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

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