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

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