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

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