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

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