2777 :     Convert a parameter into a list reference. If the parameter is undefined,
2778 :     an undefined value will be returned. Otherwise, it will be parsed as a
2779 :     comma-separated list of values.
2780 : parrello 1.69
2781 :     =over 4
2782 :    
2783 : parrello 1.93 =item string
2784 :    
2785 :     Incoming string.
2786 :    
2787 :     =item RETURN
2788 : parrello 1.69
2789 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2790 :     was undefined.
2791 : parrello 1.69
2792 :     =back
2793 :    
2794 :     =cut
2795 :    
2796 : parrello 1.93 sub ParseParm {
2797 :     # Get the parameters.
2798 :     my ($string) = @_;
2799 :     # Declare the return variable.
2800 :     my $retVal;
2801 :     # Check for data.
2802 :     if (defined $string) {
2803 :     # We have some, so split it into a list.
2804 :     $retVal = [ split /\s*,\s*/, $string];
2805 : parrello 1.72 }
2806 : parrello 1.93 # Return the result.
2807 :     return $retVal;
2808 : parrello 1.69 }
2809 :    
2810 : parrello 1.97 =head3 Now
2811 :    
2812 :     my $string = Tracer::Now();
2813 :    
2814 :     Return a displayable time stamp containing the local time. Whatever format this
2815 :     method produces must be parseable by L</ParseDate>.
2816 :    
2817 :     =cut
2818 :    
2819 :     sub Now {
2820 :     return DisplayTime(time);
2821 :     }
2822 :    
2823 :     =head3 DisplayTime
2824 :    
2825 :     my $string = Tracer::DisplayTime($time);
2826 : parrello 1.69
2827 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
2828 :     method produces must be parseable by L</ParseDate>.
2829 :    
2830 :     =over 4
2831 : parrello 1.69
2832 : parrello 1.97 =item time
2833 : parrello 1.69
2834 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2835 :    
2836 :     =item RETURN
2837 : parrello 1.69
2838 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2839 : parrello 1.69
2840 : parrello 1.97 =back
2841 : parrello 1.69
2842 : parrello 1.93 =cut
2843 : parrello 1.69
2844 : parrello 1.97 sub DisplayTime {
2845 :     my ($time) = @_;
2846 :     my $retVal = "(n/a)";
2847 :     if (defined $time) {
2848 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2849 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2850 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2851 :     }
2852 : parrello 1.93 return $retVal;
2853 :     }
2854 : parrello 1.69
2855 : parrello 1.93 # Pad a number to 2 digits.
2856 :     sub _p2 {
2857 :     my ($value) = @_;
2858 :     $value = "0$value" if ($value < 10);
2859 :     return $value;
2860 : parrello 1.69 }
2861 :    
2862 : parrello 1.93 =head3 Escape
2863 : parrello 1.69
2864 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2865 : parrello 1.69
2866 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2867 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2868 :     result is to reverse the effect of L</UnEscape>.
2869 : parrello 1.69
2870 :     =over 4
2871 :    
2872 : parrello 1.93 =item realString
2873 : parrello 1.69
2874 : parrello 1.93 String to escape.
2875 : parrello 1.69
2876 :     =item RETURN
2877 :    
2878 : parrello 1.93 Escaped equivalent of the real string.
2879 :    
2880 :     =back
2881 :    
2882 :     =cut
2883 :    
2884 :     sub Escape {
2885 :     # Get the parameter.
2886 :     my ($realString) = @_;
2887 :     # Initialize the return variable.
2888 :     my $retVal = "";
2889 :     # Loop through the parameter string, looking for sequences to escape.
2890 :     while (length $realString > 0) {
2891 :     # Look for the first sequence to escape.
2892 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2893 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2894 :     # itself is in $2. First, move the clear text to the return variable.
2895 :     $retVal .= $1;
2896 :     # Strip the processed section off the real string.
2897 :     $realString = substr $realString, (length $2) + (length $1);
2898 :     # Get the matched character.
2899 :     my $char = $2;
2900 :     # If we have a CR, we are done.
2901 :     if ($char ne "\r") {
2902 :     # It's not a CR, so encode the escape sequence.
2903 :     $char =~ tr/\t\n/tn/;
2904 :     $retVal .= "\\" . $char;
2905 :     }
2906 :     } else {
2907 :     # Here there are no more escape sequences. The rest of the string is
2908 :     # transferred unmodified.
2909 :     $retVal .= $realString;
2910 :     $realString = "";
2911 :     }
2912 :     }
2913 :     # Return the result.
2914 :     return $retVal;
2915 : parrello 1.69 }
2916 :    
2917 : parrello 1.93 =head3 UnEscape
2918 : parrello 1.69
2919 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2920 : parrello 1.69
2921 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2922 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2923 :     be deleted.
2924 : parrello 1.69
2925 :     =over 4
2926 :    
2927 : parrello 1.93 =item codedString
2928 : parrello 1.69
2929 : parrello 1.93 String to un-escape.
2930 : parrello 1.69
2931 :     =item RETURN
2932 :    
2933 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2934 :     values.
2935 : parrello 1.69
2936 :     =back
2937 :    
2938 :     =cut
2939 :    
2940 : parrello 1.93 sub UnEscape {
2941 :     # Get the parameter.
2942 :     my ($codedString) = @_;
2943 :     # Initialize the return variable.
2944 :     my $retVal = "";
2945 :     # Only proceed if the incoming string is nonempty.
2946 :     if (defined $codedString) {
2947 :     # Loop through the parameter string, looking for escape sequences. We can't do
2948 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
2949 :     # "\<tab>" no matter what we do.)
2950 :     while (length $codedString > 0) {
2951 :     # Look for the first escape sequence.
2952 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2953 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2954 :     # itself is in $2. First, move the clear text to the return variable.
2955 :     $retVal .= $1;
2956 :     $codedString = substr $codedString, (2 + length $1);
2957 :     # Get the escape value.
2958 :     my $char = $2;
2959 :     # If we have a "\r", we are done.
2960 :     if ($char ne 'r') {
2961 :     # Here it's not an 'r', so we convert it.
2962 :     $char =~ tr/\\tn/\\\t\n/;
2963 :     $retVal .= $char;
2964 :     }
2965 :     } else {
2966 :     # Here there are no more escape sequences. The rest of the string is
2967 :     # transferred unmodified.
2968 :     $retVal .= $codedString;
2969 :     $codedString = "";
2970 :     }
2971 :     }
2972 : parrello 1.35 }
2973 : parrello 1.69 # Return the result.
2974 :     return $retVal;
2975 :     }
2976 :    
2977 : parrello 1.93 =head3 Percent
2978 : parrello 1.69
2979 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
2980 : parrello 1.69
2981 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
2982 :     is zero, returns zero.
2983 : parrello 1.69
2984 :     =over 4
2985 :    
2986 : parrello 1.93 =item number
2987 : parrello 1.69
2988 : parrello 1.93 Percent numerator.
2989 : parrello 1.69
2990 : parrello 1.93 =item base
2991 : parrello 1.69
2992 : parrello 1.93 Percent base.
2993 : parrello 1.69
2994 : parrello 1.93 =item RETURN
2995 : parrello 1.69
2996 : parrello 1.93 Returns the percentage of the base represented by the numerator.
2997 : parrello 1.69
2998 :     =back
2999 :    
3000 :     =cut
3001 :    
3002 : parrello 1.93 sub Percent {
3003 : parrello 1.69 # Get the parameters.
3004 : parrello 1.93 my ($number, $base) = @_;
3005 :     # Declare the return variable.
3006 :     my $retVal = 0;
3007 :     # Compute the percent.
3008 :     if ($base != 0) {
3009 :     $retVal = $number * 100 / $base;
3010 :     }
3011 :     # Return the result.
3012 :     return $retVal;
3013 : parrello 1.69 }
3014 :    
3015 : parrello 1.97 =head3 Constrain
3016 :    
3017 :     my $constrained = Constrain($value, $min, $max);
3018 :    
3019 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3020 :    
3021 :     =over 4
3022 :    
3023 :     =item value
3024 :    
3025 :     Value to constrain.
3026 :    
3027 :     =item min (optional)
3028 :    
3029 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3030 :    
3031 :     =item max (optional)
3032 :    
3033 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3034 :    
3035 :     =item RETURN
3036 :    
3037 :     Returns the incoming value, constrained according to the other parameters.
3038 :    
3039 :     =back
3040 :    
3041 :     =cut
3042 :    
3043 :     sub Constrain {
3044 :     # Get the parameters.
3045 :     my ($value, $min, $max) = @_;
3046 :     # Declare the return variable.
3047 :     my $retVal = $value;
3048 :     # Apply the minimum constraint.
3049 :     if (defined $min && $retVal < $min) {
3050 :     $retVal = $min;
3051 :     }
3052 :     # Apply the maximum constraint.
3053 :     if (defined $max && $retVal > $max) {
3054 :     $retVal = $max;
3055 :     }
3056 :     # Return the result.
3057 :     return $retVal;
3058 :     }
3059 :    
3060 : parrello 1.93 =head3 Min
3061 : parrello 1.69
3062 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3063 : parrello 1.69
3064 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3065 : parrello 1.69
3066 :     =over 4
3067 :    
3068 : parrello 1.93 =item $value1, $value2, ... $valueN
3069 : parrello 1.69
3070 : parrello 1.93 List of numbers to compare.
3071 : parrello 1.69
3072 :     =item RETURN
3073 :    
3074 : parrello 1.93 Returns the lowest number in the list.
3075 : parrello 1.69
3076 :     =back
3077 :    
3078 :     =cut
3079 :    
3080 : parrello 1.93 sub Min {
3081 :     # Get the parameters. Note that we prime the return value with the first parameter.
3082 :     my ($retVal, @values) = @_;
3083 :     # Loop through the remaining parameters, looking for the lowest.
3084 :     for my $value (@values) {
3085 :     if ($value < $retVal) {
3086 :     $retVal = $value;
3087 : parrello 1.72 }
3088 :     }
3089 : parrello 1.93 # Return the minimum found.
3090 : parrello 1.70 return $retVal;
3091 : parrello 1.35 }
3092 :    
3093 : parrello 1.93 =head3 Max
3094 :    
3095 :     my $max = Max($value1, $value2, ... $valueN);
3096 : parrello 1.69
3097 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3098 : parrello 1.65
3099 : parrello 1.93 =over 4
3100 : parrello 1.65
3101 : parrello 1.93 =item $value1, $value2, ... $valueN
3102 : parrello 1.65
3103 : parrello 1.93 List of numbers to compare.
3104 : parrello 1.65
3105 : parrello 1.93 =item RETURN
3106 : parrello 1.65
3107 : parrello 1.93 Returns the highest number in the list.
3108 : parrello 1.65
3109 :     =back
3110 :    
3111 :     =cut
3112 :    
3113 : parrello 1.93 sub Max {
3114 :     # Get the parameters. Note that we prime the return value with the first parameter.
3115 :     my ($retVal, @values) = @_;
3116 :     # Loop through the remaining parameters, looking for the highest.
3117 :     for my $value (@values) {
3118 :     if ($value > $retVal) {
3119 :     $retVal = $value;
3120 : parrello 1.65 }
3121 :     }
3122 : parrello 1.93 # Return the maximum found.
3123 :     return $retVal;
3124 : parrello 1.65 }
3125 :    
3126 : parrello 1.35
3127 : parrello 1.93 =head3 Strip
3128 : parrello 1.37
3129 : parrello 1.93 my $string = Tracer::Strip($line);
3130 : parrello 1.37
3131 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3132 :     that may have been transferred back and forth several times among different
3133 :     operating environments.
3134 : parrello 1.37
3135 :     =over 4
3136 :    
3137 : parrello 1.93 =item line
3138 : parrello 1.37
3139 : parrello 1.93 Line of text to be stripped.
3140 : parrello 1.37
3141 : parrello 1.93 =item RETURN
3142 : parrello 1.91
3143 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3144 : parrello 1.91
3145 : parrello 1.37 =back
3146 :    
3147 :     =cut
3148 :    
3149 : parrello 1.93 sub Strip {
3150 :     # Get a copy of the parameter string.
3151 :     my ($string) = @_;
3152 :     my $retVal = (defined $string ? $string : "");
3153 :     # Strip the line terminator characters.
3154 :     $retVal =~ s/(\r|\n)+$//g;
3155 :     # Return the result.
3156 :     return $retVal;
3157 : parrello 1.43 }
3158 :    
3159 : parrello 1.93 =head3 Pad
3160 : parrello 1.43
3161 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3162 : parrello 1.43
3163 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3164 :     space, and the padding will be on the right side unless specified
3165 :     in the third parameter.
3166 : parrello 1.43
3167 :     =over 4
3168 :    
3169 : parrello 1.93 =item string
3170 :    
3171 :     String to be padded.
3172 :    
3173 :     =item len
3174 :    
3175 :     Desired length of the padded string.
3176 :    
3177 :     =item left (optional)
3178 :    
3179 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3180 :    
3181 :     =item padChar (optional)
3182 :    
3183 :     Character to use for padding. The default is a space.
3184 :    
3185 :     =item RETURN
3186 : parrello 1.43
3187 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3188 :     specified end so that it achieves the desired length.
3189 : parrello 1.43
3190 :     =back
3191 :    
3192 :     =cut
3193 :    
3194 : parrello 1.93 sub Pad {
3195 :     # Get the parameters.
3196 :     my ($string, $len, $left, $padChar) = @_;
3197 :     # Compute the padding character.
3198 :     if (! defined $padChar) {
3199 :     $padChar = " ";
3200 :     }
3201 :     # Compute the number of spaces needed.
3202 :     my $needed = $len - length $string;
3203 :     # Copy the string into the return variable.
3204 :     my $retVal = $string;
3205 :     # Only proceed if padding is needed.
3206 :     if ($needed > 0) {
3207 :     # Create the pad string.
3208 :     my $pad = $padChar x $needed;
3209 :     # Affix it to the return value.
3210 :     if ($left) {
3211 :     $retVal = $pad . $retVal;
3212 :     } else {
3213 :     $retVal .= $pad;
3214 : parrello 1.43 }
3215 : parrello 1.37 }
3216 : parrello 1.93 # Return the result.
3217 :     return $retVal;
3218 : parrello 1.37 }
3219 :    
3220 : parrello 1.93 =head3 EOF
3221 :    
3222 :     This is a constant that is lexically greater than any useful string.
3223 :    
3224 :     =cut
3225 :    
3226 :     sub EOF {
3227 :     return "\xFF\xFF\xFF\xFF\xFF";
3228 :     }
3229 : parrello 1.59
3230 : parrello 1.93 =head3 TICK
3231 : parrello 1.59
3232 : parrello 1.93 my @results = TICK($commandString);
3233 : parrello 1.59
3234 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3235 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3236 : parrello 1.59
3237 : parrello 1.93 `./protein.cgi`
3238 : parrello 1.59
3239 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3240 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3241 : parrello 1.59
3242 : parrello 1.93 TICK("./protein.cgi")
3243 : parrello 1.59
3244 : parrello 1.93 it will work correctly in both environments.
3245 : parrello 1.59
3246 : parrello 1.93 =over 4
3247 : parrello 1.59
3248 : parrello 1.93 =item commandString
3249 : parrello 1.59
3250 : parrello 1.93 The command string to pass to the system.
3251 : parrello 1.59
3252 :     =item RETURN
3253 :    
3254 : parrello 1.93 Returns the standard output from the specified command, as a list.
3255 : parrello 1.59
3256 :     =back
3257 :    
3258 :     =cut
3259 : parrello 1.93 #: Return Type @;
3260 :     sub TICK {
3261 : parrello 1.59 # Get the parameters.
3262 : parrello 1.93 my ($commandString) = @_;
3263 :     # Chop off the dot-slash if this is Windows.
3264 :     if ($FIG_Config::win_mode) {
3265 :     $commandString =~ s!^\./!!;
3266 : parrello 1.59 }
3267 : parrello 1.93 # Activate the command and return the result.
3268 :     return `$commandString`;
3269 : parrello 1.59 }
3270 :    
3271 : parrello 1.93
3272 : parrello 1.55 =head3 CommaFormat
3273 :    
3274 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3275 : parrello 1.55
3276 :     Insert commas into a number.
3277 :    
3278 :     =over 4
3279 :    
3280 :     =item number
3281 :    
3282 :     A sequence of digits.
3283 :    
3284 :     =item RETURN
3285 :    
3286 :     Returns the same digits with commas strategically inserted.
3287 :    
3288 :     =back
3289 :    
3290 :     =cut
3291 :    
3292 :     sub CommaFormat {
3293 :     # Get the parameters.
3294 :     my ($number) = @_;
3295 :     # Pad the length up to a multiple of three.
3296 :     my $padded = "$number";
3297 :     $padded = " " . $padded while length($padded) % 3 != 0;
3298 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3299 :     # cause the delimiters to be included in the output stream. The
3300 :     # GREP removes the empty strings in between the delimiters.
3301 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3302 :     # Clean out the spaces.
3303 :     $retVal =~ s/ //g;
3304 :     # Return the result.
3305 :     return $retVal;
3306 :     }
3307 : parrello 1.46
3308 :    
3309 : parrello 1.62 =head3 CompareLists
3310 :    
3311 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3312 : parrello 1.62
3313 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3314 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3315 :     The return value contains a list of items that are only in the new list
3316 :     (inserted) and only in the old list (deleted).
3317 :    
3318 :     =over 4
3319 :    
3320 :     =item newList
3321 :    
3322 :     Reference to a list of new tuples.
3323 :    
3324 :     =item oldList
3325 :    
3326 :     Reference to a list of old tuples.
3327 :    
3328 :     =item keyIndex (optional)
3329 :    
3330 :     Index into each tuple of its key field. The default is 0.
3331 :    
3332 :     =item RETURN
3333 :    
3334 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3335 :     list (inserted) followed by a reference to the list of items that are only in the old
3336 :     list (deleted).
3337 :    
3338 :     =back
3339 :    
3340 :     =cut
3341 :    
3342 :     sub CompareLists {
3343 :     # Get the parameters.
3344 :     my ($newList, $oldList, $keyIndex) = @_;
3345 :     if (! defined $keyIndex) {
3346 :     $keyIndex = 0;
3347 :     }
3348 :     # Declare the return variables.
3349 :     my ($inserted, $deleted) = ([], []);
3350 :     # Loop through the two lists simultaneously.
3351 :     my ($newI, $oldI) = (0, 0);
3352 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3353 :     while ($newI < $newN || $oldI < $oldN) {
3354 :     # Get the current object in each list. Note that if one
3355 :     # of the lists is past the end, we'll get undef.
3356 :     my $newItem = $newList->[$newI];
3357 :     my $oldItem = $oldList->[$oldI];
3358 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3359 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3360 :     push @{$deleted}, $oldItem;
3361 :     $oldI++;
3362 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3363 :     # The new item is not in the old list, so mark it inserted.
3364 :     push @{$inserted}, $newItem;
3365 :     $newI++;
3366 :     } else {
3367 :     # The item is in both lists, so push forward.
3368 :     $oldI++;
3369 :     $newI++;
3370 :     }
3371 :     }
3372 :     # Return the result.
3373 :     return ($inserted, $deleted);
3374 :     }
3375 :    
3376 : parrello 1.65 =head3 GenerateURL
3377 :    
3378 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3379 : parrello 1.65
3380 :     Generate a GET-style URL for the specified page with the specified parameter
3381 :     names and values. The values will be URL-escaped automatically. So, for
3382 :     example
3383 :    
3384 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3385 :    
3386 :     would return
3387 :    
3388 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3389 : parrello 1.65
3390 :     =over 4
3391 :    
3392 :     =item page
3393 :    
3394 :     Page URL.
3395 :    
3396 :     =item parameters
3397 :    
3398 :     Hash mapping parameter names to parameter values.
3399 :    
3400 :     =item RETURN
3401 :    
3402 :     Returns a GET-style URL that goes to the specified page and passes in the
3403 :     specified parameters and values.
3404 :    
3405 :     =back
3406 :    
3407 :     =cut
3408 :    
3409 :     sub GenerateURL {
3410 :     # Get the parameters.
3411 :     my ($page, %parameters) = @_;
3412 :     # Prime the return variable with the page URL.
3413 :     my $retVal = $page;
3414 :     # Loop through the parameters, creating parameter elements in a list.
3415 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3416 :     # If the list is nonempty, tack it on.
3417 :     if (@parmList) {
3418 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3419 : parrello 1.65 }
3420 :     # Return the result.
3421 :     return $retVal;
3422 :     }
3423 :    
3424 : parrello 1.78 =head3 ApplyURL
3425 :    
3426 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3427 : parrello 1.78
3428 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3429 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3430 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3431 :    
3432 :     This provides a simple way to process the results of a database query into something
3433 :     displayable by combining a URL with text.
3434 :    
3435 :     =over 4
3436 :    
3437 :     =item table
3438 :    
3439 :     Reference to a list of lists. The elements in the containing list will be updated by
3440 :     this method.
3441 :    
3442 :     =item target
3443 :    
3444 :     The index of the column to be converted into HTML.
3445 :    
3446 :     =item url
3447 :    
3448 :     The index of the column containing the URL. Note that the URL must have a recognizable
3449 :     C<http:> at the beginning.
3450 :    
3451 :     =back
3452 :    
3453 :     =cut
3454 :    
3455 :     sub ApplyURL {
3456 :     # Get the parameters.
3457 :     my ($table, $target, $url) = @_;
3458 :     # Loop through the table.
3459 :     for my $row (@{$table}) {
3460 :     # Apply the URL to the target cell.
3461 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3462 :     # Delete the URL from the row.
3463 :     delete $row->[$url];
3464 :     }
3465 :     }
3466 :    
3467 :     =head3 CombineURL
3468 :    
3469 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3470 : parrello 1.78
3471 :     This method will convert the specified text into HTML hyperlinked to the specified
3472 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3473 :     is defined and begins with an C<http:> header.
3474 :    
3475 :     =over 4
3476 :    
3477 :     =item text
3478 :    
3479 :     Text to return. This will be HTML-escaped automatically.
3480 :    
3481 :     =item url
3482 :    
3483 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3484 :     will be returned without any hyperlinking.
3485 :    
3486 :     =item RETURN
3487 :    
3488 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3489 :     doesn't look right, the HTML-escaped text will be returned without any further
3490 :     modification.
3491 :    
3492 :     =back
3493 :    
3494 :     =cut
3495 :    
3496 :     sub CombineURL {
3497 :     # Get the parameters.
3498 :     my ($text, $url) = @_;
3499 :     # Declare the return variable.
3500 :     my $retVal = CGI::escapeHTML($text);
3501 :     # Verify the URL.
3502 :     if (defined($url) && $url =~ m!http://!i) {
3503 :     # It's good, so we apply it to the text.
3504 :     $retVal = "<a href=\"$url\">$retVal</a>";
3505 :     }
3506 :     # Return the result.
3507 :     return $retVal;
3508 :     }
3509 :    
3510 : parrello 1.93 =head3 Cmp
3511 :    
3512 :     my $cmp = Tracer::Cmp($a, $b);
3513 :    
3514 :     This method performs a universal sort comparison. Each value coming in is
3515 :     separated into a leading text part and a trailing number part. The text
3516 :     part is string compared, and if both parts are equal, then the number
3517 :     parts are compared numerically. A stream of just numbers or a stream of
3518 :     just strings will sort correctly, and a mixed stream will sort with the
3519 :     numbers first. Strings with a label and a number will sort in the
3520 :     expected manner instead of lexically.
3521 :    
3522 :     =over 4
3523 :    
3524 :     =item a
3525 :    
3526 :     First item to compare.
3527 :    
3528 :     =item b
3529 :    
3530 :     Second item to compare.
3531 :    
3532 :     =item RETURN
3533 :    
3534 :     Returns a negative number if the first item should sort first (is less), a positive
3535 :     number if the first item should sort second (is greater), and a zero if the items are
3536 :     equal.
3537 :    
3538 :     =back
3539 :    
3540 :     =cut
3541 :    
3542 :     sub Cmp {
3543 :     # Get the parameters.
3544 :     my ($a, $b) = @_;
3545 :     # Declare the return value.
3546 :     my $retVal;
3547 :     # Check for nulls.
3548 :     if (! defined($a)) {
3549 :     $retVal = (! defined($b) ? 0 : -1);
3550 :     } elsif (! defined($b)) {
3551 :     $retVal = 1;
3552 :     } else {
3553 :     # Here we have two real values. Parse the two strings.
3554 :     $a =~ /^(\D*)(\d*)$/;
3555 :     my $aParsed = [$1, $2];
3556 :     $b =~ /^(\D*)(\d*)$/;
3557 :     my $bParsed = [$1, $2];
3558 :     # Compare the string parts.
3559 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3560 :     if (! $retVal) {
3561 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3562 :     }
3563 :     }
3564 :     # Return the result.
3565 :     return $retVal;
3566 :     }
3567 :    
3568 : parrello 1.87
3569 : parrello 1.97 =head3 TrackingCode
3570 :    
3571 :     my $html = Tracer::TrackingCode();
3572 :    
3573 :     Returns the HTML code for doing web page traffic monitoring. If the
3574 :     current environment is a test system, then it returns a null string;
3575 :     otherwise, it returns a bunch of javascript containing code for turning
3576 :     on SiteMeter and Google Analytics.
3577 :    
3578 :     =cut
3579 :    
3580 :     sub TrackingCode {
3581 :     # Declare the return variable.
3582 :     my $retVal = "<!-- tracking off -->";
3583 :     # Determine if we're in production.
3584 :     if ($FIG_Config::site_meter) {
3585 :     $retVal = <<END_HTML
3586 :     <!-- Site Meter -->
3587 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3588 :     </script>
3589 :     <noscript>
3590 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3591 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3592 :     </noscript>
3593 :     <!-- Copyright (c)2006 Site Meter -->
3594 :     END_HTML
3595 :     }
3596 :     return $retVal;
3597 :     }
3598 :    
3599 :    
3600 : olson 1.88 1;

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