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1 : gdpusch 1.95 # -*- perl -*-
2 :     ########################################################################
3 : olson 1.30 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 : parrello 1.61 #
8 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 : parrello 1.61 # Public License.
11 : olson 1.30 #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.95 ########################################################################
18 : olson 1.30
19 : olson 1.1 package Tracer;
20 :    
21 : parrello 1.12 require Exporter;
22 :     @ISA = ('Exporter');
23 : parrello 1.99 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24 : parrello 1.97 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25 : parrello 1.12 use strict;
26 : gdpusch 1.96 use Carp qw(longmess croak carp);
27 : parrello 1.12 use CGI;
28 : parrello 1.47 use Cwd;
29 : parrello 1.12 use FIG_Config;
30 : parrello 1.9 use PageBuilder;
31 : parrello 1.21 use Digest::MD5;
32 : parrello 1.36 use File::Basename;
33 : parrello 1.37 use File::Path;
34 : parrello 1.48 use File::stat;
35 : parrello 1.59 use LWP::UserAgent;
36 : parrello 1.64 use Time::HiRes 'gettimeofday';
37 : parrello 1.65 use URI::Escape;
38 : parrello 1.74 use Time::Local;
39 : parrello 1.99 use POSIX qw(strftime);
40 :     use Time::Zone;
41 :    
42 : olson 1.1
43 :     =head1 Tracing and Debugging Helpers
44 :    
45 : parrello 1.72 =head2 Tracing
46 : olson 1.1
47 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51 :     level is less than or equal to the setup trace level and whose category is activated will
52 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
53 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
54 :     appear.
55 : olson 1.1
56 : parrello 1.72 =head3 Putting Trace Messages in Your Code
57 :    
58 :     To generate a trace message, use the following syntax.
59 :    
60 :     Trace($message) if T(errors => 4);
61 : olson 1.1
62 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
64 : olson 1.1
65 : parrello 1.72 Trace($message) if T(main => 4);
66 : olson 1.1
67 :     will trace if the trace level is 4 or more.
68 :    
69 :     If the category name is the same as the package name, all you need is the number. So, if the
70 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71 :     active and the trace level is 2 or more.
72 :    
73 : parrello 1.72 Trace($message) if T(2);
74 :    
75 :     In scripts, where no package name is available, the category defaults to C<main>.
76 :    
77 :     =head3 Custom Tracing
78 :    
79 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
81 :     L</Emergency Tracing> easier to understand.
82 : olson 1.1
83 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84 :     a list of category names, and a destination. The trace level and list of category names are
85 : olson 1.1 specified as a space-delimited string. Thus
86 :    
87 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
88 : olson 1.1
89 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90 : parrello 1.72 specifies that messages should be sent to the standard output.
91 : parrello 1.12
92 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93 :     level 3 and writes the output to the standard error output. This sort of thing might be
94 :     useful in a CGI environment.
95 :    
96 : parrello 1.72 TSetup('3 *', 'WARN');
97 : olson 1.1
98 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
99 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
100 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
101 :     the page output, they can be gathered together and displayed at the end of the page. This makes
102 :     it easier to debug page formatting problems.
103 :    
104 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105 :     a file at the same time. To trace to a file, specify the filename with an output character in front
106 :     of it.
107 :    
108 :     TSetup('4 SQL', ">$fileName");
109 :    
110 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111 :     bracket.
112 :    
113 :     TSetup('3 *', "+>$fileName");
114 : parrello 1.4
115 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117 :     Thus, debugging information is available and easily retrieved even when the application is
118 :     being used out in the field.
119 :    
120 : parrello 1.72 =head3 Trace Levels
121 :    
122 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
123 :     a suggestion.
124 :    
125 :     =over 4
126 :    
127 : parrello 1.32 =item Error 0
128 : parrello 1.10
129 :     Message indicates an error that may lead to incorrect results or that has stopped the
130 :     application entirely.
131 :    
132 : parrello 1.32 =item Warning 1
133 : parrello 1.10
134 :     Message indicates something that is unexpected but that probably did not interfere
135 :     with program execution.
136 :    
137 : parrello 1.32 =item Notice 2
138 : parrello 1.10
139 :     Message indicates the beginning or end of a major task.
140 :    
141 : parrello 1.32 =item Information 3
142 : parrello 1.10
143 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
144 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
145 :    
146 : parrello 1.32 =item Detail 4
147 : parrello 1.10
148 :     Message indicates a low-level loop iteration.
149 :    
150 :     =back
151 :    
152 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
153 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
154 :     The time stamp is between square brackets and the category name between angle brackets.
155 :     After the category name there is a colon (C<:>) followed by the message text.
156 :     If the square brackets or angle brackets are missing, then the trace management
157 :     utilities assume that they are encountering a set of pre-formatted lines.
158 :    
159 :     Note, however, that this formatting is done automatically by the tracing functions. You
160 :     only need to know about it if you want to parse a trace file.
161 :    
162 :     =head3 Emergency Tracing
163 :    
164 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
165 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167 :     that you specify a tracing key. For command-line tools, the key is
168 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
169 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
170 :     the tracing in your environment without stepping on other users.
171 :    
172 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173 :     generate one for you.
174 :    
175 :     You can activate and de-activate emergency tracing from the debugging control panel, as
176 :     well as display the trace file itself.
177 :    
178 :     To enable emergency tracing in your code, call
179 :    
180 :     ETracing($cgi)
181 :    
182 :     from a web script and
183 :    
184 :     ETracing()
185 :    
186 :     from a command-line script.
187 :    
188 :     The web script will look for the tracing key in the cookies, and the command-line
189 :     script will look for it in the C<TRACING> environment variable. If you are
190 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191 : parrello 1.72 will be configured automatically.
192 :    
193 : olson 1.1 =cut
194 : parrello 1.2
195 : olson 1.1 # Declare the configuration variables.
196 :    
197 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
198 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
199 :     # standard output
200 : parrello 1.3 my %Categories = ( main => 1 );
201 : parrello 1.12 # hash of active category names
202 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
203 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
204 :     # messages
205 :     my @Queue = (); # queued list of trace messages.
206 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
207 : parrello 1.97 my $LastLevel = 0; # level of the last test call
208 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
209 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
210 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
211 :     umask 2; # Fix the damn umask so everything is group-writable.
212 : olson 1.1
213 : parrello 1.93 =head2 Tracing Methods
214 :    
215 :     =head3 Setups
216 :    
217 :     my $count = Tracer::Setups();
218 :    
219 :     Return the number of times L</TSetup> has been called.
220 :    
221 :     This method allows for the creation of conditional tracing setups where, for example, we
222 :     may want to set up tracing if nobody else has done it before us.
223 :    
224 :     =cut
225 :    
226 :     sub Setups {
227 :     return $SetupCount;
228 :     }
229 : olson 1.1
230 :     =head3 TSetup
231 :    
232 : parrello 1.92 TSetup($categoryList, $target);
233 : olson 1.1
234 :     This method is used to specify the trace options. The options are stored as package data
235 :     and interrogated by the L</Trace> and L</T> methods.
236 :    
237 :     =over 4
238 :    
239 :     =item categoryList
240 :    
241 :     A string specifying the trace level and the categories to be traced, separated by spaces.
242 :     The trace level must come first.
243 :    
244 :     =item target
245 :    
246 :     The destination for the trace output. To send the trace output to a file, specify the file
247 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
248 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
249 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
250 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
251 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
252 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
253 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
254 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
255 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
256 : parrello 1.6 cause tracing to be suppressed.
257 : olson 1.1
258 :     =back
259 :    
260 :     =cut
261 :    
262 :     sub TSetup {
263 : parrello 1.12 # Get the parameters.
264 :     my ($categoryList, $target) = @_;
265 :     # Parse the category list.
266 :     my @categoryData = split /\s+/, $categoryList;
267 :     # Extract the trace level.
268 :     $TraceLevel = shift @categoryData;
269 :     # Presume category-based tracing until we learn otherwise.
270 :     $AllTrace = 0;
271 :     # Build the category hash. Note that if we find a "*", we turn on non-category
272 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
273 : parrello 1.34 %Categories = ( main => 1 );
274 : parrello 1.12 for my $category (@categoryData) {
275 :     if ($category eq '*') {
276 :     $AllTrace = 1;
277 :     } else {
278 : parrello 1.13 $Categories{lc $category} = 1;
279 : parrello 1.12 }
280 :     }
281 :     # Now we need to process the destination information. The most important special
282 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
283 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
284 :     # the standard output (tee mode).
285 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
286 :     if ($target =~ m/^\+/) {
287 :     $TeeFlag = 1;
288 :     $target = substr($target, 1);
289 :     }
290 :     if ($target =~ m/^>[^>]/) {
291 : parrello 1.98 # We need to initialize the file (which clears it).
292 : parrello 1.12 open TRACEFILE, $target;
293 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
294 : parrello 1.12 close TRACEFILE;
295 : parrello 1.98 # Set to append mode now that the file has been cleared.
296 : parrello 1.12 $Destination = ">$target";
297 :     } else {
298 :     $Destination = $target;
299 :     }
300 :     } else {
301 :     $Destination = uc($target);
302 :     }
303 :     # Increment the setup counter.
304 :     $SetupCount++;
305 : parrello 1.11 }
306 :    
307 : parrello 1.93 =head3 SetLevel
308 : parrello 1.31
309 : parrello 1.93 Tracer::SetLevel($newLevel);
310 : parrello 1.31
311 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
312 : parrello 1.31
313 : parrello 1.93 =over 4
314 : parrello 1.31
315 : parrello 1.93 =item newLevel
316 : parrello 1.31
317 : parrello 1.93 Proposed new trace level.
318 : parrello 1.31
319 : parrello 1.93 =back
320 : parrello 1.31
321 : parrello 1.93 =cut
322 : parrello 1.31
323 : parrello 1.93 sub SetLevel {
324 :     $TraceLevel = $_[0];
325 :     }
326 : parrello 1.31
327 : parrello 1.97 =head3 ParseDate
328 :    
329 :     my $time = Tracer::ParseDate($dateString);
330 :    
331 :     Convert a date into a PERL time number. This method expects a date-like string
332 :     and parses it into a number. The string must be vaguely date-like or it will
333 :     return an undefined value. Our requirement is that a month and day be
334 :     present and that three pieces of the date string (time of day, month and day,
335 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
336 :    
337 :     If a time of day is present, it must be in military time with two digits for
338 :     everything but the hour.
339 : parrello 1.31
340 : parrello 1.97 The year must be exactly four digits.
341 : parrello 1.31
342 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
343 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
344 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
345 :    
346 :     It should be guaranteed that this method will parse the output of the L</Now> function.
347 :    
348 :     The parameters are as follows.
349 : parrello 1.31
350 : parrello 1.93 =over 4
351 : parrello 1.31
352 : parrello 1.93 =item dateString
353 : parrello 1.31
354 : parrello 1.97 The date string to convert.
355 : parrello 1.31
356 : parrello 1.93 =item RETURN
357 : parrello 1.31
358 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
359 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
360 : parrello 1.31
361 : parrello 1.93 =back
362 : parrello 1.38
363 : parrello 1.93 =cut
364 : parrello 1.38
365 : parrello 1.97 # Universal month conversion table.
366 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
367 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
368 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
369 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
370 :     May => 4, May => 4, '05' => 4, '5' => 4,
371 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
372 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
373 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
374 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
375 :     Oct => 9, October => 9, '10' => 9,
376 :     Nov => 10, November => 10, '11' => 10,
377 :     Dec => 11, December => 11, '12' => 11
378 :     };
379 :    
380 :     sub ParseDate {
381 : parrello 1.93 # Get the parameters.
382 :     my ($dateString) = @_;
383 :     # Declare the return variable.
384 :     my $retVal;
385 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
386 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
387 :     # won't be fooled into thinking the month is Sunday.
388 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
389 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
390 :     # Insist that the month and day are valid.
391 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
392 :     # Find the time.
393 :     my ($hour, $min, $sec) = (0, 0, 0);
394 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
395 :     ($hour, $min, $sec) = ($1, $2, $3);
396 :     }
397 :     # Find the year.
398 :     my $year;
399 :     if ($dateString =~ /\b(\d{4})\b/) {
400 :     $year = $1;
401 :     } else {
402 :     # Get the default year, which is this one. Note we must convert it to
403 :     # the four-digit value expected by "timelocal".
404 :     (undef, undef, undef, undef, undef, $year) = localtime();
405 :     $year += 1900;
406 :     }
407 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
408 :     }
409 : parrello 1.93 }
410 :     # Return the result.
411 :     return $retVal;
412 :     }
413 : parrello 1.31
414 : parrello 1.93 =head3 LogErrors
415 : parrello 1.42
416 : parrello 1.93 Tracer::LogErrors($fileName);
417 : parrello 1.31
418 : parrello 1.93 Route the standard error output to a log file.
419 : parrello 1.31
420 : parrello 1.93 =over 4
421 : parrello 1.31
422 : parrello 1.93 =item fileName
423 : parrello 1.31
424 : parrello 1.93 Name of the file to receive the error output.
425 : parrello 1.31
426 : parrello 1.93 =back
427 : parrello 1.31
428 : parrello 1.93 =cut
429 : parrello 1.84
430 : parrello 1.93 sub LogErrors {
431 :     # Get the file name.
432 :     my ($fileName) = @_;
433 :     # Open the file as the standard error output.
434 :     open STDERR, '>', $fileName;
435 :     }
436 : parrello 1.84
437 : parrello 1.93 =head3 Trace
438 : parrello 1.31
439 : parrello 1.93 Trace($message);
440 : parrello 1.31
441 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
442 :     any prior call to B<TSetup>.
443 : parrello 1.31
444 : parrello 1.93 =over 4
445 : parrello 1.42
446 : parrello 1.93 =item message
447 : parrello 1.42
448 : parrello 1.93 Message to write.
449 : parrello 1.42
450 : parrello 1.93 =back
451 : parrello 1.72
452 : parrello 1.93 =cut
453 : parrello 1.36
454 : parrello 1.93 sub Trace {
455 :     # Get the parameters.
456 :     my ($message) = @_;
457 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
458 :     # new-line stuff ourselves.
459 :     my $stripped = Strip($message);
460 :     # Compute the caller information.
461 :     my ($callPackage, $callFile, $callLine) = caller();
462 :     my $callFileTitle = basename($callFile);
463 :     # Check the caller.
464 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
465 : parrello 1.93 # Get the timestamp.
466 :     my $timeStamp = Now();
467 : parrello 1.97 # Build the prefix.
468 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
469 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
470 : parrello 1.97 # Format the message.
471 :     my $formatted = "$prefix $stripped";
472 : parrello 1.93 # Process according to the destination.
473 :     if ($Destination eq "TEXT") {
474 :     # Write the message to the standard output.
475 :     print "$formatted\n";
476 :     } elsif ($Destination eq "ERROR") {
477 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
478 : parrello 1.93 print STDERR "$formatted\n";
479 : parrello 1.97 } elsif ($Destination eq "WARN") {
480 :     # Emit the message to the standard error output. It is presumed that the
481 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
482 :     # the caller info.
483 :     print STDERR "$callerInfo$stripped\n";
484 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
485 :     # Push the message into the queue.
486 :     push @Queue, "$formatted";
487 :     } elsif ($Destination eq "HTML") {
488 :     # Convert the message to HTML and write it to the standard output.
489 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
490 :     print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
491 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
492 :     # Write the trace message to an output file.
493 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
494 : parrello 1.93 print TRACING "$formatted\n";
495 :     close TRACING;
496 :     # If the Tee flag is on, echo it to the standard output.
497 :     if ($TeeFlag) {
498 :     print "$formatted\n";
499 :     }
500 :     }
501 :     }
502 : parrello 1.36
503 : parrello 1.93 =head3 T
504 : parrello 1.36
505 : parrello 1.93 my $switch = T($category, $traceLevel);
506 : parrello 1.36
507 : parrello 1.93 or
508 : parrello 1.44
509 : parrello 1.93 my $switch = T($traceLevel);
510 : parrello 1.44
511 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
512 :     is active, else FALSE. If no category is specified, the caller's package name is used.
513 : parrello 1.44
514 : parrello 1.93 =over 4
515 : parrello 1.44
516 : parrello 1.93 =item category
517 : parrello 1.44
518 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
519 :     used.
520 : parrello 1.31
521 : parrello 1.93 =item traceLevel
522 : parrello 1.31
523 : parrello 1.93 Relevant tracing level.
524 : parrello 1.31
525 : parrello 1.93 =item RETURN
526 : parrello 1.31
527 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
528 : parrello 1.31
529 : parrello 1.93 =back
530 : parrello 1.36
531 : parrello 1.93 =cut
532 :    
533 :     sub T {
534 :     # Declare the return variable.
535 :     my $retVal = 0;
536 :     # Only proceed if tracing is turned on.
537 :     if ($Destination ne "NONE") {
538 :     # Get the parameters.
539 :     my ($category, $traceLevel) = @_;
540 :     if (!defined $traceLevel) {
541 :     # Here we have no category, so we need to get the calling package.
542 :     # The calling package is normally the first parameter. If it is
543 :     # omitted, the first parameter will be the tracelevel. So, the
544 :     # first thing we do is shift the so-called category into the
545 :     # $traceLevel variable where it belongs.
546 :     $traceLevel = $category;
547 :     my ($package, $fileName, $line) = caller;
548 :     # If there is no calling package, we default to "main".
549 :     if (!$package) {
550 :     $category = "main";
551 :     } else {
552 :     my @cats = split /::/, $package;
553 :     $category = $cats[$#cats];
554 :     }
555 :     }
556 : parrello 1.97 # Save the category name and level.
557 : parrello 1.93 $LastCategory = $category;
558 : parrello 1.97 $LastLevel = $traceLevel;
559 : parrello 1.93 # Convert it to lower case before we hash it.
560 :     $category = lc $category;
561 : parrello 1.100 # Validate the trace level.
562 : parrello 1.93 if (ref $traceLevel) {
563 :     Confess("Bad trace level.");
564 :     } elsif (ref $TraceLevel) {
565 :     Confess("Bad trace config.");
566 :     }
567 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
568 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
569 : parrello 1.93 }
570 :     # Return the computed result.
571 :     return $retVal;
572 :     }
573 :    
574 :     =head3 QTrace
575 :    
576 :     my $data = QTrace($format);
577 :    
578 :     Return the queued trace data in the specified format.
579 :    
580 :     =over 4
581 :    
582 :     =item format
583 :    
584 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
585 :    
586 :     =back
587 :    
588 :     =cut
589 :    
590 :     sub QTrace {
591 :     # Get the parameter.
592 :     my ($format) = @_;
593 :     # Create the return variable.
594 :     my $retVal = "";
595 :     # Only proceed if there is an actual queue.
596 :     if (@Queue) {
597 :     # Process according to the format.
598 :     if ($format =~ m/^HTML$/i) {
599 :     # Convert the queue into an HTML list.
600 :     $retVal = "<ul>\n";
601 :     for my $line (@Queue) {
602 :     my $escapedLine = CGI::escapeHTML($line);
603 :     $retVal .= "<li>$escapedLine</li>\n";
604 :     }
605 :     $retVal .= "</ul>\n";
606 :     } elsif ($format =~ m/^TEXT$/i) {
607 :     # Convert the queue into a list of text lines.
608 :     $retVal = join("\n", @Queue) . "\n";
609 :     }
610 :     # Clear the queue.
611 :     @Queue = ();
612 :     }
613 :     # Return the formatted list.
614 :     return $retVal;
615 :     }
616 :    
617 :     =head3 Confess
618 :    
619 :     Confess($message);
620 :    
621 :     Trace the call stack and abort the program with the specified message. When used with
622 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
623 :     So, for example
624 :    
625 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
626 :    
627 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
628 :    
629 :     =over 4
630 :    
631 :     =item message
632 :    
633 :     Message to include in the trace.
634 :    
635 :     =back
636 :    
637 :     =cut
638 :    
639 :     sub Confess {
640 :     # Get the parameters.
641 :     my ($message) = @_;
642 : parrello 1.97 # Set up the category and level.
643 :     $LastCategory = "(confess)";
644 :     $LastLevel = 0;
645 : parrello 1.93 if (! defined($FIG_Config::no_tool_hdr)) {
646 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
647 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
648 :     # Only proceed if the tool header file is actually present.
649 :     if (-f $toolHeaderFile) {
650 : parrello 1.97 my $fh;
651 :     if (open $fh, "<$toolHeaderFile") {
652 :     my @lines = <$fh>;
653 :     Trace("Tool header has " . scalar(@lines) . " lines.");
654 :     }
655 : parrello 1.93 }
656 :     }
657 :     # Trace the call stack.
658 :     Cluck($message);
659 :     # Abort the program.
660 :     croak(">>> $message");
661 :     }
662 :    
663 : parrello 1.99 =head3 Warn
664 :    
665 :     Warn($message);
666 :    
667 :     This method traces an important message. If an RSS feed is configured
668 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
669 :     then the message will be echoed to the feed. In general, a tracing
670 :     destination of C<WARN> indicates that the caller is running as a web
671 :     service in a production environment; however, this is not a requirement.
672 :    
673 :     The L</Cluck> method calls this one for its final message. Since
674 :     L</Confess> calls L</Cluck>, this means that any error which is caught
675 :     and confessed will put something in the feed. This insures that someone
676 :     will be alerted relatively quickly when a failure occurs.
677 :    
678 :     =over 4
679 :    
680 :     =item message
681 :    
682 :     Message to be traced.
683 :    
684 :     =back
685 :    
686 :     =cut
687 :    
688 :     sub Warn {
689 :     # Get the parameters.
690 :     my ($message) = @_;
691 :     # Trace the message.
692 :     Trace($message);
693 :     # An error here would be disastrous. Note, however, that we aren't too worried
694 :     # about losing events. The error log is always available for the occasions where
695 :     # we mess up.
696 :     eval {
697 :     # Do we need to put this in the RSS feed?
698 :     if ($FIG_Config::error_feed && $Destination eq 'WARN') {
699 :     # Yes. We now need to compute the date, the link, and the title.
700 :     # First, the date, in a very specific format.
701 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
702 :     (tz_local_offset() / 30);
703 :     # Environment data goes in here.
704 :     my $environment;
705 : parrello 1.101 # HTML-escape the message and remove excess space.
706 :     my $title = CGI::escapeHTML($message);
707 :     $title =~ s/\s+/ /gs;
708 :     # Compute the title from the message. If it's too long, we have to
709 :     # split it up.
710 :     if (length $title > 60) {
711 :     $title = substr($title, 0, 50) . "...";
712 :     }
713 :     # We'll put the link in here.
714 :     my $link;
715 : parrello 1.99 # If we have a CGI object, then this is a web error. Otherwise, it's
716 :     # command-line.
717 :     if (defined $SavedCGI) {
718 : parrello 1.101 # We're in a web service. The environment is the user's IP, and the link
719 : parrello 1.99 # is the URL that got us here.
720 :     my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
721 : parrello 1.101 $environment = "Event Reported at IP address $key.";
722 : parrello 1.99 $link = $SavedCGI->url(-full => 1, -query => 1);
723 : parrello 1.100 # We need the user agent string and (if available) the referrer.
724 : parrello 1.101 $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
725 : parrello 1.100 if ($ENV{HTTP_REFERER}) {
726 :     $environment .= " referred from $ENV{HTTP_REFERER}"
727 :     }
728 :     # Close off the sentence.
729 :     $environment .= ". ";
730 : parrello 1.99 } else {
731 :     # No CGI object, so we're a command-line tool. Use the tracing
732 : parrello 1.101 # key and the PID as the user identifier, and add the command.
733 : parrello 1.99 my $key = EmergencyKey();
734 : parrello 1.101 $environment = "Event Reported by $key Process $$. Command $ENV{_}.";
735 : parrello 1.99 # Set the link to the development NMPDR. There is really no good
736 :     # choice here.
737 :     $link = "http://$FIG_Config::dev_server";
738 :     }
739 :     # Build a GUID. We use the current time, the title, and the process ID,
740 :     # then digest the result.
741 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
742 :     # Finally, the description. This is a stack trace plus various environmental stuff.
743 : parrello 1.101 # We have a goofy thing here in that we need to HTML-escape some sections of the description
744 :     # twice. They will be unescaped once when processed by the RSS reader. First, the stack
745 :     # trace.
746 :     my $stackTrace = "";
747 : parrello 1.99 my @trace = LongMess();
748 : parrello 1.101 # Only proceed if we got something back.
749 :     if (scalar(@trace) > 0) {
750 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
751 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
752 :     }
753 :     my $basicDescription = CGI::escapeHTML($message) . "<br /><br />" .
754 :     CGI::escapeHTML($environment) . $stackTrace;
755 : parrello 1.99 # Okay, we have all the pieces. Create a hash of the new event.
756 :     my $newItem = { title => $title,
757 : parrello 1.101 description => CGI::escapeHTML($basicDescription),
758 : parrello 1.99 link => $link,
759 :     category => $LastCategory,
760 :     pubDate => $date,
761 :     guid => $guid,
762 :     };
763 :     # We need XML capability for this.
764 :     require XML::Simple;
765 :     # The RSS document goes in here.
766 :     my $rss;
767 :     # Get the name of the RSS file. It's in the FIG temporary directory.
768 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
769 :     # Does it exist?
770 :     if (-s $fileName) {
771 :     # Slurp it in.
772 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
773 :     } else {
774 :     my $size = -s $fileName;
775 :     # Create an empty channel.
776 :     $rss = {
777 :     channel => {
778 :     title => 'NMPDR Warning Feed',
779 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
780 :     description => "Important messages regarding the status of the NMPDR.",
781 :     generator => "NMPDR Trace Facility",
782 :     docs => "http://blogs.law.harvard.edu/tech/rss",
783 :     item => []
784 :     },
785 :     };
786 :     }
787 :     # Get the channel object.
788 :     my $channel = $rss->{channel};
789 :     # Update the last-build date.
790 :     $channel->{lastBuildDate} = $date;
791 :     # Get the item array.
792 :     my $items = $channel->{item};
793 :     # Insure it has only 100 entries.
794 :     while (scalar @{$items} > 100) {
795 :     pop @{$items};
796 :     }
797 :     # Add our new item at the front.
798 :     unshift @{$items}, $newItem;
799 :     # Replace the file.
800 : parrello 1.101 my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => 'rss version="2.0"', XmlDecl => '<?xml version="1.0" encoding="utf-8"?>',
801 : parrello 1.99 NoEscape => 1);
802 :     # We don't use Open here because we can't afford an error.
803 :     if (open XMLOUT, ">$fileName") {
804 :     print XMLOUT $xml;
805 :     close XMLOUT;
806 :     }
807 :     }
808 :     };
809 :     # There's no "if ($@)" here, because putting an error message in the log
810 :     # saying that we missed putting an error message in the feed of messages
811 :     # in the log is not going to help anybody.
812 :     }
813 :    
814 : parrello 1.93 =head3 Assert
815 :    
816 :     Assert($condition1, $condition2, ... $conditionN);
817 :    
818 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
819 :     the OR operator and the L</Confess> method as a debugging assert.
820 :     So, for example
821 :    
822 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
823 :    
824 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
825 :    
826 :     =cut
827 :     sub Assert {
828 :     my $retVal = 1;
829 :     LOOP: for my $condition (@_) {
830 :     if (! $condition) {
831 :     $retVal = 0;
832 :     last LOOP;
833 :     }
834 :     }
835 :     return $retVal;
836 :     }
837 :    
838 :     =head3 Cluck
839 :    
840 :     Cluck($message);
841 :    
842 :     Trace the call stack. Note that for best results, you should qualify the call with a
843 :     trace condition. For example,
844 :    
845 :     Cluck("Starting record parse.") if T(3);
846 :    
847 :     will only trace the stack if the trace level for the package is 3 or more.
848 :    
849 :     =over 4
850 :    
851 :     =item message
852 :    
853 :     Message to include in the trace.
854 :    
855 :     =back
856 :    
857 :     =cut
858 :    
859 :     sub Cluck {
860 :     # Get the parameters.
861 :     my ($message) = @_;
862 :     # Trace what's happening.
863 :     Trace("Stack trace for event: $message");
864 : parrello 1.99 # Get the stack trace.
865 :     my @trace = LongMess();
866 :     # Convert the trace to a series of messages.
867 :     for my $line (@trace) {
868 :     # Replace the tab at the beginning with spaces.
869 :     $line =~ s/^\t/ /;
870 :     # Trace the line.
871 :     Trace($line);
872 :     }
873 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
874 :     Warn($message);
875 :     }
876 :    
877 :     =head3 LongMess
878 :    
879 :     my @lines = Tracer::LongMess();
880 :    
881 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
882 :     of message strings.
883 :    
884 :     =cut
885 :    
886 :     sub LongMess {
887 :     # Declare the return variable.
888 :     my @retVal = ();
889 :     my $confession = longmess("");
890 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
891 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
892 :     # Here we have a line worth keeping. Push it onto the result list.
893 :     push @retVal, $line;
894 : parrello 1.97 }
895 : parrello 1.93 }
896 : parrello 1.99 # Return the result.
897 :     return @retVal;
898 : parrello 1.93 }
899 :    
900 : parrello 1.97 =head3 ScriptSetup (deprecated)
901 : parrello 1.93
902 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
903 :    
904 :     Perform standard tracing and debugging setup for scripts. The value returned is
905 :     the CGI object followed by a pre-built variable hash. At the end of the script,
906 :     the client should call L</ScriptFinish> to output the web page.
907 :    
908 :     This method calls L</ETracing> to configure tracing, which allows the tracing
909 :     to be configured via the emergency tracing form on the debugging control panel.
910 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
911 :     method, which includes every program that uses this method or L</StandardSetup>.
912 : parrello 1.36
913 : parrello 1.93 =over 4
914 : parrello 1.31
915 : parrello 1.93 =item noTrace (optional)
916 : parrello 1.31
917 : parrello 1.93 If specified, tracing will be suppressed. This is useful if the script wants to set up
918 :     tracing manually.
919 : parrello 1.31
920 :     =item RETURN
921 :    
922 : parrello 1.93 Returns a two-element list consisting of a CGI query object and a variable hash for
923 :     the output page.
924 : parrello 1.31
925 :     =back
926 :    
927 :     =cut
928 :    
929 : parrello 1.93 sub ScriptSetup {
930 : parrello 1.31 # Get the parameters.
931 : parrello 1.93 my ($noTrace) = @_;
932 :     # Get the CGI query object.
933 :     my $cgi = CGI->new();
934 :     # Set up tracing if it's not suppressed.
935 :     ETracing($cgi) unless $noTrace;
936 :     # Create the variable hash.
937 :     my $varHash = { results => '' };
938 :     # Return the query object and variable hash.
939 :     return ($cgi, $varHash);
940 :     }
941 :    
942 :     =head3 ETracing
943 :    
944 :     ETracing($parameter);
945 :    
946 :     Set up emergency tracing. Emergency tracing is tracing that is turned
947 :     on automatically for any program that calls this method. The emergency
948 :     tracing parameters are stored in a a file identified by a tracing key.
949 :     If this method is called with a CGI object, then the tracing key is
950 :     taken from a cookie. If it is called with no parameters, then the tracing
951 :     key is taken from an environment variable. If it is called with a string,
952 :     the tracing key is that string.
953 :    
954 :     =over 4
955 :    
956 :     =item parameter
957 :    
958 :     A parameter from which the tracing key is computed. If it is a scalar,
959 :     that scalar is used as the tracing key. If it is a CGI object, the
960 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
961 :     tracing key is taken from the C<TRACING> environment variable. If it
962 :     is a CGI object and emergency tracing is not on, the C<Trace> and
963 :     C<TF> parameters will be used to determine the type of tracing.
964 :    
965 :     =back
966 :    
967 :     =cut
968 :    
969 :     sub ETracing {
970 :     # Get the parameter.
971 :     my ($parameter) = @_;
972 :     # Check for CGI mode.
973 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
974 :     $SavedCGI = $parameter;
975 :     } else {
976 :     $SavedCGI = undef;
977 :     }
978 : parrello 1.93 # Default to no tracing except errors.
979 :     my ($tracing, $dest) = ("0", "WARN");
980 :     # Check for emergency tracing.
981 :     my $tkey = EmergencyKey($parameter);
982 :     my $emergencyFile = EmergencyFileName($tkey);
983 :     if (-e $emergencyFile) {
984 :     # We have the file. Read in the data.
985 :     my @tracing = GetFile($emergencyFile);
986 :     # Pull off the time limit.
987 :     my $expire = shift @tracing;
988 :     # Convert it to seconds.
989 :     $expire *= 3600;
990 :     # Check the file data.
991 :     my $stat = stat($emergencyFile);
992 :     my ($now) = gettimeofday;
993 :     if ($now - $stat->mtime > $expire) {
994 :     # Delete the expired file.
995 :     unlink $emergencyFile;
996 : parrello 1.44 } else {
997 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
998 :     # the trace level;
999 :     $dest = shift @tracing;
1000 :     my $level = shift @tracing;
1001 :     # Convert the destination to a real tracing destination.
1002 :     # temp directory.
1003 :     $dest = EmergencyTracingDest($tkey, $dest);
1004 :     # Insure Tracer is specified.
1005 :     my %moduleHash = map { $_ => 1 } @tracing;
1006 :     $moduleHash{Tracer} = 1;
1007 :     # Set the trace parameter.
1008 :     $tracing = join(" ", $level, sort keys %moduleHash);
1009 : parrello 1.44 }
1010 : parrello 1.99 } elsif (defined $SavedCGI) {
1011 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1012 :     # for tracing from the form parameters.
1013 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1014 : parrello 1.93 # Here the user has requested tracing via a form.
1015 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1016 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1017 : parrello 1.36 }
1018 :     }
1019 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1020 :     TSetup($tracing, $dest);
1021 : parrello 1.94 # Check to see if we're a web script.
1022 : parrello 1.99 if (defined $SavedCGI) {
1023 : parrello 1.94 # Yes we are. Trace the form and environment data.
1024 : parrello 1.99 TraceParms($SavedCGI);
1025 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1026 :     # emitted by the script in its raw form.
1027 :     if (T(Raw => 3)) {
1028 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1029 :     }
1030 : parrello 1.83 }
1031 : parrello 1.31 }
1032 :    
1033 : parrello 1.93 =head3 EmergencyFileName
1034 :    
1035 :     my $fileName = Tracer::EmergencyFileName($tkey);
1036 :    
1037 :     Return the emergency tracing file name. This is the file that specifies
1038 :     the tracing information.
1039 :    
1040 :     =over 4
1041 :    
1042 :     =item tkey
1043 :    
1044 :     Tracing key for the current program.
1045 : parrello 1.11
1046 : parrello 1.93 =item RETURN
1047 : parrello 1.11
1048 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1049 : parrello 1.11
1050 : parrello 1.93 =back
1051 : parrello 1.11
1052 :     =cut
1053 :    
1054 : parrello 1.93 sub EmergencyFileName {
1055 :     # Get the parameters.
1056 :     my ($tkey) = @_;
1057 :     # Compute the emergency tracing file name.
1058 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1059 : olson 1.1 }
1060 :    
1061 : parrello 1.93 =head3 EmergencyFileTarget
1062 : parrello 1.10
1063 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1064 : parrello 1.10
1065 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1066 :     the tracing output for file-based tracing.
1067 : parrello 1.10
1068 : parrello 1.93 =over 4
1069 : parrello 1.10
1070 : parrello 1.93 =item tkey
1071 : parrello 1.10
1072 : parrello 1.93 Tracing key for the current program.
1073 : parrello 1.10
1074 : parrello 1.93 =item RETURN
1075 : parrello 1.10
1076 : parrello 1.93 Returns the name of the file to contain the trace output.
1077 : parrello 1.10
1078 : parrello 1.93 =back
1079 : parrello 1.10
1080 : parrello 1.93 =cut
1081 : parrello 1.10
1082 : parrello 1.93 sub EmergencyFileTarget {
1083 :     # Get the parameters.
1084 :     my ($tkey) = @_;
1085 :     # Compute the emergency tracing file name.
1086 :     return "$FIG_Config::temp/trace$tkey.log";
1087 :     }
1088 : parrello 1.10
1089 : parrello 1.93 =head3 EmergencyTracingDest
1090 : parrello 1.10
1091 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1092 : parrello 1.10
1093 : parrello 1.93 This method converts an emergency tracing destination to a real
1094 :     tracing destination. The main difference is that if the
1095 :     destination is C<FILE> or C<APPEND>, we convert it to file
1096 :     output. If the destination is C<DUAL>, we convert it to file
1097 :     and standard output.
1098 : parrello 1.10
1099 :     =over 4
1100 :    
1101 : parrello 1.93 =item tkey
1102 : parrello 1.10
1103 : parrello 1.93 Tracing key for this environment.
1104 : parrello 1.10
1105 : parrello 1.93 =item myDest
1106 : parrello 1.10
1107 : parrello 1.93 Destination from the emergency tracing file.
1108 : parrello 1.10
1109 :     =item RETURN
1110 :    
1111 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1112 : parrello 1.10
1113 :     =back
1114 :    
1115 :     =cut
1116 :    
1117 : parrello 1.93 sub EmergencyTracingDest {
1118 : parrello 1.12 # Get the parameters.
1119 : parrello 1.93 my ($tkey, $myDest) = @_;
1120 :     # Declare the return variable.
1121 :     my $retVal = $myDest;
1122 :     # Process according to the destination value.
1123 :     if ($myDest eq 'FILE') {
1124 :     $retVal = ">" . EmergencyFileTarget($tkey);
1125 :     } elsif ($myDest eq 'APPEND') {
1126 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1127 :     } elsif ($myDest eq 'DUAL') {
1128 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1129 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1130 :     $retVal = "WARN";
1131 : parrello 1.12 }
1132 : parrello 1.93 # Return the result.
1133 :     return $retVal;
1134 : parrello 1.10 }
1135 :    
1136 : parrello 1.93 =head3 Emergency
1137 :    
1138 :     Emergency($key, $hours, $dest, $level, @modules);
1139 :    
1140 :     Turn on emergency tracing. This method is normally invoked over the web from
1141 :     a debugging console, but it can also be called by the C<trace.pl> script.
1142 :     The caller specifies the duration of the emergency in hours, the desired tracing
1143 :     destination, the trace level, and a list of the trace modules to activate.
1144 :     For the length of the duration, when a program in an environment with the
1145 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1146 :     turned on automatically. See L</TSetup> for more about tracing setup and
1147 :     L</ETracing> for more about emergency tracing.
1148 :    
1149 :     =over 4
1150 : parrello 1.11
1151 : parrello 1.93 =item tkey
1152 : parrello 1.11
1153 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1154 : parrello 1.11
1155 : parrello 1.93 =item hours
1156 : parrello 1.11
1157 : parrello 1.93 Number of hours to keep emergency tracing alive.
1158 : parrello 1.11
1159 : parrello 1.93 =item dest
1160 : parrello 1.11
1161 : parrello 1.93 Tracing destination. If no path information is specified for a file
1162 :     destination, it is put in the FIG temporary directory.
1163 : parrello 1.11
1164 : parrello 1.93 =item level
1165 : parrello 1.11
1166 : parrello 1.93 Tracing level. A higher level means more trace messages.
1167 : parrello 1.11
1168 : parrello 1.93 =item modules
1169 : parrello 1.11
1170 : parrello 1.93 A list of the tracing modules to activate.
1171 : parrello 1.11
1172 :     =back
1173 :    
1174 :     =cut
1175 : parrello 1.93
1176 :     sub Emergency {
1177 : parrello 1.11 # Get the parameters.
1178 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1179 :     # Create the emergency file.
1180 :     my $specFile = EmergencyFileName($tkey);
1181 :     my $outHandle = Open(undef, ">$specFile");
1182 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1183 : parrello 1.11 }
1184 :    
1185 : parrello 1.93 =head3 EmergencyKey
1186 :    
1187 :     my $tkey = EmergencyKey($parameter);
1188 :    
1189 :     Return the Key to be used for emergency tracing. This could be an IP address,
1190 :     a session ID, or a user name, depending on the environment.
1191 : parrello 1.11
1192 : parrello 1.93 =over 4
1193 : parrello 1.11
1194 : parrello 1.93 =item parameter
1195 : parrello 1.11
1196 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1197 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1198 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1199 :     taken from the C<TRACING> environment variable.
1200 : parrello 1.29
1201 : parrello 1.93 =item RETURN
1202 : parrello 1.11
1203 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1204 : parrello 1.11
1205 : parrello 1.93 =back
1206 : parrello 1.11
1207 : parrello 1.93 =cut
1208 : parrello 1.29
1209 : parrello 1.93 sub EmergencyKey {
1210 :     # Get the parameters.
1211 :     my ($parameter) = @_;
1212 :     # Declare the return variable.
1213 :     my $retVal;
1214 :     # Determine the parameter type.
1215 :     if (! defined $parameter) {
1216 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1217 :     # get the effective login ID.
1218 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1219 : parrello 1.93 } else {
1220 :     my $ptype = ref $parameter;
1221 :     if ($ptype eq 'CGI') {
1222 :     # Here we were invoked from a web page. Look for a cookie.
1223 :     $retVal = $parameter->cookie('IP');
1224 :     } elsif (! $ptype) {
1225 :     # Here the key was passed in.
1226 :     $retVal = $parameter;
1227 :     }
1228 :     }
1229 :     # If no luck finding a key, use the PID.
1230 :     if (! defined $retVal) {
1231 :     $retVal = $$;
1232 :     }
1233 :     # Return the result.
1234 :     return $retVal;
1235 :     }
1236 : parrello 1.11
1237 :    
1238 : parrello 1.93 =head3 TraceParms
1239 : parrello 1.11
1240 : parrello 1.93 Tracer::TraceParms($cgi);
1241 : parrello 1.11
1242 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1243 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1244 : parrello 1.11
1245 : parrello 1.93 =over 4
1246 : parrello 1.11
1247 : parrello 1.93 =item cgi
1248 : parrello 1.31
1249 : parrello 1.93 CGI query object containing the parameters to trace.
1250 : parrello 1.31
1251 : parrello 1.11 =back
1252 :    
1253 :     =cut
1254 : parrello 1.93
1255 :     sub TraceParms {
1256 : parrello 1.11 # Get the parameters.
1257 : parrello 1.93 my ($cgi) = @_;
1258 : parrello 1.94 if (T(CGI => 2)) {
1259 :     # Here we trace the GET-style URL for the script.
1260 : parrello 1.97 Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1261 : parrello 1.94 }
1262 : parrello 1.93 if (T(CGI => 3)) {
1263 :     # Here we want to trace the parameter data.
1264 :     my @names = $cgi->param;
1265 :     for my $parmName (sort @names) {
1266 :     # Note we skip the Trace parameters, which are for our use only.
1267 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1268 :     my @values = $cgi->param($parmName);
1269 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1270 : parrello 1.93 }
1271 :     }
1272 :     # Display the request method.
1273 :     my $method = $cgi->request_method();
1274 :     Trace("Method: $method");
1275 :     }
1276 :     if (T(CGI => 4)) {
1277 :     # Here we want the environment data too.
1278 :     for my $envName (sort keys %ENV) {
1279 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1280 : parrello 1.12 }
1281 :     }
1282 : parrello 1.11 }
1283 :    
1284 : parrello 1.94 =head3 TraceImages
1285 :    
1286 :     Tracer::TraceImages($htmlString);
1287 :    
1288 :     Trace information about all of an html document's images. The tracing
1289 :     will be for type "IMG" at level 3. The image's source string
1290 :     will be displayed. This is generally either the URL of the image or
1291 :     raw data for the image itself. If the source is too long, only the first 300
1292 :     characters will be shown at trace level 3. The entire source will be shown,
1293 :     however, at trace level 4. This method is not very smart, and might catch
1294 :     Javascript code, but it is still useful when debugging the arcane
1295 :     behavior of images in multiple browser environments.
1296 :    
1297 :     =over 4
1298 :    
1299 :     =item htmlString
1300 :    
1301 :     HTML text for an outgoing web page.
1302 :    
1303 :     =back
1304 :    
1305 :     =cut
1306 :    
1307 :     sub TraceImages {
1308 :     # Only proceed if we're at the proper trace level.
1309 :     if (T(IMG => 3)) {
1310 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1311 :     # into a variable called "$htmlString". This is because we expect html strings to be
1312 :     # long, and don't want to copy them any more than we have to.
1313 :     Trace(length($_[0]) . " characters in web page.");
1314 :     # Loop through the HTML, culling image tags.
1315 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1316 :     # Extract the source string and determine whether or not it's too long.
1317 :     my $srcString = $1;
1318 :     my $pos = pos($_[0]) - length($srcString);
1319 :     my $excess = length($srcString) - 300;
1320 :     # We'll put the display string in here.
1321 :     my $srcDisplay = $srcString;
1322 :     # If it's a data string, split it at the comma.
1323 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1324 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1325 :     # a long string, however, we only show the first 300 characters.
1326 :     if ($excess > 0 && ! T(IMG => 4)) {
1327 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1328 :     }
1329 :     # Output the trace message.
1330 :     Trace("Image tag at position $pos:\n$srcDisplay");
1331 :     }
1332 :     }
1333 :     }
1334 :    
1335 :    
1336 : parrello 1.97 =head3 ScriptFinish (deprecated)
1337 : parrello 1.93
1338 :     ScriptFinish($webData, $varHash);
1339 :    
1340 :     Output a web page at the end of a script. Either the string to be output or the
1341 :     name of a template file can be specified. If the second parameter is omitted,
1342 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1343 :     name of a template file. The template should have the variable C<DebugData>
1344 :     specified in any form that invokes a standard script. If debugging mode is turned
1345 :     on, a form field will be put in that allows the user to enter tracing data.
1346 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1347 :     the output, formatted as a list.
1348 :    
1349 :     A typical standard script would loook like the following.
1350 :    
1351 :     BEGIN {
1352 :     # Print the HTML header.
1353 :     print "CONTENT-TYPE: text/html\n\n";
1354 :     }
1355 :     use Tracer;
1356 :     use CGI;
1357 :     use FIG;
1358 :     # ... more uses ...
1359 : parrello 1.6
1360 : parrello 1.93 my ($cgi, $varHash) = ScriptSetup();
1361 :     eval {
1362 :     # ... get data from $cgi, put it in $varHash ...
1363 :     };
1364 :     if ($@) {
1365 :     Trace("Script Error: $@") if T(0);
1366 :     }
1367 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1368 : parrello 1.6
1369 : parrello 1.93 The idea here is that even if the script fails, you'll see trace messages and
1370 :     useful output.
1371 : parrello 1.6
1372 :     =over 4
1373 :    
1374 : parrello 1.93 =item webData
1375 :    
1376 :     A string containing either the full web page to be written to the output or the
1377 :     name of a template file from which the page is to be constructed. If the name
1378 :     of a template file is specified, then the second parameter must be present;
1379 :     otherwise, it must be absent.
1380 :    
1381 :     =item varHash (optional)
1382 : parrello 1.6
1383 : parrello 1.93 If specified, then a reference to a hash mapping variable names for a template
1384 :     to their values. The template file will be read into memory, and variable markers
1385 :     will be replaced by data in this hash reference.
1386 : parrello 1.6
1387 :     =back
1388 :    
1389 :     =cut
1390 :    
1391 : parrello 1.93 sub ScriptFinish {
1392 :     # Get the parameters.
1393 :     my ($webData, $varHash) = @_;
1394 :     # Check for a template file situation.
1395 :     my $outputString;
1396 :     if (defined $varHash) {
1397 :     # Here we have a template file. We need to determine the template type.
1398 :     my $template;
1399 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1400 :     $template = "$FIG_Config::template_url/$webData";
1401 :     } else {
1402 :     $template = "<<$webData";
1403 :     }
1404 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
1405 :     } else {
1406 :     # Here the user gave us a raw string.
1407 :     $outputString = $webData;
1408 :     }
1409 :     # Check for trace messages.
1410 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
1411 :     # We have trace messages, so we want to put them at the end of the body. This
1412 :     # is either at the end of the whole string or at the beginning of the BODY
1413 :     # end-tag.
1414 :     my $pos = length $outputString;
1415 :     if ($outputString =~ m#</body>#gi) {
1416 :     $pos = (pos $outputString) - 7;
1417 :     }
1418 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
1419 :     # destination.
1420 :     my $traceHtml;
1421 :     if ($Destination eq "QUEUE") {
1422 :     $traceHtml = QTrace('Html');
1423 :     } elsif ($Destination =~ /^>>(.+)$/) {
1424 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
1425 :     # can copy the file name into the clipboard easily.
1426 :     my $actualDest = $1;
1427 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1428 :     } else {
1429 :     # Here we have one of the special destinations.
1430 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1431 :     }
1432 :     substr $outputString, $pos, 0, $traceHtml;
1433 :     }
1434 :     # Write the output string.
1435 :     print $outputString;
1436 : parrello 1.6 }
1437 :    
1438 : parrello 1.93 =head2 Command-Line Utility Methods
1439 : olson 1.1
1440 : parrello 1.93 =head3 SendSMS
1441 : olson 1.1
1442 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1443 : olson 1.1
1444 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1445 :     user name, password, and API ID for the relevant account in the hash reference variable
1446 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1447 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1448 :     is C<2561022>, then the FIG_Config file must contain
1449 : olson 1.1
1450 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1451 :     password => 'silly',
1452 :     api_id => '2561022' };
1453 : olson 1.1
1454 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1455 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1456 :     when you call this method.
1457 : olson 1.1
1458 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1459 : parrello 1.74
1460 : parrello 1.93 =over 4
1461 : parrello 1.74
1462 : parrello 1.93 =item phoneNumber
1463 : parrello 1.74
1464 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1465 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1466 : parrello 1.74
1467 : parrello 1.93 =item msg
1468 : parrello 1.74
1469 : parrello 1.93 Message to send to the specified phone.
1470 : parrello 1.74
1471 :     =item RETURN
1472 :    
1473 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1474 : parrello 1.74
1475 : parrello 1.78 =back
1476 :    
1477 : parrello 1.74 =cut
1478 :    
1479 : parrello 1.93 sub SendSMS {
1480 : parrello 1.74 # Get the parameters.
1481 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1482 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1483 : parrello 1.74 my $retVal;
1484 : parrello 1.93 # Only proceed if we have phone support.
1485 :     if (! defined $FIG_Config::phone) {
1486 :     Trace("Phone support not present in FIG_Config.") if T(1);
1487 :     } else {
1488 :     # Get the phone data.
1489 :     my $parms = $FIG_Config::phone;
1490 :     # Get the Clickatell URL.
1491 :     my $url = "http://api.clickatell.com/http/";
1492 :     # Create the user agent.
1493 :     my $ua = LWP::UserAgent->new;
1494 :     # Request a Clickatell session.
1495 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1496 :     password => $parms->{password},
1497 :     api_id => $parms->{api_id},
1498 :     to => $phoneNumber,
1499 :     text => $msg});
1500 :     # Check for an error.
1501 :     if (! $resp->is_success) {
1502 :     Trace("Alert failed.") if T(1);
1503 :     } else {
1504 :     # Get the message ID.
1505 :     my $rstring = $resp->content;
1506 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1507 :     $retVal = $1;
1508 :     } else {
1509 :     Trace("Phone attempt failed with $rstring") if T(1);
1510 :     }
1511 :     }
1512 : parrello 1.74 }
1513 :     # Return the result.
1514 :     return $retVal;
1515 :     }
1516 :    
1517 : parrello 1.93 =head3 StandardSetup
1518 : olson 1.1
1519 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1520 : olson 1.1
1521 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1522 :     values are a hash of the command-line options and a list of the positional
1523 :     parameters. Tracing is automatically set up and the command-line options are
1524 :     validated.
1525 : olson 1.1
1526 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1527 :     be more easily understood, however, once they are examined individually.
1528 : olson 1.1
1529 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1530 :     special-purpose tracing categories. Most tracing categories are PERL package
1531 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1532 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1533 : olson 1.1
1534 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1535 : olson 1.1
1536 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1537 :     the output. There are two special tracing categories that are automatically
1538 :     handled by this method. In other words, if you used L</TSetup> you would need
1539 :     to include these categories manually, but if you use this method they are turned
1540 :     on automatically.
1541 : parrello 1.5
1542 :     =over 4
1543 :    
1544 : parrello 1.93 =item SQL
1545 : parrello 1.5
1546 : parrello 1.93 Traces SQL commands and activity.
1547 : parrello 1.5
1548 : parrello 1.93 =item Tracer
1549 : parrello 1.5
1550 : parrello 1.93 Traces error messages and call stacks.
1551 : parrello 1.5
1552 :     =back
1553 :    
1554 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1555 :     The trace level is specified using the C<-trace> command-line option. For example,
1556 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1557 :     all tracing at level 3.
1558 : parrello 1.5
1559 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1560 : parrello 1.5
1561 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1562 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1563 :     process ID. You can also specify the C<user> parameter to put a user ID
1564 :     instead of a process ID in the trace file name. So, for example
1565 : olson 1.1
1566 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1567 :     For a genome-by-genome update, use 3.
1568 : olson 1.1
1569 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1570 : olson 1.1
1571 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1572 : olson 1.1
1573 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1574 :     options, their default values, and an explanation of what they mean. Command-line
1575 :     options may be in the form of switches or keywords. In the case of a switch, the
1576 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1577 :     of a keyword, the value is separated from the option name by an equal sign. You
1578 :     can see this last in the command-line example above.
1579 : olson 1.1
1580 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1581 :     prior to calling this method.
1582 : olson 1.1
1583 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1584 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1585 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1586 :     the following code.
1587 : olson 1.1
1588 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1589 :     { safe => [0, "use database transactions"],
1590 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1591 :     start => [' ', "start with this genome"],
1592 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1593 :     "<command> <transactionDirectory> <IDfile>",
1594 :     @ARGV);
1595 : olson 1.1
1596 :    
1597 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1598 :     stores the actual options in a hash that is returned as C<$options>. The
1599 :     positional parameters are returned in C<@parameters>.
1600 : olson 1.1
1601 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1602 : olson 1.1
1603 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1604 : olson 1.1
1605 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1606 :     above command as
1607 : olson 1.1
1608 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1609 : olson 1.1
1610 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1611 :     parameters, and would find themselves in I<@parameters> after executing the
1612 :     above code fragment. The tracing would be set to level 2, and the categories
1613 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1614 :     and C<DocUtils> was included because it came in within the first parameter
1615 :     to this method. The I<$options> hash would be
1616 : olson 1.1
1617 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1618 :     noAlias => 1, start => ' ', tblFiles => 0 }
1619 : olson 1.1
1620 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1621 :     standard tracing setup and command-line parsing. Note that the caller is
1622 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1623 :     are used by this method to control the tracing. If additional tracing features
1624 :     need to be added in the future, they can be processed by this method without
1625 :     upsetting the command-line utilities.
1626 : olson 1.1
1627 : parrello 1.93 If the C<background> option is specified on the command line, then the
1628 :     standard and error outputs will be directed to files in the temporary
1629 :     directory, using the same suffix as the trace file. So, if the command
1630 :     line specified
1631 : olson 1.1
1632 : parrello 1.93 -user=Bruce -background
1633 : olson 1.1
1634 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1635 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1636 :     simplify starting a command in the background.
1637 : olson 1.1
1638 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1639 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1640 :     be used instead of custom tracing. If the user name is not specified,
1641 :     the tracing key is taken from the C<Tracing> environment variable. If there
1642 :     is no value for that variable, the tracing key will be computed from the PID.
1643 : olson 1.1
1644 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1645 :     names will be traced at level 0 and the program will exit without processing.
1646 :     This provides a limited help capability. For example, if the user enters
1647 : olson 1.1
1648 : parrello 1.93 TransactFeatures -help
1649 : olson 1.1
1650 : parrello 1.93 he would see the following output.
1651 : olson 1.1
1652 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1653 :     -trace tracing level (default E)
1654 :     -sql trace SQL commands
1655 :     -safe use database transactions
1656 :     -noAlias do not expect aliases in CHANGE transactions
1657 :     -start start with this genome
1658 :     -tblFiles output TBL files containing the corrected IDs
1659 : olson 1.1
1660 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1661 :     for C<trace> in the incoming options hash. The default value can be overridden,
1662 :     or the tracing to the standard output can be turned off by suffixing a minus
1663 :     sign to the trace level. So, for example,
1664 : olson 1.1
1665 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1666 :     ...
1667 : olson 1.1
1668 : parrello 1.93 would set the default trace level to 0 instead of E, while
1669 : olson 1.1
1670 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1671 :     ...
1672 : olson 1.1
1673 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1674 :     standard output.
1675 : olson 1.1
1676 : parrello 1.93 The parameters to this method are as follows.
1677 : olson 1.1
1678 : parrello 1.93 =over 4
1679 : olson 1.1
1680 : parrello 1.93 =item categories
1681 : parrello 1.2
1682 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1683 :     packages whose internal workings will need to be debugged to get the
1684 :     command working.
1685 : olson 1.1
1686 : parrello 1.93 =item options
1687 : olson 1.1
1688 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1689 :     to their default values and descriptions. The user can override the defaults
1690 :     by specifying the options as command-line switches prefixed by a hyphen.
1691 :     Tracing-related options may be added to this hash. If the C<-h> option is
1692 :     specified on the command line, the option descriptions will be used to
1693 :     explain the options. To turn off tracing to the standard output, add a
1694 :     minus sign to the value for C<trace> (see above).
1695 : olson 1.1
1696 : parrello 1.93 =item parmHelp
1697 : olson 1.1
1698 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1699 :     if the user specifies the C<-h> option.
1700 : olson 1.1
1701 : parrello 1.93 =item argv
1702 : olson 1.1
1703 : parrello 1.93 List of command line parameters, including the option switches, which must
1704 :     precede the positional parameters and be prefixed by a hyphen.
1705 : olson 1.1
1706 :     =item RETURN
1707 :    
1708 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1709 :     maps the command-line option switches to their values. These will either be the
1710 :     default values or overrides specified on the command line. The remaining
1711 :     elements of the list are the position parameters, in order.
1712 : olson 1.1
1713 :     =back
1714 :    
1715 :     =cut
1716 :    
1717 : parrello 1.93 sub StandardSetup {
1718 :     # Get the parameters.
1719 :     my ($categories, $options, $parmHelp, @argv) = @_;
1720 :     # Get the default tracing key.
1721 :     my $tkey = EmergencyKey();
1722 :     # Add the tracing options.
1723 :     if (! exists $options->{trace}) {
1724 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1725 :     }
1726 :     $options->{sql} = [0, "turn on SQL tracing"];
1727 :     $options->{help} = [0, "display command-line options"];
1728 :     $options->{user} = [$tkey, "tracing key"];
1729 :     $options->{background} = [0, "spool standard and error output"];
1730 :     # Create a parsing hash from the options hash. The parsing hash
1731 :     # contains the default values rather than the default value
1732 :     # and the description. While we're at it, we'll memorize the
1733 :     # length of the longest option name.
1734 :     my $longestName = 0;
1735 :     my %parseOptions = ();
1736 :     for my $key (keys %{$options}) {
1737 :     if (length $key > $longestName) {
1738 :     $longestName = length $key;
1739 :     }
1740 :     $parseOptions{$key} = $options->{$key}->[0];
1741 :     }
1742 :     # Parse the command line.
1743 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1744 :     # Get the logfile suffix.
1745 :     my $suffix = $retOptions->{user};
1746 :     # Check for background mode.
1747 :     if ($retOptions->{background}) {
1748 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
1749 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
1750 :     open STDOUT, ">$outFileName";
1751 :     open STDERR, ">$errFileName";
1752 :     # Check for phone support. If we have phone support and a phone number,
1753 :     # we want to turn it on.
1754 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1755 :     $retOptions->{phone} = $ENV{PHONE};
1756 :     }
1757 :     }
1758 :     # Now we want to set up tracing. First, we need to know if the user
1759 :     # wants emergency tracing.
1760 :     if ($retOptions->{trace} eq 'E') {
1761 :     ETracing($retOptions->{user});
1762 :     } else {
1763 :     # Here the tracing is controlled from the command line.
1764 :     my @cats = @{$categories};
1765 :     if ($retOptions->{sql}) {
1766 :     push @cats, "SQL";
1767 :     }
1768 :     # Add the default categories.
1769 :     push @cats, "Tracer";
1770 :     # Next, we create the category string by joining the categories.
1771 :     my $cats = join(" ", @cats);
1772 :     # Check to determine whether or not the caller wants to turn off tracing
1773 :     # to the standard output.
1774 :     my $traceLevel = $retOptions->{trace};
1775 :     my $textOKFlag = 1;
1776 :     if ($traceLevel =~ /^(.)-/) {
1777 :     $traceLevel = $1;
1778 :     $textOKFlag = 0;
1779 :     }
1780 :     # Now we set up the trace mode.
1781 :     my $traceMode;
1782 :     # Verify that we can open a file in the FIG temporary directory.
1783 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1784 :     if (open TESTTRACE, ">$traceFileName") {
1785 :     # Here we can trace to a file.
1786 :     $traceMode = ">$traceFileName";
1787 :     if ($textOKFlag) {
1788 :     # Echo to standard output if the text-OK flag is set.
1789 :     $traceMode = "+$traceMode";
1790 :     }
1791 :     # Close the test file.
1792 :     close TESTTRACE;
1793 :     } else {
1794 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1795 :     warn "Could not open trace file $traceFileName: $!\n";
1796 :     # We trace to the standard output if it's
1797 :     # okay, and the error log otherwise.
1798 : parrello 1.93 if ($textOKFlag) {
1799 :     $traceMode = "TEXT";
1800 : parrello 1.12 } else {
1801 : parrello 1.93 $traceMode = "WARN";
1802 : parrello 1.12 }
1803 :     }
1804 : parrello 1.93 # Now set up the tracing.
1805 :     TSetup("$traceLevel $cats", $traceMode);
1806 :     }
1807 :     # Check for the "help" option. If it is specified, dump the command-line
1808 :     # options and exit the program.
1809 :     if ($retOptions->{help}) {
1810 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1811 :     print "$1 [options] $parmHelp\n";
1812 :     for my $key (sort keys %{$options}) {
1813 :     my $name = Pad($key, $longestName, 0, ' ');
1814 :     my $desc = $options->{$key}->[1];
1815 :     if ($options->{$key}->[0]) {
1816 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1817 :     }
1818 :     print " $name $desc\n";
1819 : parrello 1.36 }
1820 : parrello 1.93 exit(0);
1821 :     }
1822 :     # Trace the options, if applicable.
1823 :     if (T(3)) {
1824 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1825 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1826 : parrello 1.3 }
1827 : parrello 1.93 # Return the parsed parameters.
1828 :     return ($retOptions, @retParameters);
1829 : olson 1.1 }
1830 :    
1831 : parrello 1.93 =head3 ReadOptions
1832 : olson 1.1
1833 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1834 : olson 1.1
1835 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1836 :     format
1837 : olson 1.1
1838 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1839 : olson 1.1
1840 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1841 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1842 :     character is a semi-colon will be ignored. The return hash will map each option name to
1843 :     the corresponding option value.
1844 : olson 1.1
1845 :     =over 4
1846 :    
1847 : parrello 1.93 =item fileName
1848 : olson 1.1
1849 : parrello 1.93 Name of the file containing the option data.
1850 : olson 1.1
1851 :     =item RETURN
1852 :    
1853 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1854 :     value.
1855 : olson 1.1
1856 :     =back
1857 :    
1858 :     =cut
1859 :    
1860 : parrello 1.93 sub ReadOptions {
1861 : parrello 1.12 # Get the parameters.
1862 : parrello 1.93 my ($fileName) = @_;
1863 :     # Open the file.
1864 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1865 :     # Count the number of records read.
1866 :     my ($records, $comments) = 0;
1867 :     # Create the return hash.
1868 :     my %retVal = ();
1869 :     # Loop through the file, accumulating key-value pairs.
1870 :     while (my $line = <CONFIGFILE>) {
1871 :     # Denote we've read a line.
1872 :     $records++;
1873 :     # Determine the line type.
1874 :     if ($line =~ /^\s*[\n\r]/) {
1875 :     # A blank line is a comment.
1876 :     $comments++;
1877 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1878 :     # Here we have an option assignment.
1879 :     retVal{$1} = $2;
1880 :     } elsif ($line =~ /^\s*;/) {
1881 :     # Here we have a text comment.
1882 :     $comments++;
1883 : parrello 1.12 } else {
1884 : parrello 1.93 # Here we have an invalid line.
1885 :     Trace("Invalid option statement in record $records.") if T(0);
1886 : parrello 1.12 }
1887 :     }
1888 : parrello 1.93 # Return the hash created.
1889 :     return %retVal;
1890 : olson 1.1 }
1891 :    
1892 : parrello 1.93 =head3 GetOptions
1893 : parrello 1.9
1894 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1895 : parrello 1.9
1896 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1897 :     as input and uses the data from the second to update the first. If the second does not exist,
1898 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1899 :     exist in the first.
1900 : parrello 1.9
1901 : parrello 1.93 Consider the following example.
1902 : parrello 1.9
1903 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1904 : parrello 1.9
1905 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1906 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1907 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1908 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1909 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1910 : parrello 1.9
1911 : parrello 1.93 {databaseType => 'Oracle'}
1912 : parrello 1.9
1913 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1914 : parrello 1.9
1915 : parrello 1.93 =over 4
1916 : parrello 1.9
1917 : parrello 1.93 =item defaults
1918 : parrello 1.9
1919 : parrello 1.93 Table of default option values.
1920 : parrello 1.9
1921 : parrello 1.93 =item options
1922 : olson 1.1
1923 : parrello 1.93 Table of overrides, if any.
1924 : olson 1.1
1925 :     =item RETURN
1926 :    
1927 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1928 : olson 1.1
1929 :     =back
1930 :    
1931 :     =cut
1932 :    
1933 : parrello 1.93 sub GetOptions {
1934 :     # Get the parameters.
1935 :     my ($defaults, $options) = @_;
1936 :     # Check for overrides.
1937 :     if ($options) {
1938 :     # Loop through the overrides.
1939 :     while (my ($option, $setting) = each %{$options}) {
1940 :     # Insure this override exists.
1941 :     if (!exists $defaults->{$option}) {
1942 :     croak "Unrecognized option $option encountered.";
1943 : parrello 1.12 } else {
1944 : parrello 1.93 # Apply the override.
1945 :     $defaults->{$option} = $setting;
1946 : parrello 1.12 }
1947 :     }
1948 :     }
1949 : parrello 1.93 # Return the merged table.
1950 :     return $defaults;
1951 : olson 1.1 }
1952 :    
1953 : parrello 1.93 =head3 MergeOptions
1954 : olson 1.1
1955 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1956 : olson 1.1
1957 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1958 :     second (default) hash, and if a matching key is not found in the first hash, the default
1959 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1960 :     checking and no return value.
1961 : olson 1.1
1962 :     =over 4
1963 :    
1964 : parrello 1.93 =item table
1965 : olson 1.1
1966 : parrello 1.93 Hash table to be updated with the default values.
1967 : olson 1.1
1968 : parrello 1.93 =item defaults
1969 : olson 1.1
1970 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
1971 : olson 1.1
1972 :     =back
1973 :    
1974 :     =cut
1975 :    
1976 : parrello 1.93 sub MergeOptions {
1977 :     # Get the parameters.
1978 :     my ($table, $defaults) = @_;
1979 :     # Loop through the defaults.
1980 :     while (my ($key, $value) = each %{$defaults}) {
1981 :     if (!exists $table->{$key}) {
1982 :     $table->{$key} = $value;
1983 :     }
1984 : parrello 1.12 }
1985 : olson 1.1 }
1986 :    
1987 : parrello 1.93 =head3 ParseCommand
1988 : olson 1.1
1989 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
1990 : olson 1.1
1991 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
1992 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1993 :     off and merged into a table of default options. The remainder of the command line is
1994 :     returned as a list of positional arguments. For example, consider the following invocation.
1995 : olson 1.1
1996 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
1997 : olson 1.1
1998 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
1999 :     B<errors> and B<logFile>. If @words has the following format
2000 : olson 1.1
2001 : parrello 1.93 -logFile=error.log apple orange rutabaga
2002 : olson 1.1
2003 : parrello 1.93 then at the end of the invocation, C<$options> will be
2004 : olson 1.1
2005 : parrello 1.93 { errors => 0, logFile => 'error.log' }
2006 : olson 1.1
2007 : parrello 1.93 and C<@arguments> will contain
2008 : olson 1.1
2009 : parrello 1.93 apple orange rutabaga
2010 : olson 1.1
2011 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2012 :     support for quote characters. Options can be specified with single or double hyphens.
2013 : parrello 1.54
2014 :     =over 4
2015 :    
2016 : parrello 1.93 =item optionTable
2017 : parrello 1.54
2018 : parrello 1.93 Table of default options.
2019 : parrello 1.54
2020 : parrello 1.93 =item inputList
2021 : parrello 1.54
2022 : parrello 1.93 List of words on the command line.
2023 : parrello 1.54
2024 :     =item RETURN
2025 :    
2026 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2027 : parrello 1.54
2028 :     =back
2029 :    
2030 :     =cut
2031 :    
2032 : parrello 1.93 sub ParseCommand {
2033 : parrello 1.54 # Get the parameters.
2034 : parrello 1.93 my ($optionTable, @inputList) = @_;
2035 :     # Process any options in the input list.
2036 :     my %overrides = ();
2037 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2038 :     # Get the current option.
2039 :     my $arg = shift @inputList;
2040 :     # Pull out the option name.
2041 :     $arg =~ /^--?([^=]*)/g;
2042 :     my $name = $1;
2043 :     # Check for an option value.
2044 :     if ($arg =~ /\G=(.*)$/g) {
2045 :     # Here we have a value for the option.
2046 :     $overrides{$name} = UnEscape($1);
2047 :     } else {
2048 :     # Here there is no value, so we use 1.
2049 :     $overrides{$name} = 1;
2050 :     }
2051 :     }
2052 :     # Merge the options into the defaults.
2053 :     GetOptions($optionTable, \%overrides);
2054 :     # Translate the remaining parameters.
2055 :     my @retVal = ();
2056 :     for my $inputParm (@inputList) {
2057 :     push @retVal, UnEscape($inputParm);
2058 : parrello 1.54 }
2059 : parrello 1.93 # Return the results.
2060 :     return ($optionTable, @retVal);
2061 : parrello 1.54 }
2062 :    
2063 : parrello 1.93
2064 :     =head2 File Utility Methods
2065 :    
2066 : olson 1.1 =head3 GetFile
2067 :    
2068 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2069 : olson 1.1
2070 : parrello 1.35 or
2071 :    
2072 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2073 : parrello 1.35
2074 :     Return the entire contents of a file. In list context, line-ends are removed and
2075 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2076 : olson 1.1
2077 :     =over 4
2078 :    
2079 :     =item fileName
2080 :    
2081 :     Name of the file to read.
2082 :    
2083 :     =item RETURN
2084 :    
2085 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2086 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2087 :     the file, an empty list will be returned.
2088 : olson 1.1
2089 :     =back
2090 :    
2091 :     =cut
2092 :    
2093 :     sub GetFile {
2094 : parrello 1.12 # Get the parameters.
2095 :     my ($fileName) = @_;
2096 :     # Declare the return variable.
2097 :     my @retVal = ();
2098 :     # Open the file for input.
2099 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2100 :     # Read the whole file into the return variable, stripping off any terminator
2101 :     # characters.
2102 :     my $lineCount = 0;
2103 :     while (my $line = <$handle>) {
2104 :     $lineCount++;
2105 :     $line = Strip($line);
2106 :     push @retVal, $line;
2107 :     }
2108 :     # Close it.
2109 :     close $handle;
2110 :     my $actualLines = @retVal;
2111 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2112 : parrello 1.12 # Return the file's contents in the desired format.
2113 : parrello 1.9 if (wantarray) {
2114 : parrello 1.12 return @retVal;
2115 : parrello 1.6 } else {
2116 :     return join "\n", @retVal;
2117 :     }
2118 : olson 1.1 }
2119 :    
2120 : parrello 1.60 =head3 PutFile
2121 :    
2122 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2123 : parrello 1.60
2124 :     Write out a file from a list of lines of text.
2125 :    
2126 :     =over 4
2127 :    
2128 :     =item fileName
2129 :    
2130 :     Name of the output file.
2131 :    
2132 :     =item lines
2133 :    
2134 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2135 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2136 :     modification.
2137 : parrello 1.60
2138 :     =back
2139 :    
2140 :     =cut
2141 :    
2142 :     sub PutFile {
2143 :     # Get the parameters.
2144 :     my ($fileName, $lines) = @_;
2145 :     # Open the output file.
2146 :     my $handle = Open(undef, ">$fileName");
2147 : parrello 1.77 # Count the lines written.
2148 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2149 :     # Here we have a scalar, so we write it raw.
2150 :     print $handle $lines;
2151 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2152 : parrello 1.66 } else {
2153 :     # Write the lines one at a time.
2154 : parrello 1.77 my $count = 0;
2155 : parrello 1.66 for my $line (@{$lines}) {
2156 :     print $handle "$line\n";
2157 : parrello 1.77 $count++;
2158 : parrello 1.66 }
2159 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2160 : parrello 1.60 }
2161 :     # Close the output file.
2162 :     close $handle;
2163 :     }
2164 :    
2165 : parrello 1.93 =head3 ParseRecord
2166 : olson 1.1
2167 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2168 : olson 1.1
2169 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2170 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2171 :     These will automatically be converted.
2172 : olson 1.1
2173 :     =over 4
2174 :    
2175 : parrello 1.93 =item line
2176 :    
2177 :     Line of data containing the tab-delimited fields.
2178 :    
2179 :     =item RETURN
2180 : olson 1.1
2181 : parrello 1.93 Returns a list of the fields found in the data line.
2182 : olson 1.1
2183 :     =back
2184 :    
2185 :     =cut
2186 :    
2187 : parrello 1.93 sub ParseRecord {
2188 : parrello 1.12 # Get the parameter.
2189 : parrello 1.93 my ($line) = @_;
2190 :     # Remove the trailing new-line, if any.
2191 :     chomp $line;
2192 :     # Split the line read into pieces using the tab character.
2193 :     my @retVal = split /\t/, $line;
2194 :     # Trim and fix the escapes in each piece.
2195 :     for my $value (@retVal) {
2196 :     # Trim leading whitespace.
2197 :     $value =~ s/^\s+//;
2198 :     # Trim trailing whitespace.
2199 :     $value =~ s/\s+$//;
2200 :     # Delete the carriage returns.
2201 :     $value =~ s/\r//g;
2202 :     # Convert the escapes into their real values.
2203 :     $value =~ s/\\t/"\t"/ge;
2204 :     $value =~ s/\\n/"\n"/ge;
2205 :     }
2206 :     # Return the result.
2207 :     return @retVal;
2208 :     }
2209 :    
2210 :     =head3 Merge
2211 :    
2212 :     my @mergedList = Tracer::Merge(@inputList);
2213 :    
2214 :     Sort a list of strings and remove duplicates.
2215 :    
2216 :     =over 4
2217 :    
2218 :     =item inputList
2219 :    
2220 :     List of scalars to sort and merge.
2221 :    
2222 :     =item RETURN
2223 :    
2224 :     Returns a list containing the same elements sorted in ascending order with duplicates
2225 :     removed.
2226 :    
2227 :     =back
2228 :    
2229 :     =cut
2230 :    
2231 :     sub Merge {
2232 :     # Get the input list in sort order.
2233 :     my @inputList = sort @_;
2234 :     # Only proceed if the list has at least two elements.
2235 :     if (@inputList > 1) {
2236 :     # Now we want to move through the list splicing out duplicates.
2237 :     my $i = 0;
2238 :     while ($i < @inputList) {
2239 :     # Get the current entry.
2240 :     my $thisEntry = $inputList[$i];
2241 :     # Find out how many elements duplicate the current entry.
2242 :     my $j = $i + 1;
2243 :     my $dup1 = $i + 1;
2244 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2245 :     # If the number is nonzero, splice out the duplicates found.
2246 :     if ($j > $dup1) {
2247 :     splice @inputList, $dup1, $j - $dup1;
2248 : parrello 1.14 }
2249 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2250 :     # at position $i. We push $i forward one position and start again.
2251 :     $i++;
2252 : parrello 1.14 }
2253 : parrello 1.12 }
2254 : parrello 1.93 # Return the merged list.
2255 :     return @inputList;
2256 : olson 1.1 }
2257 :    
2258 : parrello 1.93 =head3 Open
2259 : olson 1.1
2260 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2261 : olson 1.1
2262 : parrello 1.93 Open a file.
2263 : olson 1.1
2264 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2265 :     function. The mode is specified using Unix-like shell information. So, for
2266 :     example,
2267 : olson 1.1
2268 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2269 : olson 1.1
2270 : parrello 1.93 would open for output appended to the specified file, and
2271 : olson 1.1
2272 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2273 : olson 1.1
2274 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2275 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2276 :     code as follows.
2277 : olson 1.1
2278 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2279 : olson 1.1
2280 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2281 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2282 :     failed open will throw an exception and the third parameter will be used to construct
2283 :     an error message. If the parameter is omitted, a standard message is constructed
2284 :     using the file spec.
2285 : olson 1.1
2286 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2287 : olson 1.1
2288 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2289 :     The actual error message from the file system will be captured and appended to the
2290 :     message in any case.
2291 : parrello 1.6
2292 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2293 : parrello 1.6
2294 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2295 :     corresponds to the C++ C<errno> value.
2296 : parrello 1.6
2297 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2298 : parrello 1.6
2299 : parrello 1.93 =over 4
2300 : parrello 1.6
2301 : parrello 1.93 =item fileHandle
2302 : parrello 1.6
2303 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2304 :     and returned as the value of this method.
2305 : olson 1.1
2306 : parrello 1.93 =item fileSpec
2307 : olson 1.1
2308 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2309 : olson 1.1
2310 : parrello 1.93 =item message (optional)
2311 : olson 1.1
2312 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2313 :     will be generated. In either case, the error information from the file system
2314 :     is appended to the message. To specify a conditional open that does not throw
2315 :     an error if it fails, use C<0>.
2316 : olson 1.1
2317 : parrello 1.93 =item RETURN
2318 : olson 1.1
2319 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2320 :     open failed.
2321 : olson 1.1
2322 :     =back
2323 :    
2324 :     =cut
2325 :    
2326 : parrello 1.93 sub Open {
2327 : parrello 1.12 # Get the parameters.
2328 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2329 :     # Attempt to open the file.
2330 :     my $rv = open $fileHandle, $fileSpec;
2331 :     # If the open failed, generate an error message.
2332 :     if (! $rv) {
2333 :     # Save the system error message.
2334 :     my $sysMessage = $!;
2335 :     # See if we need a default message.
2336 :     if (!$message) {
2337 :     # Clean any obvious mode characters and leading spaces from the
2338 :     # filename.
2339 :     my ($fileName) = FindNamePart($fileSpec);
2340 :     $message = "Could not open \"$fileName\"";
2341 :     }
2342 :     # Terminate with an error using the supplied message and the
2343 :     # error message from the file system.
2344 :     Confess("$message: $!");
2345 : parrello 1.12 }
2346 : parrello 1.93 # Return the file handle.
2347 :     return $fileHandle;
2348 : olson 1.1 }
2349 :    
2350 : parrello 1.93 =head3 FindNamePart
2351 :    
2352 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2353 :    
2354 :     Extract the portion of a file specification that contains the file name.
2355 :    
2356 :     A file specification is the string passed to an C<open> call. It specifies the file
2357 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2358 :     method assumes that the file name is whatever follows the first angle bracket
2359 :     sequence. So, for example, in the following strings the file name is
2360 :     C</usr/fig/myfile.txt>.
2361 : parrello 1.5
2362 : parrello 1.93 >>/usr/fig/myfile.txt
2363 :     </usr/fig/myfile.txt
2364 :     | sort -u > /usr/fig/myfile.txt
2365 : parrello 1.5
2366 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2367 :     whole incoming string.
2368 : parrello 1.5
2369 :     =over 4
2370 :    
2371 : parrello 1.93 =item fileSpec
2372 : parrello 1.5
2373 : parrello 1.93 File specification string from which the file name is to be extracted.
2374 : parrello 1.5
2375 :     =item RETURN
2376 :    
2377 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2378 :     the specified string, or the whole string if a file name cannot be found via normal
2379 :     methods. The second element contains the start position of the file name portion and
2380 :     the third element contains the length.
2381 : parrello 1.5
2382 :     =back
2383 :    
2384 :     =cut
2385 : parrello 1.93 #: Return Type $;
2386 :     sub FindNamePart {
2387 :     # Get the parameters.
2388 :     my ($fileSpec) = @_;
2389 :     # Default to the whole input string.
2390 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2391 :     # Parse out the file name if we can.
2392 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2393 :     $retVal = $2;
2394 :     $len = length $retVal;
2395 :     $pos = (length $fileSpec) - (length $3) - $len;
2396 : parrello 1.12 }
2397 : parrello 1.93 # Return the result.
2398 :     return ($retVal, $pos, $len);
2399 : parrello 1.5 }
2400 :    
2401 : parrello 1.93 =head3 OpenDir
2402 : parrello 1.5
2403 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2404 : parrello 1.5
2405 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2406 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2407 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2408 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2409 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2410 :     set, an exception is thrown. So, for example,
2411 : parrello 1.5
2412 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2413 : parrello 1.5
2414 : parrello 1.93 is effectively the same as
2415 : parrello 1.5
2416 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2417 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2418 : parrello 1.5
2419 : parrello 1.93 Similarly, the following code
2420 : parrello 1.5
2421 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2422 : parrello 1.5
2423 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2424 :     automatically returns an empty list if the directory fails to open.
2425 : parrello 1.5
2426 : parrello 1.93 =over 4
2427 : parrello 1.5
2428 : parrello 1.93 =item dirName
2429 : parrello 1.5
2430 : parrello 1.93 Name of the directory to open.
2431 : parrello 1.5
2432 : parrello 1.93 =item filtered
2433 : parrello 1.5
2434 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2435 :     from the list, else FALSE.
2436 : parrello 1.5
2437 : parrello 1.93 =item flag
2438 : parrello 1.5
2439 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2440 : parrello 1.5
2441 : parrello 1.93 =back
2442 : parrello 1.5
2443 : parrello 1.93 =cut
2444 :     #: Return Type @;
2445 :     sub OpenDir {
2446 :     # Get the parameters.
2447 :     my ($dirName, $filtered, $flag) = @_;
2448 :     # Declare the return variable.
2449 :     my @retVal = ();
2450 :     # Open the directory.
2451 :     if (opendir(my $dirHandle, $dirName)) {
2452 :     # The directory opened successfully. Get the appropriate list according to the
2453 :     # strictures of the filter parameter.
2454 :     if ($filtered) {
2455 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2456 :     } else {
2457 :     @retVal = readdir $dirHandle;
2458 :     }
2459 :     } elsif (! $flag) {
2460 :     # Here the directory would not open and it's considered an error.
2461 :     Confess("Could not open directory $dirName.");
2462 :     }
2463 :     # Return the result.
2464 :     return @retVal;
2465 :     }
2466 : parrello 1.5
2467 :    
2468 : parrello 1.93 =head3 Insure
2469 : parrello 1.5
2470 : parrello 1.93 Insure($dirName, $chmod);
2471 : parrello 1.5
2472 : parrello 1.93 Insure a directory is present.
2473 : parrello 1.5
2474 : parrello 1.93 =over 4
2475 : parrello 1.5
2476 : parrello 1.93 =item dirName
2477 : olson 1.1
2478 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2479 : parrello 1.7
2480 : parrello 1.93 =item chmod (optional)
2481 : parrello 1.7
2482 : parrello 1.93 Security privileges to be given to the directory if it is created.
2483 : parrello 1.7
2484 : parrello 1.93 =back
2485 : parrello 1.7
2486 :     =cut
2487 :    
2488 : parrello 1.93 sub Insure {
2489 :     my ($dirName, $chmod) = @_;
2490 :     if (! -d $dirName) {
2491 :     Trace("Creating $dirName directory.") if T(2);
2492 :     eval {
2493 :     mkpath $dirName;
2494 :     # If we have permissions specified, set them here.
2495 :     if (defined($chmod)) {
2496 :     chmod $chmod, $dirName;
2497 :     }
2498 :     };
2499 :     if ($@) {
2500 :     Confess("Error creating $dirName: $@");
2501 :     }
2502 : parrello 1.12 }
2503 : parrello 1.9 }
2504 :    
2505 : parrello 1.93 =head3 ChDir
2506 : parrello 1.9
2507 : parrello 1.93 ChDir($dirName);
2508 : parrello 1.9
2509 : parrello 1.93 Change to the specified directory.
2510 : parrello 1.9
2511 :     =over 4
2512 :    
2513 : parrello 1.93 =item dirName
2514 : parrello 1.9
2515 : parrello 1.93 Name of the directory to which we want to change.
2516 : parrello 1.9
2517 :     =back
2518 :    
2519 :     =cut
2520 :    
2521 : parrello 1.93 sub ChDir {
2522 :     my ($dirName) = @_;
2523 :     if (! -d $dirName) {
2524 :     Confess("Cannot change to directory $dirName: no such directory.");
2525 :     } else {
2526 :     Trace("Changing to directory $dirName.") if T(File => 4);
2527 :     my $okFlag = chdir $dirName;
2528 :     if (! $okFlag) {
2529 :     Confess("Error switching to directory $dirName.");
2530 :     }
2531 :     }
2532 : parrello 1.9 }
2533 :    
2534 : parrello 1.93 =head3 SetPermissions
2535 :    
2536 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2537 : parrello 1.9
2538 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2539 :     In addition, the group ownership will be changed to the specified value.
2540 : parrello 1.9
2541 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2542 :     problems, so it does internal error recovery.
2543 : parrello 1.9
2544 :     =over 4
2545 :    
2546 : parrello 1.93 =item dirName
2547 :    
2548 :     Name of the directory to process.
2549 :    
2550 :     =item group
2551 : parrello 1.9
2552 : parrello 1.93 Name of the group to be assigned.
2553 : parrello 1.9
2554 : parrello 1.93 =item mask
2555 : parrello 1.9
2556 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2557 :     permission bits of any file or directory that does not already have them
2558 :     set to 1.
2559 : parrello 1.9
2560 : parrello 1.93 =item otherMasks
2561 : parrello 1.9
2562 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2563 :     one of the patterns, that directory and all its members and subdirectories
2564 :     will be assigned the new pattern. For example, the following would
2565 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2566 : parrello 1.9
2567 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2568 : parrello 1.9
2569 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2570 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2571 : parrello 1.22
2572 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2573 :     '^tmp' => 0666);
2574 : parrello 1.9
2575 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2576 :     names are matched, not file names.
2577 : parrello 1.9
2578 :     =back
2579 :    
2580 :     =cut
2581 :    
2582 : parrello 1.93 sub SetPermissions {
2583 : parrello 1.12 # Get the parameters.
2584 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2585 :     # Set up for error recovery.
2586 :     eval {
2587 :     # Switch to the specified directory.
2588 :     ChDir($dirName);
2589 :     # Get the group ID.
2590 :     my $gid = getgrnam($group);
2591 :     # Get the mask for tracing.
2592 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2593 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2594 :     my $fixCount = 0;
2595 :     my $lookCount = 0;
2596 :     # @dirs will be a stack of directories to be processed.
2597 :     my @dirs = (getcwd());
2598 :     while (scalar(@dirs) > 0) {
2599 :     # Get the current directory.
2600 :     my $dir = pop @dirs;
2601 :     # Check for a match to one of the specified directory names. To do
2602 :     # that, we need to pull the individual part of the name off of the
2603 :     # whole path.
2604 :     my $simpleName = $dir;
2605 :     if ($dir =~ m!/([^/]+)$!) {
2606 :     $simpleName = $1;
2607 :     }
2608 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2609 :     # Search for a match.
2610 :     my $match = 0;
2611 :     my $i;
2612 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2613 :     my $pattern = $otherMasks[$i];
2614 :     if ($simpleName =~ /$pattern/i) {
2615 :     $match = 1;
2616 :     }
2617 :     }
2618 :     # Check for a match. Note we use $i-1 because the loop added 2
2619 :     # before terminating due to the match.
2620 :     if ($match && $otherMasks[$i-1] != $mask) {
2621 :     # This directory matches one of the incoming patterns, and it's
2622 :     # a different mask, so we process it recursively with that mask.
2623 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2624 :     } else {
2625 :     # Here we can process normally. Get all of the non-hidden members.
2626 :     my @submems = OpenDir($dir, 1);
2627 :     for my $submem (@submems) {
2628 :     # Get the full name.
2629 :     my $thisMem = "$dir/$submem";
2630 :     Trace("Checking member $thisMem.") if T(4);
2631 :     $lookCount++;
2632 :     if ($lookCount % 1000 == 0) {
2633 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2634 :     }
2635 :     # Fix the group.
2636 :     chown -1, $gid, $thisMem;
2637 :     # Insure this member is not a symlink.
2638 :     if (! -l $thisMem) {
2639 :     # Get its info.
2640 :     my $fileInfo = stat $thisMem;
2641 :     # Only proceed if we got the info. Otherwise, it's a hard link
2642 :     # and we want to skip it anyway.
2643 :     if ($fileInfo) {
2644 :     my $fileMode = $fileInfo->mode;
2645 :     if (($fileMode & $mask) != $mask) {
2646 :     # Fix this member.
2647 :     $fileMode |= $mask;
2648 :     chmod $fileMode, $thisMem;
2649 :     $fixCount++;
2650 :     }
2651 :     # If it's a subdirectory, stack it.
2652 :     if (-d $thisMem) {
2653 :     push @dirs, $thisMem;
2654 :     }
2655 :     }
2656 :     }
2657 :     }
2658 :     }
2659 : parrello 1.12 }
2660 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2661 :     };
2662 :     # Check for an error.
2663 :     if ($@) {
2664 :     Confess("SetPermissions error: $@");
2665 : parrello 1.12 }
2666 : parrello 1.7 }
2667 :    
2668 : parrello 1.93 =head3 GetLine
2669 : parrello 1.29
2670 : parrello 1.93 my @data = Tracer::GetLine($handle);
2671 : parrello 1.15
2672 : parrello 1.93 Read a line of data from a tab-delimited file.
2673 : parrello 1.15
2674 :     =over 4
2675 :    
2676 : parrello 1.93 =item handle
2677 : parrello 1.15
2678 : parrello 1.93 Open file handle from which to read.
2679 : parrello 1.15
2680 :     =item RETURN
2681 :    
2682 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2683 :     tab-delimited. If we are at the end of the file, then an empty list will be
2684 :     returned. If an empty line is read, a single list item consisting of a null
2685 :     string will be returned.
2686 : parrello 1.15
2687 :     =back
2688 :    
2689 :     =cut
2690 : parrello 1.93
2691 :     sub GetLine {
2692 : parrello 1.15 # Get the parameters.
2693 : parrello 1.93 my ($handle) = @_;
2694 :     # Declare the return variable.
2695 :     my @retVal = ();
2696 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2697 :     # Read from the file.
2698 :     my $line = <$handle>;
2699 :     # Only proceed if we found something.
2700 :     if (defined $line) {
2701 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2702 :     # upload control and have a nonstandard EOL combination.
2703 :     $line =~ s/(\r|\n)+$//;
2704 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2705 :     if (T(File => 4)) {
2706 :     my $escapedLine = $line;
2707 :     $escapedLine =~ s/\n/\\n/g;
2708 :     $escapedLine =~ s/\r/\\r/g;
2709 :     $escapedLine =~ s/\t/\\t/g;
2710 :     Trace("Line read: -->$escapedLine<--");
2711 :     }
2712 :     # If the line is empty, return a single empty string; otherwise, parse
2713 :     # it into fields.
2714 :     if ($line eq "") {
2715 :     push @retVal, "";
2716 :     } else {
2717 :     push @retVal, split /\t/,$line;
2718 :     }
2719 :     } else {
2720 :     # Trace the reason the read failed.
2721 :     Trace("End of file: $!") if T(File => 3);
2722 : parrello 1.15 }
2723 : parrello 1.93 # Return the result.
2724 :     return @retVal;
2725 : parrello 1.15 }
2726 :    
2727 : parrello 1.93 =head3 PutLine
2728 :    
2729 :     Tracer::PutLine($handle, \@fields, $eol);
2730 : parrello 1.35
2731 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2732 :     output in tab-separated form, with a trailing new-line.
2733 : parrello 1.35
2734 : parrello 1.93 =over 4
2735 : parrello 1.35
2736 : parrello 1.93 =item handle
2737 : parrello 1.69
2738 : parrello 1.93 Output file handle.
2739 : parrello 1.69
2740 : parrello 1.93 =item fields
2741 : parrello 1.69
2742 : parrello 1.93 List of field values.
2743 : parrello 1.69
2744 : parrello 1.93 =item eol (optional)
2745 : parrello 1.69
2746 : parrello 1.93 End-of-line character (default is "\n").
2747 : parrello 1.69
2748 :     =back
2749 : parrello 1.35
2750 :     =cut
2751 :    
2752 : parrello 1.93 sub PutLine {
2753 : parrello 1.69 # Get the parameters.
2754 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2755 :     # Write the data.
2756 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2757 : parrello 1.69 }
2758 :    
2759 :    
2760 : parrello 1.97 =head3 PrintLine
2761 :    
2762 :     Tracer::PrintLine($line);
2763 :    
2764 :     Print a line of text with a trailing new-line.
2765 :    
2766 :     =over 4
2767 :    
2768 :     =item line
2769 :    
2770 :     Line of text to print.
2771 :    
2772 :     =back
2773 :    
2774 :     =cut
2775 :    
2776 :     sub PrintLine {
2777 :     # Get the parameters.
2778 :     my ($line) = @_;
2779 :     # Print the line.
2780 :     print "$line\n";
2781 :     }
2782 :    
2783 : parrello 1.69
2784 : parrello 1.93 =head2 Other Useful Methods
2785 :    
2786 :     =head3 ParseParm
2787 :    
2788 :     my $listValue = Tracer::ParseParm($string);
2789 :    
2790 :     Convert a parameter into a list reference. If the parameter is undefined,
2791 :     an undefined value will be returned. Otherwise, it will be parsed as a
2792 :     comma-separated list of values.
2793 : parrello 1.69
2794 :     =over 4
2795 :    
2796 : parrello 1.93 =item string
2797 :    
2798 :     Incoming string.
2799 :    
2800 :     =item RETURN
2801 : parrello 1.69
2802 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2803 :     was undefined.
2804 : parrello 1.69
2805 :     =back
2806 :    
2807 :     =cut
2808 :    
2809 : parrello 1.93 sub ParseParm {
2810 :     # Get the parameters.
2811 :     my ($string) = @_;
2812 :     # Declare the return variable.
2813 :     my $retVal;
2814 :     # Check for data.
2815 :     if (defined $string) {
2816 :     # We have some, so split it into a list.
2817 :     $retVal = [ split /\s*,\s*/, $string];
2818 : parrello 1.72 }
2819 : parrello 1.93 # Return the result.
2820 :     return $retVal;
2821 : parrello 1.69 }
2822 :    
2823 : parrello 1.97 =head3 Now
2824 :    
2825 :     my $string = Tracer::Now();
2826 :    
2827 :     Return a displayable time stamp containing the local time. Whatever format this
2828 :     method produces must be parseable by L</ParseDate>.
2829 :    
2830 :     =cut
2831 :    
2832 :     sub Now {
2833 :     return DisplayTime(time);
2834 :     }
2835 :    
2836 :     =head3 DisplayTime
2837 :    
2838 :     my $string = Tracer::DisplayTime($time);
2839 : parrello 1.69
2840 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
2841 :     method produces must be parseable by L</ParseDate>.
2842 :    
2843 :     =over 4
2844 : parrello 1.69
2845 : parrello 1.97 =item time
2846 : parrello 1.69
2847 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2848 :    
2849 :     =item RETURN
2850 : parrello 1.69
2851 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2852 : parrello 1.69
2853 : parrello 1.97 =back
2854 : parrello 1.69
2855 : parrello 1.93 =cut
2856 : parrello 1.69
2857 : parrello 1.97 sub DisplayTime {
2858 :     my ($time) = @_;
2859 :     my $retVal = "(n/a)";
2860 :     if (defined $time) {
2861 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2862 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2863 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2864 :     }
2865 : parrello 1.93 return $retVal;
2866 :     }
2867 : parrello 1.69
2868 : parrello 1.93 # Pad a number to 2 digits.
2869 :     sub _p2 {
2870 :     my ($value) = @_;
2871 :     $value = "0$value" if ($value < 10);
2872 :     return $value;
2873 : parrello 1.69 }
2874 :    
2875 : parrello 1.93 =head3 Escape
2876 : parrello 1.69
2877 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2878 : parrello 1.69
2879 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2880 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2881 :     result is to reverse the effect of L</UnEscape>.
2882 : parrello 1.69
2883 :     =over 4
2884 :    
2885 : parrello 1.93 =item realString
2886 : parrello 1.69
2887 : parrello 1.93 String to escape.
2888 : parrello 1.69
2889 :     =item RETURN
2890 :    
2891 : parrello 1.93 Escaped equivalent of the real string.
2892 :    
2893 :     =back
2894 :    
2895 :     =cut
2896 :    
2897 :     sub Escape {
2898 :     # Get the parameter.
2899 :     my ($realString) = @_;
2900 :     # Initialize the return variable.
2901 :     my $retVal = "";
2902 :     # Loop through the parameter string, looking for sequences to escape.
2903 :     while (length $realString > 0) {
2904 :     # Look for the first sequence to escape.
2905 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2906 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2907 :     # itself is in $2. First, move the clear text to the return variable.
2908 :     $retVal .= $1;
2909 :     # Strip the processed section off the real string.
2910 :     $realString = substr $realString, (length $2) + (length $1);
2911 :     # Get the matched character.
2912 :     my $char = $2;
2913 :     # If we have a CR, we are done.
2914 :     if ($char ne "\r") {
2915 :     # It's not a CR, so encode the escape sequence.
2916 :     $char =~ tr/\t\n/tn/;
2917 :     $retVal .= "\\" . $char;
2918 :     }
2919 :     } else {
2920 :     # Here there are no more escape sequences. The rest of the string is
2921 :     # transferred unmodified.
2922 :     $retVal .= $realString;
2923 :     $realString = "";
2924 :     }
2925 :     }
2926 :     # Return the result.
2927 :     return $retVal;
2928 : parrello 1.69 }
2929 :    
2930 : parrello 1.93 =head3 UnEscape
2931 : parrello 1.69
2932 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2933 : parrello 1.69
2934 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2935 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2936 :     be deleted.
2937 : parrello 1.69
2938 :     =over 4
2939 :    
2940 : parrello 1.93 =item codedString
2941 : parrello 1.69
2942 : parrello 1.93 String to un-escape.
2943 : parrello 1.69
2944 :     =item RETURN
2945 :    
2946 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2947 :     values.
2948 : parrello 1.69
2949 :     =back
2950 :    
2951 :     =cut
2952 :    
2953 : parrello 1.93 sub UnEscape {
2954 :     # Get the parameter.
2955 :     my ($codedString) = @_;
2956 :     # Initialize the return variable.
2957 :     my $retVal = "";
2958 :     # Only proceed if the incoming string is nonempty.
2959 :     if (defined $codedString) {
2960 :     # Loop through the parameter string, looking for escape sequences. We can't do
2961 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
2962 :     # "\<tab>" no matter what we do.)
2963 :     while (length $codedString > 0) {
2964 :     # Look for the first escape sequence.
2965 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
2966 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2967 :     # itself is in $2. First, move the clear text to the return variable.
2968 :     $retVal .= $1;
2969 :     $codedString = substr $codedString, (2 + length $1);
2970 :     # Get the escape value.
2971 :     my $char = $2;
2972 :     # If we have a "\r", we are done.
2973 :     if ($char ne 'r') {
2974 :     # Here it's not an 'r', so we convert it.
2975 :     $char =~ tr/\\tn/\\\t\n/;
2976 :     $retVal .= $char;
2977 :     }
2978 :     } else {
2979 :     # Here there are no more escape sequences. The rest of the string is
2980 :     # transferred unmodified.
2981 :     $retVal .= $codedString;
2982 :     $codedString = "";
2983 :     }
2984 :     }
2985 : parrello 1.35 }
2986 : parrello 1.69 # Return the result.
2987 :     return $retVal;
2988 :     }
2989 :    
2990 : parrello 1.93 =head3 Percent
2991 : parrello 1.69
2992 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
2993 : parrello 1.69
2994 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
2995 :     is zero, returns zero.
2996 : parrello 1.69
2997 :     =over 4
2998 :    
2999 : parrello 1.93 =item number
3000 : parrello 1.69
3001 : parrello 1.93 Percent numerator.
3002 : parrello 1.69
3003 : parrello 1.93 =item base
3004 : parrello 1.69
3005 : parrello 1.93 Percent base.
3006 : parrello 1.69
3007 : parrello 1.93 =item RETURN
3008 : parrello 1.69
3009 : parrello 1.93 Returns the percentage of the base represented by the numerator.
3010 : parrello 1.69
3011 :     =back
3012 :    
3013 :     =cut
3014 :    
3015 : parrello 1.93 sub Percent {
3016 : parrello 1.69 # Get the parameters.
3017 : parrello 1.93 my ($number, $base) = @_;
3018 :     # Declare the return variable.
3019 :     my $retVal = 0;
3020 :     # Compute the percent.
3021 :     if ($base != 0) {
3022 :     $retVal = $number * 100 / $base;
3023 :     }
3024 :     # Return the result.
3025 :     return $retVal;
3026 : parrello 1.69 }
3027 :    
3028 : parrello 1.97 =head3 Constrain
3029 :    
3030 :     my $constrained = Constrain($value, $min, $max);
3031 :    
3032 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3033 :    
3034 :     =over 4
3035 :    
3036 :     =item value
3037 :    
3038 :     Value to constrain.
3039 :    
3040 :     =item min (optional)
3041 :    
3042 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3043 :    
3044 :     =item max (optional)
3045 :    
3046 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3047 :    
3048 :     =item RETURN
3049 :    
3050 :     Returns the incoming value, constrained according to the other parameters.
3051 :    
3052 :     =back
3053 :    
3054 :     =cut
3055 :    
3056 :     sub Constrain {
3057 :     # Get the parameters.
3058 :     my ($value, $min, $max) = @_;
3059 :     # Declare the return variable.
3060 :     my $retVal = $value;
3061 :     # Apply the minimum constraint.
3062 :     if (defined $min && $retVal < $min) {
3063 :     $retVal = $min;
3064 :     }
3065 :     # Apply the maximum constraint.
3066 :     if (defined $max && $retVal > $max) {
3067 :     $retVal = $max;
3068 :     }
3069 :     # Return the result.
3070 :     return $retVal;
3071 :     }
3072 :    
3073 : parrello 1.93 =head3 Min
3074 : parrello 1.69
3075 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3076 : parrello 1.69
3077 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3078 : parrello 1.69
3079 :     =over 4
3080 :    
3081 : parrello 1.93 =item $value1, $value2, ... $valueN
3082 : parrello 1.69
3083 : parrello 1.93 List of numbers to compare.
3084 : parrello 1.69
3085 :     =item RETURN
3086 :    
3087 : parrello 1.93 Returns the lowest number in the list.
3088 : parrello 1.69
3089 :     =back
3090 :    
3091 :     =cut
3092 :    
3093 : parrello 1.93 sub Min {
3094 :     # Get the parameters. Note that we prime the return value with the first parameter.
3095 :     my ($retVal, @values) = @_;
3096 :     # Loop through the remaining parameters, looking for the lowest.
3097 :     for my $value (@values) {
3098 :     if ($value < $retVal) {
3099 :     $retVal = $value;
3100 : parrello 1.72 }
3101 :     }
3102 : parrello 1.93 # Return the minimum found.
3103 : parrello 1.70 return $retVal;
3104 : parrello 1.35 }
3105 :    
3106 : parrello 1.93 =head3 Max
3107 :    
3108 :     my $max = Max($value1, $value2, ... $valueN);
3109 : parrello 1.69
3110 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3111 : parrello 1.65
3112 : parrello 1.93 =over 4
3113 : parrello 1.65
3114 : parrello 1.93 =item $value1, $value2, ... $valueN
3115 : parrello 1.65
3116 : parrello 1.93 List of numbers to compare.
3117 : parrello 1.65
3118 : parrello 1.93 =item RETURN
3119 : parrello 1.65
3120 : parrello 1.93 Returns the highest number in the list.
3121 : parrello 1.65
3122 :     =back
3123 :    
3124 :     =cut
3125 :    
3126 : parrello 1.93 sub Max {
3127 :     # Get the parameters. Note that we prime the return value with the first parameter.
3128 :     my ($retVal, @values) = @_;
3129 :     # Loop through the remaining parameters, looking for the highest.
3130 :     for my $value (@values) {
3131 :     if ($value > $retVal) {
3132 :     $retVal = $value;
3133 : parrello 1.65 }
3134 :     }
3135 : parrello 1.93 # Return the maximum found.
3136 :     return $retVal;
3137 : parrello 1.65 }
3138 :    
3139 : parrello 1.35
3140 : parrello 1.93 =head3 Strip
3141 : parrello 1.37
3142 : parrello 1.93 my $string = Tracer::Strip($line);
3143 : parrello 1.37
3144 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3145 :     that may have been transferred back and forth several times among different
3146 :     operating environments.
3147 : parrello 1.37
3148 :     =over 4
3149 :    
3150 : parrello 1.93 =item line
3151 : parrello 1.37
3152 : parrello 1.93 Line of text to be stripped.
3153 : parrello 1.37
3154 : parrello 1.93 =item RETURN
3155 : parrello 1.91
3156 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3157 : parrello 1.91
3158 : parrello 1.37 =back
3159 :    
3160 :     =cut
3161 :    
3162 : parrello 1.93 sub Strip {
3163 :     # Get a copy of the parameter string.
3164 :     my ($string) = @_;
3165 :     my $retVal = (defined $string ? $string : "");
3166 :     # Strip the line terminator characters.
3167 :     $retVal =~ s/(\r|\n)+$//g;
3168 :     # Return the result.
3169 :     return $retVal;
3170 : parrello 1.43 }
3171 :    
3172 : parrello 1.93 =head3 Pad
3173 : parrello 1.43
3174 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3175 : parrello 1.43
3176 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3177 :     space, and the padding will be on the right side unless specified
3178 :     in the third parameter.
3179 : parrello 1.43
3180 :     =over 4
3181 :    
3182 : parrello 1.93 =item string
3183 :    
3184 :     String to be padded.
3185 :    
3186 :     =item len
3187 :    
3188 :     Desired length of the padded string.
3189 :    
3190 :     =item left (optional)
3191 :    
3192 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3193 :    
3194 :     =item padChar (optional)
3195 :    
3196 :     Character to use for padding. The default is a space.
3197 :    
3198 :     =item RETURN
3199 : parrello 1.43
3200 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3201 :     specified end so that it achieves the desired length.
3202 : parrello 1.43
3203 :     =back
3204 :    
3205 :     =cut
3206 :    
3207 : parrello 1.93 sub Pad {
3208 :     # Get the parameters.
3209 :     my ($string, $len, $left, $padChar) = @_;
3210 :     # Compute the padding character.
3211 :     if (! defined $padChar) {
3212 :     $padChar = " ";
3213 :     }
3214 :     # Compute the number of spaces needed.
3215 :     my $needed = $len - length $string;
3216 :     # Copy the string into the return variable.
3217 :     my $retVal = $string;
3218 :     # Only proceed if padding is needed.
3219 :     if ($needed > 0) {
3220 :     # Create the pad string.
3221 :     my $pad = $padChar x $needed;
3222 :     # Affix it to the return value.
3223 :     if ($left) {
3224 :     $retVal = $pad . $retVal;
3225 :     } else {
3226 :     $retVal .= $pad;
3227 : parrello 1.43 }
3228 : parrello 1.37 }
3229 : parrello 1.93 # Return the result.
3230 :     return $retVal;
3231 : parrello 1.37 }
3232 :    
3233 : parrello 1.93 =head3 EOF
3234 :    
3235 :     This is a constant that is lexically greater than any useful string.
3236 :    
3237 :     =cut
3238 :    
3239 :     sub EOF {
3240 :     return "\xFF\xFF\xFF\xFF\xFF";
3241 :     }
3242 : parrello 1.59
3243 : parrello 1.93 =head3 TICK
3244 : parrello 1.59
3245 : parrello 1.93 my @results = TICK($commandString);
3246 : parrello 1.59
3247 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3248 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3249 : parrello 1.59
3250 : parrello 1.93 `./protein.cgi`
3251 : parrello 1.59
3252 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3253 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3254 : parrello 1.59
3255 : parrello 1.93 TICK("./protein.cgi")
3256 : parrello 1.59
3257 : parrello 1.93 it will work correctly in both environments.
3258 : parrello 1.59
3259 : parrello 1.93 =over 4
3260 : parrello 1.59
3261 : parrello 1.93 =item commandString
3262 : parrello 1.59
3263 : parrello 1.93 The command string to pass to the system.
3264 : parrello 1.59
3265 :     =item RETURN
3266 :    
3267 : parrello 1.93 Returns the standard output from the specified command, as a list.
3268 : parrello 1.59
3269 :     =back
3270 :    
3271 :     =cut
3272 : parrello 1.93 #: Return Type @;
3273 :     sub TICK {
3274 : parrello 1.59 # Get the parameters.
3275 : parrello 1.93 my ($commandString) = @_;
3276 :     # Chop off the dot-slash if this is Windows.
3277 :     if ($FIG_Config::win_mode) {
3278 :     $commandString =~ s!^\./!!;
3279 : parrello 1.59 }
3280 : parrello 1.93 # Activate the command and return the result.
3281 :     return `$commandString`;
3282 : parrello 1.59 }
3283 :    
3284 : parrello 1.93
3285 : parrello 1.55 =head3 CommaFormat
3286 :    
3287 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3288 : parrello 1.55
3289 :     Insert commas into a number.
3290 :    
3291 :     =over 4
3292 :    
3293 :     =item number
3294 :    
3295 :     A sequence of digits.
3296 :    
3297 :     =item RETURN
3298 :    
3299 :     Returns the same digits with commas strategically inserted.
3300 :    
3301 :     =back
3302 :    
3303 :     =cut
3304 :    
3305 :     sub CommaFormat {
3306 :     # Get the parameters.
3307 :     my ($number) = @_;
3308 :     # Pad the length up to a multiple of three.
3309 :     my $padded = "$number";
3310 :     $padded = " " . $padded while length($padded) % 3 != 0;
3311 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3312 :     # cause the delimiters to be included in the output stream. The
3313 :     # GREP removes the empty strings in between the delimiters.
3314 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3315 :     # Clean out the spaces.
3316 :     $retVal =~ s/ //g;
3317 :     # Return the result.
3318 :     return $retVal;
3319 :     }
3320 : parrello 1.46
3321 :    
3322 : parrello 1.62 =head3 CompareLists
3323 :    
3324 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3325 : parrello 1.62
3326 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3327 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3328 :     The return value contains a list of items that are only in the new list
3329 :     (inserted) and only in the old list (deleted).
3330 :    
3331 :     =over 4
3332 :    
3333 :     =item newList
3334 :    
3335 :     Reference to a list of new tuples.
3336 :    
3337 :     =item oldList
3338 :    
3339 :     Reference to a list of old tuples.
3340 :    
3341 :     =item keyIndex (optional)
3342 :    
3343 :     Index into each tuple of its key field. The default is 0.
3344 :    
3345 :     =item RETURN
3346 :    
3347 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3348 :     list (inserted) followed by a reference to the list of items that are only in the old
3349 :     list (deleted).
3350 :    
3351 :     =back
3352 :    
3353 :     =cut
3354 :    
3355 :     sub CompareLists {
3356 :     # Get the parameters.
3357 :     my ($newList, $oldList, $keyIndex) = @_;
3358 :     if (! defined $keyIndex) {
3359 :     $keyIndex = 0;
3360 :     }
3361 :     # Declare the return variables.
3362 :     my ($inserted, $deleted) = ([], []);
3363 :     # Loop through the two lists simultaneously.
3364 :     my ($newI, $oldI) = (0, 0);
3365 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3366 :     while ($newI < $newN || $oldI < $oldN) {
3367 :     # Get the current object in each list. Note that if one
3368 :     # of the lists is past the end, we'll get undef.
3369 :     my $newItem = $newList->[$newI];
3370 :     my $oldItem = $oldList->[$oldI];
3371 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3372 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3373 :     push @{$deleted}, $oldItem;
3374 :     $oldI++;
3375 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3376 :     # The new item is not in the old list, so mark it inserted.
3377 :     push @{$inserted}, $newItem;
3378 :     $newI++;
3379 :     } else {
3380 :     # The item is in both lists, so push forward.
3381 :     $oldI++;
3382 :     $newI++;
3383 :     }
3384 :     }
3385 :     # Return the result.
3386 :     return ($inserted, $deleted);
3387 :     }
3388 :    
3389 : parrello 1.65 =head3 GenerateURL
3390 :    
3391 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3392 : parrello 1.65
3393 :     Generate a GET-style URL for the specified page with the specified parameter
3394 :     names and values. The values will be URL-escaped automatically. So, for
3395 :     example
3396 :    
3397 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3398 :    
3399 :     would return
3400 :    
3401 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3402 : parrello 1.65
3403 :     =over 4
3404 :    
3405 :     =item page
3406 :    
3407 :     Page URL.
3408 :    
3409 :     =item parameters
3410 :    
3411 :     Hash mapping parameter names to parameter values.
3412 :    
3413 :     =item RETURN
3414 :    
3415 :     Returns a GET-style URL that goes to the specified page and passes in the
3416 :     specified parameters and values.
3417 :    
3418 :     =back
3419 :    
3420 :     =cut
3421 :    
3422 :     sub GenerateURL {
3423 :     # Get the parameters.
3424 :     my ($page, %parameters) = @_;
3425 :     # Prime the return variable with the page URL.
3426 :     my $retVal = $page;
3427 :     # Loop through the parameters, creating parameter elements in a list.
3428 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3429 :     # If the list is nonempty, tack it on.
3430 :     if (@parmList) {
3431 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3432 : parrello 1.65 }
3433 :     # Return the result.
3434 :     return $retVal;
3435 :     }
3436 :    
3437 : parrello 1.78 =head3 ApplyURL
3438 :    
3439 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3440 : parrello 1.78
3441 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3442 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3443 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3444 :    
3445 :     This provides a simple way to process the results of a database query into something
3446 :     displayable by combining a URL with text.
3447 :    
3448 :     =over 4
3449 :    
3450 :     =item table
3451 :    
3452 :     Reference to a list of lists. The elements in the containing list will be updated by
3453 :     this method.
3454 :    
3455 :     =item target
3456 :    
3457 :     The index of the column to be converted into HTML.
3458 :    
3459 :     =item url
3460 :    
3461 :     The index of the column containing the URL. Note that the URL must have a recognizable
3462 :     C<http:> at the beginning.
3463 :    
3464 :     =back
3465 :    
3466 :     =cut
3467 :    
3468 :     sub ApplyURL {
3469 :     # Get the parameters.
3470 :     my ($table, $target, $url) = @_;
3471 :     # Loop through the table.
3472 :     for my $row (@{$table}) {
3473 :     # Apply the URL to the target cell.
3474 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3475 :     # Delete the URL from the row.
3476 :     delete $row->[$url];
3477 :     }
3478 :     }
3479 :    
3480 :     =head3 CombineURL
3481 :    
3482 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3483 : parrello 1.78
3484 :     This method will convert the specified text into HTML hyperlinked to the specified
3485 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3486 :     is defined and begins with an C<http:> header.
3487 :    
3488 :     =over 4
3489 :    
3490 :     =item text
3491 :    
3492 :     Text to return. This will be HTML-escaped automatically.
3493 :    
3494 :     =item url
3495 :    
3496 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3497 :     will be returned without any hyperlinking.
3498 :    
3499 :     =item RETURN
3500 :    
3501 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3502 :     doesn't look right, the HTML-escaped text will be returned without any further
3503 :     modification.
3504 :    
3505 :     =back
3506 :    
3507 :     =cut
3508 :    
3509 :     sub CombineURL {
3510 :     # Get the parameters.
3511 :     my ($text, $url) = @_;
3512 :     # Declare the return variable.
3513 :     my $retVal = CGI::escapeHTML($text);
3514 :     # Verify the URL.
3515 :     if (defined($url) && $url =~ m!http://!i) {
3516 :     # It's good, so we apply it to the text.
3517 :     $retVal = "<a href=\"$url\">$retVal</a>";
3518 :     }
3519 :     # Return the result.
3520 :     return $retVal;
3521 :     }
3522 :    
3523 : parrello 1.93 =head3 Cmp
3524 :    
3525 :     my $cmp = Tracer::Cmp($a, $b);
3526 :    
3527 :     This method performs a universal sort comparison. Each value coming in is
3528 :     separated into a leading text part and a trailing number part. The text
3529 :     part is string compared, and if both parts are equal, then the number
3530 :     parts are compared numerically. A stream of just numbers or a stream of
3531 :     just strings will sort correctly, and a mixed stream will sort with the
3532 :     numbers first. Strings with a label and a number will sort in the
3533 :     expected manner instead of lexically.
3534 :    
3535 :     =over 4
3536 :    
3537 :     =item a
3538 :    
3539 :     First item to compare.
3540 :    
3541 :     =item b
3542 :    
3543 :     Second item to compare.
3544 :    
3545 :     =item RETURN
3546 :    
3547 :     Returns a negative number if the first item should sort first (is less), a positive
3548 :     number if the first item should sort second (is greater), and a zero if the items are
3549 :     equal.
3550 :    
3551 :     =back
3552 :    
3553 :     =cut
3554 :    
3555 :     sub Cmp {
3556 :     # Get the parameters.
3557 :     my ($a, $b) = @_;
3558 :     # Declare the return value.
3559 :     my $retVal;
3560 :     # Check for nulls.
3561 :     if (! defined($a)) {
3562 :     $retVal = (! defined($b) ? 0 : -1);
3563 :     } elsif (! defined($b)) {
3564 :     $retVal = 1;
3565 :     } else {
3566 :     # Here we have two real values. Parse the two strings.
3567 :     $a =~ /^(\D*)(\d*)$/;
3568 :     my $aParsed = [$1, $2];
3569 :     $b =~ /^(\D*)(\d*)$/;
3570 :     my $bParsed = [$1, $2];
3571 :     # Compare the string parts.
3572 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3573 :     if (! $retVal) {
3574 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3575 :     }
3576 :     }
3577 :     # Return the result.
3578 :     return $retVal;
3579 :     }
3580 :    
3581 : parrello 1.87
3582 : parrello 1.97 =head3 TrackingCode
3583 :    
3584 :     my $html = Tracer::TrackingCode();
3585 :    
3586 :     Returns the HTML code for doing web page traffic monitoring. If the
3587 :     current environment is a test system, then it returns a null string;
3588 :     otherwise, it returns a bunch of javascript containing code for turning
3589 :     on SiteMeter and Google Analytics.
3590 :    
3591 :     =cut
3592 :    
3593 :     sub TrackingCode {
3594 :     # Declare the return variable.
3595 :     my $retVal = "<!-- tracking off -->";
3596 :     # Determine if we're in production.
3597 :     if ($FIG_Config::site_meter) {
3598 :     $retVal = <<END_HTML
3599 :     <!-- Site Meter -->
3600 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3601 :     </script>
3602 :     <noscript>
3603 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3604 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3605 :     </noscript>
3606 :     <!-- Copyright (c)2006 Site Meter -->
3607 :     END_HTML
3608 :     }
3609 :     return $retVal;
3610 :     }
3611 :    
3612 :    
3613 : olson 1.88 1;

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