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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 1.111 use Fcntl qw(:DEFAULT :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: $!";
496 : parrello 1.111 # Lock the file.
497 :     flock TRACING, LOCK_EX;
498 : parrello 1.93 print TRACING "$formatted\n";
499 :     close TRACING;
500 :     # If the Tee flag is on, echo it to the standard output.
501 :     if ($TeeFlag) {
502 :     print "$formatted\n";
503 :     }
504 :     }
505 :     }
506 : parrello 1.36
507 : parrello 1.93 =head3 T
508 : parrello 1.36
509 : parrello 1.93 my $switch = T($category, $traceLevel);
510 : parrello 1.36
511 : parrello 1.93 or
512 : parrello 1.44
513 : parrello 1.93 my $switch = T($traceLevel);
514 : parrello 1.44
515 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
516 :     is active, else FALSE. If no category is specified, the caller's package name is used.
517 : parrello 1.44
518 : parrello 1.93 =over 4
519 : parrello 1.44
520 : parrello 1.93 =item category
521 : parrello 1.44
522 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
523 :     used.
524 : parrello 1.31
525 : parrello 1.93 =item traceLevel
526 : parrello 1.31
527 : parrello 1.93 Relevant tracing level.
528 : parrello 1.31
529 : parrello 1.93 =item RETURN
530 : parrello 1.31
531 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
532 : parrello 1.31
533 : parrello 1.93 =back
534 : parrello 1.36
535 : parrello 1.93 =cut
536 :    
537 :     sub T {
538 :     # Declare the return variable.
539 :     my $retVal = 0;
540 :     # Only proceed if tracing is turned on.
541 :     if ($Destination ne "NONE") {
542 :     # Get the parameters.
543 :     my ($category, $traceLevel) = @_;
544 :     if (!defined $traceLevel) {
545 :     # Here we have no category, so we need to get the calling package.
546 :     # The calling package is normally the first parameter. If it is
547 :     # omitted, the first parameter will be the tracelevel. So, the
548 :     # first thing we do is shift the so-called category into the
549 :     # $traceLevel variable where it belongs.
550 :     $traceLevel = $category;
551 :     my ($package, $fileName, $line) = caller;
552 :     # If there is no calling package, we default to "main".
553 :     if (!$package) {
554 :     $category = "main";
555 :     } else {
556 :     my @cats = split /::/, $package;
557 :     $category = $cats[$#cats];
558 :     }
559 :     }
560 : parrello 1.97 # Save the category name and level.
561 : parrello 1.93 $LastCategory = $category;
562 : parrello 1.97 $LastLevel = $traceLevel;
563 : parrello 1.93 # Convert it to lower case before we hash it.
564 :     $category = lc $category;
565 : parrello 1.100 # Validate the trace level.
566 : parrello 1.93 if (ref $traceLevel) {
567 :     Confess("Bad trace level.");
568 :     } elsif (ref $TraceLevel) {
569 :     Confess("Bad trace config.");
570 :     }
571 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
572 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
573 : parrello 1.93 }
574 :     # Return the computed result.
575 :     return $retVal;
576 :     }
577 :    
578 :     =head3 QTrace
579 :    
580 :     my $data = QTrace($format);
581 :    
582 :     Return the queued trace data in the specified format.
583 :    
584 :     =over 4
585 :    
586 :     =item format
587 :    
588 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
589 :    
590 :     =back
591 :    
592 :     =cut
593 :    
594 :     sub QTrace {
595 :     # Get the parameter.
596 :     my ($format) = @_;
597 :     # Create the return variable.
598 :     my $retVal = "";
599 :     # Only proceed if there is an actual queue.
600 :     if (@Queue) {
601 :     # Process according to the format.
602 :     if ($format =~ m/^HTML$/i) {
603 :     # Convert the queue into an HTML list.
604 :     $retVal = "<ul>\n";
605 :     for my $line (@Queue) {
606 :     my $escapedLine = CGI::escapeHTML($line);
607 :     $retVal .= "<li>$escapedLine</li>\n";
608 :     }
609 :     $retVal .= "</ul>\n";
610 :     } elsif ($format =~ m/^TEXT$/i) {
611 :     # Convert the queue into a list of text lines.
612 :     $retVal = join("\n", @Queue) . "\n";
613 :     }
614 :     # Clear the queue.
615 :     @Queue = ();
616 :     }
617 :     # Return the formatted list.
618 :     return $retVal;
619 :     }
620 :    
621 :     =head3 Confess
622 :    
623 :     Confess($message);
624 :    
625 :     Trace the call stack and abort the program with the specified message. When used with
626 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
627 :     So, for example
628 :    
629 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
630 :    
631 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
632 :    
633 :     =over 4
634 :    
635 :     =item message
636 :    
637 :     Message to include in the trace.
638 :    
639 :     =back
640 :    
641 :     =cut
642 :    
643 :     sub Confess {
644 :     # Get the parameters.
645 :     my ($message) = @_;
646 : parrello 1.97 # Set up the category and level.
647 :     $LastCategory = "(confess)";
648 :     $LastLevel = 0;
649 : parrello 1.93 if (! defined($FIG_Config::no_tool_hdr)) {
650 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
651 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
652 :     # Only proceed if the tool header file is actually present.
653 :     if (-f $toolHeaderFile) {
654 : parrello 1.97 my $fh;
655 :     if (open $fh, "<$toolHeaderFile") {
656 :     my @lines = <$fh>;
657 :     Trace("Tool header has " . scalar(@lines) . " lines.");
658 :     }
659 : parrello 1.93 }
660 :     }
661 :     # Trace the call stack.
662 :     Cluck($message);
663 :     # Abort the program.
664 :     croak(">>> $message");
665 :     }
666 :    
667 : parrello 1.106 =head3 SaveCGI
668 :    
669 :     Tracer::SaveCGI($cgi);
670 :    
671 :     This method saves the CGI object but does not activate emergency tracing.
672 :     It is used to allow L</Warn> to work in situations where emergency
673 :     tracing is contra-indicated (e.g. the wiki).
674 :    
675 :     =over 4
676 :    
677 :     =item cgi
678 :    
679 :     Active CGI query object.
680 :    
681 :     =back
682 :    
683 :     =cut
684 :    
685 :     sub SaveCGI {
686 :     $SavedCGI = $_[0];
687 :     }
688 :    
689 : parrello 1.99 =head3 Warn
690 :    
691 : parrello 1.106 Warn($message, @options);
692 : parrello 1.99
693 :     This method traces an important message. If an RSS feed is configured
694 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
695 :     then the message will be echoed to the feed. In general, a tracing
696 :     destination of C<WARN> indicates that the caller is running as a web
697 :     service in a production environment; however, this is not a requirement.
698 :    
699 : parrello 1.103 To force warnings into the RSS feed even when the tracing destination
700 :     is not C<WARN>, simply specify the C<Feed> tracing module. This can be
701 :     configured automatically when L</StandardSetup> is used.
702 :    
703 : parrello 1.99 The L</Cluck> method calls this one for its final message. Since
704 :     L</Confess> calls L</Cluck>, this means that any error which is caught
705 :     and confessed will put something in the feed. This insures that someone
706 :     will be alerted relatively quickly when a failure occurs.
707 :    
708 :     =over 4
709 :    
710 :     =item message
711 :    
712 :     Message to be traced.
713 :    
714 : parrello 1.106 =item options
715 :    
716 :     A list containing zero or more options.
717 :    
718 :     =back
719 :    
720 :     The permissible options are as follows.
721 :    
722 :     =over 4
723 :    
724 :     =item noStack
725 :    
726 :     If specified, then the stack trace is not included in the output.
727 :    
728 : parrello 1.99 =back
729 :    
730 :     =cut
731 :    
732 :     sub Warn {
733 :     # Get the parameters.
734 : parrello 1.106 my $message = shift @_;
735 :     my %options = map { $_ => 1 } @_;
736 : parrello 1.107 # Save $@;
737 :     my $savedError = $@;
738 : parrello 1.99 # Trace the message.
739 :     Trace($message);
740 : parrello 1.106 # This will contain the lock handle. If it's defined, it means we need to unlock.
741 :     my $lock;
742 : parrello 1.103 # Check for feed forcing.
743 :     my $forceFeed = exists $Categories{feed};
744 : parrello 1.106 # An error here would be disastrous. Note that if debug mode is specified,
745 :     # we do this stuff even in a test environment.
746 : parrello 1.99 eval {
747 :     # Do we need to put this in the RSS feed?
748 : parrello 1.103 if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
749 : parrello 1.109 # Probably. We need to check first, however, to see if it's from an
750 :     # ignored IP. For non-CGI situations, we default the IP to the self-referent.
751 :     my $key = "127.0.0.1";
752 :     if (defined $SavedCGI) {
753 :     # Get the IP address.
754 :     $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
755 : parrello 1.101 }
756 : parrello 1.109 # Is the IP address in the ignore list?
757 :     my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
758 :     if (! $found) {
759 :     # No. We're good. We now need to compute the date, the link, and the title.
760 :     # First, the date, in a very specific format.
761 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
762 :     (tz_local_offset() / 30);
763 :     # Environment data goes in here. We start with the date.
764 :     my $environment = "$date. ";
765 :     # If we need to recap the message (because it's too long to be a title), we'll
766 :     # put it in here.
767 :     my $recap;
768 :     # Copy the message and remove excess space.
769 :     my $title = $message;
770 :     $title =~ s/\s+/ /gs;
771 :     # If it's too long, we have to split it up.
772 :     if (length $title > 60) {
773 :     # Put the full message in the environment string.
774 :     $recap = $title;
775 :     # Excerpt it as the title.
776 :     $title = substr($title, 0, 50) . "...";
777 :     }
778 :     # If we have a CGI object, then this is a web error. Otherwise, it's
779 :     # command-line.
780 :     if (defined $SavedCGI) {
781 :     # We're in a web service. The environment is the user's IP, and the link
782 :     # is the URL that got us here.
783 :     $environment .= "Event Reported at IP address $key process $$.";
784 :     my $url = $SavedCGI->self_url();
785 :     # We need the user agent string and (if available) the referrer.
786 :     # The referrer will be the link.
787 :     $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
788 :     if ($ENV{HTTP_REFERER}) {
789 :     my $link = $ENV{HTTP_REFERER};
790 :     $environment .= " referred from <a href=\"$link\">$link</a>.";
791 :     } else {
792 :     $environment .= " referrer unknown.";
793 :     }
794 :     # Close off the sentence with the original link.
795 :     $environment .= " URL of event is <a href=\"$url\">$url</a>.";
796 :     } else {
797 :     # No CGI object, so we're a command-line tool. Use the tracing
798 :     # key and the PID as the user identifier, and add the command.
799 :     my $key = EmergencyKey();
800 :     $environment .= "Event Reported by $key process $$.";
801 :     if ($CommandLine) {
802 :     # We're in a StandardSetup script, so we have the real command line.
803 :     $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
804 :     } elsif ($ENV{_}) {
805 :     # We're in a BASH script, so the command has been stored in the _ variable.
806 :     $environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
807 :     }
808 :     }
809 :     # Build a GUID. We use the current time, the title, and the process ID,
810 :     # then digest the result.
811 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
812 :     # Finally, the description. This is a stack trace plus various environmental stuff.
813 :     # The trace is optional.
814 :     my $stackTrace;
815 :     if ($options{noStack}) {
816 :     $stackTrace = "";
817 :     } else {
818 :     my @trace = LongMess();
819 :     # Only proceed if we got something back.
820 :     if (scalar(@trace) > 0) {
821 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
822 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
823 :     }
824 :     }
825 :     # We got the stack trace. Now it's time to put it all together.
826 :     # We have a goofy thing here in that we need to HTML-escape some sections of the description
827 :     # twice. They will be escaped once here, and then once when written by XML::Simple. They are
828 :     # unescaped once when processed by the RSS reader, and stuff in the description is treated as
829 :     # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
830 :     # our <br>s and <pre>s are used to format the description.
831 :     $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
832 :     my $description = "$recap$environment $stackTrace";
833 :     # Okay, we have all the pieces. Create a hash of the new event.
834 :     my $newItem = { title => $title,
835 :     description => $description,
836 :     category => $LastCategory,
837 :     pubDate => $date,
838 :     guid => $guid,
839 :     };
840 :     # We need XML capability for this.
841 :     require XML::Simple;
842 :     # The RSS document goes in here.
843 :     my $rss;
844 :     # Get the name of the RSS file. It's in the FIG temporary directory.
845 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
846 :     # Open the config file and lock it.
847 :     $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
848 :     flock $lock, LOCK_EX;
849 :     # Does it exist?
850 :     if (-s $fileName) {
851 :     # Slurp it in.
852 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
853 : parrello 1.102 } else {
854 : parrello 1.109 my $size = -s $fileName;
855 :     # Create an empty channel.
856 :     $rss = {
857 :     channel => {
858 :     title => 'NMPDR Warning Feed',
859 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
860 :     description => "Important messages regarding the status of the NMPDR.",
861 :     generator => "NMPDR Trace Facility",
862 :     docs => "http://blogs.law.harvard.edu/tech/rss",
863 :     item => []
864 :     },
865 :     };
866 : parrello 1.100 }
867 : parrello 1.109 # Get the channel object.
868 :     my $channel = $rss->{channel};
869 :     # Update the last-build date.
870 :     $channel->{lastBuildDate} = $date;
871 :     # Get the item array.
872 :     my $items = $channel->{item};
873 :     # Insure it has only 100 entries.
874 :     while (scalar @{$items} > 100) {
875 :     pop @{$items};
876 : parrello 1.104 }
877 : parrello 1.109 # Add our new item at the front.
878 :     unshift @{$items}, $newItem;
879 :     # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
880 :     # the requirements for those.
881 :     my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
882 :     # Here we put in the root and declaration. The problem is that the root has to have the version attribute
883 :     # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
884 :     $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
885 :     # We don't use Open here because we can't afford an error.
886 :     if (open XMLOUT, ">$fileName") {
887 :     print XMLOUT $xml;
888 :     close XMLOUT;
889 : parrello 1.106 }
890 : parrello 1.101 }
891 : parrello 1.99 }
892 :     };
893 : parrello 1.103 if ($@) {
894 :     # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
895 :     # (which is a good thing).
896 : parrello 1.102 my $error = $@;
897 : parrello 1.103 Trace("Feed Error: $error") if T(Feed => 0);
898 : parrello 1.102 }
899 : parrello 1.106 # Be sure to unlock.
900 :     if ($lock) {
901 :     flock $lock, LOCK_UN;
902 :     undef $lock;
903 :     }
904 : parrello 1.107 # Restore the error message.
905 :     $@ = $savedError;
906 : parrello 1.99 }
907 :    
908 : parrello 1.106
909 :    
910 :    
911 : parrello 1.93 =head3 Assert
912 :    
913 :     Assert($condition1, $condition2, ... $conditionN);
914 :    
915 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
916 :     the OR operator and the L</Confess> method as a debugging assert.
917 :     So, for example
918 :    
919 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
920 :    
921 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
922 :    
923 :     =cut
924 :     sub Assert {
925 :     my $retVal = 1;
926 :     LOOP: for my $condition (@_) {
927 :     if (! $condition) {
928 :     $retVal = 0;
929 :     last LOOP;
930 :     }
931 :     }
932 :     return $retVal;
933 :     }
934 :    
935 :     =head3 Cluck
936 :    
937 :     Cluck($message);
938 :    
939 :     Trace the call stack. Note that for best results, you should qualify the call with a
940 :     trace condition. For example,
941 :    
942 :     Cluck("Starting record parse.") if T(3);
943 :    
944 :     will only trace the stack if the trace level for the package is 3 or more.
945 :    
946 :     =over 4
947 :    
948 :     =item message
949 :    
950 :     Message to include in the trace.
951 :    
952 :     =back
953 :    
954 :     =cut
955 :    
956 :     sub Cluck {
957 :     # Get the parameters.
958 :     my ($message) = @_;
959 :     # Trace what's happening.
960 :     Trace("Stack trace for event: $message");
961 : parrello 1.99 # Get the stack trace.
962 :     my @trace = LongMess();
963 :     # Convert the trace to a series of messages.
964 :     for my $line (@trace) {
965 :     # Replace the tab at the beginning with spaces.
966 :     $line =~ s/^\t/ /;
967 :     # Trace the line.
968 :     Trace($line);
969 :     }
970 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
971 :     Warn($message);
972 :     }
973 :    
974 :     =head3 LongMess
975 :    
976 :     my @lines = Tracer::LongMess();
977 :    
978 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
979 :     of message strings.
980 :    
981 :     =cut
982 :    
983 :     sub LongMess {
984 :     # Declare the return variable.
985 :     my @retVal = ();
986 :     my $confession = longmess("");
987 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
988 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
989 :     # Here we have a line worth keeping. Push it onto the result list.
990 :     push @retVal, $line;
991 : parrello 1.97 }
992 : parrello 1.93 }
993 : parrello 1.99 # Return the result.
994 :     return @retVal;
995 : parrello 1.93 }
996 :    
997 :     =head3 ETracing
998 :    
999 :     ETracing($parameter);
1000 :    
1001 :     Set up emergency tracing. Emergency tracing is tracing that is turned
1002 :     on automatically for any program that calls this method. The emergency
1003 :     tracing parameters are stored in a a file identified by a tracing key.
1004 :     If this method is called with a CGI object, then the tracing key is
1005 :     taken from a cookie. If it is called with no parameters, then the tracing
1006 :     key is taken from an environment variable. If it is called with a string,
1007 :     the tracing key is that string.
1008 :    
1009 :     =over 4
1010 :    
1011 :     =item parameter
1012 :    
1013 :     A parameter from which the tracing key is computed. If it is a scalar,
1014 :     that scalar is used as the tracing key. If it is a CGI object, the
1015 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
1016 :     tracing key is taken from the C<TRACING> environment variable. If it
1017 :     is a CGI object and emergency tracing is not on, the C<Trace> and
1018 :     C<TF> parameters will be used to determine the type of tracing.
1019 :    
1020 :     =back
1021 :    
1022 :     =cut
1023 :    
1024 :     sub ETracing {
1025 :     # Get the parameter.
1026 :     my ($parameter) = @_;
1027 :     # Check for CGI mode.
1028 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
1029 :     $SavedCGI = $parameter;
1030 :     } else {
1031 :     $SavedCGI = undef;
1032 :     }
1033 : parrello 1.93 # Default to no tracing except errors.
1034 :     my ($tracing, $dest) = ("0", "WARN");
1035 :     # Check for emergency tracing.
1036 :     my $tkey = EmergencyKey($parameter);
1037 :     my $emergencyFile = EmergencyFileName($tkey);
1038 :     if (-e $emergencyFile) {
1039 :     # We have the file. Read in the data.
1040 :     my @tracing = GetFile($emergencyFile);
1041 :     # Pull off the time limit.
1042 :     my $expire = shift @tracing;
1043 :     # Convert it to seconds.
1044 :     $expire *= 3600;
1045 :     # Check the file data.
1046 :     my $stat = stat($emergencyFile);
1047 :     my ($now) = gettimeofday;
1048 :     if ($now - $stat->mtime > $expire) {
1049 :     # Delete the expired file.
1050 :     unlink $emergencyFile;
1051 : parrello 1.44 } else {
1052 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
1053 :     # the trace level;
1054 :     $dest = shift @tracing;
1055 :     my $level = shift @tracing;
1056 :     # Convert the destination to a real tracing destination.
1057 :     # temp directory.
1058 :     $dest = EmergencyTracingDest($tkey, $dest);
1059 :     # Insure Tracer is specified.
1060 :     my %moduleHash = map { $_ => 1 } @tracing;
1061 :     $moduleHash{Tracer} = 1;
1062 :     # Set the trace parameter.
1063 :     $tracing = join(" ", $level, sort keys %moduleHash);
1064 : parrello 1.44 }
1065 : parrello 1.99 } elsif (defined $SavedCGI) {
1066 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1067 :     # for tracing from the form parameters.
1068 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1069 : parrello 1.93 # Here the user has requested tracing via a form.
1070 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1071 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1072 : parrello 1.36 }
1073 :     }
1074 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1075 :     TSetup($tracing, $dest);
1076 : parrello 1.94 # Check to see if we're a web script.
1077 : parrello 1.99 if (defined $SavedCGI) {
1078 : parrello 1.94 # Yes we are. Trace the form and environment data.
1079 : parrello 1.99 TraceParms($SavedCGI);
1080 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1081 :     # emitted by the script in its raw form.
1082 :     if (T(Raw => 3)) {
1083 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1084 :     }
1085 : parrello 1.83 }
1086 : parrello 1.31 }
1087 :    
1088 : parrello 1.93 =head3 EmergencyFileName
1089 :    
1090 :     my $fileName = Tracer::EmergencyFileName($tkey);
1091 :    
1092 :     Return the emergency tracing file name. This is the file that specifies
1093 :     the tracing information.
1094 :    
1095 :     =over 4
1096 :    
1097 :     =item tkey
1098 :    
1099 :     Tracing key for the current program.
1100 : parrello 1.11
1101 : parrello 1.93 =item RETURN
1102 : parrello 1.11
1103 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1104 : parrello 1.11
1105 : parrello 1.93 =back
1106 : parrello 1.11
1107 :     =cut
1108 :    
1109 : parrello 1.93 sub EmergencyFileName {
1110 :     # Get the parameters.
1111 :     my ($tkey) = @_;
1112 :     # Compute the emergency tracing file name.
1113 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1114 : olson 1.1 }
1115 :    
1116 : parrello 1.93 =head3 EmergencyFileTarget
1117 : parrello 1.10
1118 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1119 : parrello 1.10
1120 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1121 :     the tracing output for file-based tracing.
1122 : parrello 1.10
1123 : parrello 1.93 =over 4
1124 : parrello 1.10
1125 : parrello 1.93 =item tkey
1126 : parrello 1.10
1127 : parrello 1.93 Tracing key for the current program.
1128 : parrello 1.10
1129 : parrello 1.93 =item RETURN
1130 : parrello 1.10
1131 : parrello 1.93 Returns the name of the file to contain the trace output.
1132 : parrello 1.10
1133 : parrello 1.93 =back
1134 : parrello 1.10
1135 : parrello 1.93 =cut
1136 : parrello 1.10
1137 : parrello 1.93 sub EmergencyFileTarget {
1138 :     # Get the parameters.
1139 :     my ($tkey) = @_;
1140 :     # Compute the emergency tracing file name.
1141 :     return "$FIG_Config::temp/trace$tkey.log";
1142 :     }
1143 : parrello 1.10
1144 : parrello 1.93 =head3 EmergencyTracingDest
1145 : parrello 1.10
1146 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1147 : parrello 1.10
1148 : parrello 1.93 This method converts an emergency tracing destination to a real
1149 :     tracing destination. The main difference is that if the
1150 :     destination is C<FILE> or C<APPEND>, we convert it to file
1151 :     output. If the destination is C<DUAL>, we convert it to file
1152 :     and standard output.
1153 : parrello 1.10
1154 :     =over 4
1155 :    
1156 : parrello 1.93 =item tkey
1157 : parrello 1.10
1158 : parrello 1.93 Tracing key for this environment.
1159 : parrello 1.10
1160 : parrello 1.93 =item myDest
1161 : parrello 1.10
1162 : parrello 1.93 Destination from the emergency tracing file.
1163 : parrello 1.10
1164 :     =item RETURN
1165 :    
1166 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1167 : parrello 1.10
1168 :     =back
1169 :    
1170 :     =cut
1171 :    
1172 : parrello 1.93 sub EmergencyTracingDest {
1173 : parrello 1.12 # Get the parameters.
1174 : parrello 1.93 my ($tkey, $myDest) = @_;
1175 :     # Declare the return variable.
1176 :     my $retVal = $myDest;
1177 :     # Process according to the destination value.
1178 :     if ($myDest eq 'FILE') {
1179 :     $retVal = ">" . EmergencyFileTarget($tkey);
1180 :     } elsif ($myDest eq 'APPEND') {
1181 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1182 :     } elsif ($myDest eq 'DUAL') {
1183 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1184 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1185 :     $retVal = "WARN";
1186 : parrello 1.12 }
1187 : parrello 1.93 # Return the result.
1188 :     return $retVal;
1189 : parrello 1.10 }
1190 :    
1191 : parrello 1.93 =head3 Emergency
1192 :    
1193 :     Emergency($key, $hours, $dest, $level, @modules);
1194 :    
1195 :     Turn on emergency tracing. This method is normally invoked over the web from
1196 :     a debugging console, but it can also be called by the C<trace.pl> script.
1197 :     The caller specifies the duration of the emergency in hours, the desired tracing
1198 :     destination, the trace level, and a list of the trace modules to activate.
1199 :     For the length of the duration, when a program in an environment with the
1200 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1201 :     turned on automatically. See L</TSetup> for more about tracing setup and
1202 :     L</ETracing> for more about emergency tracing.
1203 :    
1204 :     =over 4
1205 : parrello 1.11
1206 : parrello 1.93 =item tkey
1207 : parrello 1.11
1208 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1209 : parrello 1.11
1210 : parrello 1.93 =item hours
1211 : parrello 1.11
1212 : parrello 1.93 Number of hours to keep emergency tracing alive.
1213 : parrello 1.11
1214 : parrello 1.93 =item dest
1215 : parrello 1.11
1216 : parrello 1.93 Tracing destination. If no path information is specified for a file
1217 :     destination, it is put in the FIG temporary directory.
1218 : parrello 1.11
1219 : parrello 1.93 =item level
1220 : parrello 1.11
1221 : parrello 1.93 Tracing level. A higher level means more trace messages.
1222 : parrello 1.11
1223 : parrello 1.93 =item modules
1224 : parrello 1.11
1225 : parrello 1.93 A list of the tracing modules to activate.
1226 : parrello 1.11
1227 :     =back
1228 :    
1229 :     =cut
1230 : parrello 1.93
1231 :     sub Emergency {
1232 : parrello 1.11 # Get the parameters.
1233 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1234 :     # Create the emergency file.
1235 :     my $specFile = EmergencyFileName($tkey);
1236 :     my $outHandle = Open(undef, ">$specFile");
1237 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1238 : parrello 1.11 }
1239 :    
1240 : parrello 1.93 =head3 EmergencyKey
1241 :    
1242 :     my $tkey = EmergencyKey($parameter);
1243 :    
1244 :     Return the Key to be used for emergency tracing. This could be an IP address,
1245 :     a session ID, or a user name, depending on the environment.
1246 : parrello 1.11
1247 : parrello 1.93 =over 4
1248 : parrello 1.11
1249 : parrello 1.93 =item parameter
1250 : parrello 1.11
1251 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1252 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1253 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1254 :     taken from the C<TRACING> environment variable.
1255 : parrello 1.29
1256 : parrello 1.93 =item RETURN
1257 : parrello 1.11
1258 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1259 : parrello 1.11
1260 : parrello 1.93 =back
1261 : parrello 1.11
1262 : parrello 1.93 =cut
1263 : parrello 1.29
1264 : parrello 1.93 sub EmergencyKey {
1265 :     # Get the parameters.
1266 :     my ($parameter) = @_;
1267 :     # Declare the return variable.
1268 :     my $retVal;
1269 :     # Determine the parameter type.
1270 :     if (! defined $parameter) {
1271 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1272 :     # get the effective login ID.
1273 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1274 : parrello 1.93 } else {
1275 :     my $ptype = ref $parameter;
1276 :     if ($ptype eq 'CGI') {
1277 :     # Here we were invoked from a web page. Look for a cookie.
1278 :     $retVal = $parameter->cookie('IP');
1279 :     } elsif (! $ptype) {
1280 :     # Here the key was passed in.
1281 :     $retVal = $parameter;
1282 :     }
1283 :     }
1284 :     # If no luck finding a key, use the PID.
1285 :     if (! defined $retVal) {
1286 :     $retVal = $$;
1287 :     }
1288 :     # Return the result.
1289 :     return $retVal;
1290 :     }
1291 : parrello 1.11
1292 :    
1293 : parrello 1.93 =head3 TraceParms
1294 : parrello 1.11
1295 : parrello 1.93 Tracer::TraceParms($cgi);
1296 : parrello 1.11
1297 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1298 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1299 : parrello 1.11
1300 : parrello 1.93 =over 4
1301 : parrello 1.11
1302 : parrello 1.93 =item cgi
1303 : parrello 1.31
1304 : parrello 1.93 CGI query object containing the parameters to trace.
1305 : parrello 1.31
1306 : parrello 1.11 =back
1307 :    
1308 :     =cut
1309 : parrello 1.93
1310 :     sub TraceParms {
1311 : parrello 1.11 # Get the parameters.
1312 : parrello 1.93 my ($cgi) = @_;
1313 : parrello 1.94 if (T(CGI => 2)) {
1314 :     # Here we trace the GET-style URL for the script.
1315 : parrello 1.97 Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1316 : parrello 1.94 }
1317 : parrello 1.93 if (T(CGI => 3)) {
1318 :     # Here we want to trace the parameter data.
1319 :     my @names = $cgi->param;
1320 :     for my $parmName (sort @names) {
1321 :     # Note we skip the Trace parameters, which are for our use only.
1322 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1323 :     my @values = $cgi->param($parmName);
1324 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1325 : parrello 1.93 }
1326 :     }
1327 :     # Display the request method.
1328 :     my $method = $cgi->request_method();
1329 :     Trace("Method: $method");
1330 :     }
1331 :     if (T(CGI => 4)) {
1332 :     # Here we want the environment data too.
1333 :     for my $envName (sort keys %ENV) {
1334 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1335 : parrello 1.12 }
1336 :     }
1337 : parrello 1.11 }
1338 :    
1339 : parrello 1.94 =head3 TraceImages
1340 :    
1341 :     Tracer::TraceImages($htmlString);
1342 :    
1343 :     Trace information about all of an html document's images. The tracing
1344 :     will be for type "IMG" at level 3. The image's source string
1345 :     will be displayed. This is generally either the URL of the image or
1346 :     raw data for the image itself. If the source is too long, only the first 300
1347 :     characters will be shown at trace level 3. The entire source will be shown,
1348 :     however, at trace level 4. This method is not very smart, and might catch
1349 :     Javascript code, but it is still useful when debugging the arcane
1350 :     behavior of images in multiple browser environments.
1351 :    
1352 :     =over 4
1353 :    
1354 :     =item htmlString
1355 :    
1356 :     HTML text for an outgoing web page.
1357 :    
1358 :     =back
1359 :    
1360 :     =cut
1361 :    
1362 :     sub TraceImages {
1363 :     # Only proceed if we're at the proper trace level.
1364 :     if (T(IMG => 3)) {
1365 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1366 :     # into a variable called "$htmlString". This is because we expect html strings to be
1367 :     # long, and don't want to copy them any more than we have to.
1368 :     Trace(length($_[0]) . " characters in web page.");
1369 :     # Loop through the HTML, culling image tags.
1370 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1371 :     # Extract the source string and determine whether or not it's too long.
1372 :     my $srcString = $1;
1373 :     my $pos = pos($_[0]) - length($srcString);
1374 :     my $excess = length($srcString) - 300;
1375 :     # We'll put the display string in here.
1376 :     my $srcDisplay = $srcString;
1377 :     # If it's a data string, split it at the comma.
1378 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1379 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1380 :     # a long string, however, we only show the first 300 characters.
1381 :     if ($excess > 0 && ! T(IMG => 4)) {
1382 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1383 :     }
1384 :     # Output the trace message.
1385 :     Trace("Image tag at position $pos:\n$srcDisplay");
1386 :     }
1387 :     }
1388 :     }
1389 :    
1390 : parrello 1.93 =head2 Command-Line Utility Methods
1391 : olson 1.1
1392 : parrello 1.93 =head3 SendSMS
1393 : olson 1.1
1394 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1395 : olson 1.1
1396 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1397 :     user name, password, and API ID for the relevant account in the hash reference variable
1398 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1399 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1400 :     is C<2561022>, then the FIG_Config file must contain
1401 : olson 1.1
1402 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1403 :     password => 'silly',
1404 :     api_id => '2561022' };
1405 : olson 1.1
1406 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1407 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1408 :     when you call this method.
1409 : olson 1.1
1410 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1411 : parrello 1.74
1412 : parrello 1.93 =over 4
1413 : parrello 1.74
1414 : parrello 1.93 =item phoneNumber
1415 : parrello 1.74
1416 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1417 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1418 : parrello 1.74
1419 : parrello 1.93 =item msg
1420 : parrello 1.74
1421 : parrello 1.93 Message to send to the specified phone.
1422 : parrello 1.74
1423 :     =item RETURN
1424 :    
1425 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1426 : parrello 1.74
1427 : parrello 1.78 =back
1428 :    
1429 : parrello 1.74 =cut
1430 :    
1431 : parrello 1.93 sub SendSMS {
1432 : parrello 1.74 # Get the parameters.
1433 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1434 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1435 : parrello 1.74 my $retVal;
1436 : parrello 1.93 # Only proceed if we have phone support.
1437 :     if (! defined $FIG_Config::phone) {
1438 :     Trace("Phone support not present in FIG_Config.") if T(1);
1439 :     } else {
1440 :     # Get the phone data.
1441 :     my $parms = $FIG_Config::phone;
1442 :     # Get the Clickatell URL.
1443 :     my $url = "http://api.clickatell.com/http/";
1444 :     # Create the user agent.
1445 :     my $ua = LWP::UserAgent->new;
1446 :     # Request a Clickatell session.
1447 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1448 :     password => $parms->{password},
1449 :     api_id => $parms->{api_id},
1450 :     to => $phoneNumber,
1451 :     text => $msg});
1452 :     # Check for an error.
1453 :     if (! $resp->is_success) {
1454 :     Trace("Alert failed.") if T(1);
1455 :     } else {
1456 :     # Get the message ID.
1457 :     my $rstring = $resp->content;
1458 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1459 :     $retVal = $1;
1460 :     } else {
1461 :     Trace("Phone attempt failed with $rstring") if T(1);
1462 :     }
1463 :     }
1464 : parrello 1.74 }
1465 :     # Return the result.
1466 :     return $retVal;
1467 :     }
1468 :    
1469 : parrello 1.93 =head3 StandardSetup
1470 : olson 1.1
1471 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1472 : olson 1.1
1473 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1474 :     values are a hash of the command-line options and a list of the positional
1475 :     parameters. Tracing is automatically set up and the command-line options are
1476 :     validated.
1477 : olson 1.1
1478 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1479 :     be more easily understood, however, once they are examined individually.
1480 : olson 1.1
1481 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1482 :     special-purpose tracing categories. Most tracing categories are PERL package
1483 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1484 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1485 : olson 1.1
1486 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1487 : olson 1.1
1488 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1489 :     the output. There are two special tracing categories that are automatically
1490 :     handled by this method. In other words, if you used L</TSetup> you would need
1491 :     to include these categories manually, but if you use this method they are turned
1492 :     on automatically.
1493 : parrello 1.5
1494 :     =over 4
1495 :    
1496 : parrello 1.93 =item SQL
1497 : parrello 1.5
1498 : parrello 1.93 Traces SQL commands and activity.
1499 : parrello 1.5
1500 : parrello 1.93 =item Tracer
1501 : parrello 1.5
1502 : parrello 1.93 Traces error messages and call stacks.
1503 : parrello 1.5
1504 :     =back
1505 :    
1506 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1507 :     The trace level is specified using the C<-trace> command-line option. For example,
1508 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1509 :     all tracing at level 3.
1510 : parrello 1.5
1511 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1512 : parrello 1.5
1513 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1514 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1515 :     process ID. You can also specify the C<user> parameter to put a user ID
1516 :     instead of a process ID in the trace file name. So, for example
1517 : olson 1.1
1518 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1519 :     For a genome-by-genome update, use 3.
1520 : olson 1.1
1521 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1522 : olson 1.1
1523 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1524 : olson 1.1
1525 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1526 :     options, their default values, and an explanation of what they mean. Command-line
1527 :     options may be in the form of switches or keywords. In the case of a switch, the
1528 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1529 :     of a keyword, the value is separated from the option name by an equal sign. You
1530 :     can see this last in the command-line example above.
1531 : olson 1.1
1532 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1533 :     prior to calling this method.
1534 : olson 1.1
1535 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1536 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1537 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1538 :     the following code.
1539 : olson 1.1
1540 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1541 :     { safe => [0, "use database transactions"],
1542 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1543 :     start => [' ', "start with this genome"],
1544 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1545 :     "<command> <transactionDirectory> <IDfile>",
1546 :     @ARGV);
1547 : olson 1.1
1548 :    
1549 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1550 :     stores the actual options in a hash that is returned as C<$options>. The
1551 :     positional parameters are returned in C<@parameters>.
1552 : olson 1.1
1553 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1554 : olson 1.1
1555 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1556 : olson 1.1
1557 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1558 :     above command as
1559 : olson 1.1
1560 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1561 : olson 1.1
1562 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1563 :     parameters, and would find themselves in I<@parameters> after executing the
1564 :     above code fragment. The tracing would be set to level 2, and the categories
1565 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1566 :     and C<DocUtils> was included because it came in within the first parameter
1567 :     to this method. The I<$options> hash would be
1568 : olson 1.1
1569 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1570 :     noAlias => 1, start => ' ', tblFiles => 0 }
1571 : olson 1.1
1572 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1573 :     standard tracing setup and command-line parsing. Note that the caller is
1574 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1575 :     are used by this method to control the tracing. If additional tracing features
1576 :     need to be added in the future, they can be processed by this method without
1577 :     upsetting the command-line utilities.
1578 : olson 1.1
1579 : parrello 1.93 If the C<background> option is specified on the command line, then the
1580 :     standard and error outputs will be directed to files in the temporary
1581 :     directory, using the same suffix as the trace file. So, if the command
1582 :     line specified
1583 : olson 1.1
1584 : parrello 1.93 -user=Bruce -background
1585 : olson 1.1
1586 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1587 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1588 :     simplify starting a command in the background.
1589 : olson 1.1
1590 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1591 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1592 :     be used instead of custom tracing. If the user name is not specified,
1593 :     the tracing key is taken from the C<Tracing> environment variable. If there
1594 : parrello 1.103 is no value for that variable, the tracing key will be computed from the active
1595 :     login ID.
1596 :    
1597 :     Since the default situation in StandardSetup is to trace to the standard
1598 :     output, errors that occur in command-line scripts will not generate
1599 :     RSS events. To force the events, use the C<warn> option.
1600 :    
1601 :     TransactFeatures -background -warn register ../xacts IDs.tbl
1602 : olson 1.1
1603 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1604 :     names will be traced at level 0 and the program will exit without processing.
1605 :     This provides a limited help capability. For example, if the user enters
1606 : olson 1.1
1607 : parrello 1.93 TransactFeatures -help
1608 : olson 1.1
1609 : parrello 1.93 he would see the following output.
1610 : olson 1.1
1611 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1612 :     -trace tracing level (default E)
1613 :     -sql trace SQL commands
1614 :     -safe use database transactions
1615 :     -noAlias do not expect aliases in CHANGE transactions
1616 :     -start start with this genome
1617 :     -tblFiles output TBL files containing the corrected IDs
1618 : parrello 1.111 -forked do not erase the trace file before tracing
1619 : olson 1.1
1620 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1621 :     for C<trace> in the incoming options hash. The default value can be overridden,
1622 :     or the tracing to the standard output can be turned off by suffixing a minus
1623 :     sign to the trace level. So, for example,
1624 : olson 1.1
1625 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1626 :     ...
1627 : olson 1.1
1628 : parrello 1.93 would set the default trace level to 0 instead of E, while
1629 : olson 1.1
1630 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1631 :     ...
1632 : olson 1.1
1633 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1634 :     standard output.
1635 : olson 1.1
1636 : parrello 1.93 The parameters to this method are as follows.
1637 : olson 1.1
1638 : parrello 1.93 =over 4
1639 : olson 1.1
1640 : parrello 1.93 =item categories
1641 : parrello 1.2
1642 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1643 :     packages whose internal workings will need to be debugged to get the
1644 :     command working.
1645 : olson 1.1
1646 : parrello 1.93 =item options
1647 : olson 1.1
1648 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1649 :     to their default values and descriptions. The user can override the defaults
1650 :     by specifying the options as command-line switches prefixed by a hyphen.
1651 :     Tracing-related options may be added to this hash. If the C<-h> option is
1652 :     specified on the command line, the option descriptions will be used to
1653 :     explain the options. To turn off tracing to the standard output, add a
1654 :     minus sign to the value for C<trace> (see above).
1655 : olson 1.1
1656 : parrello 1.93 =item parmHelp
1657 : olson 1.1
1658 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1659 :     if the user specifies the C<-h> option.
1660 : olson 1.1
1661 : parrello 1.93 =item argv
1662 : olson 1.1
1663 : parrello 1.93 List of command line parameters, including the option switches, which must
1664 :     precede the positional parameters and be prefixed by a hyphen.
1665 : olson 1.1
1666 :     =item RETURN
1667 :    
1668 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1669 :     maps the command-line option switches to their values. These will either be the
1670 :     default values or overrides specified on the command line. The remaining
1671 :     elements of the list are the position parameters, in order.
1672 : olson 1.1
1673 :     =back
1674 :    
1675 :     =cut
1676 :    
1677 : parrello 1.93 sub StandardSetup {
1678 :     # Get the parameters.
1679 :     my ($categories, $options, $parmHelp, @argv) = @_;
1680 :     # Get the default tracing key.
1681 :     my $tkey = EmergencyKey();
1682 : parrello 1.104 # Save the command line.
1683 :     $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1684 : parrello 1.93 # Add the tracing options.
1685 :     if (! exists $options->{trace}) {
1686 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1687 :     }
1688 : parrello 1.112 if (! exists $options->{forked}) {
1689 :     $options->{forked} = [0, "keep old trace file"];
1690 :     }
1691 : parrello 1.93 $options->{sql} = [0, "turn on SQL tracing"];
1692 :     $options->{help} = [0, "display command-line options"];
1693 :     $options->{user} = [$tkey, "tracing key"];
1694 :     $options->{background} = [0, "spool standard and error output"];
1695 : parrello 1.103 $options->{warn} = [0, "send errors to RSS feed"];
1696 : parrello 1.113 $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1697 : parrello 1.93 # Create a parsing hash from the options hash. The parsing hash
1698 :     # contains the default values rather than the default value
1699 :     # and the description. While we're at it, we'll memorize the
1700 :     # length of the longest option name.
1701 :     my $longestName = 0;
1702 :     my %parseOptions = ();
1703 :     for my $key (keys %{$options}) {
1704 :     if (length $key > $longestName) {
1705 :     $longestName = length $key;
1706 :     }
1707 :     $parseOptions{$key} = $options->{$key}->[0];
1708 :     }
1709 :     # Parse the command line.
1710 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1711 :     # Get the logfile suffix.
1712 :     my $suffix = $retOptions->{user};
1713 : parrello 1.113 # We'll put the trace file name in here. We need it later if background
1714 :     # mode is on.
1715 :     my $traceFileName;
1716 : parrello 1.93 # Now we want to set up tracing. First, we need to know if the user
1717 :     # wants emergency tracing.
1718 :     if ($retOptions->{trace} eq 'E') {
1719 :     ETracing($retOptions->{user});
1720 :     } else {
1721 :     # Here the tracing is controlled from the command line.
1722 :     my @cats = @{$categories};
1723 :     if ($retOptions->{sql}) {
1724 :     push @cats, "SQL";
1725 :     }
1726 : parrello 1.103 if ($retOptions->{warn}) {
1727 :     push @cats, "Feed";
1728 :     }
1729 : parrello 1.93 # Add the default categories.
1730 :     push @cats, "Tracer";
1731 : parrello 1.113 # Check for more tracing groups.
1732 :     if ($retOptions->{moreTracing}) {
1733 :     push @cats, split /,/, $retOptions->{moreTracing};
1734 :     }
1735 : parrello 1.93 # Next, we create the category string by joining the categories.
1736 :     my $cats = join(" ", @cats);
1737 :     # Check to determine whether or not the caller wants to turn off tracing
1738 :     # to the standard output.
1739 :     my $traceLevel = $retOptions->{trace};
1740 :     my $textOKFlag = 1;
1741 :     if ($traceLevel =~ /^(.)-/) {
1742 :     $traceLevel = $1;
1743 :     $textOKFlag = 0;
1744 :     }
1745 :     # Now we set up the trace mode.
1746 :     my $traceMode;
1747 :     # Verify that we can open a file in the FIG temporary directory.
1748 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1749 : parrello 1.111 my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1750 :     if (open TESTTRACE, "$traceFileSpec") {
1751 : parrello 1.93 # Here we can trace to a file.
1752 : parrello 1.111 $traceMode = ">>$traceFileName";
1753 : parrello 1.93 if ($textOKFlag) {
1754 :     # Echo to standard output if the text-OK flag is set.
1755 :     $traceMode = "+$traceMode";
1756 :     }
1757 :     # Close the test file.
1758 :     close TESTTRACE;
1759 :     } else {
1760 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1761 :     warn "Could not open trace file $traceFileName: $!\n";
1762 :     # We trace to the standard output if it's
1763 :     # okay, and the error log otherwise.
1764 : parrello 1.93 if ($textOKFlag) {
1765 :     $traceMode = "TEXT";
1766 : parrello 1.12 } else {
1767 : parrello 1.93 $traceMode = "WARN";
1768 : parrello 1.12 }
1769 :     }
1770 : parrello 1.93 # Now set up the tracing.
1771 :     TSetup("$traceLevel $cats", $traceMode);
1772 :     }
1773 : parrello 1.113 # Check for background mode.
1774 :     if ($retOptions->{background}) {
1775 :     my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1776 :     my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1777 :     # Spool the output.
1778 :     open STDOUT, ">$outFileName";
1779 :     # If we have a trace file, trace the errors to the log. Otherwise,
1780 :     # spool the errors.
1781 :     if (defined $traceFileName) {
1782 :     open STDERR, "| Tracer $traceFileName";
1783 :     } else {
1784 :     open STDERR, ">$errFileName";
1785 :     }
1786 :     # Check for phone support. If we have phone support and a phone number,
1787 :     # we want to turn it on.
1788 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1789 :     $retOptions->{phone} = $ENV{PHONE};
1790 :     }
1791 :     }
1792 : parrello 1.93 # Check for the "help" option. If it is specified, dump the command-line
1793 :     # options and exit the program.
1794 :     if ($retOptions->{help}) {
1795 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1796 :     print "$1 [options] $parmHelp\n";
1797 :     for my $key (sort keys %{$options}) {
1798 :     my $name = Pad($key, $longestName, 0, ' ');
1799 :     my $desc = $options->{$key}->[1];
1800 :     if ($options->{$key}->[0]) {
1801 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1802 :     }
1803 :     print " $name $desc\n";
1804 : parrello 1.36 }
1805 : parrello 1.93 exit(0);
1806 :     }
1807 :     # Trace the options, if applicable.
1808 :     if (T(3)) {
1809 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1810 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1811 : parrello 1.3 }
1812 : parrello 1.93 # Return the parsed parameters.
1813 :     return ($retOptions, @retParameters);
1814 : olson 1.1 }
1815 :    
1816 : parrello 1.93 =head3 ReadOptions
1817 : olson 1.1
1818 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1819 : olson 1.1
1820 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1821 :     format
1822 : olson 1.1
1823 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1824 : olson 1.1
1825 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1826 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1827 :     character is a semi-colon will be ignored. The return hash will map each option name to
1828 :     the corresponding option value.
1829 : olson 1.1
1830 :     =over 4
1831 :    
1832 : parrello 1.93 =item fileName
1833 : olson 1.1
1834 : parrello 1.93 Name of the file containing the option data.
1835 : olson 1.1
1836 :     =item RETURN
1837 :    
1838 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1839 :     value.
1840 : olson 1.1
1841 :     =back
1842 :    
1843 :     =cut
1844 :    
1845 : parrello 1.93 sub ReadOptions {
1846 : parrello 1.12 # Get the parameters.
1847 : parrello 1.93 my ($fileName) = @_;
1848 :     # Open the file.
1849 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1850 :     # Count the number of records read.
1851 :     my ($records, $comments) = 0;
1852 :     # Create the return hash.
1853 :     my %retVal = ();
1854 :     # Loop through the file, accumulating key-value pairs.
1855 :     while (my $line = <CONFIGFILE>) {
1856 :     # Denote we've read a line.
1857 :     $records++;
1858 :     # Determine the line type.
1859 :     if ($line =~ /^\s*[\n\r]/) {
1860 :     # A blank line is a comment.
1861 :     $comments++;
1862 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1863 :     # Here we have an option assignment.
1864 :     retVal{$1} = $2;
1865 :     } elsif ($line =~ /^\s*;/) {
1866 :     # Here we have a text comment.
1867 :     $comments++;
1868 : parrello 1.12 } else {
1869 : parrello 1.93 # Here we have an invalid line.
1870 :     Trace("Invalid option statement in record $records.") if T(0);
1871 : parrello 1.12 }
1872 :     }
1873 : parrello 1.93 # Return the hash created.
1874 :     return %retVal;
1875 : olson 1.1 }
1876 :    
1877 : parrello 1.93 =head3 GetOptions
1878 : parrello 1.9
1879 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1880 : parrello 1.9
1881 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1882 :     as input and uses the data from the second to update the first. If the second does not exist,
1883 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1884 :     exist in the first.
1885 : parrello 1.9
1886 : parrello 1.93 Consider the following example.
1887 : parrello 1.9
1888 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1889 : parrello 1.9
1890 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1891 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1892 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1893 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1894 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1895 : parrello 1.9
1896 : parrello 1.93 {databaseType => 'Oracle'}
1897 : parrello 1.9
1898 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1899 : parrello 1.9
1900 : parrello 1.93 =over 4
1901 : parrello 1.9
1902 : parrello 1.93 =item defaults
1903 : parrello 1.9
1904 : parrello 1.93 Table of default option values.
1905 : parrello 1.9
1906 : parrello 1.93 =item options
1907 : olson 1.1
1908 : parrello 1.93 Table of overrides, if any.
1909 : olson 1.1
1910 :     =item RETURN
1911 :    
1912 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1913 : olson 1.1
1914 :     =back
1915 :    
1916 :     =cut
1917 :    
1918 : parrello 1.93 sub GetOptions {
1919 :     # Get the parameters.
1920 :     my ($defaults, $options) = @_;
1921 :     # Check for overrides.
1922 :     if ($options) {
1923 :     # Loop through the overrides.
1924 :     while (my ($option, $setting) = each %{$options}) {
1925 :     # Insure this override exists.
1926 :     if (!exists $defaults->{$option}) {
1927 :     croak "Unrecognized option $option encountered.";
1928 : parrello 1.12 } else {
1929 : parrello 1.93 # Apply the override.
1930 :     $defaults->{$option} = $setting;
1931 : parrello 1.12 }
1932 :     }
1933 :     }
1934 : parrello 1.93 # Return the merged table.
1935 :     return $defaults;
1936 : olson 1.1 }
1937 :    
1938 : parrello 1.93 =head3 MergeOptions
1939 : olson 1.1
1940 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1941 : olson 1.1
1942 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1943 :     second (default) hash, and if a matching key is not found in the first hash, the default
1944 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1945 :     checking and no return value.
1946 : olson 1.1
1947 :     =over 4
1948 :    
1949 : parrello 1.93 =item table
1950 : olson 1.1
1951 : parrello 1.93 Hash table to be updated with the default values.
1952 : olson 1.1
1953 : parrello 1.93 =item defaults
1954 : olson 1.1
1955 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1956 : olson 1.1
1957 :     =back
1958 :    
1959 :     =cut
1960 :    
1961 : parrello 1.93 sub MergeOptions {
1962 :     # Get the parameters.
1963 :     my ($table, $defaults) = @_;
1964 :     # Loop through the defaults.
1965 :     while (my ($key, $value) = each %{$defaults}) {
1966 :     if (!exists $table->{$key}) {
1967 :     $table->{$key} = $value;
1968 :     }
1969 : parrello 1.12 }
1970 : olson 1.1 }
1971 :    
1972 : parrello 1.111 =head3 UnparseOptions
1973 :    
1974 :     my $optionString = Tracer::UnparseOptions(\%options);
1975 :    
1976 :     Convert an option hash into a command-line string. This will not
1977 :     necessarily be the same text that came in, but it will nonetheless
1978 :     produce the same ultimate result when parsed by L</StandardSetup>.
1979 :    
1980 :     =over 4
1981 :    
1982 :     =item options
1983 :    
1984 :     Reference to a hash of options to convert into an option string.
1985 :    
1986 :     =item RETURN
1987 :    
1988 :     Returns a string that will parse to the same set of options when
1989 :     parsed by L</StandardSetup>.
1990 :    
1991 :     =back
1992 :    
1993 :     =cut
1994 :    
1995 :     sub UnparseOptions {
1996 :     # Get the parameters.
1997 :     my ($options) = @_;
1998 :     # The option segments will be put in here.
1999 :     my @retVal = ();
2000 :     # Loop through the options.
2001 :     for my $key (keys %$options) {
2002 :     # Get the option value.
2003 :     my $value = $options->{$key};
2004 :     # Only use it if it's nonempty.
2005 :     if (defined $value && $value ne "") {
2006 :     my $segment = "--$key=$value";
2007 :     # Quote it if necessary.
2008 :     if ($segment =~ /[ |<>*]/) {
2009 :     $segment = '"' . $segment . '"';
2010 :     }
2011 :     # Add it to the return list.
2012 :     push @retVal, $segment;
2013 :     }
2014 :     }
2015 :     # Return the result.
2016 :     return join(" ", @retVal);
2017 :     }
2018 :    
2019 : parrello 1.93 =head3 ParseCommand
2020 : olson 1.1
2021 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2022 : olson 1.1
2023 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
2024 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2025 :     off and merged into a table of default options. The remainder of the command line is
2026 :     returned as a list of positional arguments. For example, consider the following invocation.
2027 : olson 1.1
2028 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2029 : olson 1.1
2030 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
2031 :     B<errors> and B<logFile>. If @words has the following format
2032 : olson 1.1
2033 : parrello 1.93 -logFile=error.log apple orange rutabaga
2034 : olson 1.1
2035 : parrello 1.93 then at the end of the invocation, C<$options> will be
2036 : olson 1.1
2037 : parrello 1.93 { errors => 0, logFile => 'error.log' }
2038 : olson 1.1
2039 : parrello 1.93 and C<@arguments> will contain
2040 : olson 1.1
2041 : parrello 1.93 apple orange rutabaga
2042 : olson 1.1
2043 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2044 :     support for quote characters. Options can be specified with single or double hyphens.
2045 : parrello 1.54
2046 :     =over 4
2047 :    
2048 : parrello 1.93 =item optionTable
2049 : parrello 1.54
2050 : parrello 1.93 Table of default options.
2051 : parrello 1.54
2052 : parrello 1.93 =item inputList
2053 : parrello 1.54
2054 : parrello 1.93 List of words on the command line.
2055 : parrello 1.54
2056 :     =item RETURN
2057 :    
2058 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2059 : parrello 1.54
2060 :     =back
2061 :    
2062 :     =cut
2063 :    
2064 : parrello 1.93 sub ParseCommand {
2065 : parrello 1.54 # Get the parameters.
2066 : parrello 1.93 my ($optionTable, @inputList) = @_;
2067 :     # Process any options in the input list.
2068 :     my %overrides = ();
2069 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2070 :     # Get the current option.
2071 :     my $arg = shift @inputList;
2072 :     # Pull out the option name.
2073 :     $arg =~ /^--?([^=]*)/g;
2074 :     my $name = $1;
2075 :     # Check for an option value.
2076 :     if ($arg =~ /\G=(.*)$/g) {
2077 :     # Here we have a value for the option.
2078 :     $overrides{$name} = UnEscape($1);
2079 :     } else {
2080 :     # Here there is no value, so we use 1.
2081 :     $overrides{$name} = 1;
2082 :     }
2083 :     }
2084 :     # Merge the options into the defaults.
2085 :     GetOptions($optionTable, \%overrides);
2086 :     # Translate the remaining parameters.
2087 :     my @retVal = ();
2088 :     for my $inputParm (@inputList) {
2089 :     push @retVal, UnEscape($inputParm);
2090 : parrello 1.54 }
2091 : parrello 1.93 # Return the results.
2092 :     return ($optionTable, @retVal);
2093 : parrello 1.54 }
2094 :    
2095 : parrello 1.93
2096 :     =head2 File Utility Methods
2097 :    
2098 : olson 1.1 =head3 GetFile
2099 :    
2100 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2101 : olson 1.1
2102 : parrello 1.35 or
2103 :    
2104 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2105 : parrello 1.35
2106 :     Return the entire contents of a file. In list context, line-ends are removed and
2107 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2108 : olson 1.1
2109 :     =over 4
2110 :    
2111 :     =item fileName
2112 :    
2113 :     Name of the file to read.
2114 :    
2115 :     =item RETURN
2116 :    
2117 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2118 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2119 :     the file, an empty list will be returned.
2120 : olson 1.1
2121 :     =back
2122 :    
2123 :     =cut
2124 :    
2125 :     sub GetFile {
2126 : parrello 1.12 # Get the parameters.
2127 :     my ($fileName) = @_;
2128 :     # Declare the return variable.
2129 :     my @retVal = ();
2130 :     # Open the file for input.
2131 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2132 :     # Read the whole file into the return variable, stripping off any terminator
2133 :     # characters.
2134 :     my $lineCount = 0;
2135 :     while (my $line = <$handle>) {
2136 :     $lineCount++;
2137 :     $line = Strip($line);
2138 :     push @retVal, $line;
2139 :     }
2140 :     # Close it.
2141 :     close $handle;
2142 :     my $actualLines = @retVal;
2143 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2144 : parrello 1.12 # Return the file's contents in the desired format.
2145 : parrello 1.9 if (wantarray) {
2146 : parrello 1.12 return @retVal;
2147 : parrello 1.6 } else {
2148 :     return join "\n", @retVal;
2149 :     }
2150 : olson 1.1 }
2151 :    
2152 : parrello 1.60 =head3 PutFile
2153 :    
2154 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2155 : parrello 1.60
2156 :     Write out a file from a list of lines of text.
2157 :    
2158 :     =over 4
2159 :    
2160 :     =item fileName
2161 :    
2162 :     Name of the output file.
2163 :    
2164 :     =item lines
2165 :    
2166 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2167 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2168 :     modification.
2169 : parrello 1.60
2170 :     =back
2171 :    
2172 :     =cut
2173 :    
2174 :     sub PutFile {
2175 :     # Get the parameters.
2176 :     my ($fileName, $lines) = @_;
2177 :     # Open the output file.
2178 :     my $handle = Open(undef, ">$fileName");
2179 : parrello 1.77 # Count the lines written.
2180 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2181 :     # Here we have a scalar, so we write it raw.
2182 :     print $handle $lines;
2183 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2184 : parrello 1.66 } else {
2185 :     # Write the lines one at a time.
2186 : parrello 1.77 my $count = 0;
2187 : parrello 1.66 for my $line (@{$lines}) {
2188 :     print $handle "$line\n";
2189 : parrello 1.77 $count++;
2190 : parrello 1.66 }
2191 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2192 : parrello 1.60 }
2193 :     # Close the output file.
2194 :     close $handle;
2195 :     }
2196 :    
2197 : parrello 1.93 =head3 ParseRecord
2198 : olson 1.1
2199 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2200 : olson 1.1
2201 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2202 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2203 :     These will automatically be converted.
2204 : olson 1.1
2205 :     =over 4
2206 :    
2207 : parrello 1.93 =item line
2208 :    
2209 :     Line of data containing the tab-delimited fields.
2210 :    
2211 :     =item RETURN
2212 : olson 1.1
2213 : parrello 1.93 Returns a list of the fields found in the data line.
2214 : olson 1.1
2215 :     =back
2216 :    
2217 :     =cut
2218 :    
2219 : parrello 1.93 sub ParseRecord {
2220 : parrello 1.12 # Get the parameter.
2221 : parrello 1.93 my ($line) = @_;
2222 :     # Remove the trailing new-line, if any.
2223 :     chomp $line;
2224 :     # Split the line read into pieces using the tab character.
2225 :     my @retVal = split /\t/, $line;
2226 :     # Trim and fix the escapes in each piece.
2227 :     for my $value (@retVal) {
2228 :     # Trim leading whitespace.
2229 :     $value =~ s/^\s+//;
2230 :     # Trim trailing whitespace.
2231 :     $value =~ s/\s+$//;
2232 :     # Delete the carriage returns.
2233 :     $value =~ s/\r//g;
2234 :     # Convert the escapes into their real values.
2235 :     $value =~ s/\\t/"\t"/ge;
2236 :     $value =~ s/\\n/"\n"/ge;
2237 :     }
2238 :     # Return the result.
2239 :     return @retVal;
2240 :     }
2241 :    
2242 :     =head3 Merge
2243 :    
2244 :     my @mergedList = Tracer::Merge(@inputList);
2245 :    
2246 :     Sort a list of strings and remove duplicates.
2247 :    
2248 :     =over 4
2249 :    
2250 :     =item inputList
2251 :    
2252 :     List of scalars to sort and merge.
2253 :    
2254 :     =item RETURN
2255 :    
2256 :     Returns a list containing the same elements sorted in ascending order with duplicates
2257 :     removed.
2258 :    
2259 :     =back
2260 :    
2261 :     =cut
2262 :    
2263 :     sub Merge {
2264 :     # Get the input list in sort order.
2265 :     my @inputList = sort @_;
2266 :     # Only proceed if the list has at least two elements.
2267 :     if (@inputList > 1) {
2268 :     # Now we want to move through the list splicing out duplicates.
2269 :     my $i = 0;
2270 :     while ($i < @inputList) {
2271 :     # Get the current entry.
2272 :     my $thisEntry = $inputList[$i];
2273 :     # Find out how many elements duplicate the current entry.
2274 :     my $j = $i + 1;
2275 :     my $dup1 = $i + 1;
2276 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2277 :     # If the number is nonzero, splice out the duplicates found.
2278 :     if ($j > $dup1) {
2279 :     splice @inputList, $dup1, $j - $dup1;
2280 : parrello 1.14 }
2281 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2282 :     # at position $i. We push $i forward one position and start again.
2283 :     $i++;
2284 : parrello 1.14 }
2285 : parrello 1.12 }
2286 : parrello 1.93 # Return the merged list.
2287 :     return @inputList;
2288 : olson 1.1 }
2289 :    
2290 : parrello 1.93 =head3 Open
2291 : olson 1.1
2292 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2293 : olson 1.1
2294 : parrello 1.93 Open a file.
2295 : olson 1.1
2296 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2297 :     function. The mode is specified using Unix-like shell information. So, for
2298 :     example,
2299 : olson 1.1
2300 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2301 : olson 1.1
2302 : parrello 1.93 would open for output appended to the specified file, and
2303 : olson 1.1
2304 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2305 : olson 1.1
2306 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2307 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2308 :     code as follows.
2309 : olson 1.1
2310 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2311 : olson 1.1
2312 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2313 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2314 :     failed open will throw an exception and the third parameter will be used to construct
2315 :     an error message. If the parameter is omitted, a standard message is constructed
2316 :     using the file spec.
2317 : olson 1.1
2318 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2319 : olson 1.1
2320 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2321 :     The actual error message from the file system will be captured and appended to the
2322 :     message in any case.
2323 : parrello 1.6
2324 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2325 : parrello 1.6
2326 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2327 :     corresponds to the C++ C<errno> value.
2328 : parrello 1.6
2329 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2330 : parrello 1.6
2331 : parrello 1.93 =over 4
2332 : parrello 1.6
2333 : parrello 1.93 =item fileHandle
2334 : parrello 1.6
2335 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2336 :     and returned as the value of this method.
2337 : olson 1.1
2338 : parrello 1.93 =item fileSpec
2339 : olson 1.1
2340 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2341 : olson 1.1
2342 : parrello 1.93 =item message (optional)
2343 : olson 1.1
2344 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2345 :     will be generated. In either case, the error information from the file system
2346 :     is appended to the message. To specify a conditional open that does not throw
2347 :     an error if it fails, use C<0>.
2348 : olson 1.1
2349 : parrello 1.93 =item RETURN
2350 : olson 1.1
2351 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2352 :     open failed.
2353 : olson 1.1
2354 :     =back
2355 :    
2356 :     =cut
2357 :    
2358 : parrello 1.93 sub Open {
2359 : parrello 1.12 # Get the parameters.
2360 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2361 :     # Attempt to open the file.
2362 :     my $rv = open $fileHandle, $fileSpec;
2363 :     # If the open failed, generate an error message.
2364 :     if (! $rv) {
2365 :     # Save the system error message.
2366 :     my $sysMessage = $!;
2367 :     # See if we need a default message.
2368 :     if (!$message) {
2369 :     # Clean any obvious mode characters and leading spaces from the
2370 :     # filename.
2371 :     my ($fileName) = FindNamePart($fileSpec);
2372 :     $message = "Could not open \"$fileName\"";
2373 :     }
2374 :     # Terminate with an error using the supplied message and the
2375 :     # error message from the file system.
2376 :     Confess("$message: $!");
2377 : parrello 1.12 }
2378 : parrello 1.93 # Return the file handle.
2379 :     return $fileHandle;
2380 : olson 1.1 }
2381 :    
2382 : parrello 1.93 =head3 FindNamePart
2383 :    
2384 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2385 :    
2386 :     Extract the portion of a file specification that contains the file name.
2387 :    
2388 :     A file specification is the string passed to an C<open> call. It specifies the file
2389 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2390 :     method assumes that the file name is whatever follows the first angle bracket
2391 :     sequence. So, for example, in the following strings the file name is
2392 :     C</usr/fig/myfile.txt>.
2393 : parrello 1.5
2394 : parrello 1.93 >>/usr/fig/myfile.txt
2395 :     </usr/fig/myfile.txt
2396 :     | sort -u > /usr/fig/myfile.txt
2397 : parrello 1.5
2398 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2399 :     whole incoming string.
2400 : parrello 1.5
2401 :     =over 4
2402 :    
2403 : parrello 1.93 =item fileSpec
2404 : parrello 1.5
2405 : parrello 1.93 File specification string from which the file name is to be extracted.
2406 : parrello 1.5
2407 :     =item RETURN
2408 :    
2409 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2410 :     the specified string, or the whole string if a file name cannot be found via normal
2411 :     methods. The second element contains the start position of the file name portion and
2412 :     the third element contains the length.
2413 : parrello 1.5
2414 :     =back
2415 :    
2416 :     =cut
2417 : parrello 1.93 #: Return Type $;
2418 :     sub FindNamePart {
2419 :     # Get the parameters.
2420 :     my ($fileSpec) = @_;
2421 :     # Default to the whole input string.
2422 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2423 :     # Parse out the file name if we can.
2424 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2425 :     $retVal = $2;
2426 :     $len = length $retVal;
2427 :     $pos = (length $fileSpec) - (length $3) - $len;
2428 : parrello 1.12 }
2429 : parrello 1.93 # Return the result.
2430 :     return ($retVal, $pos, $len);
2431 : parrello 1.5 }
2432 :    
2433 : parrello 1.93 =head3 OpenDir
2434 : parrello 1.5
2435 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2436 : parrello 1.5
2437 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2438 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2439 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2440 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2441 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2442 :     set, an exception is thrown. So, for example,
2443 : parrello 1.5
2444 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2445 : parrello 1.5
2446 : parrello 1.93 is effectively the same as
2447 : parrello 1.5
2448 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2449 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2450 : parrello 1.5
2451 : parrello 1.93 Similarly, the following code
2452 : parrello 1.5
2453 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2454 : parrello 1.5
2455 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2456 :     automatically returns an empty list if the directory fails to open.
2457 : parrello 1.5
2458 : parrello 1.93 =over 4
2459 : parrello 1.5
2460 : parrello 1.93 =item dirName
2461 : parrello 1.5
2462 : parrello 1.93 Name of the directory to open.
2463 : parrello 1.5
2464 : parrello 1.93 =item filtered
2465 : parrello 1.5
2466 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2467 :     from the list, else FALSE.
2468 : parrello 1.5
2469 : parrello 1.93 =item flag
2470 : parrello 1.5
2471 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2472 : parrello 1.5
2473 : parrello 1.93 =back
2474 : parrello 1.5
2475 : parrello 1.93 =cut
2476 :     #: Return Type @;
2477 :     sub OpenDir {
2478 :     # Get the parameters.
2479 :     my ($dirName, $filtered, $flag) = @_;
2480 :     # Declare the return variable.
2481 :     my @retVal = ();
2482 :     # Open the directory.
2483 :     if (opendir(my $dirHandle, $dirName)) {
2484 :     # The directory opened successfully. Get the appropriate list according to the
2485 :     # strictures of the filter parameter.
2486 :     if ($filtered) {
2487 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2488 :     } else {
2489 :     @retVal = readdir $dirHandle;
2490 :     }
2491 :     } elsif (! $flag) {
2492 :     # Here the directory would not open and it's considered an error.
2493 :     Confess("Could not open directory $dirName.");
2494 :     }
2495 :     # Return the result.
2496 :     return @retVal;
2497 :     }
2498 : parrello 1.5
2499 :    
2500 : parrello 1.93 =head3 Insure
2501 : parrello 1.5
2502 : parrello 1.93 Insure($dirName, $chmod);
2503 : parrello 1.5
2504 : parrello 1.93 Insure a directory is present.
2505 : parrello 1.5
2506 : parrello 1.93 =over 4
2507 : parrello 1.5
2508 : parrello 1.93 =item dirName
2509 : olson 1.1
2510 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2511 : parrello 1.7
2512 : parrello 1.93 =item chmod (optional)
2513 : parrello 1.7
2514 : parrello 1.93 Security privileges to be given to the directory if it is created.
2515 : parrello 1.7
2516 : parrello 1.93 =back
2517 : parrello 1.7
2518 :     =cut
2519 :    
2520 : parrello 1.93 sub Insure {
2521 :     my ($dirName, $chmod) = @_;
2522 :     if (! -d $dirName) {
2523 :     Trace("Creating $dirName directory.") if T(2);
2524 :     eval {
2525 :     mkpath $dirName;
2526 :     # If we have permissions specified, set them here.
2527 :     if (defined($chmod)) {
2528 :     chmod $chmod, $dirName;
2529 :     }
2530 :     };
2531 :     if ($@) {
2532 :     Confess("Error creating $dirName: $@");
2533 :     }
2534 : parrello 1.12 }
2535 : parrello 1.9 }
2536 :    
2537 : parrello 1.93 =head3 ChDir
2538 : parrello 1.9
2539 : parrello 1.93 ChDir($dirName);
2540 : parrello 1.9
2541 : parrello 1.93 Change to the specified directory.
2542 : parrello 1.9
2543 :     =over 4
2544 :    
2545 : parrello 1.93 =item dirName
2546 : parrello 1.9
2547 : parrello 1.93 Name of the directory to which we want to change.
2548 : parrello 1.9
2549 :     =back
2550 :    
2551 :     =cut
2552 :    
2553 : parrello 1.93 sub ChDir {
2554 :     my ($dirName) = @_;
2555 :     if (! -d $dirName) {
2556 :     Confess("Cannot change to directory $dirName: no such directory.");
2557 :     } else {
2558 :     Trace("Changing to directory $dirName.") if T(File => 4);
2559 :     my $okFlag = chdir $dirName;
2560 :     if (! $okFlag) {
2561 :     Confess("Error switching to directory $dirName.");
2562 :     }
2563 :     }
2564 : parrello 1.9 }
2565 :    
2566 : parrello 1.93 =head3 SetPermissions
2567 :    
2568 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2569 : parrello 1.9
2570 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2571 :     In addition, the group ownership will be changed to the specified value.
2572 : parrello 1.9
2573 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2574 :     problems, so it does internal error recovery.
2575 : parrello 1.9
2576 :     =over 4
2577 :    
2578 : parrello 1.93 =item dirName
2579 :    
2580 :     Name of the directory to process.
2581 :    
2582 :     =item group
2583 : parrello 1.9
2584 : parrello 1.93 Name of the group to be assigned.
2585 : parrello 1.9
2586 : parrello 1.93 =item mask
2587 : parrello 1.9
2588 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2589 :     permission bits of any file or directory that does not already have them
2590 :     set to 1.
2591 : parrello 1.9
2592 : parrello 1.93 =item otherMasks
2593 : parrello 1.9
2594 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2595 :     one of the patterns, that directory and all its members and subdirectories
2596 :     will be assigned the new pattern. For example, the following would
2597 : parrello 1.110 assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2598 : parrello 1.9
2599 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2600 : parrello 1.9
2601 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2602 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2603 : parrello 1.22
2604 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2605 :     '^tmp' => 0666);
2606 : parrello 1.9
2607 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2608 :     names are matched, not file names.
2609 : parrello 1.9
2610 :     =back
2611 :    
2612 :     =cut
2613 :    
2614 : parrello 1.93 sub SetPermissions {
2615 : parrello 1.12 # Get the parameters.
2616 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2617 :     # Set up for error recovery.
2618 :     eval {
2619 :     # Switch to the specified directory.
2620 :     ChDir($dirName);
2621 :     # Get the group ID.
2622 :     my $gid = getgrnam($group);
2623 :     # Get the mask for tracing.
2624 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2625 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2626 :     my $fixCount = 0;
2627 :     my $lookCount = 0;
2628 :     # @dirs will be a stack of directories to be processed.
2629 :     my @dirs = (getcwd());
2630 :     while (scalar(@dirs) > 0) {
2631 :     # Get the current directory.
2632 :     my $dir = pop @dirs;
2633 :     # Check for a match to one of the specified directory names. To do
2634 :     # that, we need to pull the individual part of the name off of the
2635 :     # whole path.
2636 :     my $simpleName = $dir;
2637 :     if ($dir =~ m!/([^/]+)$!) {
2638 :     $simpleName = $1;
2639 :     }
2640 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2641 :     # Search for a match.
2642 :     my $match = 0;
2643 :     my $i;
2644 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2645 :     my $pattern = $otherMasks[$i];
2646 :     if ($simpleName =~ /$pattern/i) {
2647 :     $match = 1;
2648 :     }
2649 :     }
2650 : parrello 1.110 # Find out if we have a match. Note we use $i-1 because the loop added 2
2651 : parrello 1.93 # before terminating due to the match.
2652 :     if ($match && $otherMasks[$i-1] != $mask) {
2653 :     # This directory matches one of the incoming patterns, and it's
2654 :     # a different mask, so we process it recursively with that mask.
2655 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2656 :     } else {
2657 :     # Here we can process normally. Get all of the non-hidden members.
2658 :     my @submems = OpenDir($dir, 1);
2659 :     for my $submem (@submems) {
2660 :     # Get the full name.
2661 :     my $thisMem = "$dir/$submem";
2662 :     Trace("Checking member $thisMem.") if T(4);
2663 :     $lookCount++;
2664 :     if ($lookCount % 1000 == 0) {
2665 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2666 :     }
2667 :     # Fix the group.
2668 :     chown -1, $gid, $thisMem;
2669 :     # Insure this member is not a symlink.
2670 :     if (! -l $thisMem) {
2671 :     # Get its info.
2672 :     my $fileInfo = stat $thisMem;
2673 :     # Only proceed if we got the info. Otherwise, it's a hard link
2674 :     # and we want to skip it anyway.
2675 :     if ($fileInfo) {
2676 :     my $fileMode = $fileInfo->mode;
2677 :     if (($fileMode & $mask) != $mask) {
2678 :     # Fix this member.
2679 :     $fileMode |= $mask;
2680 :     chmod $fileMode, $thisMem;
2681 :     $fixCount++;
2682 :     }
2683 :     # If it's a subdirectory, stack it.
2684 :     if (-d $thisMem) {
2685 :     push @dirs, $thisMem;
2686 :     }
2687 :     }
2688 :     }
2689 :     }
2690 :     }
2691 : parrello 1.12 }
2692 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2693 :     };
2694 :     # Check for an error.
2695 :     if ($@) {
2696 :     Confess("SetPermissions error: $@");
2697 : parrello 1.12 }
2698 : parrello 1.7 }
2699 :    
2700 : parrello 1.93 =head3 GetLine
2701 : parrello 1.29
2702 : parrello 1.93 my @data = Tracer::GetLine($handle);
2703 : parrello 1.15
2704 : parrello 1.93 Read a line of data from a tab-delimited file.
2705 : parrello 1.15
2706 :     =over 4
2707 :    
2708 : parrello 1.93 =item handle
2709 : parrello 1.15
2710 : parrello 1.93 Open file handle from which to read.
2711 : parrello 1.15
2712 :     =item RETURN
2713 :    
2714 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2715 :     tab-delimited. If we are at the end of the file, then an empty list will be
2716 :     returned. If an empty line is read, a single list item consisting of a null
2717 :     string will be returned.
2718 : parrello 1.15
2719 :     =back
2720 :    
2721 :     =cut
2722 : parrello 1.93
2723 :     sub GetLine {
2724 : parrello 1.15 # Get the parameters.
2725 : parrello 1.93 my ($handle) = @_;
2726 :     # Declare the return variable.
2727 :     my @retVal = ();
2728 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2729 :     # Read from the file.
2730 :     my $line = <$handle>;
2731 :     # Only proceed if we found something.
2732 :     if (defined $line) {
2733 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2734 :     # upload control and have a nonstandard EOL combination.
2735 :     $line =~ s/(\r|\n)+$//;
2736 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2737 :     if (T(File => 4)) {
2738 :     my $escapedLine = $line;
2739 :     $escapedLine =~ s/\n/\\n/g;
2740 :     $escapedLine =~ s/\r/\\r/g;
2741 :     $escapedLine =~ s/\t/\\t/g;
2742 :     Trace("Line read: -->$escapedLine<--");
2743 :     }
2744 :     # If the line is empty, return a single empty string; otherwise, parse
2745 :     # it into fields.
2746 :     if ($line eq "") {
2747 :     push @retVal, "";
2748 :     } else {
2749 :     push @retVal, split /\t/,$line;
2750 :     }
2751 :     } else {
2752 :     # Trace the reason the read failed.
2753 :     Trace("End of file: $!") if T(File => 3);
2754 : parrello 1.15 }
2755 : parrello 1.93 # Return the result.
2756 :     return @retVal;
2757 : parrello 1.15 }
2758 :    
2759 : parrello 1.93 =head3 PutLine
2760 :    
2761 :     Tracer::PutLine($handle, \@fields, $eol);
2762 : parrello 1.35
2763 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2764 :     output in tab-separated form, with a trailing new-line.
2765 : parrello 1.35
2766 : parrello 1.93 =over 4
2767 : parrello 1.35
2768 : parrello 1.93 =item handle
2769 : parrello 1.69
2770 : parrello 1.93 Output file handle.
2771 : parrello 1.69
2772 : parrello 1.93 =item fields
2773 : parrello 1.69
2774 : parrello 1.93 List of field values.
2775 : parrello 1.69
2776 : parrello 1.93 =item eol (optional)
2777 : parrello 1.69
2778 : parrello 1.93 End-of-line character (default is "\n").
2779 : parrello 1.69
2780 :     =back
2781 : parrello 1.35
2782 :     =cut
2783 :    
2784 : parrello 1.93 sub PutLine {
2785 : parrello 1.69 # Get the parameters.
2786 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2787 :     # Write the data.
2788 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2789 : parrello 1.69 }
2790 :    
2791 :    
2792 : parrello 1.97 =head3 PrintLine
2793 :    
2794 :     Tracer::PrintLine($line);
2795 :    
2796 :     Print a line of text with a trailing new-line.
2797 :    
2798 :     =over 4
2799 :    
2800 :     =item line
2801 :    
2802 :     Line of text to print.
2803 :    
2804 :     =back
2805 :    
2806 :     =cut
2807 :    
2808 :     sub PrintLine {
2809 :     # Get the parameters.
2810 :     my ($line) = @_;
2811 :     # Print the line.
2812 :     print "$line\n";
2813 :     }
2814 :    
2815 : parrello 1.69
2816 : parrello 1.93 =head2 Other Useful Methods
2817 :    
2818 :     =head3 ParseParm
2819 :    
2820 :     my $listValue = Tracer::ParseParm($string);
2821 :    
2822 :     Convert a parameter into a list reference. If the parameter is undefined,
2823 :     an undefined value will be returned. Otherwise, it will be parsed as a
2824 :     comma-separated list of values.
2825 : parrello 1.69
2826 :     =over 4
2827 :    
2828 : parrello 1.93 =item string
2829 :    
2830 :     Incoming string.
2831 :    
2832 :     =item RETURN
2833 : parrello 1.69
2834 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2835 :     was undefined.
2836 : parrello 1.69
2837 :     =back
2838 :    
2839 :     =cut
2840 :    
2841 : parrello 1.93 sub ParseParm {
2842 :     # Get the parameters.
2843 :     my ($string) = @_;
2844 :     # Declare the return variable.
2845 :     my $retVal;
2846 :     # Check for data.
2847 :     if (defined $string) {
2848 :     # We have some, so split it into a list.
2849 :     $retVal = [ split /\s*,\s*/, $string];
2850 : parrello 1.72 }
2851 : parrello 1.93 # Return the result.
2852 :     return $retVal;
2853 : parrello 1.69 }
2854 :    
2855 : parrello 1.97 =head3 Now
2856 :    
2857 :     my $string = Tracer::Now();
2858 :    
2859 :     Return a displayable time stamp containing the local time. Whatever format this
2860 :     method produces must be parseable by L</ParseDate>.
2861 :    
2862 :     =cut
2863 :    
2864 :     sub Now {
2865 :     return DisplayTime(time);
2866 :     }
2867 :    
2868 :     =head3 DisplayTime
2869 :    
2870 :     my $string = Tracer::DisplayTime($time);
2871 : parrello 1.69
2872 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
2873 :     method produces must be parseable by L</ParseDate>.
2874 :    
2875 :     =over 4
2876 : parrello 1.69
2877 : parrello 1.97 =item time
2878 : parrello 1.69
2879 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2880 :    
2881 :     =item RETURN
2882 : parrello 1.69
2883 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2884 : parrello 1.69
2885 : parrello 1.97 =back
2886 : parrello 1.69
2887 : parrello 1.93 =cut
2888 : parrello 1.69
2889 : parrello 1.97 sub DisplayTime {
2890 :     my ($time) = @_;
2891 :     my $retVal = "(n/a)";
2892 :     if (defined $time) {
2893 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2894 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2895 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2896 :     }
2897 : parrello 1.93 return $retVal;
2898 :     }
2899 : parrello 1.69
2900 : parrello 1.93 # Pad a number to 2 digits.
2901 :     sub _p2 {
2902 :     my ($value) = @_;
2903 :     $value = "0$value" if ($value < 10);
2904 :     return $value;
2905 : parrello 1.69 }
2906 :    
2907 : parrello 1.93 =head3 Escape
2908 : parrello 1.69
2909 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2910 : parrello 1.69
2911 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2912 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2913 :     result is to reverse the effect of L</UnEscape>.
2914 : parrello 1.69
2915 :     =over 4
2916 :    
2917 : parrello 1.93 =item realString
2918 : parrello 1.69
2919 : parrello 1.93 String to escape.
2920 : parrello 1.69
2921 :     =item RETURN
2922 :    
2923 : parrello 1.93 Escaped equivalent of the real string.
2924 :    
2925 :     =back
2926 :    
2927 :     =cut
2928 :    
2929 :     sub Escape {
2930 :     # Get the parameter.
2931 :     my ($realString) = @_;
2932 :     # Initialize the return variable.
2933 :     my $retVal = "";
2934 :     # Loop through the parameter string, looking for sequences to escape.
2935 :     while (length $realString > 0) {
2936 :     # Look for the first sequence to escape.
2937 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2938 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2939 :     # itself is in $2. First, move the clear text to the return variable.
2940 :     $retVal .= $1;
2941 :     # Strip the processed section off the real string.
2942 :     $realString = substr $realString, (length $2) + (length $1);
2943 :     # Get the matched character.
2944 :     my $char = $2;
2945 :     # If we have a CR, we are done.
2946 :     if ($char ne "\r") {
2947 :     # It's not a CR, so encode the escape sequence.
2948 :     $char =~ tr/\t\n/tn/;
2949 :     $retVal .= "\\" . $char;
2950 :     }
2951 :     } else {
2952 :     # Here there are no more escape sequences. The rest of the string is
2953 :     # transferred unmodified.
2954 :     $retVal .= $realString;
2955 :     $realString = "";
2956 :     }
2957 :     }
2958 :     # Return the result.
2959 :     return $retVal;
2960 : parrello 1.69 }
2961 :    
2962 : parrello 1.93 =head3 UnEscape
2963 : parrello 1.69
2964 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2965 : parrello 1.69
2966 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2967 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2968 :     be deleted.
2969 : parrello 1.69
2970 :     =over 4
2971 :    
2972 : parrello 1.93 =item codedString
2973 : parrello 1.69
2974 : parrello 1.93 String to un-escape.
2975 : parrello 1.69
2976 :     =item RETURN
2977 :    
2978 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2979 :     values.
2980 : parrello 1.69
2981 :     =back
2982 :    
2983 :     =cut
2984 :    
2985 : parrello 1.93 sub UnEscape {
2986 :     # Get the parameter.
2987 :     my ($codedString) = @_;
2988 :     # Initialize the return variable.
2989 :     my $retVal = "";
2990 :     # Only proceed if the incoming string is nonempty.
2991 :     if (defined $codedString) {
2992 :     # Loop through the parameter string, looking for escape sequences. We can't do
2993 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
2994 :     # "\<tab>" no matter what we do.)
2995 :     while (length $codedString > 0) {
2996 :     # Look for the first escape sequence.
2997 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2998 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2999 :     # itself is in $2. First, move the clear text to the return variable.
3000 :     $retVal .= $1;
3001 :     $codedString = substr $codedString, (2 + length $1);
3002 :     # Get the escape value.
3003 :     my $char = $2;
3004 :     # If we have a "\r", we are done.
3005 :     if ($char ne 'r') {
3006 :     # Here it's not an 'r', so we convert it.
3007 :     $char =~ tr/\\tn/\\\t\n/;
3008 :     $retVal .= $char;
3009 :     }
3010 :     } else {
3011 :     # Here there are no more escape sequences. The rest of the string is
3012 :     # transferred unmodified.
3013 :     $retVal .= $codedString;
3014 :     $codedString = "";
3015 :     }
3016 :     }
3017 : parrello 1.35 }
3018 : parrello 1.69 # Return the result.
3019 :     return $retVal;
3020 :     }
3021 :    
3022 : parrello 1.93 =head3 Percent
3023 : parrello 1.69
3024 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
3025 : parrello 1.69
3026 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
3027 :     is zero, returns zero.
3028 : parrello 1.69
3029 :     =over 4
3030 :    
3031 : parrello 1.93 =item number
3032 : parrello 1.69
3033 : parrello 1.93 Percent numerator.
3034 : parrello 1.69
3035 : parrello 1.93 =item base
3036 : parrello 1.69
3037 : parrello 1.93 Percent base.
3038 : parrello 1.69
3039 : parrello 1.93 =item RETURN
3040 : parrello 1.69
3041 : parrello 1.93 Returns the percentage of the base represented by the numerator.
3042 : parrello 1.69
3043 :     =back
3044 :    
3045 :     =cut
3046 :    
3047 : parrello 1.93 sub Percent {
3048 : parrello 1.69 # Get the parameters.
3049 : parrello 1.93 my ($number, $base) = @_;
3050 :     # Declare the return variable.
3051 :     my $retVal = 0;
3052 :     # Compute the percent.
3053 :     if ($base != 0) {
3054 :     $retVal = $number * 100 / $base;
3055 :     }
3056 :     # Return the result.
3057 :     return $retVal;
3058 : parrello 1.69 }
3059 :    
3060 : parrello 1.97 =head3 Constrain
3061 :    
3062 :     my $constrained = Constrain($value, $min, $max);
3063 :    
3064 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3065 :    
3066 :     =over 4
3067 :    
3068 :     =item value
3069 :    
3070 :     Value to constrain.
3071 :    
3072 :     =item min (optional)
3073 :    
3074 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3075 :    
3076 :     =item max (optional)
3077 :    
3078 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3079 :    
3080 :     =item RETURN
3081 :    
3082 :     Returns the incoming value, constrained according to the other parameters.
3083 :    
3084 :     =back
3085 :    
3086 :     =cut
3087 :    
3088 :     sub Constrain {
3089 :     # Get the parameters.
3090 :     my ($value, $min, $max) = @_;
3091 :     # Declare the return variable.
3092 :     my $retVal = $value;
3093 :     # Apply the minimum constraint.
3094 :     if (defined $min && $retVal < $min) {
3095 :     $retVal = $min;
3096 :     }
3097 :     # Apply the maximum constraint.
3098 :     if (defined $max && $retVal > $max) {
3099 :     $retVal = $max;
3100 :     }
3101 :     # Return the result.
3102 :     return $retVal;
3103 :     }
3104 :    
3105 : parrello 1.93 =head3 Min
3106 : parrello 1.69
3107 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3108 : parrello 1.69
3109 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3110 : parrello 1.69
3111 :     =over 4
3112 :    
3113 : parrello 1.93 =item $value1, $value2, ... $valueN
3114 : parrello 1.69
3115 : parrello 1.93 List of numbers to compare.
3116 : parrello 1.69
3117 :     =item RETURN
3118 :    
3119 : parrello 1.93 Returns the lowest number in the list.
3120 : parrello 1.69
3121 :     =back
3122 :    
3123 :     =cut
3124 :    
3125 : parrello 1.93 sub Min {
3126 :     # Get the parameters. Note that we prime the return value with the first parameter.
3127 :     my ($retVal, @values) = @_;
3128 :     # Loop through the remaining parameters, looking for the lowest.
3129 :     for my $value (@values) {
3130 :     if ($value < $retVal) {
3131 :     $retVal = $value;
3132 : parrello 1.72 }
3133 :     }
3134 : parrello 1.93 # Return the minimum found.
3135 : parrello 1.70 return $retVal;
3136 : parrello 1.35 }
3137 :    
3138 : parrello 1.93 =head3 Max
3139 :    
3140 :     my $max = Max($value1, $value2, ... $valueN);
3141 : parrello 1.69
3142 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3143 : parrello 1.65
3144 : parrello 1.93 =over 4
3145 : parrello 1.65
3146 : parrello 1.93 =item $value1, $value2, ... $valueN
3147 : parrello 1.65
3148 : parrello 1.93 List of numbers to compare.
3149 : parrello 1.65
3150 : parrello 1.93 =item RETURN
3151 : parrello 1.65
3152 : parrello 1.93 Returns the highest number in the list.
3153 : parrello 1.65
3154 :     =back
3155 :    
3156 :     =cut
3157 :    
3158 : parrello 1.93 sub Max {
3159 :     # Get the parameters. Note that we prime the return value with the first parameter.
3160 :     my ($retVal, @values) = @_;
3161 :     # Loop through the remaining parameters, looking for the highest.
3162 :     for my $value (@values) {
3163 :     if ($value > $retVal) {
3164 :     $retVal = $value;
3165 : parrello 1.65 }
3166 :     }
3167 : parrello 1.93 # Return the maximum found.
3168 :     return $retVal;
3169 : parrello 1.65 }
3170 :    
3171 : parrello 1.93 =head3 Strip
3172 : parrello 1.37
3173 : parrello 1.93 my $string = Tracer::Strip($line);
3174 : parrello 1.37
3175 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3176 :     that may have been transferred back and forth several times among different
3177 :     operating environments.
3178 : parrello 1.37
3179 :     =over 4
3180 :    
3181 : parrello 1.93 =item line
3182 : parrello 1.37
3183 : parrello 1.93 Line of text to be stripped.
3184 : parrello 1.37
3185 : parrello 1.93 =item RETURN
3186 : parrello 1.91
3187 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3188 : parrello 1.91
3189 : parrello 1.37 =back
3190 :    
3191 :     =cut
3192 :    
3193 : parrello 1.93 sub Strip {
3194 :     # Get a copy of the parameter string.
3195 :     my ($string) = @_;
3196 :     my $retVal = (defined $string ? $string : "");
3197 :     # Strip the line terminator characters.
3198 :     $retVal =~ s/(\r|\n)+$//g;
3199 :     # Return the result.
3200 :     return $retVal;
3201 : parrello 1.43 }
3202 :    
3203 : parrello 1.93 =head3 Pad
3204 : parrello 1.43
3205 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3206 : parrello 1.43
3207 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3208 :     space, and the padding will be on the right side unless specified
3209 :     in the third parameter.
3210 : parrello 1.43
3211 :     =over 4
3212 :    
3213 : parrello 1.93 =item string
3214 :    
3215 :     String to be padded.
3216 :    
3217 :     =item len
3218 :    
3219 :     Desired length of the padded string.
3220 :    
3221 :     =item left (optional)
3222 :    
3223 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3224 :    
3225 :     =item padChar (optional)
3226 :    
3227 :     Character to use for padding. The default is a space.
3228 :    
3229 :     =item RETURN
3230 : parrello 1.43
3231 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3232 :     specified end so that it achieves the desired length.
3233 : parrello 1.43
3234 :     =back
3235 :    
3236 :     =cut
3237 :    
3238 : parrello 1.93 sub Pad {
3239 :     # Get the parameters.
3240 :     my ($string, $len, $left, $padChar) = @_;
3241 :     # Compute the padding character.
3242 :     if (! defined $padChar) {
3243 :     $padChar = " ";
3244 :     }
3245 :     # Compute the number of spaces needed.
3246 :     my $needed = $len - length $string;
3247 :     # Copy the string into the return variable.
3248 :     my $retVal = $string;
3249 :     # Only proceed if padding is needed.
3250 :     if ($needed > 0) {
3251 :     # Create the pad string.
3252 :     my $pad = $padChar x $needed;
3253 :     # Affix it to the return value.
3254 :     if ($left) {
3255 :     $retVal = $pad . $retVal;
3256 :     } else {
3257 :     $retVal .= $pad;
3258 : parrello 1.43 }
3259 : parrello 1.37 }
3260 : parrello 1.93 # Return the result.
3261 :     return $retVal;
3262 : parrello 1.37 }
3263 :    
3264 : parrello 1.93 =head3 EOF
3265 :    
3266 :     This is a constant that is lexically greater than any useful string.
3267 :    
3268 :     =cut
3269 :    
3270 :     sub EOF {
3271 :     return "\xFF\xFF\xFF\xFF\xFF";
3272 :     }
3273 : parrello 1.59
3274 : parrello 1.93 =head3 TICK
3275 : parrello 1.59
3276 : parrello 1.93 my @results = TICK($commandString);
3277 : parrello 1.59
3278 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3279 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3280 : parrello 1.59
3281 : parrello 1.93 `./protein.cgi`
3282 : parrello 1.59
3283 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3284 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3285 : parrello 1.59
3286 : parrello 1.93 TICK("./protein.cgi")
3287 : parrello 1.59
3288 : parrello 1.93 it will work correctly in both environments.
3289 : parrello 1.59
3290 : parrello 1.93 =over 4
3291 : parrello 1.59
3292 : parrello 1.93 =item commandString
3293 : parrello 1.59
3294 : parrello 1.93 The command string to pass to the system.
3295 : parrello 1.59
3296 :     =item RETURN
3297 :    
3298 : parrello 1.93 Returns the standard output from the specified command, as a list.
3299 : parrello 1.59
3300 :     =back
3301 :    
3302 :     =cut
3303 : parrello 1.93 #: Return Type @;
3304 :     sub TICK {
3305 : parrello 1.59 # Get the parameters.
3306 : parrello 1.93 my ($commandString) = @_;
3307 :     # Chop off the dot-slash if this is Windows.
3308 :     if ($FIG_Config::win_mode) {
3309 :     $commandString =~ s!^\./!!;
3310 : parrello 1.59 }
3311 : parrello 1.93 # Activate the command and return the result.
3312 :     return `$commandString`;
3313 : parrello 1.59 }
3314 :    
3315 : parrello 1.93
3316 : parrello 1.55 =head3 CommaFormat
3317 :    
3318 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3319 : parrello 1.55
3320 :     Insert commas into a number.
3321 :    
3322 :     =over 4
3323 :    
3324 :     =item number
3325 :    
3326 :     A sequence of digits.
3327 :    
3328 :     =item RETURN
3329 :    
3330 :     Returns the same digits with commas strategically inserted.
3331 :    
3332 :     =back
3333 :    
3334 :     =cut
3335 :    
3336 :     sub CommaFormat {
3337 :     # Get the parameters.
3338 :     my ($number) = @_;
3339 :     # Pad the length up to a multiple of three.
3340 :     my $padded = "$number";
3341 :     $padded = " " . $padded while length($padded) % 3 != 0;
3342 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3343 :     # cause the delimiters to be included in the output stream. The
3344 :     # GREP removes the empty strings in between the delimiters.
3345 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3346 :     # Clean out the spaces.
3347 :     $retVal =~ s/ //g;
3348 :     # Return the result.
3349 :     return $retVal;
3350 :     }
3351 : parrello 1.46
3352 :    
3353 : parrello 1.62 =head3 CompareLists
3354 :    
3355 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3356 : parrello 1.62
3357 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3358 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3359 :     The return value contains a list of items that are only in the new list
3360 :     (inserted) and only in the old list (deleted).
3361 :    
3362 :     =over 4
3363 :    
3364 :     =item newList
3365 :    
3366 :     Reference to a list of new tuples.
3367 :    
3368 :     =item oldList
3369 :    
3370 :     Reference to a list of old tuples.
3371 :    
3372 :     =item keyIndex (optional)
3373 :    
3374 :     Index into each tuple of its key field. The default is 0.
3375 :    
3376 :     =item RETURN
3377 :    
3378 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3379 :     list (inserted) followed by a reference to the list of items that are only in the old
3380 :     list (deleted).
3381 :    
3382 :     =back
3383 :    
3384 :     =cut
3385 :    
3386 :     sub CompareLists {
3387 :     # Get the parameters.
3388 :     my ($newList, $oldList, $keyIndex) = @_;
3389 :     if (! defined $keyIndex) {
3390 :     $keyIndex = 0;
3391 :     }
3392 :     # Declare the return variables.
3393 :     my ($inserted, $deleted) = ([], []);
3394 :     # Loop through the two lists simultaneously.
3395 :     my ($newI, $oldI) = (0, 0);
3396 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3397 :     while ($newI < $newN || $oldI < $oldN) {
3398 :     # Get the current object in each list. Note that if one
3399 :     # of the lists is past the end, we'll get undef.
3400 :     my $newItem = $newList->[$newI];
3401 :     my $oldItem = $oldList->[$oldI];
3402 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3403 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3404 :     push @{$deleted}, $oldItem;
3405 :     $oldI++;
3406 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3407 :     # The new item is not in the old list, so mark it inserted.
3408 :     push @{$inserted}, $newItem;
3409 :     $newI++;
3410 :     } else {
3411 :     # The item is in both lists, so push forward.
3412 :     $oldI++;
3413 :     $newI++;
3414 :     }
3415 :     }
3416 :     # Return the result.
3417 :     return ($inserted, $deleted);
3418 :     }
3419 :    
3420 : parrello 1.105 =head3 Cmp
3421 :    
3422 :     my $cmp = Tracer::Cmp($a, $b);
3423 :    
3424 :     This method performs a universal sort comparison. Each value coming in is
3425 :     separated into a leading text part and a trailing number part. The text
3426 :     part is string compared, and if both parts are equal, then the number
3427 :     parts are compared numerically. A stream of just numbers or a stream of
3428 :     just strings will sort correctly, and a mixed stream will sort with the
3429 :     numbers first. Strings with a label and a number will sort in the
3430 :     expected manner instead of lexically.
3431 :    
3432 :     =over 4
3433 :    
3434 :     =item a
3435 :    
3436 :     First item to compare.
3437 :    
3438 :     =item b
3439 :    
3440 :     Second item to compare.
3441 :    
3442 :     =item RETURN
3443 :    
3444 :     Returns a negative number if the first item should sort first (is less), a positive
3445 :     number if the first item should sort second (is greater), and a zero if the items are
3446 :     equal.
3447 :    
3448 :     =back
3449 :    
3450 :     =cut
3451 :    
3452 :     sub Cmp {
3453 :     # Get the parameters.
3454 :     my ($a, $b) = @_;
3455 :     # Declare the return value.
3456 :     my $retVal;
3457 :     # Check for nulls.
3458 :     if (! defined($a)) {
3459 :     $retVal = (! defined($b) ? 0 : -1);
3460 :     } elsif (! defined($b)) {
3461 :     $retVal = 1;
3462 :     } else {
3463 :     # Here we have two real values. Parse the two strings.
3464 :     $a =~ /^(\D*)(\d*)$/;
3465 :     my $aParsed = [$1, $2];
3466 :     $b =~ /^(\D*)(\d*)$/;
3467 :     my $bParsed = [$1, $2];
3468 :     # Compare the string parts.
3469 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3470 :     if (! $retVal) {
3471 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3472 :     }
3473 :     }
3474 :     # Return the result.
3475 :     return $retVal;
3476 :     }
3477 :    
3478 : parrello 1.108 =head3 ListEQ
3479 :    
3480 :     my $flag = Tracer::ListEQ(\@a, \@b);
3481 :    
3482 :     Return TRUE if the specified lists contain the same strings in the same
3483 :     order, else FALSE.
3484 :    
3485 :     =over 4
3486 :    
3487 :     =item a
3488 :    
3489 :     Reference to the first list.
3490 :    
3491 :     =item b
3492 :    
3493 :     Reference to the second list.
3494 :    
3495 :     =item RETURN
3496 :    
3497 :     Returns TRUE if the two parameters are identical string lists, else FALSE.
3498 :    
3499 :     =back
3500 :    
3501 :     =cut
3502 :    
3503 :     sub ListEQ {
3504 :     # Get the parameters.
3505 :     my ($a, $b) = @_;
3506 :     # Declare the return variable. Start by checking the lengths.
3507 :     my $n = scalar(@$a);
3508 :     my $retVal = ($n == scalar(@$b));
3509 :     # Now compare the list elements.
3510 :     for (my $i = 0; $retVal && $i < $n; $i++) {
3511 :     $retVal = ($a->[$i] eq $b->[$i]);
3512 :     }
3513 :     # Return the result.
3514 :     return $retVal;
3515 :     }
3516 :    
3517 : parrello 1.105 =head2 CGI Script Utilities
3518 :    
3519 :     =head3 ScriptSetup (deprecated)
3520 :    
3521 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
3522 :    
3523 :     Perform standard tracing and debugging setup for scripts. The value returned is
3524 :     the CGI object followed by a pre-built variable hash. At the end of the script,
3525 :     the client should call L</ScriptFinish> to output the web page.
3526 :    
3527 :     This method calls L</ETracing> to configure tracing, which allows the tracing
3528 :     to be configured via the emergency tracing form on the debugging control panel.
3529 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
3530 :     method, which includes every program that uses this method or L</StandardSetup>.
3531 :    
3532 :     =over 4
3533 :    
3534 :     =item noTrace (optional)
3535 :    
3536 :     If specified, tracing will be suppressed. This is useful if the script wants to set up
3537 :     tracing manually.
3538 :    
3539 :     =item RETURN
3540 :    
3541 :     Returns a two-element list consisting of a CGI query object and a variable hash for
3542 :     the output page.
3543 :    
3544 :     =back
3545 :    
3546 :     =cut
3547 :    
3548 :     sub ScriptSetup {
3549 :     # Get the parameters.
3550 :     my ($noTrace) = @_;
3551 :     # Get the CGI query object.
3552 :     my $cgi = CGI->new();
3553 :     # Set up tracing if it's not suppressed.
3554 :     ETracing($cgi) unless $noTrace;
3555 :     # Create the variable hash.
3556 :     my $varHash = { results => '' };
3557 :     # Return the query object and variable hash.
3558 :     return ($cgi, $varHash);
3559 :     }
3560 :    
3561 :     =head3 ScriptFinish (deprecated)
3562 :    
3563 :     ScriptFinish($webData, $varHash);
3564 :    
3565 :     Output a web page at the end of a script. Either the string to be output or the
3566 :     name of a template file can be specified. If the second parameter is omitted,
3567 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
3568 :     name of a template file. The template should have the variable C<DebugData>
3569 :     specified in any form that invokes a standard script. If debugging mode is turned
3570 :     on, a form field will be put in that allows the user to enter tracing data.
3571 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
3572 :     the output, formatted as a list.
3573 :    
3574 :     A typical standard script would loook like the following.
3575 :    
3576 :     BEGIN {
3577 :     # Print the HTML header.
3578 :     print "CONTENT-TYPE: text/html\n\n";
3579 :     }
3580 :     use Tracer;
3581 :     use CGI;
3582 :     use FIG;
3583 :     # ... more uses ...
3584 :    
3585 :     my ($cgi, $varHash) = ScriptSetup();
3586 :     eval {
3587 :     # ... get data from $cgi, put it in $varHash ...
3588 :     };
3589 :     if ($@) {
3590 :     Trace("Script Error: $@") if T(0);
3591 :     }
3592 :     ScriptFinish("Html/MyTemplate.html", $varHash);
3593 :    
3594 :     The idea here is that even if the script fails, you'll see trace messages and
3595 :     useful output.
3596 :    
3597 :     =over 4
3598 :    
3599 :     =item webData
3600 :    
3601 :     A string containing either the full web page to be written to the output or the
3602 :     name of a template file from which the page is to be constructed. If the name
3603 :     of a template file is specified, then the second parameter must be present;
3604 :     otherwise, it must be absent.
3605 :    
3606 :     =item varHash (optional)
3607 :    
3608 :     If specified, then a reference to a hash mapping variable names for a template
3609 :     to their values. The template file will be read into memory, and variable markers
3610 :     will be replaced by data in this hash reference.
3611 :    
3612 :     =back
3613 :    
3614 :     =cut
3615 :    
3616 :     sub ScriptFinish {
3617 :     # Get the parameters.
3618 :     my ($webData, $varHash) = @_;
3619 :     # Check for a template file situation.
3620 :     my $outputString;
3621 :     if (defined $varHash) {
3622 :     # Here we have a template file. We need to determine the template type.
3623 :     my $template;
3624 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
3625 :     $template = "$FIG_Config::template_url/$webData";
3626 :     } else {
3627 :     $template = "<<$webData";
3628 :     }
3629 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
3630 :     } else {
3631 :     # Here the user gave us a raw string.
3632 :     $outputString = $webData;
3633 :     }
3634 :     # Check for trace messages.
3635 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
3636 :     # We have trace messages, so we want to put them at the end of the body. This
3637 :     # is either at the end of the whole string or at the beginning of the BODY
3638 :     # end-tag.
3639 :     my $pos = length $outputString;
3640 :     if ($outputString =~ m#</body>#gi) {
3641 :     $pos = (pos $outputString) - 7;
3642 :     }
3643 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
3644 :     # destination.
3645 :     my $traceHtml;
3646 :     if ($Destination eq "QUEUE") {
3647 :     $traceHtml = QTrace('Html');
3648 :     } elsif ($Destination =~ /^>>(.+)$/) {
3649 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
3650 :     # can copy the file name into the clipboard easily.
3651 :     my $actualDest = $1;
3652 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
3653 :     } else {
3654 :     # Here we have one of the special destinations.
3655 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
3656 :     }
3657 :     substr $outputString, $pos, 0, $traceHtml;
3658 :     }
3659 :     # Write the output string.
3660 :     print $outputString;
3661 :     }
3662 :    
3663 : parrello 1.65 =head3 GenerateURL
3664 :    
3665 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3666 : parrello 1.65
3667 :     Generate a GET-style URL for the specified page with the specified parameter
3668 :     names and values. The values will be URL-escaped automatically. So, for
3669 :     example
3670 :    
3671 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3672 :    
3673 :     would return
3674 :    
3675 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3676 : parrello 1.65
3677 :     =over 4
3678 :    
3679 :     =item page
3680 :    
3681 :     Page URL.
3682 :    
3683 :     =item parameters
3684 :    
3685 :     Hash mapping parameter names to parameter values.
3686 :    
3687 :     =item RETURN
3688 :    
3689 :     Returns a GET-style URL that goes to the specified page and passes in the
3690 :     specified parameters and values.
3691 :    
3692 :     =back
3693 :    
3694 :     =cut
3695 :    
3696 :     sub GenerateURL {
3697 :     # Get the parameters.
3698 :     my ($page, %parameters) = @_;
3699 :     # Prime the return variable with the page URL.
3700 :     my $retVal = $page;
3701 :     # Loop through the parameters, creating parameter elements in a list.
3702 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3703 :     # If the list is nonempty, tack it on.
3704 :     if (@parmList) {
3705 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3706 : parrello 1.65 }
3707 :     # Return the result.
3708 :     return $retVal;
3709 :     }
3710 :    
3711 : parrello 1.78 =head3 ApplyURL
3712 :    
3713 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3714 : parrello 1.78
3715 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3716 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3717 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3718 :    
3719 :     This provides a simple way to process the results of a database query into something
3720 :     displayable by combining a URL with text.
3721 :    
3722 :     =over 4
3723 :    
3724 :     =item table
3725 :    
3726 :     Reference to a list of lists. The elements in the containing list will be updated by
3727 :     this method.
3728 :    
3729 :     =item target
3730 :    
3731 :     The index of the column to be converted into HTML.
3732 :    
3733 :     =item url
3734 :    
3735 :     The index of the column containing the URL. Note that the URL must have a recognizable
3736 :     C<http:> at the beginning.
3737 :    
3738 :     =back
3739 :    
3740 :     =cut
3741 :    
3742 :     sub ApplyURL {
3743 :     # Get the parameters.
3744 :     my ($table, $target, $url) = @_;
3745 :     # Loop through the table.
3746 :     for my $row (@{$table}) {
3747 :     # Apply the URL to the target cell.
3748 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3749 :     # Delete the URL from the row.
3750 :     delete $row->[$url];
3751 :     }
3752 :     }
3753 :    
3754 :     =head3 CombineURL
3755 :    
3756 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3757 : parrello 1.78
3758 :     This method will convert the specified text into HTML hyperlinked to the specified
3759 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3760 :     is defined and begins with an C<http:> header.
3761 :    
3762 :     =over 4
3763 :    
3764 :     =item text
3765 :    
3766 :     Text to return. This will be HTML-escaped automatically.
3767 :    
3768 :     =item url
3769 :    
3770 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3771 :     will be returned without any hyperlinking.
3772 :    
3773 :     =item RETURN
3774 :    
3775 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3776 :     doesn't look right, the HTML-escaped text will be returned without any further
3777 :     modification.
3778 :    
3779 :     =back
3780 :    
3781 :     =cut
3782 :    
3783 :     sub CombineURL {
3784 :     # Get the parameters.
3785 :     my ($text, $url) = @_;
3786 :     # Declare the return variable.
3787 :     my $retVal = CGI::escapeHTML($text);
3788 :     # Verify the URL.
3789 :     if (defined($url) && $url =~ m!http://!i) {
3790 :     # It's good, so we apply it to the text.
3791 :     $retVal = "<a href=\"$url\">$retVal</a>";
3792 :     }
3793 :     # Return the result.
3794 :     return $retVal;
3795 :     }
3796 :    
3797 : parrello 1.97 =head3 TrackingCode
3798 :    
3799 :     my $html = Tracer::TrackingCode();
3800 :    
3801 :     Returns the HTML code for doing web page traffic monitoring. If the
3802 :     current environment is a test system, then it returns a null string;
3803 :     otherwise, it returns a bunch of javascript containing code for turning
3804 :     on SiteMeter and Google Analytics.
3805 :    
3806 :     =cut
3807 :    
3808 :     sub TrackingCode {
3809 :     # Declare the return variable.
3810 :     my $retVal = "<!-- tracking off -->";
3811 :     # Determine if we're in production.
3812 :     if ($FIG_Config::site_meter) {
3813 :     $retVal = <<END_HTML
3814 :     <!-- Site Meter -->
3815 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3816 :     </script>
3817 :     <noscript>
3818 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3819 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3820 :     </noscript>
3821 :     <!-- Copyright (c)2006 Site Meter -->
3822 :     END_HTML
3823 :     }
3824 :     return $retVal;
3825 :     }
3826 :    
3827 : parrello 1.105 =head3 Clean
3828 :    
3829 :     my $cleaned = Tracer::Clean($string);
3830 :    
3831 :     Clean up a string for HTML display. This not only converts special
3832 :     characters to HTML entity names, it also removes control characters.
3833 :    
3834 :     =over 4
3835 :    
3836 :     =item string
3837 :    
3838 :     String to convert.
3839 :    
3840 :     =item RETURN
3841 :    
3842 :     Returns the input string with anything that might disrupt an HTML literal removed. An
3843 :     undefined value will be converted to an empty string.
3844 :    
3845 :     =back
3846 :    
3847 :     =cut
3848 :    
3849 :     sub Clean {
3850 :     # Get the parameters.
3851 :     my ($string) = @_;
3852 :     # Declare the return variable.
3853 :     my $retVal = "";
3854 :     # Only proceed if the value exists.
3855 :     if (defined $string) {
3856 :     # Get the string.
3857 :     $retVal = $string;
3858 :     # Clean the control characters.
3859 :     $retVal =~ tr/\x00-\x1F/?/;
3860 :     # Escape the rest.
3861 :     $retVal = CGI::escapeHTML($retVal);
3862 :     }
3863 :     # Return the result.
3864 :     return $retVal;
3865 :     }
3866 :    
3867 :    
3868 :    
3869 : parrello 1.97
3870 : olson 1.88 1;

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