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1 : gdpusch 1.95 # -*- perl -*-
2 :     ########################################################################
3 : olson 1.30 # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 : parrello 1.61 #
8 : olson 1.30 # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 : parrello 1.61 # Public License.
11 : olson 1.30 #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 : gdpusch 1.95 ########################################################################
18 : olson 1.30
19 : olson 1.1 package Tracer;
20 :    
21 : parrello 1.12 require Exporter;
22 :     @ISA = ('Exporter');
23 : parrello 1.99 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn);
24 : parrello 1.97 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
25 : parrello 1.12 use strict;
26 : gdpusch 1.96 use Carp qw(longmess croak carp);
27 : parrello 1.12 use CGI;
28 : parrello 1.47 use Cwd;
29 : parrello 1.12 use FIG_Config;
30 : parrello 1.9 use PageBuilder;
31 : parrello 1.21 use Digest::MD5;
32 : parrello 1.36 use File::Basename;
33 : parrello 1.37 use File::Path;
34 : parrello 1.48 use File::stat;
35 : parrello 1.59 use LWP::UserAgent;
36 : parrello 1.64 use Time::HiRes 'gettimeofday';
37 : parrello 1.65 use URI::Escape;
38 : parrello 1.74 use Time::Local;
39 : parrello 1.99 use POSIX qw(strftime);
40 :     use Time::Zone;
41 :    
42 : olson 1.1
43 :     =head1 Tracing and Debugging Helpers
44 :    
45 : parrello 1.72 =head2 Tracing
46 : olson 1.1
47 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
48 : parrello 1.72 L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
49 :     L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
50 :     each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
51 :     level is less than or equal to the setup trace level and whose category is activated will
52 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
53 : parrello 1.72 is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
54 :     appear.
55 : olson 1.1
56 : parrello 1.72 =head3 Putting Trace Messages in Your Code
57 :    
58 :     To generate a trace message, use the following syntax.
59 :    
60 :     Trace($message) if T(errors => 4);
61 : olson 1.1
62 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
63 : parrello 1.72 category is active. There is a special category C<main> that is always active, so
64 : olson 1.1
65 : parrello 1.72 Trace($message) if T(main => 4);
66 : olson 1.1
67 :     will trace if the trace level is 4 or more.
68 :    
69 :     If the category name is the same as the package name, all you need is the number. So, if the
70 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
71 :     active and the trace level is 2 or more.
72 :    
73 : parrello 1.72 Trace($message) if T(2);
74 :    
75 :     In scripts, where no package name is available, the category defaults to C<main>.
76 :    
77 :     =head3 Custom Tracing
78 :    
79 :     Many programs have customized tracing configured using the L</TSetup> method. This is no longer
80 :     the preferred method, but a knowledge of how custom tracing works can make the more modern
81 :     L</Emergency Tracing> easier to understand.
82 : olson 1.1
83 : parrello 1.72 To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
84 :     a list of category names, and a destination. The trace level and list of category names are
85 : olson 1.1 specified as a space-delimited string. Thus
86 :    
87 : parrello 1.72 TSetup('3 errors Sprout ERDB', 'TEXT');
88 : olson 1.1
89 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
90 : parrello 1.72 specifies that messages should be sent to the standard output.
91 : parrello 1.12
92 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
93 :     level 3 and writes the output to the standard error output. This sort of thing might be
94 :     useful in a CGI environment.
95 :    
96 : parrello 1.72 TSetup('3 *', 'WARN');
97 : olson 1.1
98 : parrello 1.72 In addition standard error and file output for trace messages, you can specify that the trace messages
99 : olson 1.1 be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
100 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
101 :     the page output, they can be gathered together and displayed at the end of the page. This makes
102 :     it easier to debug page formatting problems.
103 :    
104 : parrello 1.72 Finally, you can specify that all trace messages be emitted to a file, or the standard output and
105 :     a file at the same time. To trace to a file, specify the filename with an output character in front
106 :     of it.
107 :    
108 :     TSetup('4 SQL', ">$fileName");
109 :    
110 :     To trace to the standard output and a file at the same time, put a C<+> in front of the angle
111 :     bracket.
112 :    
113 :     TSetup('3 *', "+>$fileName");
114 : parrello 1.4
115 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
116 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
117 :     Thus, debugging information is available and easily retrieved even when the application is
118 :     being used out in the field.
119 :    
120 : parrello 1.72 =head3 Trace Levels
121 :    
122 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
123 :     a suggestion.
124 :    
125 :     =over 4
126 :    
127 : parrello 1.32 =item Error 0
128 : parrello 1.10
129 :     Message indicates an error that may lead to incorrect results or that has stopped the
130 :     application entirely.
131 :    
132 : parrello 1.32 =item Warning 1
133 : parrello 1.10
134 :     Message indicates something that is unexpected but that probably did not interfere
135 :     with program execution.
136 :    
137 : parrello 1.32 =item Notice 2
138 : parrello 1.10
139 :     Message indicates the beginning or end of a major task.
140 :    
141 : parrello 1.32 =item Information 3
142 : parrello 1.10
143 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
144 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
145 :    
146 : parrello 1.32 =item Detail 4
147 : parrello 1.10
148 :     Message indicates a low-level loop iteration.
149 :    
150 :     =back
151 :    
152 : parrello 1.69 The format of trace messages is important because some utilities analyze trace files.
153 : parrello 1.72 There are three fields-- the time stamp, the category name, and the text.
154 :     The time stamp is between square brackets and the category name between angle brackets.
155 :     After the category name there is a colon (C<:>) followed by the message text.
156 :     If the square brackets or angle brackets are missing, then the trace management
157 :     utilities assume that they are encountering a set of pre-formatted lines.
158 :    
159 :     Note, however, that this formatting is done automatically by the tracing functions. You
160 :     only need to know about it if you want to parse a trace file.
161 :    
162 :     =head3 Emergency Tracing
163 :    
164 :     Sometimes, you need a way for tracing to happen automatically without putting parameters
165 :     in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
166 : parrello 1.97 from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
167 :     that you specify a tracing key. For command-line tools, the key is
168 : parrello 1.72 taken from the C<TRACING> environment variable. For web services, the key is taken from
169 :     a cookie. Either way, the key tells the tracing facility who you are, so that you control
170 :     the tracing in your environment without stepping on other users.
171 :    
172 :     The key can be anything you want. If you don't have a key, the C<SetPassword> page will
173 :     generate one for you.
174 :    
175 :     You can activate and de-activate emergency tracing from the debugging control panel, as
176 :     well as display the trace file itself.
177 :    
178 :     To enable emergency tracing in your code, call
179 :    
180 :     ETracing($cgi)
181 :    
182 :     from a web script and
183 :    
184 :     ETracing()
185 :    
186 :     from a command-line script.
187 :    
188 :     The web script will look for the tracing key in the cookies, and the command-line
189 :     script will look for it in the C<TRACING> environment variable. If you are
190 : parrello 1.97 using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
191 : parrello 1.72 will be configured automatically.
192 :    
193 : olson 1.1 =cut
194 : parrello 1.2
195 : olson 1.1 # Declare the configuration variables.
196 :    
197 : parrello 1.94 my $Destination = "WARN"; # Description of where to send the trace output.
198 : parrello 1.12 my $TeeFlag = 0; # TRUE if output is going to a file and to the
199 :     # standard output
200 : parrello 1.3 my %Categories = ( main => 1 );
201 : parrello 1.12 # hash of active category names
202 : parrello 1.97 my @LevelNames = qw(error warn notice info detail);
203 : parrello 1.12 my $TraceLevel = 0; # trace level; a higher trace level produces more
204 :     # messages
205 :     my @Queue = (); # queued list of trace messages.
206 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
207 : parrello 1.97 my $LastLevel = 0; # level of the last test call
208 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
209 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
210 : parrello 1.99 my $SavedCGI; # CGI object passed to ETracing
211 : parrello 1.104 my $CommandLine; # Command line passed to StandardSetup
212 : parrello 1.99 umask 2; # Fix the damn umask so everything is group-writable.
213 : olson 1.1
214 : parrello 1.93 =head2 Tracing Methods
215 :    
216 :     =head3 Setups
217 :    
218 :     my $count = Tracer::Setups();
219 :    
220 :     Return the number of times L</TSetup> has been called.
221 :    
222 :     This method allows for the creation of conditional tracing setups where, for example, we
223 :     may want to set up tracing if nobody else has done it before us.
224 :    
225 :     =cut
226 :    
227 :     sub Setups {
228 :     return $SetupCount;
229 :     }
230 : olson 1.1
231 :     =head3 TSetup
232 :    
233 : parrello 1.92 TSetup($categoryList, $target);
234 : olson 1.1
235 :     This method is used to specify the trace options. The options are stored as package data
236 :     and interrogated by the L</Trace> and L</T> methods.
237 :    
238 :     =over 4
239 :    
240 :     =item categoryList
241 :    
242 :     A string specifying the trace level and the categories to be traced, separated by spaces.
243 :     The trace level must come first.
244 :    
245 :     =item target
246 :    
247 :     The destination for the trace output. To send the trace output to a file, specify the file
248 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
249 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
250 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
251 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
252 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
253 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
254 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
255 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
256 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
257 : parrello 1.6 cause tracing to be suppressed.
258 : olson 1.1
259 :     =back
260 :    
261 :     =cut
262 :    
263 :     sub TSetup {
264 : parrello 1.12 # Get the parameters.
265 :     my ($categoryList, $target) = @_;
266 :     # Parse the category list.
267 :     my @categoryData = split /\s+/, $categoryList;
268 :     # Extract the trace level.
269 :     $TraceLevel = shift @categoryData;
270 :     # Presume category-based tracing until we learn otherwise.
271 :     $AllTrace = 0;
272 :     # Build the category hash. Note that if we find a "*", we turn on non-category
273 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
274 : parrello 1.34 %Categories = ( main => 1 );
275 : parrello 1.12 for my $category (@categoryData) {
276 :     if ($category eq '*') {
277 :     $AllTrace = 1;
278 :     } else {
279 : parrello 1.13 $Categories{lc $category} = 1;
280 : parrello 1.12 }
281 :     }
282 :     # Now we need to process the destination information. The most important special
283 : parrello 1.98 # case is when we're writing to a file. This is indicated by ">" (overwrite) and
284 :     # ">>" (append). A leading "+" for either indicates that we are also writing to
285 :     # the standard output (tee mode).
286 : parrello 1.12 if ($target =~ m/^\+?>>?/) {
287 :     if ($target =~ m/^\+/) {
288 :     $TeeFlag = 1;
289 :     $target = substr($target, 1);
290 :     }
291 :     if ($target =~ m/^>[^>]/) {
292 : parrello 1.98 # We need to initialize the file (which clears it).
293 : parrello 1.12 open TRACEFILE, $target;
294 : parrello 1.98 print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
295 : parrello 1.12 close TRACEFILE;
296 : parrello 1.98 # Set to append mode now that the file has been cleared.
297 : parrello 1.12 $Destination = ">$target";
298 :     } else {
299 :     $Destination = $target;
300 :     }
301 :     } else {
302 :     $Destination = uc($target);
303 :     }
304 :     # Increment the setup counter.
305 :     $SetupCount++;
306 : parrello 1.11 }
307 :    
308 : parrello 1.93 =head3 SetLevel
309 : parrello 1.31
310 : parrello 1.93 Tracer::SetLevel($newLevel);
311 : parrello 1.31
312 : parrello 1.93 Modify the trace level. A higher trace level will cause more messages to appear.
313 : parrello 1.31
314 : parrello 1.93 =over 4
315 : parrello 1.31
316 : parrello 1.93 =item newLevel
317 : parrello 1.31
318 : parrello 1.93 Proposed new trace level.
319 : parrello 1.31
320 : parrello 1.93 =back
321 : parrello 1.31
322 : parrello 1.93 =cut
323 : parrello 1.31
324 : parrello 1.93 sub SetLevel {
325 :     $TraceLevel = $_[0];
326 :     }
327 : parrello 1.31
328 : parrello 1.97 =head3 ParseDate
329 :    
330 :     my $time = Tracer::ParseDate($dateString);
331 :    
332 :     Convert a date into a PERL time number. This method expects a date-like string
333 :     and parses it into a number. The string must be vaguely date-like or it will
334 :     return an undefined value. Our requirement is that a month and day be
335 :     present and that three pieces of the date string (time of day, month and day,
336 :     year) be separated by likely delimiters, such as spaces, commas, and such-like.
337 :    
338 :     If a time of day is present, it must be in military time with two digits for
339 :     everything but the hour.
340 : parrello 1.31
341 : parrello 1.97 The year must be exactly four digits.
342 : parrello 1.31
343 : parrello 1.97 Additional stuff can be in the string. We presume it's time zones or weekdays or something
344 :     equally innocuous. This means, however, that a sufficiently long sentence with date-like
345 :     parts in it may be interpreted as a date. Hopefully this will not be a problem.
346 :    
347 :     It should be guaranteed that this method will parse the output of the L</Now> function.
348 :    
349 :     The parameters are as follows.
350 : parrello 1.31
351 : parrello 1.93 =over 4
352 : parrello 1.31
353 : parrello 1.93 =item dateString
354 : parrello 1.31
355 : parrello 1.97 The date string to convert.
356 : parrello 1.31
357 : parrello 1.93 =item RETURN
358 : parrello 1.31
359 : parrello 1.93 Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
360 : parrello 1.97 the date string is invalid. A valid date string must contain a month and day.
361 : parrello 1.31
362 : parrello 1.93 =back
363 : parrello 1.38
364 : parrello 1.93 =cut
365 : parrello 1.38
366 : parrello 1.97 # Universal month conversion table.
367 :     use constant MONTHS => { Jan => 0, January => 0, '01' => 0, '1' => 0,
368 :     Feb => 1, February => 1, '02' => 1, '2' => 1,
369 :     Mar => 2, March => 2, '03' => 2, '3' => 2,
370 :     Apr => 3, April => 3, '04' => 3, '4' => 3,
371 :     May => 4, May => 4, '05' => 4, '5' => 4,
372 :     Jun => 5, June => 5, '06' => 5, '6' => 5,
373 :     Jul => 6, July => 6, '07' => 6, '7' => 6,
374 :     Aug => 7, August => 7, '08' => 7, '8' => 7,
375 :     Sep => 8, September => 8, '09' => 8, '9' => 8,
376 :     Oct => 9, October => 9, '10' => 9,
377 :     Nov => 10, November => 10, '11' => 10,
378 :     Dec => 11, December => 11, '12' => 11
379 :     };
380 :    
381 :     sub ParseDate {
382 : parrello 1.93 # Get the parameters.
383 :     my ($dateString) = @_;
384 :     # Declare the return variable.
385 :     my $retVal;
386 : parrello 1.97 # Find the month and day of month. There are two ways that can happen. We check for the
387 :     # numeric style first. That way, if the user's done something like "Sun 12/22", then we
388 :     # won't be fooled into thinking the month is Sunday.
389 :     if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
390 :     my ($mon, $mday) = (MONTHS->{$1}, $2);
391 :     # Insist that the month and day are valid.
392 :     if (defined($mon) && $2 >= 1 && $2 <= 31) {
393 :     # Find the time.
394 :     my ($hour, $min, $sec) = (0, 0, 0);
395 :     if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
396 :     ($hour, $min, $sec) = ($1, $2, $3);
397 :     }
398 :     # Find the year.
399 :     my $year;
400 :     if ($dateString =~ /\b(\d{4})\b/) {
401 :     $year = $1;
402 :     } else {
403 :     # Get the default year, which is this one. Note we must convert it to
404 :     # the four-digit value expected by "timelocal".
405 :     (undef, undef, undef, undef, undef, $year) = localtime();
406 :     $year += 1900;
407 :     }
408 :     $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
409 :     }
410 : parrello 1.93 }
411 :     # Return the result.
412 :     return $retVal;
413 :     }
414 : parrello 1.31
415 : parrello 1.93 =head3 LogErrors
416 : parrello 1.42
417 : parrello 1.93 Tracer::LogErrors($fileName);
418 : parrello 1.31
419 : parrello 1.93 Route the standard error output to a log file.
420 : parrello 1.31
421 : parrello 1.93 =over 4
422 : parrello 1.31
423 : parrello 1.93 =item fileName
424 : parrello 1.31
425 : parrello 1.93 Name of the file to receive the error output.
426 : parrello 1.31
427 : parrello 1.93 =back
428 : parrello 1.31
429 : parrello 1.93 =cut
430 : parrello 1.84
431 : parrello 1.93 sub LogErrors {
432 :     # Get the file name.
433 :     my ($fileName) = @_;
434 :     # Open the file as the standard error output.
435 :     open STDERR, '>', $fileName;
436 :     }
437 : parrello 1.84
438 : parrello 1.93 =head3 Trace
439 : parrello 1.31
440 : parrello 1.93 Trace($message);
441 : parrello 1.31
442 : parrello 1.93 Write a trace message to the target location specified in L</TSetup>. If there has not been
443 :     any prior call to B<TSetup>.
444 : parrello 1.31
445 : parrello 1.93 =over 4
446 : parrello 1.42
447 : parrello 1.93 =item message
448 : parrello 1.42
449 : parrello 1.93 Message to write.
450 : parrello 1.42
451 : parrello 1.93 =back
452 : parrello 1.72
453 : parrello 1.93 =cut
454 : parrello 1.36
455 : parrello 1.93 sub Trace {
456 :     # Get the parameters.
457 :     my ($message) = @_;
458 : parrello 1.97 # Strip off any line terminators at the end of the message. We will add
459 :     # new-line stuff ourselves.
460 :     my $stripped = Strip($message);
461 :     # Compute the caller information.
462 :     my ($callPackage, $callFile, $callLine) = caller();
463 :     my $callFileTitle = basename($callFile);
464 :     # Check the caller.
465 : parrello 1.98 my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
466 : parrello 1.93 # Get the timestamp.
467 :     my $timeStamp = Now();
468 : parrello 1.97 # Build the prefix.
469 :     my $level = $LevelNames[$LastLevel] || "($LastLevel)";
470 : parrello 1.98 my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
471 : parrello 1.97 # Format the message.
472 :     my $formatted = "$prefix $stripped";
473 : parrello 1.93 # Process according to the destination.
474 :     if ($Destination eq "TEXT") {
475 :     # Write the message to the standard output.
476 :     print "$formatted\n";
477 :     } elsif ($Destination eq "ERROR") {
478 : parrello 1.97 # Write the message to the error output. Here, we want our prefix fields.
479 : parrello 1.93 print STDERR "$formatted\n";
480 : parrello 1.97 } elsif ($Destination eq "WARN") {
481 :     # Emit the message to the standard error output. It is presumed that the
482 : parrello 1.98 # error logger will add its own prefix fields, the notable exception being
483 :     # the caller info.
484 :     print STDERR "$callerInfo$stripped\n";
485 : parrello 1.93 } elsif ($Destination eq "QUEUE") {
486 :     # Push the message into the queue.
487 :     push @Queue, "$formatted";
488 :     } elsif ($Destination eq "HTML") {
489 :     # Convert the message to HTML and write it to the standard output.
490 : parrello 1.97 my $escapedMessage = CGI::escapeHTML($stripped);
491 :     print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
492 : parrello 1.93 } elsif ($Destination =~ m/^>>/) {
493 :     # Write the trace message to an output file.
494 : parrello 1.97 open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
495 : parrello 1.93 print TRACING "$formatted\n";
496 :     close TRACING;
497 :     # If the Tee flag is on, echo it to the standard output.
498 :     if ($TeeFlag) {
499 :     print "$formatted\n";
500 :     }
501 :     }
502 :     }
503 : parrello 1.36
504 : parrello 1.93 =head3 T
505 : parrello 1.36
506 : parrello 1.93 my $switch = T($category, $traceLevel);
507 : parrello 1.36
508 : parrello 1.93 or
509 : parrello 1.44
510 : parrello 1.93 my $switch = T($traceLevel);
511 : parrello 1.44
512 : parrello 1.93 Return TRUE if the trace level is at or above a specified value and the specified category
513 :     is active, else FALSE. If no category is specified, the caller's package name is used.
514 : parrello 1.44
515 : parrello 1.93 =over 4
516 : parrello 1.44
517 : parrello 1.93 =item category
518 : parrello 1.44
519 : parrello 1.93 Category to which the message belongs. If not specified, the caller's package name is
520 :     used.
521 : parrello 1.31
522 : parrello 1.93 =item traceLevel
523 : parrello 1.31
524 : parrello 1.93 Relevant tracing level.
525 : parrello 1.31
526 : parrello 1.93 =item RETURN
527 : parrello 1.31
528 : parrello 1.93 TRUE if a message at the specified trace level would appear in the trace, else FALSE.
529 : parrello 1.31
530 : parrello 1.93 =back
531 : parrello 1.36
532 : parrello 1.93 =cut
533 :    
534 :     sub T {
535 :     # Declare the return variable.
536 :     my $retVal = 0;
537 :     # Only proceed if tracing is turned on.
538 :     if ($Destination ne "NONE") {
539 :     # Get the parameters.
540 :     my ($category, $traceLevel) = @_;
541 :     if (!defined $traceLevel) {
542 :     # Here we have no category, so we need to get the calling package.
543 :     # The calling package is normally the first parameter. If it is
544 :     # omitted, the first parameter will be the tracelevel. So, the
545 :     # first thing we do is shift the so-called category into the
546 :     # $traceLevel variable where it belongs.
547 :     $traceLevel = $category;
548 :     my ($package, $fileName, $line) = caller;
549 :     # If there is no calling package, we default to "main".
550 :     if (!$package) {
551 :     $category = "main";
552 :     } else {
553 :     my @cats = split /::/, $package;
554 :     $category = $cats[$#cats];
555 :     }
556 :     }
557 : parrello 1.97 # Save the category name and level.
558 : parrello 1.93 $LastCategory = $category;
559 : parrello 1.97 $LastLevel = $traceLevel;
560 : parrello 1.93 # Convert it to lower case before we hash it.
561 :     $category = lc $category;
562 : parrello 1.100 # Validate the trace level.
563 : parrello 1.93 if (ref $traceLevel) {
564 :     Confess("Bad trace level.");
565 :     } elsif (ref $TraceLevel) {
566 :     Confess("Bad trace config.");
567 :     }
568 : parrello 1.100 # Make the check. Note that level 0 shows even if the category is turned off.
569 :     $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
570 : parrello 1.93 }
571 :     # Return the computed result.
572 :     return $retVal;
573 :     }
574 :    
575 :     =head3 QTrace
576 :    
577 :     my $data = QTrace($format);
578 :    
579 :     Return the queued trace data in the specified format.
580 :    
581 :     =over 4
582 :    
583 :     =item format
584 :    
585 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
586 :    
587 :     =back
588 :    
589 :     =cut
590 :    
591 :     sub QTrace {
592 :     # Get the parameter.
593 :     my ($format) = @_;
594 :     # Create the return variable.
595 :     my $retVal = "";
596 :     # Only proceed if there is an actual queue.
597 :     if (@Queue) {
598 :     # Process according to the format.
599 :     if ($format =~ m/^HTML$/i) {
600 :     # Convert the queue into an HTML list.
601 :     $retVal = "<ul>\n";
602 :     for my $line (@Queue) {
603 :     my $escapedLine = CGI::escapeHTML($line);
604 :     $retVal .= "<li>$escapedLine</li>\n";
605 :     }
606 :     $retVal .= "</ul>\n";
607 :     } elsif ($format =~ m/^TEXT$/i) {
608 :     # Convert the queue into a list of text lines.
609 :     $retVal = join("\n", @Queue) . "\n";
610 :     }
611 :     # Clear the queue.
612 :     @Queue = ();
613 :     }
614 :     # Return the formatted list.
615 :     return $retVal;
616 :     }
617 :    
618 :     =head3 Confess
619 :    
620 :     Confess($message);
621 :    
622 :     Trace the call stack and abort the program with the specified message. When used with
623 :     the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
624 :     So, for example
625 :    
626 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
627 :    
628 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
629 :    
630 :     =over 4
631 :    
632 :     =item message
633 :    
634 :     Message to include in the trace.
635 :    
636 :     =back
637 :    
638 :     =cut
639 :    
640 :     sub Confess {
641 :     # Get the parameters.
642 :     my ($message) = @_;
643 : parrello 1.97 # Set up the category and level.
644 :     $LastCategory = "(confess)";
645 :     $LastLevel = 0;
646 : parrello 1.93 if (! defined($FIG_Config::no_tool_hdr)) {
647 :     # Here we have a tool header. Display its length so that the user can adjust the line numbers.
648 :     my $toolHeaderFile = "$FIG_Config::fig_disk/dist/releases/current/$FIG_Config::arch/tool_hdr";
649 :     # Only proceed if the tool header file is actually present.
650 :     if (-f $toolHeaderFile) {
651 : parrello 1.97 my $fh;
652 :     if (open $fh, "<$toolHeaderFile") {
653 :     my @lines = <$fh>;
654 :     Trace("Tool header has " . scalar(@lines) . " lines.");
655 :     }
656 : parrello 1.93 }
657 :     }
658 :     # Trace the call stack.
659 :     Cluck($message);
660 :     # Abort the program.
661 :     croak(">>> $message");
662 :     }
663 :    
664 : parrello 1.99 =head3 Warn
665 :    
666 :     Warn($message);
667 :    
668 :     This method traces an important message. If an RSS feed is configured
669 :     (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
670 :     then the message will be echoed to the feed. In general, a tracing
671 :     destination of C<WARN> indicates that the caller is running as a web
672 :     service in a production environment; however, this is not a requirement.
673 :    
674 : parrello 1.103 To force warnings into the RSS feed even when the tracing destination
675 :     is not C<WARN>, simply specify the C<Feed> tracing module. This can be
676 :     configured automatically when L</StandardSetup> is used.
677 :    
678 : parrello 1.99 The L</Cluck> method calls this one for its final message. Since
679 :     L</Confess> calls L</Cluck>, this means that any error which is caught
680 :     and confessed will put something in the feed. This insures that someone
681 :     will be alerted relatively quickly when a failure occurs.
682 :    
683 :     =over 4
684 :    
685 :     =item message
686 :    
687 :     Message to be traced.
688 :    
689 :     =back
690 :    
691 :     =cut
692 :    
693 :     sub Warn {
694 :     # Get the parameters.
695 :     my ($message) = @_;
696 :     # Trace the message.
697 :     Trace($message);
698 : parrello 1.103 # Check for feed forcing.
699 :     my $forceFeed = exists $Categories{feed};
700 : parrello 1.99 # An error here would be disastrous. Note, however, that we aren't too worried
701 :     # about losing events. The error log is always available for the occasions where
702 : parrello 1.102 # we mess up. Note that if debug mode is specified, we do this stuff even in a
703 :     # test environment.
704 : parrello 1.99 eval {
705 :     # Do we need to put this in the RSS feed?
706 : parrello 1.103 if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
707 : parrello 1.99 # Yes. We now need to compute the date, the link, and the title.
708 :     # First, the date, in a very specific format.
709 :     my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
710 :     (tz_local_offset() / 30);
711 : parrello 1.102 # Environment data goes in here. We start with the date.
712 :     my $environment = "$date. ";
713 :     # If we need to recap the message (because it's too long to be a title), we'll
714 :     # put it in here.
715 :     my $recap;
716 :     # Copy the message and remove excess space.
717 :     my $title = $message;
718 : parrello 1.101 $title =~ s/\s+/ /gs;
719 : parrello 1.102 # If it's too long, we have to split it up.
720 : parrello 1.101 if (length $title > 60) {
721 : parrello 1.102 # Put the full message in the environment string.
722 :     $recap = $title;
723 :     # Excerpt it as the title.
724 : parrello 1.101 $title = substr($title, 0, 50) . "...";
725 :     }
726 : parrello 1.99 # If we have a CGI object, then this is a web error. Otherwise, it's
727 :     # command-line.
728 :     if (defined $SavedCGI) {
729 : parrello 1.101 # We're in a web service. The environment is the user's IP, and the link
730 : parrello 1.99 # is the URL that got us here.
731 :     my $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
732 : parrello 1.102 $environment .= "Event Reported at IP address $key.";
733 :     my $url = $SavedCGI->url(-full => 1, -query => 1);
734 : parrello 1.100 # We need the user agent string and (if available) the referrer.
735 : parrello 1.102 # The referrer will be the link.
736 : parrello 1.101 $environment .= "User Agent $ENV{HTTP_USER_AGENT}";
737 : parrello 1.100 if ($ENV{HTTP_REFERER}) {
738 : parrello 1.102 my $link = $ENV{HTTP_REFERER};
739 :     $environment .= " referred from <a href=\"$link\">$link</a>.";
740 :     } else {
741 :     $environment .= " referrer unknown.";
742 : parrello 1.100 }
743 : parrello 1.102 # Close off the sentence with the original link.
744 :     $environment .= " URL of error is <a href=\"$url\">$url</a>.";
745 : parrello 1.99 } else {
746 :     # No CGI object, so we're a command-line tool. Use the tracing
747 : parrello 1.101 # key and the PID as the user identifier, and add the command.
748 : parrello 1.99 my $key = EmergencyKey();
749 : parrello 1.104 $environment .= "Event Reported by $key Process $$.";
750 :     if ($CommandLine) {
751 :     # We're in a StandardSetup script, so we have the real command line.
752 :     $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
753 :     } elsif ($ENV{_}) {
754 :     # We're in a BASH script, so the command has been stored in the _ variable.
755 :     $environment .= " Command = " . CGI::escapeHTML($ENV{_}) . "\n";
756 :     }
757 : parrello 1.99 }
758 :     # Build a GUID. We use the current time, the title, and the process ID,
759 :     # then digest the result.
760 :     my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
761 :     # Finally, the description. This is a stack trace plus various environmental stuff.
762 : parrello 1.101 my $stackTrace = "";
763 : parrello 1.99 my @trace = LongMess();
764 : parrello 1.101 # Only proceed if we got something back.
765 :     if (scalar(@trace) > 0) {
766 :     $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
767 :     $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
768 :     }
769 : parrello 1.102 # We got the stack trace. Now it's time to put it all together.
770 :     # We have a goofy thing here in that we need to HTML-escape some sections of the description
771 :     # twice. They will be escaped once here, and then once when written by XML::Simple. They are
772 :     # unescaped once when processed by the RSS reader, and stuff in the description is treated as
773 :     # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
774 :     # our <br>s and <pre>s are used to format the description.
775 :     $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
776 :     my $description = "$recap$environment $stackTrace";
777 : parrello 1.99 # Okay, we have all the pieces. Create a hash of the new event.
778 :     my $newItem = { title => $title,
779 : parrello 1.102 description => $description,
780 : parrello 1.99 category => $LastCategory,
781 :     pubDate => $date,
782 :     guid => $guid,
783 :     };
784 :     # We need XML capability for this.
785 :     require XML::Simple;
786 :     # The RSS document goes in here.
787 :     my $rss;
788 :     # Get the name of the RSS file. It's in the FIG temporary directory.
789 :     my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
790 :     # Does it exist?
791 :     if (-s $fileName) {
792 :     # Slurp it in.
793 :     $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
794 :     } else {
795 :     my $size = -s $fileName;
796 :     # Create an empty channel.
797 :     $rss = {
798 :     channel => {
799 :     title => 'NMPDR Warning Feed',
800 :     link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
801 :     description => "Important messages regarding the status of the NMPDR.",
802 :     generator => "NMPDR Trace Facility",
803 :     docs => "http://blogs.law.harvard.edu/tech/rss",
804 :     item => []
805 :     },
806 :     };
807 :     }
808 :     # Get the channel object.
809 :     my $channel = $rss->{channel};
810 :     # Update the last-build date.
811 :     $channel->{lastBuildDate} = $date;
812 :     # Get the item array.
813 :     my $items = $channel->{item};
814 :     # Insure it has only 100 entries.
815 :     while (scalar @{$items} > 100) {
816 :     pop @{$items};
817 :     }
818 :     # Add our new item at the front.
819 :     unshift @{$items}, $newItem;
820 : parrello 1.102 # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
821 :     # the requirements for those.
822 :     my $xml = XML::Simple::XMLout($rss, NoAttr => 1, RootName => undef, XmlDecl => '');
823 :     # Here we put in the root and declaration. The problem is that the root has to have the version attribute
824 :     # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
825 :     $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
826 : parrello 1.99 # We don't use Open here because we can't afford an error.
827 :     if (open XMLOUT, ">$fileName") {
828 :     print XMLOUT $xml;
829 :     close XMLOUT;
830 :     }
831 :     }
832 :     };
833 : parrello 1.103 if ($@) {
834 :     # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
835 :     # (which is a good thing).
836 : parrello 1.102 my $error = $@;
837 : parrello 1.103 Trace("Feed Error: $error") if T(Feed => 0);
838 : parrello 1.102 }
839 : parrello 1.99 }
840 :    
841 : parrello 1.93 =head3 Assert
842 :    
843 :     Assert($condition1, $condition2, ... $conditionN);
844 :    
845 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
846 :     the OR operator and the L</Confess> method as a debugging assert.
847 :     So, for example
848 :    
849 :     Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
850 :    
851 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
852 :    
853 :     =cut
854 :     sub Assert {
855 :     my $retVal = 1;
856 :     LOOP: for my $condition (@_) {
857 :     if (! $condition) {
858 :     $retVal = 0;
859 :     last LOOP;
860 :     }
861 :     }
862 :     return $retVal;
863 :     }
864 :    
865 :     =head3 Cluck
866 :    
867 :     Cluck($message);
868 :    
869 :     Trace the call stack. Note that for best results, you should qualify the call with a
870 :     trace condition. For example,
871 :    
872 :     Cluck("Starting record parse.") if T(3);
873 :    
874 :     will only trace the stack if the trace level for the package is 3 or more.
875 :    
876 :     =over 4
877 :    
878 :     =item message
879 :    
880 :     Message to include in the trace.
881 :    
882 :     =back
883 :    
884 :     =cut
885 :    
886 :     sub Cluck {
887 :     # Get the parameters.
888 :     my ($message) = @_;
889 :     # Trace what's happening.
890 :     Trace("Stack trace for event: $message");
891 : parrello 1.99 # Get the stack trace.
892 :     my @trace = LongMess();
893 :     # Convert the trace to a series of messages.
894 :     for my $line (@trace) {
895 :     # Replace the tab at the beginning with spaces.
896 :     $line =~ s/^\t/ /;
897 :     # Trace the line.
898 :     Trace($line);
899 :     }
900 :     # Issue a warning. This displays the event message and inserts it into the RSS error feed.
901 :     Warn($message);
902 :     }
903 :    
904 :     =head3 LongMess
905 :    
906 :     my @lines = Tracer::LongMess();
907 :    
908 :     Return a stack trace with all tracing methods removed. The return will be in the form of a list
909 :     of message strings.
910 :    
911 :     =cut
912 :    
913 :     sub LongMess {
914 :     # Declare the return variable.
915 :     my @retVal = ();
916 :     my $confession = longmess("");
917 : parrello 1.93 for my $line (split /\s*\n/, $confession) {
918 : parrello 1.99 unless ($line =~ /Tracer\.pm/) {
919 :     # Here we have a line worth keeping. Push it onto the result list.
920 :     push @retVal, $line;
921 : parrello 1.97 }
922 : parrello 1.93 }
923 : parrello 1.99 # Return the result.
924 :     return @retVal;
925 : parrello 1.93 }
926 :    
927 : parrello 1.97 =head3 ScriptSetup (deprecated)
928 : parrello 1.93
929 :     my ($cgi, $varHash) = ScriptSetup($noTrace);
930 :    
931 :     Perform standard tracing and debugging setup for scripts. The value returned is
932 :     the CGI object followed by a pre-built variable hash. At the end of the script,
933 :     the client should call L</ScriptFinish> to output the web page.
934 :    
935 :     This method calls L</ETracing> to configure tracing, which allows the tracing
936 :     to be configured via the emergency tracing form on the debugging control panel.
937 :     Tracing will then be turned on automatically for all programs that use the L</ETracing>
938 :     method, which includes every program that uses this method or L</StandardSetup>.
939 : parrello 1.36
940 : parrello 1.93 =over 4
941 : parrello 1.31
942 : parrello 1.93 =item noTrace (optional)
943 : parrello 1.31
944 : parrello 1.93 If specified, tracing will be suppressed. This is useful if the script wants to set up
945 :     tracing manually.
946 : parrello 1.31
947 :     =item RETURN
948 :    
949 : parrello 1.93 Returns a two-element list consisting of a CGI query object and a variable hash for
950 :     the output page.
951 : parrello 1.31
952 :     =back
953 :    
954 :     =cut
955 :    
956 : parrello 1.93 sub ScriptSetup {
957 : parrello 1.31 # Get the parameters.
958 : parrello 1.93 my ($noTrace) = @_;
959 :     # Get the CGI query object.
960 :     my $cgi = CGI->new();
961 :     # Set up tracing if it's not suppressed.
962 :     ETracing($cgi) unless $noTrace;
963 :     # Create the variable hash.
964 :     my $varHash = { results => '' };
965 :     # Return the query object and variable hash.
966 :     return ($cgi, $varHash);
967 :     }
968 :    
969 :     =head3 ETracing
970 :    
971 :     ETracing($parameter);
972 :    
973 :     Set up emergency tracing. Emergency tracing is tracing that is turned
974 :     on automatically for any program that calls this method. The emergency
975 :     tracing parameters are stored in a a file identified by a tracing key.
976 :     If this method is called with a CGI object, then the tracing key is
977 :     taken from a cookie. If it is called with no parameters, then the tracing
978 :     key is taken from an environment variable. If it is called with a string,
979 :     the tracing key is that string.
980 :    
981 :     =over 4
982 :    
983 :     =item parameter
984 :    
985 :     A parameter from which the tracing key is computed. If it is a scalar,
986 :     that scalar is used as the tracing key. If it is a CGI object, the
987 :     tracing key is taken from the C<IP> cookie. If it is omitted, the
988 :     tracing key is taken from the C<TRACING> environment variable. If it
989 :     is a CGI object and emergency tracing is not on, the C<Trace> and
990 :     C<TF> parameters will be used to determine the type of tracing.
991 :    
992 :     =back
993 :    
994 :     =cut
995 :    
996 :     sub ETracing {
997 :     # Get the parameter.
998 :     my ($parameter) = @_;
999 :     # Check for CGI mode.
1000 : parrello 1.99 if (defined $parameter && ref $parameter eq 'CGI') {
1001 :     $SavedCGI = $parameter;
1002 :     } else {
1003 :     $SavedCGI = undef;
1004 :     }
1005 : parrello 1.93 # Default to no tracing except errors.
1006 :     my ($tracing, $dest) = ("0", "WARN");
1007 :     # Check for emergency tracing.
1008 :     my $tkey = EmergencyKey($parameter);
1009 :     my $emergencyFile = EmergencyFileName($tkey);
1010 :     if (-e $emergencyFile) {
1011 :     # We have the file. Read in the data.
1012 :     my @tracing = GetFile($emergencyFile);
1013 :     # Pull off the time limit.
1014 :     my $expire = shift @tracing;
1015 :     # Convert it to seconds.
1016 :     $expire *= 3600;
1017 :     # Check the file data.
1018 :     my $stat = stat($emergencyFile);
1019 :     my ($now) = gettimeofday;
1020 :     if ($now - $stat->mtime > $expire) {
1021 :     # Delete the expired file.
1022 :     unlink $emergencyFile;
1023 : parrello 1.44 } else {
1024 : parrello 1.93 # Emergency tracing is on. Pull off the destination and
1025 :     # the trace level;
1026 :     $dest = shift @tracing;
1027 :     my $level = shift @tracing;
1028 :     # Convert the destination to a real tracing destination.
1029 :     # temp directory.
1030 :     $dest = EmergencyTracingDest($tkey, $dest);
1031 :     # Insure Tracer is specified.
1032 :     my %moduleHash = map { $_ => 1 } @tracing;
1033 :     $moduleHash{Tracer} = 1;
1034 :     # Set the trace parameter.
1035 :     $tracing = join(" ", $level, sort keys %moduleHash);
1036 : parrello 1.44 }
1037 : parrello 1.99 } elsif (defined $SavedCGI) {
1038 : parrello 1.93 # There's no emergency tracing, but we have a CGI object, so check
1039 :     # for tracing from the form parameters.
1040 : parrello 1.99 if ($SavedCGI->param('Trace')) {
1041 : parrello 1.93 # Here the user has requested tracing via a form.
1042 : parrello 1.99 $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1043 :     $tracing = $SavedCGI->param('Trace') . " Tracer";
1044 : parrello 1.36 }
1045 :     }
1046 : parrello 1.93 # Setup the tracing we've determined from all the stuff above.
1047 :     TSetup($tracing, $dest);
1048 : parrello 1.94 # Check to see if we're a web script.
1049 : parrello 1.99 if (defined $SavedCGI) {
1050 : parrello 1.94 # Yes we are. Trace the form and environment data.
1051 : parrello 1.99 TraceParms($SavedCGI);
1052 : parrello 1.94 # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1053 :     # emitted by the script in its raw form.
1054 :     if (T(Raw => 3)) {
1055 :     print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1056 :     }
1057 : parrello 1.83 }
1058 : parrello 1.31 }
1059 :    
1060 : parrello 1.93 =head3 EmergencyFileName
1061 :    
1062 :     my $fileName = Tracer::EmergencyFileName($tkey);
1063 :    
1064 :     Return the emergency tracing file name. This is the file that specifies
1065 :     the tracing information.
1066 :    
1067 :     =over 4
1068 :    
1069 :     =item tkey
1070 :    
1071 :     Tracing key for the current program.
1072 : parrello 1.11
1073 : parrello 1.93 =item RETURN
1074 : parrello 1.11
1075 : parrello 1.93 Returns the name of the file to contain the emergency tracing information.
1076 : parrello 1.11
1077 : parrello 1.93 =back
1078 : parrello 1.11
1079 :     =cut
1080 :    
1081 : parrello 1.93 sub EmergencyFileName {
1082 :     # Get the parameters.
1083 :     my ($tkey) = @_;
1084 :     # Compute the emergency tracing file name.
1085 :     return "$FIG_Config::temp/Emergency$tkey.txt";
1086 : olson 1.1 }
1087 :    
1088 : parrello 1.93 =head3 EmergencyFileTarget
1089 : parrello 1.10
1090 : parrello 1.93 my $fileName = Tracer::EmergencyFileTarget($tkey);
1091 : parrello 1.10
1092 : parrello 1.93 Return the emergency tracing target file name. This is the file that receives
1093 :     the tracing output for file-based tracing.
1094 : parrello 1.10
1095 : parrello 1.93 =over 4
1096 : parrello 1.10
1097 : parrello 1.93 =item tkey
1098 : parrello 1.10
1099 : parrello 1.93 Tracing key for the current program.
1100 : parrello 1.10
1101 : parrello 1.93 =item RETURN
1102 : parrello 1.10
1103 : parrello 1.93 Returns the name of the file to contain the trace output.
1104 : parrello 1.10
1105 : parrello 1.93 =back
1106 : parrello 1.10
1107 : parrello 1.93 =cut
1108 : parrello 1.10
1109 : parrello 1.93 sub EmergencyFileTarget {
1110 :     # Get the parameters.
1111 :     my ($tkey) = @_;
1112 :     # Compute the emergency tracing file name.
1113 :     return "$FIG_Config::temp/trace$tkey.log";
1114 :     }
1115 : parrello 1.10
1116 : parrello 1.93 =head3 EmergencyTracingDest
1117 : parrello 1.10
1118 : parrello 1.93 my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1119 : parrello 1.10
1120 : parrello 1.93 This method converts an emergency tracing destination to a real
1121 :     tracing destination. The main difference is that if the
1122 :     destination is C<FILE> or C<APPEND>, we convert it to file
1123 :     output. If the destination is C<DUAL>, we convert it to file
1124 :     and standard output.
1125 : parrello 1.10
1126 :     =over 4
1127 :    
1128 : parrello 1.93 =item tkey
1129 : parrello 1.10
1130 : parrello 1.93 Tracing key for this environment.
1131 : parrello 1.10
1132 : parrello 1.93 =item myDest
1133 : parrello 1.10
1134 : parrello 1.93 Destination from the emergency tracing file.
1135 : parrello 1.10
1136 :     =item RETURN
1137 :    
1138 : parrello 1.93 Returns a destination that can be passed into L</TSetup>.
1139 : parrello 1.10
1140 :     =back
1141 :    
1142 :     =cut
1143 :    
1144 : parrello 1.93 sub EmergencyTracingDest {
1145 : parrello 1.12 # Get the parameters.
1146 : parrello 1.93 my ($tkey, $myDest) = @_;
1147 :     # Declare the return variable.
1148 :     my $retVal = $myDest;
1149 :     # Process according to the destination value.
1150 :     if ($myDest eq 'FILE') {
1151 :     $retVal = ">" . EmergencyFileTarget($tkey);
1152 :     } elsif ($myDest eq 'APPEND') {
1153 :     $retVal = ">>" . EmergencyFileTarget($tkey);
1154 :     } elsif ($myDest eq 'DUAL') {
1155 :     $retVal = "+>" . EmergencyFileTarget($tkey);
1156 : parrello 1.97 } elsif ($myDest eq 'WARN') {
1157 :     $retVal = "WARN";
1158 : parrello 1.12 }
1159 : parrello 1.93 # Return the result.
1160 :     return $retVal;
1161 : parrello 1.10 }
1162 :    
1163 : parrello 1.93 =head3 Emergency
1164 :    
1165 :     Emergency($key, $hours, $dest, $level, @modules);
1166 :    
1167 :     Turn on emergency tracing. This method is normally invoked over the web from
1168 :     a debugging console, but it can also be called by the C<trace.pl> script.
1169 :     The caller specifies the duration of the emergency in hours, the desired tracing
1170 :     destination, the trace level, and a list of the trace modules to activate.
1171 :     For the length of the duration, when a program in an environment with the
1172 :     specified tracing key active invokes a Sprout CGI script, tracing will be
1173 :     turned on automatically. See L</TSetup> for more about tracing setup and
1174 :     L</ETracing> for more about emergency tracing.
1175 :    
1176 :     =over 4
1177 : parrello 1.11
1178 : parrello 1.93 =item tkey
1179 : parrello 1.11
1180 : parrello 1.93 The tracing key. This is used to identify the control file and the trace file.
1181 : parrello 1.11
1182 : parrello 1.93 =item hours
1183 : parrello 1.11
1184 : parrello 1.93 Number of hours to keep emergency tracing alive.
1185 : parrello 1.11
1186 : parrello 1.93 =item dest
1187 : parrello 1.11
1188 : parrello 1.93 Tracing destination. If no path information is specified for a file
1189 :     destination, it is put in the FIG temporary directory.
1190 : parrello 1.11
1191 : parrello 1.93 =item level
1192 : parrello 1.11
1193 : parrello 1.93 Tracing level. A higher level means more trace messages.
1194 : parrello 1.11
1195 : parrello 1.93 =item modules
1196 : parrello 1.11
1197 : parrello 1.93 A list of the tracing modules to activate.
1198 : parrello 1.11
1199 :     =back
1200 :    
1201 :     =cut
1202 : parrello 1.93
1203 :     sub Emergency {
1204 : parrello 1.11 # Get the parameters.
1205 : parrello 1.93 my ($tkey, $hours, $dest, $level, @modules) = @_;
1206 :     # Create the emergency file.
1207 :     my $specFile = EmergencyFileName($tkey);
1208 :     my $outHandle = Open(undef, ">$specFile");
1209 :     print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1210 : parrello 1.11 }
1211 :    
1212 : parrello 1.93 =head3 EmergencyKey
1213 :    
1214 :     my $tkey = EmergencyKey($parameter);
1215 :    
1216 :     Return the Key to be used for emergency tracing. This could be an IP address,
1217 :     a session ID, or a user name, depending on the environment.
1218 : parrello 1.11
1219 : parrello 1.93 =over 4
1220 : parrello 1.11
1221 : parrello 1.93 =item parameter
1222 : parrello 1.11
1223 : parrello 1.93 Parameter defining the method for finding the tracing key. If it is a scalar,
1224 :     then it is presumed to be the tracing key itself. If it is a CGI object, then
1225 :     the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1226 :     taken from the C<TRACING> environment variable.
1227 : parrello 1.29
1228 : parrello 1.93 =item RETURN
1229 : parrello 1.11
1230 : parrello 1.93 Returns the key to be used for labels in emergency tracing.
1231 : parrello 1.11
1232 : parrello 1.93 =back
1233 : parrello 1.11
1234 : parrello 1.93 =cut
1235 : parrello 1.29
1236 : parrello 1.93 sub EmergencyKey {
1237 :     # Get the parameters.
1238 :     my ($parameter) = @_;
1239 :     # Declare the return variable.
1240 :     my $retVal;
1241 :     # Determine the parameter type.
1242 :     if (! defined $parameter) {
1243 : parrello 1.99 # Here we're supposed to check the environment. If that fails, we
1244 :     # get the effective login ID.
1245 :     $retVal = $ENV{TRACING} || scalar getpwuid($<);
1246 : parrello 1.93 } else {
1247 :     my $ptype = ref $parameter;
1248 :     if ($ptype eq 'CGI') {
1249 :     # Here we were invoked from a web page. Look for a cookie.
1250 :     $retVal = $parameter->cookie('IP');
1251 :     } elsif (! $ptype) {
1252 :     # Here the key was passed in.
1253 :     $retVal = $parameter;
1254 :     }
1255 :     }
1256 :     # If no luck finding a key, use the PID.
1257 :     if (! defined $retVal) {
1258 :     $retVal = $$;
1259 :     }
1260 :     # Return the result.
1261 :     return $retVal;
1262 :     }
1263 : parrello 1.11
1264 :    
1265 : parrello 1.93 =head3 TraceParms
1266 : parrello 1.11
1267 : parrello 1.93 Tracer::TraceParms($cgi);
1268 : parrello 1.11
1269 : parrello 1.93 Trace the CGI parameters at trace level CGI => 3 and the environment variables
1270 : parrello 1.94 at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1271 : parrello 1.11
1272 : parrello 1.93 =over 4
1273 : parrello 1.11
1274 : parrello 1.93 =item cgi
1275 : parrello 1.31
1276 : parrello 1.93 CGI query object containing the parameters to trace.
1277 : parrello 1.31
1278 : parrello 1.11 =back
1279 :    
1280 :     =cut
1281 : parrello 1.93
1282 :     sub TraceParms {
1283 : parrello 1.11 # Get the parameters.
1284 : parrello 1.93 my ($cgi) = @_;
1285 : parrello 1.94 if (T(CGI => 2)) {
1286 :     # Here we trace the GET-style URL for the script.
1287 : parrello 1.97 Trace("[URL] " . $cgi->url(-relative => 1, -query => 1));
1288 : parrello 1.94 }
1289 : parrello 1.93 if (T(CGI => 3)) {
1290 :     # Here we want to trace the parameter data.
1291 :     my @names = $cgi->param;
1292 :     for my $parmName (sort @names) {
1293 :     # Note we skip the Trace parameters, which are for our use only.
1294 :     if ($parmName ne 'Trace' && $parmName ne 'TF') {
1295 :     my @values = $cgi->param($parmName);
1296 : parrello 1.97 Trace("[CGI] $parmName = " . join(", ", @values));
1297 : parrello 1.93 }
1298 :     }
1299 :     # Display the request method.
1300 :     my $method = $cgi->request_method();
1301 :     Trace("Method: $method");
1302 :     }
1303 :     if (T(CGI => 4)) {
1304 :     # Here we want the environment data too.
1305 :     for my $envName (sort keys %ENV) {
1306 : parrello 1.97 Trace("[ENV] $envName = $ENV{$envName}");
1307 : parrello 1.12 }
1308 :     }
1309 : parrello 1.11 }
1310 :    
1311 : parrello 1.94 =head3 TraceImages
1312 :    
1313 :     Tracer::TraceImages($htmlString);
1314 :    
1315 :     Trace information about all of an html document's images. The tracing
1316 :     will be for type "IMG" at level 3. The image's source string
1317 :     will be displayed. This is generally either the URL of the image or
1318 :     raw data for the image itself. If the source is too long, only the first 300
1319 :     characters will be shown at trace level 3. The entire source will be shown,
1320 :     however, at trace level 4. This method is not very smart, and might catch
1321 :     Javascript code, but it is still useful when debugging the arcane
1322 :     behavior of images in multiple browser environments.
1323 :    
1324 :     =over 4
1325 :    
1326 :     =item htmlString
1327 :    
1328 :     HTML text for an outgoing web page.
1329 :    
1330 :     =back
1331 :    
1332 :     =cut
1333 :    
1334 :     sub TraceImages {
1335 :     # Only proceed if we're at the proper trace level.
1336 :     if (T(IMG => 3)) {
1337 :     # For performance reasons we're manipulating $_[0] instead of retrieving the string
1338 :     # into a variable called "$htmlString". This is because we expect html strings to be
1339 :     # long, and don't want to copy them any more than we have to.
1340 :     Trace(length($_[0]) . " characters in web page.");
1341 :     # Loop through the HTML, culling image tags.
1342 :     while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1343 :     # Extract the source string and determine whether or not it's too long.
1344 :     my $srcString = $1;
1345 :     my $pos = pos($_[0]) - length($srcString);
1346 :     my $excess = length($srcString) - 300;
1347 :     # We'll put the display string in here.
1348 :     my $srcDisplay = $srcString;
1349 :     # If it's a data string, split it at the comma.
1350 :     $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1351 :     # If there's no excess or we're at trace level 4, we're done. At level 3 with
1352 :     # a long string, however, we only show the first 300 characters.
1353 :     if ($excess > 0 && ! T(IMG => 4)) {
1354 :     $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1355 :     }
1356 :     # Output the trace message.
1357 :     Trace("Image tag at position $pos:\n$srcDisplay");
1358 :     }
1359 :     }
1360 :     }
1361 :    
1362 :    
1363 : parrello 1.97 =head3 ScriptFinish (deprecated)
1364 : parrello 1.93
1365 :     ScriptFinish($webData, $varHash);
1366 :    
1367 :     Output a web page at the end of a script. Either the string to be output or the
1368 :     name of a template file can be specified. If the second parameter is omitted,
1369 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1370 :     name of a template file. The template should have the variable C<DebugData>
1371 :     specified in any form that invokes a standard script. If debugging mode is turned
1372 :     on, a form field will be put in that allows the user to enter tracing data.
1373 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1374 :     the output, formatted as a list.
1375 :    
1376 :     A typical standard script would loook like the following.
1377 :    
1378 :     BEGIN {
1379 :     # Print the HTML header.
1380 :     print "CONTENT-TYPE: text/html\n\n";
1381 :     }
1382 :     use Tracer;
1383 :     use CGI;
1384 :     use FIG;
1385 :     # ... more uses ...
1386 : parrello 1.6
1387 : parrello 1.93 my ($cgi, $varHash) = ScriptSetup();
1388 :     eval {
1389 :     # ... get data from $cgi, put it in $varHash ...
1390 :     };
1391 :     if ($@) {
1392 :     Trace("Script Error: $@") if T(0);
1393 :     }
1394 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1395 : parrello 1.6
1396 : parrello 1.93 The idea here is that even if the script fails, you'll see trace messages and
1397 :     useful output.
1398 : parrello 1.6
1399 :     =over 4
1400 :    
1401 : parrello 1.93 =item webData
1402 :    
1403 :     A string containing either the full web page to be written to the output or the
1404 :     name of a template file from which the page is to be constructed. If the name
1405 :     of a template file is specified, then the second parameter must be present;
1406 :     otherwise, it must be absent.
1407 :    
1408 :     =item varHash (optional)
1409 : parrello 1.6
1410 : parrello 1.93 If specified, then a reference to a hash mapping variable names for a template
1411 :     to their values. The template file will be read into memory, and variable markers
1412 :     will be replaced by data in this hash reference.
1413 : parrello 1.6
1414 :     =back
1415 :    
1416 :     =cut
1417 :    
1418 : parrello 1.93 sub ScriptFinish {
1419 :     # Get the parameters.
1420 :     my ($webData, $varHash) = @_;
1421 :     # Check for a template file situation.
1422 :     my $outputString;
1423 :     if (defined $varHash) {
1424 :     # Here we have a template file. We need to determine the template type.
1425 :     my $template;
1426 :     if ($FIG_Config::template_url && $webData =~ /\.php$/) {
1427 :     $template = "$FIG_Config::template_url/$webData";
1428 :     } else {
1429 :     $template = "<<$webData";
1430 :     }
1431 :     $outputString = PageBuilder::Build($template, $varHash, "Html");
1432 :     } else {
1433 :     # Here the user gave us a raw string.
1434 :     $outputString = $webData;
1435 :     }
1436 :     # Check for trace messages.
1437 :     if ($Destination ne "NONE" && $TraceLevel > 0) {
1438 :     # We have trace messages, so we want to put them at the end of the body. This
1439 :     # is either at the end of the whole string or at the beginning of the BODY
1440 :     # end-tag.
1441 :     my $pos = length $outputString;
1442 :     if ($outputString =~ m#</body>#gi) {
1443 :     $pos = (pos $outputString) - 7;
1444 :     }
1445 :     # If the trace messages were queued, we unroll them. Otherwise, we display the
1446 :     # destination.
1447 :     my $traceHtml;
1448 :     if ($Destination eq "QUEUE") {
1449 :     $traceHtml = QTrace('Html');
1450 :     } elsif ($Destination =~ /^>>(.+)$/) {
1451 :     # Here the tracing output it to a file. We code it as a hyperlink so the user
1452 :     # can copy the file name into the clipboard easily.
1453 :     my $actualDest = $1;
1454 :     $traceHtml = "<p>Tracing output to $actualDest.</p>\n";
1455 :     } else {
1456 :     # Here we have one of the special destinations.
1457 :     $traceHtml = "<P>Tracing output type is $Destination.</p>\n";
1458 :     }
1459 :     substr $outputString, $pos, 0, $traceHtml;
1460 :     }
1461 :     # Write the output string.
1462 :     print $outputString;
1463 : parrello 1.6 }
1464 :    
1465 : parrello 1.93 =head2 Command-Line Utility Methods
1466 : olson 1.1
1467 : parrello 1.93 =head3 SendSMS
1468 : olson 1.1
1469 : parrello 1.93 my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1470 : olson 1.1
1471 : parrello 1.93 Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1472 :     user name, password, and API ID for the relevant account in the hash reference variable
1473 :     I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1474 :     example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1475 :     is C<2561022>, then the FIG_Config file must contain
1476 : olson 1.1
1477 : parrello 1.93 $phone = { user => 'BruceTheHumanPet',
1478 :     password => 'silly',
1479 :     api_id => '2561022' };
1480 : olson 1.1
1481 : parrello 1.93 The original purpose of this method was to insure Bruce would be notified immediately when the
1482 :     Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1483 :     when you call this method.
1484 : olson 1.1
1485 : parrello 1.93 The message ID will be returned if successful, and C<undef> if an error occurs.
1486 : parrello 1.74
1487 : parrello 1.93 =over 4
1488 : parrello 1.74
1489 : parrello 1.93 =item phoneNumber
1490 : parrello 1.74
1491 : parrello 1.93 Phone number to receive the message, in international format. A United States phone number
1492 :     would be prefixed by "1". A British phone number would be prefixed by "44".
1493 : parrello 1.74
1494 : parrello 1.93 =item msg
1495 : parrello 1.74
1496 : parrello 1.93 Message to send to the specified phone.
1497 : parrello 1.74
1498 :     =item RETURN
1499 :    
1500 : parrello 1.93 Returns the message ID if successful, and C<undef> if the message could not be sent.
1501 : parrello 1.74
1502 : parrello 1.78 =back
1503 :    
1504 : parrello 1.74 =cut
1505 :    
1506 : parrello 1.93 sub SendSMS {
1507 : parrello 1.74 # Get the parameters.
1508 : parrello 1.93 my ($phoneNumber, $msg) = @_;
1509 :     # Declare the return variable. If we do not change it, C<undef> will be returned.
1510 : parrello 1.74 my $retVal;
1511 : parrello 1.93 # Only proceed if we have phone support.
1512 :     if (! defined $FIG_Config::phone) {
1513 :     Trace("Phone support not present in FIG_Config.") if T(1);
1514 :     } else {
1515 :     # Get the phone data.
1516 :     my $parms = $FIG_Config::phone;
1517 :     # Get the Clickatell URL.
1518 :     my $url = "http://api.clickatell.com/http/";
1519 :     # Create the user agent.
1520 :     my $ua = LWP::UserAgent->new;
1521 :     # Request a Clickatell session.
1522 :     my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1523 :     password => $parms->{password},
1524 :     api_id => $parms->{api_id},
1525 :     to => $phoneNumber,
1526 :     text => $msg});
1527 :     # Check for an error.
1528 :     if (! $resp->is_success) {
1529 :     Trace("Alert failed.") if T(1);
1530 :     } else {
1531 :     # Get the message ID.
1532 :     my $rstring = $resp->content;
1533 :     if ($rstring =~ /^ID:\s+(.*)$/) {
1534 :     $retVal = $1;
1535 :     } else {
1536 :     Trace("Phone attempt failed with $rstring") if T(1);
1537 :     }
1538 :     }
1539 : parrello 1.74 }
1540 :     # Return the result.
1541 :     return $retVal;
1542 :     }
1543 :    
1544 : parrello 1.93 =head3 StandardSetup
1545 : olson 1.1
1546 : parrello 1.93 my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1547 : olson 1.1
1548 : parrello 1.93 This method performs standard command-line parsing and tracing setup. The return
1549 :     values are a hash of the command-line options and a list of the positional
1550 :     parameters. Tracing is automatically set up and the command-line options are
1551 :     validated.
1552 : olson 1.1
1553 : parrello 1.93 This is a complex method that does a lot of grunt work. The parameters can
1554 :     be more easily understood, however, once they are examined individually.
1555 : olson 1.1
1556 : parrello 1.93 The I<categories> parameter is the most obtuse. It is a reference to a list of
1557 :     special-purpose tracing categories. Most tracing categories are PERL package
1558 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1559 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1560 : olson 1.1
1561 : parrello 1.93 ["Sprout", "SproutLoad", "ERDB"]
1562 : olson 1.1
1563 : parrello 1.93 This would cause trace messages in the specified three packages to appear in
1564 :     the output. There are two special tracing categories that are automatically
1565 :     handled by this method. In other words, if you used L</TSetup> you would need
1566 :     to include these categories manually, but if you use this method they are turned
1567 :     on automatically.
1568 : parrello 1.5
1569 :     =over 4
1570 :    
1571 : parrello 1.93 =item SQL
1572 : parrello 1.5
1573 : parrello 1.93 Traces SQL commands and activity.
1574 : parrello 1.5
1575 : parrello 1.93 =item Tracer
1576 : parrello 1.5
1577 : parrello 1.93 Traces error messages and call stacks.
1578 : parrello 1.5
1579 :     =back
1580 :    
1581 : parrello 1.93 C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1582 :     The trace level is specified using the C<-trace> command-line option. For example,
1583 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
1584 :     all tracing at level 3.
1585 : parrello 1.5
1586 : parrello 1.93 TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1587 : parrello 1.5
1588 : parrello 1.93 Standard tracing is output to the standard output and echoed to the file
1589 :     C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1590 :     process ID. You can also specify the C<user> parameter to put a user ID
1591 :     instead of a process ID in the trace file name. So, for example
1592 : olson 1.1
1593 : parrello 1.93 The default trace level is 2. To get all messages, specify a trace level of 4.
1594 :     For a genome-by-genome update, use 3.
1595 : olson 1.1
1596 : parrello 1.93 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1597 : olson 1.1
1598 : parrello 1.93 would send the trace output to C<traceBruce.log> in the temporary directory.
1599 : olson 1.1
1600 : parrello 1.93 The I<options> parameter is a reference to a hash containing the command-line
1601 :     options, their default values, and an explanation of what they mean. Command-line
1602 :     options may be in the form of switches or keywords. In the case of a switch, the
1603 :     option value is 1 if it is specified and 0 if it is not specified. In the case
1604 :     of a keyword, the value is separated from the option name by an equal sign. You
1605 :     can see this last in the command-line example above.
1606 : olson 1.1
1607 : parrello 1.93 You can specify a different default trace level by setting C<$options->{trace}>
1608 :     prior to calling this method.
1609 : olson 1.1
1610 : parrello 1.93 An example at this point would help. Consider, for example, the command-line utility
1611 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
1612 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1613 :     the following code.
1614 : olson 1.1
1615 : parrello 1.93 my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1616 :     { safe => [0, "use database transactions"],
1617 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
1618 :     start => [' ', "start with this genome"],
1619 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
1620 :     "<command> <transactionDirectory> <IDfile>",
1621 :     @ARGV);
1622 : olson 1.1
1623 :    
1624 : parrello 1.93 The call to C<ParseCommand> specifies the default values for the options and
1625 :     stores the actual options in a hash that is returned as C<$options>. The
1626 :     positional parameters are returned in C<@parameters>.
1627 : olson 1.1
1628 : parrello 1.93 The following is a sample command line for C<TransactFeatures>.
1629 : olson 1.1
1630 : parrello 1.93 TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1631 : olson 1.1
1632 : parrello 1.93 Single and double hyphens are equivalent. So, you could also code the
1633 :     above command as
1634 : olson 1.1
1635 : parrello 1.93 TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1636 : olson 1.1
1637 : parrello 1.93 In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1638 :     parameters, and would find themselves in I<@parameters> after executing the
1639 :     above code fragment. The tracing would be set to level 2, and the categories
1640 :     would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1641 :     and C<DocUtils> was included because it came in within the first parameter
1642 :     to this method. The I<$options> hash would be
1643 : olson 1.1
1644 : parrello 1.93 { trace => 2, sql => 0, safe => 0,
1645 :     noAlias => 1, start => ' ', tblFiles => 0 }
1646 : olson 1.1
1647 : parrello 1.93 Use of C<StandardSetup> in this way provides a simple way of performing
1648 :     standard tracing setup and command-line parsing. Note that the caller is
1649 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
1650 :     are used by this method to control the tracing. If additional tracing features
1651 :     need to be added in the future, they can be processed by this method without
1652 :     upsetting the command-line utilities.
1653 : olson 1.1
1654 : parrello 1.93 If the C<background> option is specified on the command line, then the
1655 :     standard and error outputs will be directed to files in the temporary
1656 :     directory, using the same suffix as the trace file. So, if the command
1657 :     line specified
1658 : olson 1.1
1659 : parrello 1.93 -user=Bruce -background
1660 : olson 1.1
1661 : parrello 1.93 then the trace output would go to C<traceBruce.log>, the standard output to
1662 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1663 :     simplify starting a command in the background.
1664 : olson 1.1
1665 : parrello 1.93 The user name is also used as the tracing key for L</Emergency Tracing>.
1666 :     Specifying a value of C<E> for the trace level causes emergency tracing to
1667 :     be used instead of custom tracing. If the user name is not specified,
1668 :     the tracing key is taken from the C<Tracing> environment variable. If there
1669 : parrello 1.103 is no value for that variable, the tracing key will be computed from the active
1670 :     login ID.
1671 :    
1672 :     Since the default situation in StandardSetup is to trace to the standard
1673 :     output, errors that occur in command-line scripts will not generate
1674 :     RSS events. To force the events, use the C<warn> option.
1675 :    
1676 :     TransactFeatures -background -warn register ../xacts IDs.tbl
1677 : olson 1.1
1678 : parrello 1.93 Finally, if the special option C<-help> is specified, the option
1679 :     names will be traced at level 0 and the program will exit without processing.
1680 :     This provides a limited help capability. For example, if the user enters
1681 : olson 1.1
1682 : parrello 1.93 TransactFeatures -help
1683 : olson 1.1
1684 : parrello 1.93 he would see the following output.
1685 : olson 1.1
1686 : parrello 1.93 TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1687 :     -trace tracing level (default E)
1688 :     -sql trace SQL commands
1689 :     -safe use database transactions
1690 :     -noAlias do not expect aliases in CHANGE transactions
1691 :     -start start with this genome
1692 :     -tblFiles output TBL files containing the corrected IDs
1693 : olson 1.1
1694 : parrello 1.93 The caller has the option of modifying the tracing scheme by placing a value
1695 :     for C<trace> in the incoming options hash. The default value can be overridden,
1696 :     or the tracing to the standard output can be turned off by suffixing a minus
1697 :     sign to the trace level. So, for example,
1698 : olson 1.1
1699 : parrello 1.93 { trace => [0, "tracing level (default 0)"],
1700 :     ...
1701 : olson 1.1
1702 : parrello 1.93 would set the default trace level to 0 instead of E, while
1703 : olson 1.1
1704 : parrello 1.93 { trace => ["2-", "tracing level (default 2)"],
1705 :     ...
1706 : olson 1.1
1707 : parrello 1.93 would set the default to 2, but trace only to the log file, not to the
1708 :     standard output.
1709 : olson 1.1
1710 : parrello 1.93 The parameters to this method are as follows.
1711 : olson 1.1
1712 : parrello 1.93 =over 4
1713 : olson 1.1
1714 : parrello 1.93 =item categories
1715 : parrello 1.2
1716 : parrello 1.93 Reference to a list of tracing category names. These should be names of
1717 :     packages whose internal workings will need to be debugged to get the
1718 :     command working.
1719 : olson 1.1
1720 : parrello 1.93 =item options
1721 : olson 1.1
1722 : parrello 1.93 Reference to a hash containing the legal options for the current command mapped
1723 :     to their default values and descriptions. The user can override the defaults
1724 :     by specifying the options as command-line switches prefixed by a hyphen.
1725 :     Tracing-related options may be added to this hash. If the C<-h> option is
1726 :     specified on the command line, the option descriptions will be used to
1727 :     explain the options. To turn off tracing to the standard output, add a
1728 :     minus sign to the value for C<trace> (see above).
1729 : olson 1.1
1730 : parrello 1.93 =item parmHelp
1731 : olson 1.1
1732 : parrello 1.93 A string that vaguely describes the positional parameters. This is used
1733 :     if the user specifies the C<-h> option.
1734 : olson 1.1
1735 : parrello 1.93 =item argv
1736 : olson 1.1
1737 : parrello 1.93 List of command line parameters, including the option switches, which must
1738 :     precede the positional parameters and be prefixed by a hyphen.
1739 : olson 1.1
1740 :     =item RETURN
1741 :    
1742 : parrello 1.93 Returns a list. The first element of the list is the reference to a hash that
1743 :     maps the command-line option switches to their values. These will either be the
1744 :     default values or overrides specified on the command line. The remaining
1745 :     elements of the list are the position parameters, in order.
1746 : olson 1.1
1747 :     =back
1748 :    
1749 :     =cut
1750 :    
1751 : parrello 1.93 sub StandardSetup {
1752 :     # Get the parameters.
1753 :     my ($categories, $options, $parmHelp, @argv) = @_;
1754 :     # Get the default tracing key.
1755 :     my $tkey = EmergencyKey();
1756 : parrello 1.104 # Save the command line.
1757 :     $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1758 : parrello 1.93 # Add the tracing options.
1759 :     if (! exists $options->{trace}) {
1760 :     $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1761 :     }
1762 :     $options->{sql} = [0, "turn on SQL tracing"];
1763 :     $options->{help} = [0, "display command-line options"];
1764 :     $options->{user} = [$tkey, "tracing key"];
1765 :     $options->{background} = [0, "spool standard and error output"];
1766 : parrello 1.103 $options->{warn} = [0, "send errors to RSS feed"];
1767 : parrello 1.93 # Create a parsing hash from the options hash. The parsing hash
1768 :     # contains the default values rather than the default value
1769 :     # and the description. While we're at it, we'll memorize the
1770 :     # length of the longest option name.
1771 :     my $longestName = 0;
1772 :     my %parseOptions = ();
1773 :     for my $key (keys %{$options}) {
1774 :     if (length $key > $longestName) {
1775 :     $longestName = length $key;
1776 :     }
1777 :     $parseOptions{$key} = $options->{$key}->[0];
1778 :     }
1779 :     # Parse the command line.
1780 :     my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1781 :     # Get the logfile suffix.
1782 :     my $suffix = $retOptions->{user};
1783 :     # Check for background mode.
1784 :     if ($retOptions->{background}) {
1785 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
1786 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
1787 :     open STDOUT, ">$outFileName";
1788 :     open STDERR, ">$errFileName";
1789 :     # Check for phone support. If we have phone support and a phone number,
1790 :     # we want to turn it on.
1791 :     if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1792 :     $retOptions->{phone} = $ENV{PHONE};
1793 :     }
1794 :     }
1795 :     # Now we want to set up tracing. First, we need to know if the user
1796 :     # wants emergency tracing.
1797 :     if ($retOptions->{trace} eq 'E') {
1798 :     ETracing($retOptions->{user});
1799 :     } else {
1800 :     # Here the tracing is controlled from the command line.
1801 :     my @cats = @{$categories};
1802 :     if ($retOptions->{sql}) {
1803 :     push @cats, "SQL";
1804 :     }
1805 : parrello 1.103 if ($retOptions->{warn}) {
1806 :     push @cats, "Feed";
1807 :     }
1808 : parrello 1.93 # Add the default categories.
1809 :     push @cats, "Tracer";
1810 :     # Next, we create the category string by joining the categories.
1811 :     my $cats = join(" ", @cats);
1812 :     # Check to determine whether or not the caller wants to turn off tracing
1813 :     # to the standard output.
1814 :     my $traceLevel = $retOptions->{trace};
1815 :     my $textOKFlag = 1;
1816 :     if ($traceLevel =~ /^(.)-/) {
1817 :     $traceLevel = $1;
1818 :     $textOKFlag = 0;
1819 :     }
1820 :     # Now we set up the trace mode.
1821 :     my $traceMode;
1822 :     # Verify that we can open a file in the FIG temporary directory.
1823 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1824 :     if (open TESTTRACE, ">$traceFileName") {
1825 :     # Here we can trace to a file.
1826 :     $traceMode = ">$traceFileName";
1827 :     if ($textOKFlag) {
1828 :     # Echo to standard output if the text-OK flag is set.
1829 :     $traceMode = "+$traceMode";
1830 :     }
1831 :     # Close the test file.
1832 :     close TESTTRACE;
1833 :     } else {
1834 : parrello 1.98 # Here we can't trace to a file. Complain about this.
1835 :     warn "Could not open trace file $traceFileName: $!\n";
1836 :     # We trace to the standard output if it's
1837 :     # okay, and the error log otherwise.
1838 : parrello 1.93 if ($textOKFlag) {
1839 :     $traceMode = "TEXT";
1840 : parrello 1.12 } else {
1841 : parrello 1.93 $traceMode = "WARN";
1842 : parrello 1.12 }
1843 :     }
1844 : parrello 1.93 # Now set up the tracing.
1845 :     TSetup("$traceLevel $cats", $traceMode);
1846 :     }
1847 :     # Check for the "help" option. If it is specified, dump the command-line
1848 :     # options and exit the program.
1849 :     if ($retOptions->{help}) {
1850 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1851 :     print "$1 [options] $parmHelp\n";
1852 :     for my $key (sort keys %{$options}) {
1853 :     my $name = Pad($key, $longestName, 0, ' ');
1854 :     my $desc = $options->{$key}->[1];
1855 :     if ($options->{$key}->[0]) {
1856 :     $desc .= " (default " . $options->{$key}->[0] . ")";
1857 :     }
1858 :     print " $name $desc\n";
1859 : parrello 1.36 }
1860 : parrello 1.93 exit(0);
1861 :     }
1862 :     # Trace the options, if applicable.
1863 :     if (T(3)) {
1864 :     my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1865 :     Trace("Selected options: " . join(", ", sort @parms) . ".");
1866 : parrello 1.3 }
1867 : parrello 1.93 # Return the parsed parameters.
1868 :     return ($retOptions, @retParameters);
1869 : olson 1.1 }
1870 :    
1871 : parrello 1.93 =head3 ReadOptions
1872 : olson 1.1
1873 : parrello 1.93 my %options = Tracer::ReadOptions($fileName);
1874 : olson 1.1
1875 : parrello 1.93 Read a set of options from a file. Each option is encoded in a line of text that has the
1876 :     format
1877 : olson 1.1
1878 : parrello 1.93 I<optionName>C<=>I<optionValue>C<; >I<comment>
1879 : olson 1.1
1880 : parrello 1.93 The option name must consist entirely of letters, digits, and the punctuation characters
1881 :     C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1882 :     character is a semi-colon will be ignored. The return hash will map each option name to
1883 :     the corresponding option value.
1884 : olson 1.1
1885 :     =over 4
1886 :    
1887 : parrello 1.93 =item fileName
1888 : olson 1.1
1889 : parrello 1.93 Name of the file containing the option data.
1890 : olson 1.1
1891 :     =item RETURN
1892 :    
1893 : parrello 1.93 Returns a hash mapping the option names specified in the file to their corresponding option
1894 :     value.
1895 : olson 1.1
1896 :     =back
1897 :    
1898 :     =cut
1899 :    
1900 : parrello 1.93 sub ReadOptions {
1901 : parrello 1.12 # Get the parameters.
1902 : parrello 1.93 my ($fileName) = @_;
1903 :     # Open the file.
1904 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1905 :     # Count the number of records read.
1906 :     my ($records, $comments) = 0;
1907 :     # Create the return hash.
1908 :     my %retVal = ();
1909 :     # Loop through the file, accumulating key-value pairs.
1910 :     while (my $line = <CONFIGFILE>) {
1911 :     # Denote we've read a line.
1912 :     $records++;
1913 :     # Determine the line type.
1914 :     if ($line =~ /^\s*[\n\r]/) {
1915 :     # A blank line is a comment.
1916 :     $comments++;
1917 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1918 :     # Here we have an option assignment.
1919 :     retVal{$1} = $2;
1920 :     } elsif ($line =~ /^\s*;/) {
1921 :     # Here we have a text comment.
1922 :     $comments++;
1923 : parrello 1.12 } else {
1924 : parrello 1.93 # Here we have an invalid line.
1925 :     Trace("Invalid option statement in record $records.") if T(0);
1926 : parrello 1.12 }
1927 :     }
1928 : parrello 1.93 # Return the hash created.
1929 :     return %retVal;
1930 : olson 1.1 }
1931 :    
1932 : parrello 1.93 =head3 GetOptions
1933 : parrello 1.9
1934 : parrello 1.93 Tracer::GetOptions(\%defaults, \%options);
1935 : parrello 1.9
1936 : parrello 1.93 Merge a specified set of options into a table of defaults. This method takes two hash references
1937 :     as input and uses the data from the second to update the first. If the second does not exist,
1938 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
1939 :     exist in the first.
1940 : parrello 1.9
1941 : parrello 1.93 Consider the following example.
1942 : parrello 1.9
1943 : parrello 1.93 my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1944 : parrello 1.9
1945 : parrello 1.93 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1946 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1947 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1948 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1949 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1950 : parrello 1.9
1951 : parrello 1.93 {databaseType => 'Oracle'}
1952 : parrello 1.9
1953 : parrello 1.93 an error will occur because the B<databaseType> option does not exist.
1954 : parrello 1.9
1955 : parrello 1.93 =over 4
1956 : parrello 1.9
1957 : parrello 1.93 =item defaults
1958 : parrello 1.9
1959 : parrello 1.93 Table of default option values.
1960 : parrello 1.9
1961 : parrello 1.93 =item options
1962 : olson 1.1
1963 : parrello 1.93 Table of overrides, if any.
1964 : olson 1.1
1965 :     =item RETURN
1966 :    
1967 : parrello 1.93 Returns a reference to the default table passed in as the first parameter.
1968 : olson 1.1
1969 :     =back
1970 :    
1971 :     =cut
1972 :    
1973 : parrello 1.93 sub GetOptions {
1974 :     # Get the parameters.
1975 :     my ($defaults, $options) = @_;
1976 :     # Check for overrides.
1977 :     if ($options) {
1978 :     # Loop through the overrides.
1979 :     while (my ($option, $setting) = each %{$options}) {
1980 :     # Insure this override exists.
1981 :     if (!exists $defaults->{$option}) {
1982 :     croak "Unrecognized option $option encountered.";
1983 : parrello 1.12 } else {
1984 : parrello 1.93 # Apply the override.
1985 :     $defaults->{$option} = $setting;
1986 : parrello 1.12 }
1987 :     }
1988 :     }
1989 : parrello 1.93 # Return the merged table.
1990 :     return $defaults;
1991 : olson 1.1 }
1992 :    
1993 : parrello 1.93 =head3 MergeOptions
1994 : olson 1.1
1995 : parrello 1.93 Tracer::MergeOptions(\%table, \%defaults);
1996 : olson 1.1
1997 : parrello 1.93 Merge default values into a hash table. This method looks at the key-value pairs in the
1998 :     second (default) hash, and if a matching key is not found in the first hash, the default
1999 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
2000 :     checking and no return value.
2001 : olson 1.1
2002 :     =over 4
2003 :    
2004 : parrello 1.93 =item table
2005 : olson 1.1
2006 : parrello 1.93 Hash table to be updated with the default values.
2007 : olson 1.1
2008 : parrello 1.93 =item defaults
2009 : olson 1.1
2010 : parrello 1.93 Default values to be merged into the first hash table if they are not already present.
2011 : olson 1.1
2012 :     =back
2013 :    
2014 :     =cut
2015 :    
2016 : parrello 1.93 sub MergeOptions {
2017 :     # Get the parameters.
2018 :     my ($table, $defaults) = @_;
2019 :     # Loop through the defaults.
2020 :     while (my ($key, $value) = each %{$defaults}) {
2021 :     if (!exists $table->{$key}) {
2022 :     $table->{$key} = $value;
2023 :     }
2024 : parrello 1.12 }
2025 : olson 1.1 }
2026 :    
2027 : parrello 1.93 =head3 ParseCommand
2028 : olson 1.1
2029 : parrello 1.93 my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2030 : olson 1.1
2031 : parrello 1.93 Parse a command line consisting of a list of parameters. The initial parameters may be option
2032 :     specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2033 :     off and merged into a table of default options. The remainder of the command line is
2034 :     returned as a list of positional arguments. For example, consider the following invocation.
2035 : olson 1.1
2036 : parrello 1.93 my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2037 : olson 1.1
2038 : parrello 1.93 In this case, the list @words will be treated as a command line and there are two options available,
2039 :     B<errors> and B<logFile>. If @words has the following format
2040 : olson 1.1
2041 : parrello 1.93 -logFile=error.log apple orange rutabaga
2042 : olson 1.1
2043 : parrello 1.93 then at the end of the invocation, C<$options> will be
2044 : olson 1.1
2045 : parrello 1.93 { errors => 0, logFile => 'error.log' }
2046 : olson 1.1
2047 : parrello 1.93 and C<@arguments> will contain
2048 : olson 1.1
2049 : parrello 1.93 apple orange rutabaga
2050 : olson 1.1
2051 : parrello 1.93 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2052 :     support for quote characters. Options can be specified with single or double hyphens.
2053 : parrello 1.54
2054 :     =over 4
2055 :    
2056 : parrello 1.93 =item optionTable
2057 : parrello 1.54
2058 : parrello 1.93 Table of default options.
2059 : parrello 1.54
2060 : parrello 1.93 =item inputList
2061 : parrello 1.54
2062 : parrello 1.93 List of words on the command line.
2063 : parrello 1.54
2064 :     =item RETURN
2065 :    
2066 : parrello 1.93 Returns a reference to the option table and a list of the positional arguments.
2067 : parrello 1.54
2068 :     =back
2069 :    
2070 :     =cut
2071 :    
2072 : parrello 1.93 sub ParseCommand {
2073 : parrello 1.54 # Get the parameters.
2074 : parrello 1.93 my ($optionTable, @inputList) = @_;
2075 :     # Process any options in the input list.
2076 :     my %overrides = ();
2077 :     while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2078 :     # Get the current option.
2079 :     my $arg = shift @inputList;
2080 :     # Pull out the option name.
2081 :     $arg =~ /^--?([^=]*)/g;
2082 :     my $name = $1;
2083 :     # Check for an option value.
2084 :     if ($arg =~ /\G=(.*)$/g) {
2085 :     # Here we have a value for the option.
2086 :     $overrides{$name} = UnEscape($1);
2087 :     } else {
2088 :     # Here there is no value, so we use 1.
2089 :     $overrides{$name} = 1;
2090 :     }
2091 :     }
2092 :     # Merge the options into the defaults.
2093 :     GetOptions($optionTable, \%overrides);
2094 :     # Translate the remaining parameters.
2095 :     my @retVal = ();
2096 :     for my $inputParm (@inputList) {
2097 :     push @retVal, UnEscape($inputParm);
2098 : parrello 1.54 }
2099 : parrello 1.93 # Return the results.
2100 :     return ($optionTable, @retVal);
2101 : parrello 1.54 }
2102 :    
2103 : parrello 1.93
2104 :     =head2 File Utility Methods
2105 :    
2106 : olson 1.1 =head3 GetFile
2107 :    
2108 : parrello 1.92 my @fileContents = Tracer::GetFile($fileName);
2109 : olson 1.1
2110 : parrello 1.35 or
2111 :    
2112 : parrello 1.92 my $fileContents = Tracer::GetFile($fileName);
2113 : parrello 1.35
2114 :     Return the entire contents of a file. In list context, line-ends are removed and
2115 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2116 : olson 1.1
2117 :     =over 4
2118 :    
2119 :     =item fileName
2120 :    
2121 :     Name of the file to read.
2122 :    
2123 :     =item RETURN
2124 :    
2125 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
2126 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
2127 :     the file, an empty list will be returned.
2128 : olson 1.1
2129 :     =back
2130 :    
2131 :     =cut
2132 :    
2133 :     sub GetFile {
2134 : parrello 1.12 # Get the parameters.
2135 :     my ($fileName) = @_;
2136 :     # Declare the return variable.
2137 :     my @retVal = ();
2138 :     # Open the file for input.
2139 : parrello 1.60 my $handle = Open(undef, "<$fileName");
2140 :     # Read the whole file into the return variable, stripping off any terminator
2141 :     # characters.
2142 :     my $lineCount = 0;
2143 :     while (my $line = <$handle>) {
2144 :     $lineCount++;
2145 :     $line = Strip($line);
2146 :     push @retVal, $line;
2147 :     }
2148 :     # Close it.
2149 :     close $handle;
2150 :     my $actualLines = @retVal;
2151 : parrello 1.77 Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2152 : parrello 1.12 # Return the file's contents in the desired format.
2153 : parrello 1.9 if (wantarray) {
2154 : parrello 1.12 return @retVal;
2155 : parrello 1.6 } else {
2156 :     return join "\n", @retVal;
2157 :     }
2158 : olson 1.1 }
2159 :    
2160 : parrello 1.60 =head3 PutFile
2161 :    
2162 : parrello 1.92 Tracer::PutFile($fileName, \@lines);
2163 : parrello 1.60
2164 :     Write out a file from a list of lines of text.
2165 :    
2166 :     =over 4
2167 :    
2168 :     =item fileName
2169 :    
2170 :     Name of the output file.
2171 :    
2172 :     =item lines
2173 :    
2174 :     Reference to a list of text lines. The lines will be written to the file in order, with trailing
2175 : parrello 1.66 new-line characters. Alternatively, may be a string, in which case the string will be written without
2176 :     modification.
2177 : parrello 1.60
2178 :     =back
2179 :    
2180 :     =cut
2181 :    
2182 :     sub PutFile {
2183 :     # Get the parameters.
2184 :     my ($fileName, $lines) = @_;
2185 :     # Open the output file.
2186 :     my $handle = Open(undef, ">$fileName");
2187 : parrello 1.77 # Count the lines written.
2188 : parrello 1.66 if (ref $lines ne 'ARRAY') {
2189 :     # Here we have a scalar, so we write it raw.
2190 :     print $handle $lines;
2191 : parrello 1.77 Trace("Scalar put to file $fileName.") if T(File => 3);
2192 : parrello 1.66 } else {
2193 :     # Write the lines one at a time.
2194 : parrello 1.77 my $count = 0;
2195 : parrello 1.66 for my $line (@{$lines}) {
2196 :     print $handle "$line\n";
2197 : parrello 1.77 $count++;
2198 : parrello 1.66 }
2199 : parrello 1.77 Trace("$count lines put to file $fileName.") if T(File => 3);
2200 : parrello 1.60 }
2201 :     # Close the output file.
2202 :     close $handle;
2203 :     }
2204 :    
2205 : parrello 1.93 =head3 ParseRecord
2206 : olson 1.1
2207 : parrello 1.93 my @fields = Tracer::ParseRecord($line);
2208 : olson 1.1
2209 : parrello 1.93 Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2210 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2211 :     These will automatically be converted.
2212 : olson 1.1
2213 :     =over 4
2214 :    
2215 : parrello 1.93 =item line
2216 :    
2217 :     Line of data containing the tab-delimited fields.
2218 :    
2219 :     =item RETURN
2220 : olson 1.1
2221 : parrello 1.93 Returns a list of the fields found in the data line.
2222 : olson 1.1
2223 :     =back
2224 :    
2225 :     =cut
2226 :    
2227 : parrello 1.93 sub ParseRecord {
2228 : parrello 1.12 # Get the parameter.
2229 : parrello 1.93 my ($line) = @_;
2230 :     # Remove the trailing new-line, if any.
2231 :     chomp $line;
2232 :     # Split the line read into pieces using the tab character.
2233 :     my @retVal = split /\t/, $line;
2234 :     # Trim and fix the escapes in each piece.
2235 :     for my $value (@retVal) {
2236 :     # Trim leading whitespace.
2237 :     $value =~ s/^\s+//;
2238 :     # Trim trailing whitespace.
2239 :     $value =~ s/\s+$//;
2240 :     # Delete the carriage returns.
2241 :     $value =~ s/\r//g;
2242 :     # Convert the escapes into their real values.
2243 :     $value =~ s/\\t/"\t"/ge;
2244 :     $value =~ s/\\n/"\n"/ge;
2245 :     }
2246 :     # Return the result.
2247 :     return @retVal;
2248 :     }
2249 :    
2250 :     =head3 Merge
2251 :    
2252 :     my @mergedList = Tracer::Merge(@inputList);
2253 :    
2254 :     Sort a list of strings and remove duplicates.
2255 :    
2256 :     =over 4
2257 :    
2258 :     =item inputList
2259 :    
2260 :     List of scalars to sort and merge.
2261 :    
2262 :     =item RETURN
2263 :    
2264 :     Returns a list containing the same elements sorted in ascending order with duplicates
2265 :     removed.
2266 :    
2267 :     =back
2268 :    
2269 :     =cut
2270 :    
2271 :     sub Merge {
2272 :     # Get the input list in sort order.
2273 :     my @inputList = sort @_;
2274 :     # Only proceed if the list has at least two elements.
2275 :     if (@inputList > 1) {
2276 :     # Now we want to move through the list splicing out duplicates.
2277 :     my $i = 0;
2278 :     while ($i < @inputList) {
2279 :     # Get the current entry.
2280 :     my $thisEntry = $inputList[$i];
2281 :     # Find out how many elements duplicate the current entry.
2282 :     my $j = $i + 1;
2283 :     my $dup1 = $i + 1;
2284 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2285 :     # If the number is nonzero, splice out the duplicates found.
2286 :     if ($j > $dup1) {
2287 :     splice @inputList, $dup1, $j - $dup1;
2288 : parrello 1.14 }
2289 : parrello 1.93 # Now the element at position $dup1 is different from the element before it
2290 :     # at position $i. We push $i forward one position and start again.
2291 :     $i++;
2292 : parrello 1.14 }
2293 : parrello 1.12 }
2294 : parrello 1.93 # Return the merged list.
2295 :     return @inputList;
2296 : olson 1.1 }
2297 :    
2298 : parrello 1.93 =head3 Open
2299 : olson 1.1
2300 : parrello 1.93 my $handle = Open($fileHandle, $fileSpec, $message);
2301 : olson 1.1
2302 : parrello 1.93 Open a file.
2303 : olson 1.1
2304 : parrello 1.93 The I<$fileSpec> is essentially the second argument of the PERL C<open>
2305 :     function. The mode is specified using Unix-like shell information. So, for
2306 :     example,
2307 : olson 1.1
2308 : parrello 1.93 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2309 : olson 1.1
2310 : parrello 1.93 would open for output appended to the specified file, and
2311 : olson 1.1
2312 : parrello 1.93 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2313 : olson 1.1
2314 : parrello 1.93 would open a pipe that sorts the records written and removes duplicates. Note
2315 :     the use of file handle syntax in the Open call. To use anonymous file handles,
2316 :     code as follows.
2317 : olson 1.1
2318 : parrello 1.93 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2319 : olson 1.1
2320 : parrello 1.93 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2321 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2322 :     failed open will throw an exception and the third parameter will be used to construct
2323 :     an error message. If the parameter is omitted, a standard message is constructed
2324 :     using the file spec.
2325 : olson 1.1
2326 : parrello 1.93 Could not open "/usr/spool/news/twitlog"
2327 : olson 1.1
2328 : parrello 1.93 Note that the mode characters are automatically cleaned from the file name.
2329 :     The actual error message from the file system will be captured and appended to the
2330 :     message in any case.
2331 : parrello 1.6
2332 : parrello 1.93 Could not open "/usr/spool/news/twitlog": file not found.
2333 : parrello 1.6
2334 : parrello 1.93 In some versions of PERL the only error message we get is a number, which
2335 :     corresponds to the C++ C<errno> value.
2336 : parrello 1.6
2337 : parrello 1.93 Could not open "/usr/spool/news/twitlog": 6.
2338 : parrello 1.6
2339 : parrello 1.93 =over 4
2340 : parrello 1.6
2341 : parrello 1.93 =item fileHandle
2342 : parrello 1.6
2343 : parrello 1.93 File handle. If this parameter is C<undef>, a file handle will be generated
2344 :     and returned as the value of this method.
2345 : olson 1.1
2346 : parrello 1.93 =item fileSpec
2347 : olson 1.1
2348 : parrello 1.93 File name and mode, as per the PERL C<open> function.
2349 : olson 1.1
2350 : parrello 1.93 =item message (optional)
2351 : olson 1.1
2352 : parrello 1.93 Error message to use if the open fails. If omitted, a standard error message
2353 :     will be generated. In either case, the error information from the file system
2354 :     is appended to the message. To specify a conditional open that does not throw
2355 :     an error if it fails, use C<0>.
2356 : olson 1.1
2357 : parrello 1.93 =item RETURN
2358 : olson 1.1
2359 : parrello 1.93 Returns the name of the file handle assigned to the file, or C<undef> if the
2360 :     open failed.
2361 : olson 1.1
2362 :     =back
2363 :    
2364 :     =cut
2365 :    
2366 : parrello 1.93 sub Open {
2367 : parrello 1.12 # Get the parameters.
2368 : parrello 1.93 my ($fileHandle, $fileSpec, $message) = @_;
2369 :     # Attempt to open the file.
2370 :     my $rv = open $fileHandle, $fileSpec;
2371 :     # If the open failed, generate an error message.
2372 :     if (! $rv) {
2373 :     # Save the system error message.
2374 :     my $sysMessage = $!;
2375 :     # See if we need a default message.
2376 :     if (!$message) {
2377 :     # Clean any obvious mode characters and leading spaces from the
2378 :     # filename.
2379 :     my ($fileName) = FindNamePart($fileSpec);
2380 :     $message = "Could not open \"$fileName\"";
2381 :     }
2382 :     # Terminate with an error using the supplied message and the
2383 :     # error message from the file system.
2384 :     Confess("$message: $!");
2385 : parrello 1.12 }
2386 : parrello 1.93 # Return the file handle.
2387 :     return $fileHandle;
2388 : olson 1.1 }
2389 :    
2390 : parrello 1.93 =head3 FindNamePart
2391 :    
2392 :     my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2393 :    
2394 :     Extract the portion of a file specification that contains the file name.
2395 :    
2396 :     A file specification is the string passed to an C<open> call. It specifies the file
2397 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
2398 :     method assumes that the file name is whatever follows the first angle bracket
2399 :     sequence. So, for example, in the following strings the file name is
2400 :     C</usr/fig/myfile.txt>.
2401 : parrello 1.5
2402 : parrello 1.93 >>/usr/fig/myfile.txt
2403 :     </usr/fig/myfile.txt
2404 :     | sort -u > /usr/fig/myfile.txt
2405 : parrello 1.5
2406 : parrello 1.93 If the method cannot find a file name using its normal methods, it will return the
2407 :     whole incoming string.
2408 : parrello 1.5
2409 :     =over 4
2410 :    
2411 : parrello 1.93 =item fileSpec
2412 : parrello 1.5
2413 : parrello 1.93 File specification string from which the file name is to be extracted.
2414 : parrello 1.5
2415 :     =item RETURN
2416 :    
2417 : parrello 1.93 Returns a three-element list. The first element contains the file name portion of
2418 :     the specified string, or the whole string if a file name cannot be found via normal
2419 :     methods. The second element contains the start position of the file name portion and
2420 :     the third element contains the length.
2421 : parrello 1.5
2422 :     =back
2423 :    
2424 :     =cut
2425 : parrello 1.93 #: Return Type $;
2426 :     sub FindNamePart {
2427 :     # Get the parameters.
2428 :     my ($fileSpec) = @_;
2429 :     # Default to the whole input string.
2430 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2431 :     # Parse out the file name if we can.
2432 :     if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2433 :     $retVal = $2;
2434 :     $len = length $retVal;
2435 :     $pos = (length $fileSpec) - (length $3) - $len;
2436 : parrello 1.12 }
2437 : parrello 1.93 # Return the result.
2438 :     return ($retVal, $pos, $len);
2439 : parrello 1.5 }
2440 :    
2441 : parrello 1.93 =head3 OpenDir
2442 : parrello 1.5
2443 : parrello 1.93 my @files = OpenDir($dirName, $filtered, $flag);
2444 : parrello 1.5
2445 : parrello 1.93 Open a directory and return all the file names. This function essentially performs
2446 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2447 :     set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2448 :     or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2449 :     filtered out of the return list. If the directory does not open and I<$flag> is not
2450 :     set, an exception is thrown. So, for example,
2451 : parrello 1.5
2452 : parrello 1.93 my @files = OpenDir("/Volumes/fig/contigs", 1);
2453 : parrello 1.5
2454 : parrello 1.93 is effectively the same as
2455 : parrello 1.5
2456 : parrello 1.93 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2457 :     my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2458 : parrello 1.5
2459 : parrello 1.93 Similarly, the following code
2460 : parrello 1.5
2461 : parrello 1.93 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2462 : parrello 1.5
2463 : parrello 1.93 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2464 :     automatically returns an empty list if the directory fails to open.
2465 : parrello 1.5
2466 : parrello 1.93 =over 4
2467 : parrello 1.5
2468 : parrello 1.93 =item dirName
2469 : parrello 1.5
2470 : parrello 1.93 Name of the directory to open.
2471 : parrello 1.5
2472 : parrello 1.93 =item filtered
2473 : parrello 1.5
2474 : parrello 1.93 TRUE if files whose names begin with a period (C<.>) should be automatically removed
2475 :     from the list, else FALSE.
2476 : parrello 1.5
2477 : parrello 1.93 =item flag
2478 : parrello 1.5
2479 : parrello 1.93 TRUE if a failure to open is okay, else FALSE
2480 : parrello 1.5
2481 : parrello 1.93 =back
2482 : parrello 1.5
2483 : parrello 1.93 =cut
2484 :     #: Return Type @;
2485 :     sub OpenDir {
2486 :     # Get the parameters.
2487 :     my ($dirName, $filtered, $flag) = @_;
2488 :     # Declare the return variable.
2489 :     my @retVal = ();
2490 :     # Open the directory.
2491 :     if (opendir(my $dirHandle, $dirName)) {
2492 :     # The directory opened successfully. Get the appropriate list according to the
2493 :     # strictures of the filter parameter.
2494 :     if ($filtered) {
2495 :     @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2496 :     } else {
2497 :     @retVal = readdir $dirHandle;
2498 :     }
2499 :     } elsif (! $flag) {
2500 :     # Here the directory would not open and it's considered an error.
2501 :     Confess("Could not open directory $dirName.");
2502 :     }
2503 :     # Return the result.
2504 :     return @retVal;
2505 :     }
2506 : parrello 1.5
2507 :    
2508 : parrello 1.93 =head3 Insure
2509 : parrello 1.5
2510 : parrello 1.93 Insure($dirName, $chmod);
2511 : parrello 1.5
2512 : parrello 1.93 Insure a directory is present.
2513 : parrello 1.5
2514 : parrello 1.93 =over 4
2515 : parrello 1.5
2516 : parrello 1.93 =item dirName
2517 : olson 1.1
2518 : parrello 1.93 Name of the directory to check. If it does not exist, it will be created.
2519 : parrello 1.7
2520 : parrello 1.93 =item chmod (optional)
2521 : parrello 1.7
2522 : parrello 1.93 Security privileges to be given to the directory if it is created.
2523 : parrello 1.7
2524 : parrello 1.93 =back
2525 : parrello 1.7
2526 :     =cut
2527 :    
2528 : parrello 1.93 sub Insure {
2529 :     my ($dirName, $chmod) = @_;
2530 :     if (! -d $dirName) {
2531 :     Trace("Creating $dirName directory.") if T(2);
2532 :     eval {
2533 :     mkpath $dirName;
2534 :     # If we have permissions specified, set them here.
2535 :     if (defined($chmod)) {
2536 :     chmod $chmod, $dirName;
2537 :     }
2538 :     };
2539 :     if ($@) {
2540 :     Confess("Error creating $dirName: $@");
2541 :     }
2542 : parrello 1.12 }
2543 : parrello 1.9 }
2544 :    
2545 : parrello 1.93 =head3 ChDir
2546 : parrello 1.9
2547 : parrello 1.93 ChDir($dirName);
2548 : parrello 1.9
2549 : parrello 1.93 Change to the specified directory.
2550 : parrello 1.9
2551 :     =over 4
2552 :    
2553 : parrello 1.93 =item dirName
2554 : parrello 1.9
2555 : parrello 1.93 Name of the directory to which we want to change.
2556 : parrello 1.9
2557 :     =back
2558 :    
2559 :     =cut
2560 :    
2561 : parrello 1.93 sub ChDir {
2562 :     my ($dirName) = @_;
2563 :     if (! -d $dirName) {
2564 :     Confess("Cannot change to directory $dirName: no such directory.");
2565 :     } else {
2566 :     Trace("Changing to directory $dirName.") if T(File => 4);
2567 :     my $okFlag = chdir $dirName;
2568 :     if (! $okFlag) {
2569 :     Confess("Error switching to directory $dirName.");
2570 :     }
2571 :     }
2572 : parrello 1.9 }
2573 :    
2574 : parrello 1.93 =head3 SetPermissions
2575 :    
2576 :     Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2577 : parrello 1.9
2578 : parrello 1.93 Set the permissions for a directory and all the files and folders inside it.
2579 :     In addition, the group ownership will be changed to the specified value.
2580 : parrello 1.9
2581 : parrello 1.93 This method is more vulnerable than most to permission and compatability
2582 :     problems, so it does internal error recovery.
2583 : parrello 1.9
2584 :     =over 4
2585 :    
2586 : parrello 1.93 =item dirName
2587 :    
2588 :     Name of the directory to process.
2589 :    
2590 :     =item group
2591 : parrello 1.9
2592 : parrello 1.93 Name of the group to be assigned.
2593 : parrello 1.9
2594 : parrello 1.93 =item mask
2595 : parrello 1.9
2596 : parrello 1.93 Permission mask. Bits that are C<1> in this mask will be ORed into the
2597 :     permission bits of any file or directory that does not already have them
2598 :     set to 1.
2599 : parrello 1.9
2600 : parrello 1.93 =item otherMasks
2601 : parrello 1.9
2602 : parrello 1.93 Map of search patterns to permission masks. If a directory name matches
2603 :     one of the patterns, that directory and all its members and subdirectories
2604 :     will be assigned the new pattern. For example, the following would
2605 :     assign 01664 to most files, but would use 01777 for directories named C<tmp>.
2606 : parrello 1.9
2607 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2608 : parrello 1.9
2609 : parrello 1.93 The list is ordered, so the following would use 0777 for C<tmp1> and
2610 :     0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2611 : parrello 1.22
2612 : parrello 1.93 Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2613 :     '^tmp' => 0666);
2614 : parrello 1.9
2615 : parrello 1.93 Note that the pattern matches are all case-insensitive, and only directory
2616 :     names are matched, not file names.
2617 : parrello 1.9
2618 :     =back
2619 :    
2620 :     =cut
2621 :    
2622 : parrello 1.93 sub SetPermissions {
2623 : parrello 1.12 # Get the parameters.
2624 : parrello 1.93 my ($dirName, $group, $mask, @otherMasks) = @_;
2625 :     # Set up for error recovery.
2626 :     eval {
2627 :     # Switch to the specified directory.
2628 :     ChDir($dirName);
2629 :     # Get the group ID.
2630 :     my $gid = getgrnam($group);
2631 :     # Get the mask for tracing.
2632 :     my $traceMask = sprintf("%04o", $mask) . "($mask)";
2633 :     Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2634 :     my $fixCount = 0;
2635 :     my $lookCount = 0;
2636 :     # @dirs will be a stack of directories to be processed.
2637 :     my @dirs = (getcwd());
2638 :     while (scalar(@dirs) > 0) {
2639 :     # Get the current directory.
2640 :     my $dir = pop @dirs;
2641 :     # Check for a match to one of the specified directory names. To do
2642 :     # that, we need to pull the individual part of the name off of the
2643 :     # whole path.
2644 :     my $simpleName = $dir;
2645 :     if ($dir =~ m!/([^/]+)$!) {
2646 :     $simpleName = $1;
2647 :     }
2648 :     Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2649 :     # Search for a match.
2650 :     my $match = 0;
2651 :     my $i;
2652 :     for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2653 :     my $pattern = $otherMasks[$i];
2654 :     if ($simpleName =~ /$pattern/i) {
2655 :     $match = 1;
2656 :     }
2657 :     }
2658 :     # Check for a match. Note we use $i-1 because the loop added 2
2659 :     # before terminating due to the match.
2660 :     if ($match && $otherMasks[$i-1] != $mask) {
2661 :     # This directory matches one of the incoming patterns, and it's
2662 :     # a different mask, so we process it recursively with that mask.
2663 :     SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2664 :     } else {
2665 :     # Here we can process normally. Get all of the non-hidden members.
2666 :     my @submems = OpenDir($dir, 1);
2667 :     for my $submem (@submems) {
2668 :     # Get the full name.
2669 :     my $thisMem = "$dir/$submem";
2670 :     Trace("Checking member $thisMem.") if T(4);
2671 :     $lookCount++;
2672 :     if ($lookCount % 1000 == 0) {
2673 :     Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2674 :     }
2675 :     # Fix the group.
2676 :     chown -1, $gid, $thisMem;
2677 :     # Insure this member is not a symlink.
2678 :     if (! -l $thisMem) {
2679 :     # Get its info.
2680 :     my $fileInfo = stat $thisMem;
2681 :     # Only proceed if we got the info. Otherwise, it's a hard link
2682 :     # and we want to skip it anyway.
2683 :     if ($fileInfo) {
2684 :     my $fileMode = $fileInfo->mode;
2685 :     if (($fileMode & $mask) != $mask) {
2686 :     # Fix this member.
2687 :     $fileMode |= $mask;
2688 :     chmod $fileMode, $thisMem;
2689 :     $fixCount++;
2690 :     }
2691 :     # If it's a subdirectory, stack it.
2692 :     if (-d $thisMem) {
2693 :     push @dirs, $thisMem;
2694 :     }
2695 :     }
2696 :     }
2697 :     }
2698 :     }
2699 : parrello 1.12 }
2700 : parrello 1.93 Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2701 :     };
2702 :     # Check for an error.
2703 :     if ($@) {
2704 :     Confess("SetPermissions error: $@");
2705 : parrello 1.12 }
2706 : parrello 1.7 }
2707 :    
2708 : parrello 1.93 =head3 GetLine
2709 : parrello 1.29
2710 : parrello 1.93 my @data = Tracer::GetLine($handle);
2711 : parrello 1.15
2712 : parrello 1.93 Read a line of data from a tab-delimited file.
2713 : parrello 1.15
2714 :     =over 4
2715 :    
2716 : parrello 1.93 =item handle
2717 : parrello 1.15
2718 : parrello 1.93 Open file handle from which to read.
2719 : parrello 1.15
2720 :     =item RETURN
2721 :    
2722 : parrello 1.93 Returns a list of the fields in the record read. The fields are presumed to be
2723 :     tab-delimited. If we are at the end of the file, then an empty list will be
2724 :     returned. If an empty line is read, a single list item consisting of a null
2725 :     string will be returned.
2726 : parrello 1.15
2727 :     =back
2728 :    
2729 :     =cut
2730 : parrello 1.93
2731 :     sub GetLine {
2732 : parrello 1.15 # Get the parameters.
2733 : parrello 1.93 my ($handle) = @_;
2734 :     # Declare the return variable.
2735 :     my @retVal = ();
2736 :     Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2737 :     # Read from the file.
2738 :     my $line = <$handle>;
2739 :     # Only proceed if we found something.
2740 :     if (defined $line) {
2741 :     # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2742 :     # upload control and have a nonstandard EOL combination.
2743 :     $line =~ s/(\r|\n)+$//;
2744 :     # Here we do some fancy tracing to help in debugging complicated EOL marks.
2745 :     if (T(File => 4)) {
2746 :     my $escapedLine = $line;
2747 :     $escapedLine =~ s/\n/\\n/g;
2748 :     $escapedLine =~ s/\r/\\r/g;
2749 :     $escapedLine =~ s/\t/\\t/g;
2750 :     Trace("Line read: -->$escapedLine<--");
2751 :     }
2752 :     # If the line is empty, return a single empty string; otherwise, parse
2753 :     # it into fields.
2754 :     if ($line eq "") {
2755 :     push @retVal, "";
2756 :     } else {
2757 :     push @retVal, split /\t/,$line;
2758 :     }
2759 :     } else {
2760 :     # Trace the reason the read failed.
2761 :     Trace("End of file: $!") if T(File => 3);
2762 : parrello 1.15 }
2763 : parrello 1.93 # Return the result.
2764 :     return @retVal;
2765 : parrello 1.15 }
2766 :    
2767 : parrello 1.93 =head3 PutLine
2768 :    
2769 :     Tracer::PutLine($handle, \@fields, $eol);
2770 : parrello 1.35
2771 : parrello 1.93 Write a line of data to a tab-delimited file. The specified field values will be
2772 :     output in tab-separated form, with a trailing new-line.
2773 : parrello 1.35
2774 : parrello 1.93 =over 4
2775 : parrello 1.35
2776 : parrello 1.93 =item handle
2777 : parrello 1.69
2778 : parrello 1.93 Output file handle.
2779 : parrello 1.69
2780 : parrello 1.93 =item fields
2781 : parrello 1.69
2782 : parrello 1.93 List of field values.
2783 : parrello 1.69
2784 : parrello 1.93 =item eol (optional)
2785 : parrello 1.69
2786 : parrello 1.93 End-of-line character (default is "\n").
2787 : parrello 1.69
2788 :     =back
2789 : parrello 1.35
2790 :     =cut
2791 :    
2792 : parrello 1.93 sub PutLine {
2793 : parrello 1.69 # Get the parameters.
2794 : parrello 1.93 my ($handle, $fields, $eol) = @_;
2795 :     # Write the data.
2796 :     print $handle join("\t", @{$fields}) . ($eol || "\n");
2797 : parrello 1.69 }
2798 :    
2799 :    
2800 : parrello 1.97 =head3 PrintLine
2801 :    
2802 :     Tracer::PrintLine($line);
2803 :    
2804 :     Print a line of text with a trailing new-line.
2805 :    
2806 :     =over 4
2807 :    
2808 :     =item line
2809 :    
2810 :     Line of text to print.
2811 :    
2812 :     =back
2813 :    
2814 :     =cut
2815 :    
2816 :     sub PrintLine {
2817 :     # Get the parameters.
2818 :     my ($line) = @_;
2819 :     # Print the line.
2820 :     print "$line\n";
2821 :     }
2822 :    
2823 : parrello 1.69
2824 : parrello 1.93 =head2 Other Useful Methods
2825 :    
2826 :     =head3 ParseParm
2827 :    
2828 :     my $listValue = Tracer::ParseParm($string);
2829 :    
2830 :     Convert a parameter into a list reference. If the parameter is undefined,
2831 :     an undefined value will be returned. Otherwise, it will be parsed as a
2832 :     comma-separated list of values.
2833 : parrello 1.69
2834 :     =over 4
2835 :    
2836 : parrello 1.93 =item string
2837 :    
2838 :     Incoming string.
2839 :    
2840 :     =item RETURN
2841 : parrello 1.69
2842 : parrello 1.93 Returns a reference to a list of values, or C<undef> if the incoming value
2843 :     was undefined.
2844 : parrello 1.69
2845 :     =back
2846 :    
2847 :     =cut
2848 :    
2849 : parrello 1.93 sub ParseParm {
2850 :     # Get the parameters.
2851 :     my ($string) = @_;
2852 :     # Declare the return variable.
2853 :     my $retVal;
2854 :     # Check for data.
2855 :     if (defined $string) {
2856 :     # We have some, so split it into a list.
2857 :     $retVal = [ split /\s*,\s*/, $string];
2858 : parrello 1.72 }
2859 : parrello 1.93 # Return the result.
2860 :     return $retVal;
2861 : parrello 1.69 }
2862 :    
2863 : parrello 1.97 =head3 Now
2864 :    
2865 :     my $string = Tracer::Now();
2866 :    
2867 :     Return a displayable time stamp containing the local time. Whatever format this
2868 :     method produces must be parseable by L</ParseDate>.
2869 :    
2870 :     =cut
2871 :    
2872 :     sub Now {
2873 :     return DisplayTime(time);
2874 :     }
2875 :    
2876 :     =head3 DisplayTime
2877 :    
2878 :     my $string = Tracer::DisplayTime($time);
2879 : parrello 1.69
2880 : parrello 1.97 Convert a time value to a displayable time stamp. Whatever format this
2881 :     method produces must be parseable by L</ParseDate>.
2882 :    
2883 :     =over 4
2884 : parrello 1.69
2885 : parrello 1.97 =item time
2886 : parrello 1.69
2887 : parrello 1.97 Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
2888 :    
2889 :     =item RETURN
2890 : parrello 1.69
2891 : parrello 1.97 Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
2892 : parrello 1.69
2893 : parrello 1.97 =back
2894 : parrello 1.69
2895 : parrello 1.93 =cut
2896 : parrello 1.69
2897 : parrello 1.97 sub DisplayTime {
2898 :     my ($time) = @_;
2899 :     my $retVal = "(n/a)";
2900 :     if (defined $time) {
2901 :     my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
2902 :     $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
2903 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
2904 :     }
2905 : parrello 1.93 return $retVal;
2906 :     }
2907 : parrello 1.69
2908 : parrello 1.93 # Pad a number to 2 digits.
2909 :     sub _p2 {
2910 :     my ($value) = @_;
2911 :     $value = "0$value" if ($value < 10);
2912 :     return $value;
2913 : parrello 1.69 }
2914 :    
2915 : parrello 1.93 =head3 Escape
2916 : parrello 1.69
2917 : parrello 1.93 my $codedString = Tracer::Escape($realString);
2918 : parrello 1.69
2919 : parrello 1.93 Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
2920 :     replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
2921 :     result is to reverse the effect of L</UnEscape>.
2922 : parrello 1.69
2923 :     =over 4
2924 :    
2925 : parrello 1.93 =item realString
2926 : parrello 1.69
2927 : parrello 1.93 String to escape.
2928 : parrello 1.69
2929 :     =item RETURN
2930 :    
2931 : parrello 1.93 Escaped equivalent of the real string.
2932 :    
2933 :     =back
2934 :    
2935 :     =cut
2936 :    
2937 :     sub Escape {
2938 :     # Get the parameter.
2939 :     my ($realString) = @_;
2940 :     # Initialize the return variable.
2941 :     my $retVal = "";
2942 :     # Loop through the parameter string, looking for sequences to escape.
2943 :     while (length $realString > 0) {
2944 :     # Look for the first sequence to escape.
2945 :     if ($realString =~ /^(.*?)([\n\t\r\\])/) {
2946 :     # Here we found it. The text preceding the sequence is in $1. The sequence
2947 :     # itself is in $2. First, move the clear text to the return variable.
2948 :     $retVal .= $1;
2949 :     # Strip the processed section off the real string.
2950 :     $realString = substr $realString, (length $2) + (length $1);
2951 :     # Get the matched character.
2952 :     my $char = $2;
2953 :     # If we have a CR, we are done.
2954 :     if ($char ne "\r") {
2955 :     # It's not a CR, so encode the escape sequence.
2956 :     $char =~ tr/\t\n/tn/;
2957 :     $retVal .= "\\" . $char;
2958 :     }
2959 :     } else {
2960 :     # Here there are no more escape sequences. The rest of the string is
2961 :     # transferred unmodified.
2962 :     $retVal .= $realString;
2963 :     $realString = "";
2964 :     }
2965 :     }
2966 :     # Return the result.
2967 :     return $retVal;
2968 : parrello 1.69 }
2969 :    
2970 : parrello 1.93 =head3 UnEscape
2971 : parrello 1.69
2972 : parrello 1.93 my $realString = Tracer::UnEscape($codedString);
2973 : parrello 1.69
2974 : parrello 1.93 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
2975 :     a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
2976 :     be deleted.
2977 : parrello 1.69
2978 :     =over 4
2979 :    
2980 : parrello 1.93 =item codedString
2981 : parrello 1.69
2982 : parrello 1.93 String to un-escape.
2983 : parrello 1.69
2984 :     =item RETURN
2985 :    
2986 : parrello 1.93 Returns a copy of the original string with the escape sequences converted to their actual
2987 :     values.
2988 : parrello 1.69
2989 :     =back
2990 :    
2991 :     =cut
2992 :    
2993 : parrello 1.93 sub UnEscape {
2994 :     # Get the parameter.
2995 :     my ($codedString) = @_;
2996 :     # Initialize the return variable.
2997 :     my $retVal = "";
2998 :     # Only proceed if the incoming string is nonempty.
2999 :     if (defined $codedString) {
3000 :     # Loop through the parameter string, looking for escape sequences. We can't do
3001 :     # translating because it causes problems with the escaped slash. ("\\t" becomes
3002 :     # "\<tab>" no matter what we do.)
3003 :     while (length $codedString > 0) {
3004 :     # Look for the first escape sequence.
3005 :     if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3006 :     # Here we found it. The text preceding the sequence is in $1. The sequence
3007 :     # itself is in $2. First, move the clear text to the return variable.
3008 :     $retVal .= $1;
3009 :     $codedString = substr $codedString, (2 + length $1);
3010 :     # Get the escape value.
3011 :     my $char = $2;
3012 :     # If we have a "\r", we are done.
3013 :     if ($char ne 'r') {
3014 :     # Here it's not an 'r', so we convert it.
3015 :     $char =~ tr/\\tn/\\\t\n/;
3016 :     $retVal .= $char;
3017 :     }
3018 :     } else {
3019 :     # Here there are no more escape sequences. The rest of the string is
3020 :     # transferred unmodified.
3021 :     $retVal .= $codedString;
3022 :     $codedString = "";
3023 :     }
3024 :     }
3025 : parrello 1.35 }
3026 : parrello 1.69 # Return the result.
3027 :     return $retVal;
3028 :     }
3029 :    
3030 : parrello 1.93 =head3 Percent
3031 : parrello 1.69
3032 : parrello 1.93 my $percent = Tracer::Percent($number, $base);
3033 : parrello 1.69
3034 : parrello 1.93 Returns the percent of the base represented by the given number. If the base
3035 :     is zero, returns zero.
3036 : parrello 1.69
3037 :     =over 4
3038 :    
3039 : parrello 1.93 =item number
3040 : parrello 1.69
3041 : parrello 1.93 Percent numerator.
3042 : parrello 1.69
3043 : parrello 1.93 =item base
3044 : parrello 1.69
3045 : parrello 1.93 Percent base.
3046 : parrello 1.69
3047 : parrello 1.93 =item RETURN
3048 : parrello 1.69
3049 : parrello 1.93 Returns the percentage of the base represented by the numerator.
3050 : parrello 1.69
3051 :     =back
3052 :    
3053 :     =cut
3054 :    
3055 : parrello 1.93 sub Percent {
3056 : parrello 1.69 # Get the parameters.
3057 : parrello 1.93 my ($number, $base) = @_;
3058 :     # Declare the return variable.
3059 :     my $retVal = 0;
3060 :     # Compute the percent.
3061 :     if ($base != 0) {
3062 :     $retVal = $number * 100 / $base;
3063 :     }
3064 :     # Return the result.
3065 :     return $retVal;
3066 : parrello 1.69 }
3067 :    
3068 : parrello 1.97 =head3 Constrain
3069 :    
3070 :     my $constrained = Constrain($value, $min, $max);
3071 :    
3072 :     Modify a numeric value to bring it to a point in between a maximum and a minimum.
3073 :    
3074 :     =over 4
3075 :    
3076 :     =item value
3077 :    
3078 :     Value to constrain.
3079 :    
3080 :     =item min (optional)
3081 :    
3082 :     Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3083 :    
3084 :     =item max (optional)
3085 :    
3086 :     Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3087 :    
3088 :     =item RETURN
3089 :    
3090 :     Returns the incoming value, constrained according to the other parameters.
3091 :    
3092 :     =back
3093 :    
3094 :     =cut
3095 :    
3096 :     sub Constrain {
3097 :     # Get the parameters.
3098 :     my ($value, $min, $max) = @_;
3099 :     # Declare the return variable.
3100 :     my $retVal = $value;
3101 :     # Apply the minimum constraint.
3102 :     if (defined $min && $retVal < $min) {
3103 :     $retVal = $min;
3104 :     }
3105 :     # Apply the maximum constraint.
3106 :     if (defined $max && $retVal > $max) {
3107 :     $retVal = $max;
3108 :     }
3109 :     # Return the result.
3110 :     return $retVal;
3111 :     }
3112 :    
3113 : parrello 1.93 =head3 Min
3114 : parrello 1.69
3115 : parrello 1.93 my $min = Min($value1, $value2, ... $valueN);
3116 : parrello 1.69
3117 : parrello 1.93 Return the minimum argument. The arguments are treated as numbers.
3118 : parrello 1.69
3119 :     =over 4
3120 :    
3121 : parrello 1.93 =item $value1, $value2, ... $valueN
3122 : parrello 1.69
3123 : parrello 1.93 List of numbers to compare.
3124 : parrello 1.69
3125 :     =item RETURN
3126 :    
3127 : parrello 1.93 Returns the lowest number in the list.
3128 : parrello 1.69
3129 :     =back
3130 :    
3131 :     =cut
3132 :    
3133 : parrello 1.93 sub Min {
3134 :     # Get the parameters. Note that we prime the return value with the first parameter.
3135 :     my ($retVal, @values) = @_;
3136 :     # Loop through the remaining parameters, looking for the lowest.
3137 :     for my $value (@values) {
3138 :     if ($value < $retVal) {
3139 :     $retVal = $value;
3140 : parrello 1.72 }
3141 :     }
3142 : parrello 1.93 # Return the minimum found.
3143 : parrello 1.70 return $retVal;
3144 : parrello 1.35 }
3145 :    
3146 : parrello 1.93 =head3 Max
3147 :    
3148 :     my $max = Max($value1, $value2, ... $valueN);
3149 : parrello 1.69
3150 : parrello 1.93 Return the maximum argument. The arguments are treated as numbers.
3151 : parrello 1.65
3152 : parrello 1.93 =over 4
3153 : parrello 1.65
3154 : parrello 1.93 =item $value1, $value2, ... $valueN
3155 : parrello 1.65
3156 : parrello 1.93 List of numbers to compare.
3157 : parrello 1.65
3158 : parrello 1.93 =item RETURN
3159 : parrello 1.65
3160 : parrello 1.93 Returns the highest number in the list.
3161 : parrello 1.65
3162 :     =back
3163 :    
3164 :     =cut
3165 :    
3166 : parrello 1.93 sub Max {
3167 :     # Get the parameters. Note that we prime the return value with the first parameter.
3168 :     my ($retVal, @values) = @_;
3169 :     # Loop through the remaining parameters, looking for the highest.
3170 :     for my $value (@values) {
3171 :     if ($value > $retVal) {
3172 :     $retVal = $value;
3173 : parrello 1.65 }
3174 :     }
3175 : parrello 1.93 # Return the maximum found.
3176 :     return $retVal;
3177 : parrello 1.65 }
3178 :    
3179 : parrello 1.35
3180 : parrello 1.93 =head3 Strip
3181 : parrello 1.37
3182 : parrello 1.93 my $string = Tracer::Strip($line);
3183 : parrello 1.37
3184 : parrello 1.93 Strip all line terminators off a string. This is necessary when dealing with files
3185 :     that may have been transferred back and forth several times among different
3186 :     operating environments.
3187 : parrello 1.37
3188 :     =over 4
3189 :    
3190 : parrello 1.93 =item line
3191 : parrello 1.37
3192 : parrello 1.93 Line of text to be stripped.
3193 : parrello 1.37
3194 : parrello 1.93 =item RETURN
3195 : parrello 1.91
3196 : parrello 1.93 The same line of text with all the line-ending characters chopped from the end.
3197 : parrello 1.91
3198 : parrello 1.37 =back
3199 :    
3200 :     =cut
3201 :    
3202 : parrello 1.93 sub Strip {
3203 :     # Get a copy of the parameter string.
3204 :     my ($string) = @_;
3205 :     my $retVal = (defined $string ? $string : "");
3206 :     # Strip the line terminator characters.
3207 :     $retVal =~ s/(\r|\n)+$//g;
3208 :     # Return the result.
3209 :     return $retVal;
3210 : parrello 1.43 }
3211 :    
3212 : parrello 1.93 =head3 Pad
3213 : parrello 1.43
3214 : parrello 1.93 my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3215 : parrello 1.43
3216 : parrello 1.93 Pad a string to a specified length. The pad character will be a
3217 :     space, and the padding will be on the right side unless specified
3218 :     in the third parameter.
3219 : parrello 1.43
3220 :     =over 4
3221 :    
3222 : parrello 1.93 =item string
3223 :    
3224 :     String to be padded.
3225 :    
3226 :     =item len
3227 :    
3228 :     Desired length of the padded string.
3229 :    
3230 :     =item left (optional)
3231 :    
3232 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3233 :    
3234 :     =item padChar (optional)
3235 :    
3236 :     Character to use for padding. The default is a space.
3237 :    
3238 :     =item RETURN
3239 : parrello 1.43
3240 : parrello 1.93 Returns a copy of the original string with the pad character added to the
3241 :     specified end so that it achieves the desired length.
3242 : parrello 1.43
3243 :     =back
3244 :    
3245 :     =cut
3246 :    
3247 : parrello 1.93 sub Pad {
3248 :     # Get the parameters.
3249 :     my ($string, $len, $left, $padChar) = @_;
3250 :     # Compute the padding character.
3251 :     if (! defined $padChar) {
3252 :     $padChar = " ";
3253 :     }
3254 :     # Compute the number of spaces needed.
3255 :     my $needed = $len - length $string;
3256 :     # Copy the string into the return variable.
3257 :     my $retVal = $string;
3258 :     # Only proceed if padding is needed.
3259 :     if ($needed > 0) {
3260 :     # Create the pad string.
3261 :     my $pad = $padChar x $needed;
3262 :     # Affix it to the return value.
3263 :     if ($left) {
3264 :     $retVal = $pad . $retVal;
3265 :     } else {
3266 :     $retVal .= $pad;
3267 : parrello 1.43 }
3268 : parrello 1.37 }
3269 : parrello 1.93 # Return the result.
3270 :     return $retVal;
3271 : parrello 1.37 }
3272 :    
3273 : parrello 1.93 =head3 EOF
3274 :    
3275 :     This is a constant that is lexically greater than any useful string.
3276 :    
3277 :     =cut
3278 :    
3279 :     sub EOF {
3280 :     return "\xFF\xFF\xFF\xFF\xFF";
3281 :     }
3282 : parrello 1.59
3283 : parrello 1.93 =head3 TICK
3284 : parrello 1.59
3285 : parrello 1.93 my @results = TICK($commandString);
3286 : parrello 1.59
3287 : parrello 1.93 Perform a back-tick operation on a command. If this is a Windows environment, any leading
3288 :     dot-slash (C<./> will be removed. So, for example, if you were doing
3289 : parrello 1.59
3290 : parrello 1.93 `./protein.cgi`
3291 : parrello 1.59
3292 : parrello 1.93 from inside a CGI script, it would work fine in Unix, but would issue an error message
3293 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
3294 : parrello 1.59
3295 : parrello 1.93 TICK("./protein.cgi")
3296 : parrello 1.59
3297 : parrello 1.93 it will work correctly in both environments.
3298 : parrello 1.59
3299 : parrello 1.93 =over 4
3300 : parrello 1.59
3301 : parrello 1.93 =item commandString
3302 : parrello 1.59
3303 : parrello 1.93 The command string to pass to the system.
3304 : parrello 1.59
3305 :     =item RETURN
3306 :    
3307 : parrello 1.93 Returns the standard output from the specified command, as a list.
3308 : parrello 1.59
3309 :     =back
3310 :    
3311 :     =cut
3312 : parrello 1.93 #: Return Type @;
3313 :     sub TICK {
3314 : parrello 1.59 # Get the parameters.
3315 : parrello 1.93 my ($commandString) = @_;
3316 :     # Chop off the dot-slash if this is Windows.
3317 :     if ($FIG_Config::win_mode) {
3318 :     $commandString =~ s!^\./!!;
3319 : parrello 1.59 }
3320 : parrello 1.93 # Activate the command and return the result.
3321 :     return `$commandString`;
3322 : parrello 1.59 }
3323 :    
3324 : parrello 1.93
3325 : parrello 1.55 =head3 CommaFormat
3326 :    
3327 : parrello 1.92 my $formatted = Tracer::CommaFormat($number);
3328 : parrello 1.55
3329 :     Insert commas into a number.
3330 :    
3331 :     =over 4
3332 :    
3333 :     =item number
3334 :    
3335 :     A sequence of digits.
3336 :    
3337 :     =item RETURN
3338 :    
3339 :     Returns the same digits with commas strategically inserted.
3340 :    
3341 :     =back
3342 :    
3343 :     =cut
3344 :    
3345 :     sub CommaFormat {
3346 :     # Get the parameters.
3347 :     my ($number) = @_;
3348 :     # Pad the length up to a multiple of three.
3349 :     my $padded = "$number";
3350 :     $padded = " " . $padded while length($padded) % 3 != 0;
3351 :     # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3352 :     # cause the delimiters to be included in the output stream. The
3353 :     # GREP removes the empty strings in between the delimiters.
3354 :     my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3355 :     # Clean out the spaces.
3356 :     $retVal =~ s/ //g;
3357 :     # Return the result.
3358 :     return $retVal;
3359 :     }
3360 : parrello 1.46
3361 :    
3362 : parrello 1.62 =head3 CompareLists
3363 :    
3364 : parrello 1.92 my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3365 : parrello 1.62
3366 :     Compare two lists of tuples, and return a hash analyzing the differences. The lists
3367 :     are presumed to be sorted alphabetically by the value in the $keyIndex column.
3368 :     The return value contains a list of items that are only in the new list
3369 :     (inserted) and only in the old list (deleted).
3370 :    
3371 :     =over 4
3372 :    
3373 :     =item newList
3374 :    
3375 :     Reference to a list of new tuples.
3376 :    
3377 :     =item oldList
3378 :    
3379 :     Reference to a list of old tuples.
3380 :    
3381 :     =item keyIndex (optional)
3382 :    
3383 :     Index into each tuple of its key field. The default is 0.
3384 :    
3385 :     =item RETURN
3386 :    
3387 :     Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3388 :     list (inserted) followed by a reference to the list of items that are only in the old
3389 :     list (deleted).
3390 :    
3391 :     =back
3392 :    
3393 :     =cut
3394 :    
3395 :     sub CompareLists {
3396 :     # Get the parameters.
3397 :     my ($newList, $oldList, $keyIndex) = @_;
3398 :     if (! defined $keyIndex) {
3399 :     $keyIndex = 0;
3400 :     }
3401 :     # Declare the return variables.
3402 :     my ($inserted, $deleted) = ([], []);
3403 :     # Loop through the two lists simultaneously.
3404 :     my ($newI, $oldI) = (0, 0);
3405 :     my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3406 :     while ($newI < $newN || $oldI < $oldN) {
3407 :     # Get the current object in each list. Note that if one
3408 :     # of the lists is past the end, we'll get undef.
3409 :     my $newItem = $newList->[$newI];
3410 :     my $oldItem = $oldList->[$oldI];
3411 : parrello 1.63 if (! defined($newItem) || defined($oldItem) && $newItem->[$keyIndex] gt $oldItem->[$keyIndex]) {
3412 : parrello 1.62 # The old item is not in the new list, so mark it deleted.
3413 :     push @{$deleted}, $oldItem;
3414 :     $oldI++;
3415 :     } elsif (! defined($oldItem) || $oldItem->[$keyIndex] gt $newItem->[$keyIndex]) {
3416 :     # The new item is not in the old list, so mark it inserted.
3417 :     push @{$inserted}, $newItem;
3418 :     $newI++;
3419 :     } else {
3420 :     # The item is in both lists, so push forward.
3421 :     $oldI++;
3422 :     $newI++;
3423 :     }
3424 :     }
3425 :     # Return the result.
3426 :     return ($inserted, $deleted);
3427 :     }
3428 :    
3429 : parrello 1.65 =head3 GenerateURL
3430 :    
3431 : parrello 1.92 my $queryUrl = Tracer::GenerateURL($page, %parameters);
3432 : parrello 1.65
3433 :     Generate a GET-style URL for the specified page with the specified parameter
3434 :     names and values. The values will be URL-escaped automatically. So, for
3435 :     example
3436 :    
3437 :     Tracer::GenerateURL("form.cgi", type => 1, string => "\"high pass\" or highway")
3438 :    
3439 :     would return
3440 :    
3441 : parrello 1.79 form.cgi?type=1;string=%22high%20pass%22%20or%20highway
3442 : parrello 1.65
3443 :     =over 4
3444 :    
3445 :     =item page
3446 :    
3447 :     Page URL.
3448 :    
3449 :     =item parameters
3450 :    
3451 :     Hash mapping parameter names to parameter values.
3452 :    
3453 :     =item RETURN
3454 :    
3455 :     Returns a GET-style URL that goes to the specified page and passes in the
3456 :     specified parameters and values.
3457 :    
3458 :     =back
3459 :    
3460 :     =cut
3461 :    
3462 :     sub GenerateURL {
3463 :     # Get the parameters.
3464 :     my ($page, %parameters) = @_;
3465 :     # Prime the return variable with the page URL.
3466 :     my $retVal = $page;
3467 :     # Loop through the parameters, creating parameter elements in a list.
3468 :     my @parmList = map { "$_=" . uri_escape($parameters{$_}) } keys %parameters;
3469 :     # If the list is nonempty, tack it on.
3470 :     if (@parmList) {
3471 : parrello 1.79 $retVal .= "?" . join(";", @parmList);
3472 : parrello 1.65 }
3473 :     # Return the result.
3474 :     return $retVal;
3475 :     }
3476 :    
3477 : parrello 1.78 =head3 ApplyURL
3478 :    
3479 : parrello 1.92 Tracer::ApplyURL($table, $target, $url);
3480 : parrello 1.78
3481 :     Run through a two-dimensional table (or more accurately, a list of lists), converting the
3482 :     I<$target> column to HTML text having a hyperlink to a URL in the I<$url> column. The
3483 :     URL column will be deleted by this process and the target column will be HTML-escaped.
3484 :    
3485 :     This provides a simple way to process the results of a database query into something
3486 :     displayable by combining a URL with text.
3487 :    
3488 :     =over 4
3489 :    
3490 :     =item table
3491 :    
3492 :     Reference to a list of lists. The elements in the containing list will be updated by
3493 :     this method.
3494 :    
3495 :     =item target
3496 :    
3497 :     The index of the column to be converted into HTML.
3498 :    
3499 :     =item url
3500 :    
3501 :     The index of the column containing the URL. Note that the URL must have a recognizable
3502 :     C<http:> at the beginning.
3503 :    
3504 :     =back
3505 :    
3506 :     =cut
3507 :    
3508 :     sub ApplyURL {
3509 :     # Get the parameters.
3510 :     my ($table, $target, $url) = @_;
3511 :     # Loop through the table.
3512 :     for my $row (@{$table}) {
3513 :     # Apply the URL to the target cell.
3514 :     $row->[$target] = CombineURL($row->[$target], $row->[$url]);
3515 :     # Delete the URL from the row.
3516 :     delete $row->[$url];
3517 :     }
3518 :     }
3519 :    
3520 :     =head3 CombineURL
3521 :    
3522 : parrello 1.92 my $combinedHtml = Tracer::CombineURL($text, $url);
3523 : parrello 1.78
3524 :     This method will convert the specified text into HTML hyperlinked to the specified
3525 :     URL. The hyperlinking will only take place if the URL looks legitimate: that is, it
3526 :     is defined and begins with an C<http:> header.
3527 :    
3528 :     =over 4
3529 :    
3530 :     =item text
3531 :    
3532 :     Text to return. This will be HTML-escaped automatically.
3533 :    
3534 :     =item url
3535 :    
3536 :     A URL to be hyperlinked to the text. If it does not look like a URL, then the text
3537 :     will be returned without any hyperlinking.
3538 :    
3539 :     =item RETURN
3540 :    
3541 :     Returns the original text, HTML-escaped, with the URL hyperlinked to it. If the URL
3542 :     doesn't look right, the HTML-escaped text will be returned without any further
3543 :     modification.
3544 :    
3545 :     =back
3546 :    
3547 :     =cut
3548 :    
3549 :     sub CombineURL {
3550 :     # Get the parameters.
3551 :     my ($text, $url) = @_;
3552 :     # Declare the return variable.
3553 :     my $retVal = CGI::escapeHTML($text);
3554 :     # Verify the URL.
3555 :     if (defined($url) && $url =~ m!http://!i) {
3556 :     # It's good, so we apply it to the text.
3557 :     $retVal = "<a href=\"$url\">$retVal</a>";
3558 :     }
3559 :     # Return the result.
3560 :     return $retVal;
3561 :     }
3562 :    
3563 : parrello 1.93 =head3 Cmp
3564 :    
3565 :     my $cmp = Tracer::Cmp($a, $b);
3566 :    
3567 :     This method performs a universal sort comparison. Each value coming in is
3568 :     separated into a leading text part and a trailing number part. The text
3569 :     part is string compared, and if both parts are equal, then the number
3570 :     parts are compared numerically. A stream of just numbers or a stream of
3571 :     just strings will sort correctly, and a mixed stream will sort with the
3572 :     numbers first. Strings with a label and a number will sort in the
3573 :     expected manner instead of lexically.
3574 :    
3575 :     =over 4
3576 :    
3577 :     =item a
3578 :    
3579 :     First item to compare.
3580 :    
3581 :     =item b
3582 :    
3583 :     Second item to compare.
3584 :    
3585 :     =item RETURN
3586 :    
3587 :     Returns a negative number if the first item should sort first (is less), a positive
3588 :     number if the first item should sort second (is greater), and a zero if the items are
3589 :     equal.
3590 :    
3591 :     =back
3592 :    
3593 :     =cut
3594 :    
3595 :     sub Cmp {
3596 :     # Get the parameters.
3597 :     my ($a, $b) = @_;
3598 :     # Declare the return value.
3599 :     my $retVal;
3600 :     # Check for nulls.
3601 :     if (! defined($a)) {
3602 :     $retVal = (! defined($b) ? 0 : -1);
3603 :     } elsif (! defined($b)) {
3604 :     $retVal = 1;
3605 :     } else {
3606 :     # Here we have two real values. Parse the two strings.
3607 :     $a =~ /^(\D*)(\d*)$/;
3608 :     my $aParsed = [$1, $2];
3609 :     $b =~ /^(\D*)(\d*)$/;
3610 :     my $bParsed = [$1, $2];
3611 :     # Compare the string parts.
3612 :     $retVal = $aParsed->[0] cmp $bParsed->[0];
3613 :     if (! $retVal) {
3614 :     $retVal = $aParsed->[1] <=> $bParsed->[1];
3615 :     }
3616 :     }
3617 :     # Return the result.
3618 :     return $retVal;
3619 :     }
3620 :    
3621 : parrello 1.87
3622 : parrello 1.97 =head3 TrackingCode
3623 :    
3624 :     my $html = Tracer::TrackingCode();
3625 :    
3626 :     Returns the HTML code for doing web page traffic monitoring. If the
3627 :     current environment is a test system, then it returns a null string;
3628 :     otherwise, it returns a bunch of javascript containing code for turning
3629 :     on SiteMeter and Google Analytics.
3630 :    
3631 :     =cut
3632 :    
3633 :     sub TrackingCode {
3634 :     # Declare the return variable.
3635 :     my $retVal = "<!-- tracking off -->";
3636 :     # Determine if we're in production.
3637 :     if ($FIG_Config::site_meter) {
3638 :     $retVal = <<END_HTML
3639 :     <!-- Site Meter -->
3640 :     <script type="text/javascript" src="http://s20.sitemeter.com/js/counter.js?site=s20nmpdr">
3641 :     </script>
3642 :     <noscript>
3643 :     <a href="http://s20.sitemeter.com/stats.asp?site=s20nmpdr" target="_top">
3644 :     <img src="http://s20.sitemeter.com/meter.asp?site=s20nmpdr" alt="Site Meter" border="0"/></a>
3645 :     </noscript>
3646 :     <!-- Copyright (c)2006 Site Meter -->
3647 :     END_HTML
3648 :     }
3649 :     return $retVal;
3650 :     }
3651 :    
3652 :    
3653 : olson 1.88 1;

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