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1 : olson 1.30 #
2 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
3 :     # for Interpretations of Genomes. All Rights Reserved.
4 :     #
5 :     # This file is part of the SEED Toolkit.
6 :     #
7 :     # The SEED Toolkit is free software. You can redistribute
8 :     # it and/or modify it under the terms of the SEED Toolkit
9 :     # Public License.
10 :     #
11 :     # You should have received a copy of the SEED Toolkit Public License
12 :     # along with this program; if not write to the University of Chicago
13 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
14 :     # Genomes at veronika@thefig.info or download a copy from
15 :     # http://www.theseed.org/LICENSE.TXT.
16 :     #
17 :    
18 : olson 1.1 package Tracer;
19 :    
20 : parrello 1.12 require Exporter;
21 :     @ISA = ('Exporter');
22 : parrello 1.37 @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup ScriptSetup ScriptFinish Insure);
23 : parrello 1.12 @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);
24 :     use strict;
25 :     use Carp qw(longmess croak);
26 :     use CGI;
27 :     use FIG_Config;
28 : parrello 1.9 use PageBuilder;
29 : parrello 1.21 use Digest::MD5;
30 : parrello 1.36 use File::Basename;
31 : parrello 1.37 use File::Path;
32 : olson 1.1
33 :     =head1 Tracing and Debugging Helpers
34 :    
35 :     =head2 Introduction
36 :    
37 :     This package provides simple tracing for debugging and reporting purposes. To use it simply call the
38 :     L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace
39 : parrello 1.2 message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself
40 :     has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace
41 : olson 1.1 level is less than or equal to this package's trace level and whose category is activated will
42 : parrello 1.2 be written. Thus, a higher trace level on a message indicates that the message
43 : parrello 1.10 is less likely to be seen. A higher trace level passed to B<TSetup> means more trace messages will
44 : olson 1.1 appear. To generate a trace message, use the following syntax.
45 :    
46 :     C<< Trace($message) if T(errors => 4); >>
47 :    
48 : parrello 1.2 This statement will produce a trace message if the trace level is 4 or more and the C<errors>
49 : parrello 1.3 category is active. Note that the special category C<main> is always active, so
50 : olson 1.1
51 : parrello 1.3 C<< Trace($message) if T(main => 4); >>
52 : olson 1.1
53 :     will trace if the trace level is 4 or more.
54 :    
55 :     If the category name is the same as the package name, all you need is the number. So, if the
56 :     following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
57 :     active and the trace level is 2 or more.
58 :    
59 :     C<< Trace($message) if T(2); >>
60 :    
61 : parrello 1.10 To set up tracing, you call the L</TSetup> method. The method takes as input a trace level, a list
62 : olson 1.1 of category names, and a set of options. The trace level and list of category names are
63 :     specified as a space-delimited string. Thus
64 :    
65 :     C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>
66 :    
67 : parrello 1.7 sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
68 : parrello 1.12 specifies that messages should be output as HTML paragraphs.
69 :    
70 :     To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
71 :     level 3 and writes the output to the standard error output. This sort of thing might be
72 :     useful in a CGI environment.
73 :    
74 :     C<< TSetup('3 *', 'WARN'); >>
75 : olson 1.1
76 :     In addition to HTML and file output for trace messages, you can specify that the trace messages
77 :     be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
78 :     is useful if you are building a web page. Instead of having the trace messages interspersed with
79 :     the page output, they can be gathered together and displayed at the end of the page. This makes
80 :     it easier to debug page formatting problems.
81 :    
82 : parrello 1.4 Finally, you can specify that all trace messages be emitted as warnings.
83 :    
84 : olson 1.1 The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
85 :     Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
86 :     Thus, debugging information is available and easily retrieved even when the application is
87 :     being used out in the field.
88 :    
89 : parrello 1.10 There is no hard and fast rule on how to use trace levels. The following is therefore only
90 :     a suggestion.
91 :    
92 :     =over 4
93 :    
94 : parrello 1.32 =item Error 0
95 : parrello 1.10
96 :     Message indicates an error that may lead to incorrect results or that has stopped the
97 :     application entirely.
98 :    
99 : parrello 1.32 =item Warning 1
100 : parrello 1.10
101 :     Message indicates something that is unexpected but that probably did not interfere
102 :     with program execution.
103 :    
104 : parrello 1.32 =item Notice 2
105 : parrello 1.10
106 :     Message indicates the beginning or end of a major task.
107 :    
108 : parrello 1.32 =item Information 3
109 : parrello 1.10
110 :     Message indicates a subtask. In the FIG system, a subtask generally relates to a single
111 :     genome. This would be a big loop that is not expected to execute more than 500 times or so.
112 :    
113 : parrello 1.32 =item Detail 4
114 : parrello 1.10
115 :     Message indicates a low-level loop iteration.
116 :    
117 :     =back
118 :    
119 : olson 1.1 =cut
120 : parrello 1.2
121 : olson 1.1 # Declare the configuration variables.
122 :    
123 : parrello 1.12 my $Destination = "NONE"; # Description of where to send the trace output.
124 :     my $TeeFlag = 0; # TRUE if output is going to a file and to the
125 :     # standard output
126 : parrello 1.3 my %Categories = ( main => 1 );
127 : parrello 1.12 # hash of active category names
128 :     my $TraceLevel = 0; # trace level; a higher trace level produces more
129 :     # messages
130 :     my @Queue = (); # queued list of trace messages.
131 : parrello 1.7 my $LastCategory = "main"; # name of the last category interrogated
132 : parrello 1.11 my $SetupCount = 0; # number of times TSetup called
133 : parrello 1.12 my $AllTrace = 0; # TRUE if we are tracing all categories.
134 : olson 1.1
135 :     =head2 Public Methods
136 :    
137 :     =head3 TSetup
138 :    
139 :     C<< TSetup($categoryList, $target); >>
140 :    
141 :     This method is used to specify the trace options. The options are stored as package data
142 :     and interrogated by the L</Trace> and L</T> methods.
143 :    
144 :     =over 4
145 :    
146 :     =item categoryList
147 :    
148 :     A string specifying the trace level and the categories to be traced, separated by spaces.
149 :     The trace level must come first.
150 :    
151 :     =item target
152 :    
153 :     The destination for the trace output. To send the trace output to a file, specify the file
154 :     name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
155 : parrello 1.10 to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
156 :     symbol with a C<+> to echo output to a file AND to the standard output. In addition to
157 :     sending the trace messages to a file, you can specify a special destination. C<HTML> will
158 :     cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
159 : parrello 1.5 will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
160 : parrello 1.9 messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
161 : parrello 1.6 messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
162 : parrello 1.9 cause trace messages to be emitted as warnings using the B<warn> directive. C<NONE> will
163 : parrello 1.6 cause tracing to be suppressed.
164 : olson 1.1
165 :     =back
166 :    
167 :     =cut
168 :    
169 :     sub TSetup {
170 : parrello 1.12 # Get the parameters.
171 :     my ($categoryList, $target) = @_;
172 :     # Parse the category list.
173 :     my @categoryData = split /\s+/, $categoryList;
174 :     # Extract the trace level.
175 :     $TraceLevel = shift @categoryData;
176 :     # Presume category-based tracing until we learn otherwise.
177 :     $AllTrace = 0;
178 :     # Build the category hash. Note that if we find a "*", we turn on non-category
179 : parrello 1.33 # tracing. We must also clear away any pre-existing data.
180 : parrello 1.34 %Categories = ( main => 1 );
181 : parrello 1.12 for my $category (@categoryData) {
182 :     if ($category eq '*') {
183 :     $AllTrace = 1;
184 :     } else {
185 : parrello 1.13 $Categories{lc $category} = 1;
186 : parrello 1.12 }
187 :     }
188 :     # Now we need to process the destination information. The most important special
189 :     # cases are the single ">", which requires we clear the file first, and the
190 :     # "+" prefix which indicates a double echo.
191 :     if ($target =~ m/^\+?>>?/) {
192 :     if ($target =~ m/^\+/) {
193 :     $TeeFlag = 1;
194 :     $target = substr($target, 1);
195 :     }
196 :     if ($target =~ m/^>[^>]/) {
197 :     open TRACEFILE, $target;
198 :     print TRACEFILE Now() . " Tracing initialized.\n";
199 :     close TRACEFILE;
200 :     $Destination = ">$target";
201 :     } else {
202 :     $Destination = $target;
203 :     }
204 :     } else {
205 :     $Destination = uc($target);
206 :     }
207 :     # Increment the setup counter.
208 :     $SetupCount++;
209 : parrello 1.11 }
210 :    
211 : parrello 1.31 =head3 StandardSetup
212 :    
213 : parrello 1.36 C<< my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV); >>
214 : parrello 1.31
215 :     This method performs standard command-line parsing and tracing setup. The return
216 :     values are a hash of the command-line options and a list of the positional
217 :     parameters. Tracing is automatically set up and the command-line options are
218 :     validated.
219 :    
220 :     This is a complex method that does a lot of grunt work. The parameters can
221 :     be more easily understood, however, once they are examined individually.
222 :    
223 :     The I<categories> parameter is the most obtuse. It is a reference to a list of
224 :     special-purpose tracing categories. Most tracing categories are PERL package
225 :     names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
226 :     B<ERDB>, and B<SproutLoad> packages, you would specify the categories
227 :    
228 :     ["Sprout", "SproutLoad", "ERDB"]
229 :    
230 :     This would cause trace messages in the specified three packages to appear in
231 :     the output. There are threer special tracing categories that are automatically
232 :     handled by this method. In other words, if you used L</TSetup> you would need
233 :     to include these categories manually, but if you use this method they are turned
234 :     on automatically.
235 :    
236 :     =over 4
237 :    
238 :     =item FIG
239 :    
240 :     Turns on trace messages inside the B<FIG> package.
241 :    
242 :     =item SQL
243 :    
244 :     Traces SQL commands and activity.
245 :    
246 :     =item Tracer
247 :    
248 :     Traces error messages and call stacks.
249 :    
250 :     =back
251 :    
252 :     C<SQL> is only turned on if the C<-sql> option is specified in the command line.
253 :     The trace level is specified using the C<-trace> command-line option. For example,
254 :     the following command line for C<TransactFeatures> turns on SQL tracing and runs
255 :     all tracing at level 3.
256 :    
257 :     TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
258 :    
259 :     Standard tracing is output to the standard output and echoed to the file
260 : parrello 1.38 C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
261 :     process ID. You can also specify the C<user> parameter to put a user ID
262 :     instead of a process ID in the trace file name. So, for example
263 : parrello 1.31
264 : parrello 1.35 The default trace level is 2. To get all messages, specify a trace level of 4.
265 :     For a genome-by-genome update, use 3.
266 : parrello 1.31
267 : parrello 1.38 TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
268 :    
269 :     would send the trace output to C<traceBruce.log> in the temporary directory.
270 :    
271 : parrello 1.31 The I<options> parameter is a reference to a hash containing the command-line
272 : parrello 1.36 options, their default values, and an explanation of what they mean. Command-line
273 :     options may be in the form of switches or keywords. In the case of a switch, the
274 :     option value is 1 if it is specified and 0 if it is not specified. In the case
275 :     of a keyword, the value is separated from the option name by an equal sign. You
276 :     can see this last in the command-line example above.
277 : parrello 1.31
278 :     An example at this point would help. Consider, for example, the command-line utility
279 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
280 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
281 :     the following code.
282 :    
283 :     my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
284 : parrello 1.36 { safe => [0, "use database transactions"],
285 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
286 :     start => [' ', "start with this genome"],
287 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
288 :     "command transactionDirectory IDfile",
289 :     @ARGV);
290 : parrello 1.31
291 :    
292 :     The call to C<ParseCommand> specifies the default values for the options and
293 :     stores the actual options in a hash that is returned as C<$options>. The
294 :     positional parameters are returned in C<@parameters>.
295 :    
296 :     The following is a sample command line for C<TransactFeatures>.
297 :    
298 :     TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
299 :    
300 :     In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
301 :     parameters, and would find themselves in I<@parameters> after executing the
302 :     above code fragment. The tracing would be set to level 2, and the categories
303 :     would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
304 :     and C<DocUtils> was included because it came in within the first parameter
305 :     to this method. The I<$options> hash would be
306 :    
307 :     { trace => 2, sql => 0, safe => 0,
308 :     noAlias => 1, start => ' ', tblFiles => 0 }
309 :    
310 :     Use of C<StandardSetup> in this way provides a simple way of performing
311 :     standard tracing setup and command-line parsing. Note that the caller is
312 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
313 :     are used by this method to control the tracing. If additional tracing features
314 :     need to be added in the future, they can be processed by this method without
315 :     upsetting the command-line utilities.
316 :    
317 : parrello 1.36 Finally, if the special option C<-h> is specified, the option names will
318 :     be traced at level 0 and the program will exit without processing.
319 :     This provides a limited help capability. For example, if the user enters
320 :    
321 :     TransactFeatures -h
322 :    
323 :     he would see the following output.
324 :    
325 :     TransactFeatures [options] command transactionDirectory IDfile
326 :     -trace tracing level (default 2)
327 :     -sql trace SQL commands
328 :     -safe use database transactions
329 :     -noAlias do not expect aliases in CHANGE transactions
330 :     -start start with this genome
331 :     -tblFiles output TBL files containing the corrected IDs
332 :    
333 : parrello 1.31 The parameters to this method are as follows.
334 :    
335 :     =over 4
336 :    
337 :     =item categories
338 :    
339 :     Reference to a list of tracing category names. These should be names of
340 :     packages whose internal workings will need to be debugged to get the
341 :     command working.
342 :    
343 :     =item options
344 :    
345 :     Reference to a hash containing the legal options for the current command mapped
346 : parrello 1.36 to their default values and descriptions. The user can override the defaults
347 :     by specifying the options as command-line switches prefixed by a hyphen.
348 :     Tracing-related options may be added to this hash. If the C<-h> option is
349 :     specified on the command line, the option descriptions will be used to
350 :     explain the options.
351 :    
352 :     =item parmHelp
353 :    
354 :     A string that vaguely describes the positional parameters. This is used
355 :     if the user specifies the C<-h> option.
356 : parrello 1.31
357 :     =item ARGV
358 :    
359 :     List of command line parameters, including the option switches, which must
360 :     precede the positional parameters and be prefixed by a hyphen.
361 :    
362 :     =item RETURN
363 :    
364 :     Returns a list. The first element of the list is the reference to a hash that
365 :     maps the command-line option switches to their values. These will either be the
366 :     default values or overrides specified on the command line. The remaining
367 :     elements of the list are the position parameters, in order.
368 :    
369 :     =back
370 :    
371 :     =cut
372 :    
373 :     sub StandardSetup {
374 :     # Get the parameters.
375 : parrello 1.36 my ($categories, $options, $parmHelp, @argv) = @_;
376 : parrello 1.31 # Add the tracing options.
377 : parrello 1.36 $options->{trace} = [2, "tracing level"];
378 :     $options->{sql} = [0, "turn on SQL tracing"];
379 :     $options->{h} = [0, "display command-line options"];
380 : parrello 1.38 $options->{user} = [$$, "trace log file name suffix"];
381 : parrello 1.36 # Create a parsing hash from the options hash. The parsing hash
382 :     # contains the default values rather than the default value
383 :     # and the description. While we're at it, we'll memorize the
384 :     # length of the longest option name.
385 :     my $longestName = 0;
386 :     my %parseOptions = ();
387 :     for my $key (keys %{$options}) {
388 :     if (length $key > $longestName) {
389 :     $longestName = length $key;
390 :     }
391 :     $parseOptions{$key} = $options->{$key}->[0];
392 :     }
393 : parrello 1.31 # Parse the command line.
394 : parrello 1.36 my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
395 : parrello 1.31 # Now we want to set up tracing. First, we need to know if SQL is to
396 :     # be traced.
397 :     my @cats = @{$categories};
398 :     if ($retOptions->{sql}) {
399 :     push @cats, "SQL";
400 :     }
401 :     # Add the default categories.
402 :     push @cats, "Tracer", "FIG";
403 :     # Next, we create the category string by prefixing the trace level
404 :     # and joining the categories.
405 : parrello 1.36 my $cats = join(" ", $parseOptions{trace}, @cats);
406 : parrello 1.31 # Now set up the tracing.
407 : parrello 1.38 my $suffix = $retOptions->{user};
408 :     TSetup($cats, "+>$FIG_Config::temp/trace$suffix.log");
409 : parrello 1.36 # Check for the "h" option. If it is specified, dump the command-line
410 :     # options and exit the program.
411 :     if ($retOptions->{h}) {
412 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
413 :     Trace("$1 [options] $parmHelp") if T(0);
414 :     for my $key (sort keys %{$options}) {
415 :     my $name = Pad($key, $longestName, 0, ' ');
416 :     my $desc = $options->{$key}->[1];
417 :     if ($options->{$key}->[0]) {
418 :     $desc .= " (default " . $options->{$key}->[0] . ")";
419 :     }
420 :     Trace(" $name $desc") if T(0);
421 :     }
422 :     exit(0);
423 :     }
424 : parrello 1.31 # Return the parsed parameters.
425 :     return ($retOptions, @retParameters);
426 :     }
427 :    
428 : parrello 1.11 =head3 Setups
429 :    
430 :     C<< my $count = Tracer::Setups(); >>
431 :    
432 :     Return the number of times L</TSetup> has been called.
433 :    
434 :     This method allows for the creation of conditional tracing setups where, for example, we
435 :     may want to set up tracing if nobody else has done it before us.
436 :    
437 :     =cut
438 :    
439 :     sub Setups {
440 : parrello 1.12 return $SetupCount;
441 : olson 1.1 }
442 :    
443 : parrello 1.10 =head3 Open
444 :    
445 :     C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
446 :    
447 : parrello 1.11 Open a file.
448 : parrello 1.10
449 :     The I<$fileSpec> is essentially the second argument of the PERL C<open>
450 :     function. The mode is specified using Unix-like shell information. So, for
451 :     example,
452 :    
453 : parrello 1.12 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
454 : parrello 1.10
455 :     would open for output appended to the specified file, and
456 :    
457 : parrello 1.12 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
458 : parrello 1.10
459 :     would open a pipe that sorts the records written and removes duplicates. Note
460 : parrello 1.11 the use of file handle syntax in the Open call. To use anonymous file handles,
461 :     code as follows.
462 : parrello 1.10
463 : parrello 1.12 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
464 : parrello 1.10
465 : parrello 1.11 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
466 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
467 :     failed open will throw an exception and the third parameter will be used to construct
468 :     an error message. If the parameter is omitted, a standard message is constructed
469 :     using the file spec.
470 : parrello 1.10
471 : parrello 1.12 Could not open "/usr/spool/news/twitlog"
472 : parrello 1.10
473 :     Note that the mode characters are automatically cleaned from the file name.
474 :     The actual error message from the file system will be captured and appended to the
475 :     message in any case.
476 :    
477 : parrello 1.12 Could not open "/usr/spool/news/twitlog": file not found.
478 : parrello 1.10
479 :     In some versions of PERL the only error message we get is a number, which
480 :     corresponds to the C++ C<errno> value.
481 :    
482 : parrello 1.12 Could not open "/usr/spool/news/twitlog": 6.
483 : parrello 1.10
484 :     =over 4
485 :    
486 :     =item fileHandle
487 :    
488 :     File handle. If this parameter is C<undef>, a file handle will be generated
489 :     and returned as the value of this method.
490 :    
491 :     =item fileSpec
492 :    
493 :     File name and mode, as per the PERL C<open> function.
494 :    
495 :     =item message (optional)
496 :    
497 :     Error message to use if the open fails. If omitted, a standard error message
498 :     will be generated. In either case, the error information from the file system
499 : parrello 1.11 is appended to the message. To specify a conditional open that does not throw
500 :     an error if it fails, use C<0>.
501 : parrello 1.10
502 :     =item RETURN
503 :    
504 : parrello 1.11 Returns the name of the file handle assigned to the file, or C<undef> if the
505 :     open failed.
506 : parrello 1.10
507 :     =back
508 :    
509 :     =cut
510 :    
511 :     sub Open {
512 : parrello 1.12 # Get the parameters.
513 :     my ($fileHandle, $fileSpec, $message) = @_;
514 :     # Attempt to open the file.
515 :     my $rv = open $fileHandle, $fileSpec;
516 :     # If the open failed, generate an error message.
517 :     if (! $rv) {
518 :     # Save the system error message.
519 :     my $sysMessage = $!;
520 :     # See if we need a default message.
521 :     if (!$message) {
522 :     # Clean any obvious mode characters and leading spaces from the
523 :     # filename.
524 :     my ($fileName) = FindNamePart($fileSpec);
525 :     $message = "Could not open \"$fileName\"";
526 :     }
527 :     # Terminate with an error using the supplied message and the
528 :     # error message from the file system.
529 :     Confess("$message: $!");
530 :     }
531 :     # Return the file handle.
532 :     return $fileHandle;
533 : parrello 1.10 }
534 :    
535 : parrello 1.11 =head3 FindNamePart
536 :    
537 :     C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
538 :    
539 :     Extract the portion of a file specification that contains the file name.
540 :    
541 :     A file specification is the string passed to an C<open> call. It specifies the file
542 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
543 :     method assumes that the file name is whatever follows the first angle bracket
544 :     sequence. So, for example, in the following strings the file name is
545 :     C</usr/fig/myfile.txt>.
546 :    
547 :     >>/usr/fig/myfile.txt
548 :     </usr/fig/myfile.txt
549 :     | sort -u > /usr/fig/myfile.txt
550 :    
551 :     If the method cannot find a file name using its normal methods, it will return the
552 :     whole incoming string.
553 :    
554 :     =over 4
555 :    
556 :     =item fileSpec
557 :    
558 :     File specification string from which the file name is to be extracted.
559 :    
560 :     =item RETURN
561 :    
562 :     Returns a three-element list. The first element contains the file name portion of
563 :     the specified string, or the whole string if a file name cannot be found via normal
564 :     methods. The second element contains the start position of the file name portion and
565 :     the third element contains the length.
566 :    
567 :     =back
568 :    
569 :     =cut
570 :     #: Return Type $;
571 :     sub FindNamePart {
572 :     # Get the parameters.
573 :     my ($fileSpec) = @_;
574 : parrello 1.12 # Default to the whole input string.
575 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
576 : parrello 1.11 # Parse out the file name if we can.
577 : parrello 1.12 if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
578 :     $retVal = $2;
579 :     $len = length $retVal;
580 :     $pos = (length $fileSpec) - (length $3) - $len;
581 :     }
582 : parrello 1.11 # Return the result.
583 :     return ($retVal, $pos, $len);
584 :     }
585 :    
586 :     =head3 OpenDir
587 :    
588 : parrello 1.31 C<< my @files = OpenDir($dirName, $filtered, $flag); >>
589 : parrello 1.11
590 :     Open a directory and return all the file names. This function essentially performs
591 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
592 : parrello 1.31 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
593 : parrello 1.33 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
594 :     filtered out of the return list. If the directory does not open and I<$flag> is not
595 :     set, an exception is thrown. So, for example,
596 : parrello 1.11
597 : parrello 1.12 my @files = OpenDir("/Volumes/fig/contigs", 1);
598 : parrello 1.29
599 : parrello 1.11 is effectively the same as
600 :    
601 : parrello 1.12 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
602 : parrello 1.33 my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
603 : parrello 1.11
604 :     Similarly, the following code
605 :    
606 : parrello 1.31 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
607 : parrello 1.29
608 : parrello 1.11 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
609 : parrello 1.31 automatically returns an empty list if the directory fails to open.
610 : parrello 1.11
611 :     =over 4
612 :    
613 :     =item dirName
614 :    
615 :     Name of the directory to open.
616 :    
617 :     =item filtered
618 :    
619 :     TRUE if files whose names begin with a period (C<.>) should be automatically removed
620 :     from the list, else FALSE.
621 :    
622 : parrello 1.31 =item flag
623 :    
624 :     TRUE if a failure to open is okay, else FALSE
625 :    
626 : parrello 1.11 =back
627 :    
628 :     =cut
629 :     #: Return Type @;
630 :     sub OpenDir {
631 :     # Get the parameters.
632 : parrello 1.31 my ($dirName, $filtered, $flag) = @_;
633 : parrello 1.11 # Declare the return variable.
634 : parrello 1.31 my @retVal = ();
635 : parrello 1.12 # Open the directory.
636 :     if (opendir(my $dirHandle, $dirName)) {
637 :     # The directory opened successfully. Get the appropriate list according to the
638 :     # strictures of the filter parameter.
639 :     if ($filtered) {
640 : parrello 1.33 @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
641 : parrello 1.12 } else {
642 :     @retVal = readdir $dirHandle;
643 :     }
644 : parrello 1.31 } elsif (! $flag) {
645 :     # Here the directory would not open and it's considered an error.
646 : parrello 1.12 Confess("Could not open directory $dirName.");
647 :     }
648 : parrello 1.11 # Return the result.
649 :     return @retVal;
650 :     }
651 :    
652 : parrello 1.6 =head3 SetLevel
653 :    
654 :     C<< Tracer::SetLevel($newLevel); >>
655 :    
656 :     Modify the trace level. A higher trace level will cause more messages to appear.
657 :    
658 :     =over 4
659 :    
660 :     =item newLevel
661 :    
662 :     Proposed new trace level.
663 :    
664 :     =back
665 :    
666 :     =cut
667 :    
668 :     sub SetLevel {
669 :     $TraceLevel = $_[0];
670 :     }
671 :    
672 : olson 1.1 =head3 Now
673 :    
674 :     C<< my $string = Tracer::Now(); >>
675 :    
676 :     Return a displayable time stamp containing the local time.
677 :    
678 :     =cut
679 :    
680 :     sub Now {
681 : parrello 1.12 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
682 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
683 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
684 :     return $retVal;
685 : olson 1.1 }
686 :    
687 :     # Pad a number to 2 digits.
688 :     sub _p2 {
689 : parrello 1.12 my ($value) = @_;
690 :     $value = "0$value" if ($value < 10);
691 :     return $value;
692 : olson 1.1 }
693 :    
694 :     =head3 LogErrors
695 :    
696 :     C<< Tracer::LogErrors($fileName); >>
697 :    
698 :     Route the standard error output to a log file.
699 :    
700 :     =over 4
701 :    
702 :     =item fileName
703 :    
704 :     Name of the file to receive the error output.
705 :    
706 :     =back
707 :    
708 :     =cut
709 :    
710 :     sub LogErrors {
711 : parrello 1.12 # Get the file name.
712 :     my ($fileName) = @_;
713 :     # Open the file as the standard error output.
714 :     open STDERR, '>', $fileName;
715 : olson 1.1 }
716 :    
717 : parrello 1.5 =head3 ReadOptions
718 :    
719 :     C<< my %options = Tracer::ReadOptions($fileName); >>
720 :    
721 :     Read a set of options from a file. Each option is encoded in a line of text that has the
722 :     format
723 :    
724 :     I<optionName>C<=>I<optionValue>C<; >I<comment>
725 :    
726 :     The option name must consist entirely of letters, digits, and the punctuation characters
727 : parrello 1.9 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
728 :     character is a semi-colon will be ignored. The return hash will map each option name to
729 : parrello 1.5 the corresponding option value.
730 :    
731 :     =over 4
732 :    
733 :     =item fileName
734 :    
735 :     Name of the file containing the option data.
736 :    
737 :     =item RETURN
738 :    
739 :     Returns a hash mapping the option names specified in the file to their corresponding option
740 :     value.
741 :    
742 :     =back
743 :    
744 :     =cut
745 :    
746 :     sub ReadOptions {
747 : parrello 1.12 # Get the parameters.
748 :     my ($fileName) = @_;
749 :     # Open the file.
750 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
751 :     # Count the number of records read.
752 :     my ($records, $comments) = 0;
753 :     # Create the return hash.
754 :     my %retVal = ();
755 :     # Loop through the file, accumulating key-value pairs.
756 :     while (my $line = <CONFIGFILE>) {
757 :     # Denote we've read a line.
758 :     $records++;
759 :     # Determine the line type.
760 :     if ($line =~ /^\s*[\n\r]/) {
761 :     # A blank line is a comment.
762 :     $comments++;
763 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
764 :     # Here we have an option assignment.
765 :     retVal{$1} = $2;
766 :     } elsif ($line =~ /^\s*;/) {
767 :     # Here we have a text comment.
768 :     $comments++;
769 :     } else {
770 :     # Here we have an invalid line.
771 :     Trace("Invalid option statement in record $records.") if T(0);
772 :     }
773 :     }
774 :     # Return the hash created.
775 :     return %retVal;
776 : parrello 1.5 }
777 :    
778 : olson 1.1 =head3 GetOptions
779 :    
780 :     C<< Tracer::GetOptions(\%defaults, \%options); >>
781 :    
782 :     Merge a specified set of options into a table of defaults. This method takes two hash references
783 :     as input and uses the data from the second to update the first. If the second does not exist,
784 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
785 :     exist in the first.
786 :    
787 :     Consider the following example.
788 :    
789 :     C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
790 :    
791 :     In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
792 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
793 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
794 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
795 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
796 :    
797 :     C<< {databaseType => 'Oracle'} >>
798 :    
799 :     an error will occur because the B<databaseType> option does not exist.
800 :    
801 :     =over 4
802 :    
803 :     =item defaults
804 :    
805 :     Table of default option values.
806 :    
807 :     =item options
808 :    
809 :     Table of overrides, if any.
810 :    
811 :     =item RETURN
812 :    
813 :     Returns a reference to the default table passed in as the first parameter.
814 :    
815 :     =back
816 :    
817 :     =cut
818 :    
819 :     sub GetOptions {
820 : parrello 1.12 # Get the parameters.
821 :     my ($defaults, $options) = @_;
822 :     # Check for overrides.
823 :     if ($options) {
824 :     # Loop through the overrides.
825 :     while (my ($option, $setting) = each %{$options}) {
826 :     # Insure this override exists.
827 :     if (!exists $defaults->{$option}) {
828 :     croak "Unrecognized option $option encountered.";
829 :     } else {
830 :     # Apply the override.
831 :     $defaults->{$option} = $setting;
832 :     }
833 :     }
834 :     }
835 :     # Return the merged table.
836 :     return $defaults;
837 : olson 1.1 }
838 :    
839 :     =head3 MergeOptions
840 :    
841 :     C<< Tracer::MergeOptions(\%table, \%defaults); >>
842 :    
843 :     Merge default values into a hash table. This method looks at the key-value pairs in the
844 :     second (default) hash, and if a matching key is not found in the first hash, the default
845 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
846 :     checking and no return value.
847 :    
848 :     =over 4
849 :    
850 :     =item table
851 :    
852 :     Hash table to be updated with the default values.
853 :    
854 :     =item defaults
855 :    
856 :     Default values to be merged into the first hash table if they are not already present.
857 :    
858 :     =back
859 :    
860 :     =cut
861 :    
862 :     sub MergeOptions {
863 : parrello 1.12 # Get the parameters.
864 :     my ($table, $defaults) = @_;
865 :     # Loop through the defaults.
866 :     while (my ($key, $value) = each %{$defaults}) {
867 :     if (!exists $table->{$key}) {
868 :     $table->{$key} = $value;
869 :     }
870 :     }
871 : olson 1.1 }
872 :    
873 :     =head3 Trace
874 :    
875 :     C<< Trace($message); >>
876 :    
877 :     Write a trace message to the target location specified in L</TSetup>. If there has not been
878 :     any prior call to B<TSetup>.
879 :    
880 :     =over 4
881 :    
882 :     =item message
883 :    
884 :     Message to write.
885 :    
886 :     =back
887 :    
888 :     =cut
889 :    
890 :     sub Trace {
891 : parrello 1.12 # Get the parameters.
892 :     my ($message) = @_;
893 :     # Get the timestamp.
894 :     my $timeStamp = Now();
895 :     # Format the message. Note we strip off any line terminators at the end.
896 :     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);
897 :     # Process according to the destination.
898 :     if ($Destination eq "TEXT") {
899 :     # Write the message to the standard output.
900 :     print "$formatted\n";
901 :     } elsif ($Destination eq "ERROR") {
902 :     # Write the message to the error output.
903 :     print STDERR "$formatted\n";
904 :     } elsif ($Destination eq "QUEUE") {
905 :     # Push the message into the queue.
906 :     push @Queue, "$formatted";
907 :     } elsif ($Destination eq "HTML") {
908 :     # Convert the message to HTML and write it to the standard output.
909 :     my $escapedMessage = CGI::escapeHTML($message);
910 :     print "<p>$formatted</p>\n";
911 : parrello 1.4 } elsif ($Destination eq "WARN") {
912 :     # Emit the message as a warning.
913 :     warn $message;
914 : parrello 1.12 } elsif ($Destination =~ m/^>>/) {
915 :     # Write the trace message to an output file.
916 : parrello 1.14 (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
917 : parrello 1.12 print TRACING "$formatted\n";
918 :     close TRACING;
919 :     # If the Tee flag is on, echo it to the standard output.
920 :     if ($TeeFlag) {
921 :     print "$formatted\n";
922 :     }
923 :     }
924 : olson 1.1 }
925 :    
926 :     =head3 T
927 :    
928 : parrello 1.2 C<< my $switch = T($category, $traceLevel); >>
929 : olson 1.1
930 : parrello 1.12 or
931 : parrello 1.2
932 : olson 1.1 C<< my $switch = T($traceLevel); >>
933 :    
934 :     Return TRUE if the trace level is at or above a specified value and the specified category
935 :     is active, else FALSE. If no category is specified, the caller's package name is used.
936 :    
937 :     =over 4
938 :    
939 :     =item category
940 :    
941 :     Category to which the message belongs. If not specified, the caller's package name is
942 :     used.
943 :    
944 :     =item traceLevel
945 :    
946 :     Relevant tracing level.
947 :    
948 :     =item RETURN
949 :    
950 :     TRUE if a message at the specified trace level would appear in the trace, else FALSE.
951 :    
952 :     =back
953 :    
954 :     =cut
955 :    
956 :     sub T {
957 : parrello 1.12 # Declare the return variable.
958 :     my $retVal = 0;
959 :     # Only proceed if tracing is turned on.
960 :     if ($Destination ne "NONE") {
961 :     # Get the parameters.
962 :     my ($category, $traceLevel) = @_;
963 :     if (!defined $traceLevel) {
964 :     # Here we have no category, so we need to get the calling package.
965 :     # The calling package is normally the first parameter. If it is
966 :     # omitted, the first parameter will be the tracelevel. So, the
967 :     # first thing we do is shift the so-called category into the
968 :     # $traceLevel variable where it belongs.
969 :     $traceLevel = $category;
970 :     my ($package, $fileName, $line) = caller;
971 : parrello 1.3 # If there is no calling package, we default to "main".
972 : parrello 1.12 if (!$package) {
973 : parrello 1.3 $category = "main";
974 : parrello 1.12 } else {
975 :     $category = $package;
976 :     }
977 :     }
978 : parrello 1.7 # Save the category name.
979 :     $LastCategory = $category;
980 : parrello 1.13 # Convert it to lower case before we hash it.
981 :     $category = lc $category;
982 : parrello 1.12 # Use the category and tracelevel to compute the result.
983 : parrello 1.36 if (ref $traceLevel) {
984 :     Confess("Bad trace level.");
985 :     } elsif (ref $TraceLevel) {
986 :     Confess("Bad trace config.");
987 :     }
988 : parrello 1.12 $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
989 : parrello 1.3 }
990 : parrello 1.12 # Return the computed result.
991 : parrello 1.3 return $retVal;
992 : olson 1.1 }
993 :    
994 :     =head3 ParseCommand
995 :    
996 :     C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
997 :    
998 :     Parse a command line consisting of a list of parameters. The initial parameters may be option
999 : parrello 1.2 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1000 :     off and merged into a table of default options. The remainder of the command line is
1001 : olson 1.1 returned as a list of positional arguments. For example, consider the following invocation.
1002 :    
1003 :     C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1004 :    
1005 :     In this case, the list @words will be treated as a command line. There are two options available,
1006 :     B<errors> and B<logFile>. If @words has the following format
1007 :    
1008 :     C<< -logFile=error.log apple orange rutabaga >>
1009 :    
1010 :     then at the end of the invocation, C<$options> will be
1011 :    
1012 :     C<< { errors => 0, logFile => 'error.log' } >>
1013 :    
1014 :     and C<@arguments> will contain
1015 :    
1016 :     C<< apple orange rutabaga >>
1017 :    
1018 : parrello 1.2 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1019 : olson 1.1 support for quote characters.
1020 :    
1021 :     =over 4
1022 :    
1023 :     =item optionTable
1024 :    
1025 :     Table of default options.
1026 :    
1027 :     =item inputList
1028 :    
1029 :     List of words on the command line.
1030 :    
1031 :     =item RETURN
1032 :    
1033 :     Returns a reference to the option table and a list of the positional arguments.
1034 :    
1035 :     =back
1036 :    
1037 :     =cut
1038 :    
1039 :     sub ParseCommand {
1040 : parrello 1.12 # Get the parameters.
1041 :     my ($optionTable, @inputList) = @_;
1042 :     # Process any options in the input list.
1043 :     my %overrides = ();
1044 :     while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1045 :     # Get the current option.
1046 :     my $arg = shift @inputList;
1047 :     # Pull out the option name.
1048 :     $arg =~ /^-([^=]*)/g;
1049 :     my $name = $1;
1050 :     # Check for an option value.
1051 :     if ($arg =~ /\G=(.*)$/g) {
1052 :     # Here we have a value for the option.
1053 :     $overrides{$name} = UnEscape($1);
1054 :     } else {
1055 :     # Here there is no value, so we use 1.
1056 :     $overrides{$name} = 1;
1057 :     }
1058 :     }
1059 :     # Merge the options into the defaults.
1060 :     GetOptions($optionTable, \%overrides);
1061 :     # Translate the remaining parameters.
1062 :     my @retVal = ();
1063 :     for my $inputParm (@inputList) {
1064 :     push @retVal, UnEscape($inputParm);
1065 :     }
1066 :     # Return the results.
1067 :     return ($optionTable, @retVal);
1068 : olson 1.1 }
1069 :    
1070 : parrello 1.9 =head3 Escape
1071 :    
1072 :     C<< my $codedString = Tracer::Escape($realString); >>
1073 :    
1074 : parrello 1.25 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1075 : parrello 1.28 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1076 :     result is to reverse the effect of L</UnEscape>.
1077 : parrello 1.9
1078 :     =over 4
1079 :    
1080 :     =item realString
1081 :    
1082 :     String to escape.
1083 :    
1084 :     =item RETURN
1085 :    
1086 :     Escaped equivalent of the real string.
1087 :    
1088 :     =back
1089 :    
1090 :     =cut
1091 :    
1092 :     sub Escape {
1093 : parrello 1.12 # Get the parameter.
1094 :     my ($realString) = @_;
1095 :     # Initialize the return variable.
1096 :     my $retVal = "";
1097 :     # Loop through the parameter string, looking for sequences to escape.
1098 :     while (length $realString > 0) {
1099 :     # Look for the first sequence to escape.
1100 : parrello 1.27 if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1101 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1102 :     # itself is in $2. First, move the clear text to the return variable.
1103 :     $retVal .= $1;
1104 : parrello 1.14 # Strip the processed section off the real string.
1105 :     $realString = substr $realString, (length $2) + (length $1);
1106 : parrello 1.28 # Get the matched character.
1107 : parrello 1.12 my $char = $2;
1108 : parrello 1.28 # If we have a CR, we are done.
1109 :     if ($char ne "\r") {
1110 :     # It's not a CR, so encode the escape sequence.
1111 :     $char =~ tr/\t\n/tn/;
1112 :     $retVal .= "\\" . $char;
1113 :     }
1114 : parrello 1.12 } else {
1115 :     # Here there are no more escape sequences. The rest of the string is
1116 :     # transferred unmodified.
1117 :     $retVal .= $realString;
1118 :     $realString = "";
1119 :     }
1120 :     }
1121 :     # Return the result.
1122 :     return $retVal;
1123 : parrello 1.9 }
1124 :    
1125 : olson 1.1 =head3 UnEscape
1126 :    
1127 :     C<< my $realString = Tracer::UnEscape($codedString); >>
1128 :    
1129 : parrello 1.25 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1130 : parrello 1.28 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1131 :     be deleted.
1132 : olson 1.1
1133 :     =over 4
1134 :    
1135 :     =item codedString
1136 :    
1137 :     String to un-escape.
1138 :    
1139 :     =item RETURN
1140 :    
1141 :     Returns a copy of the original string with the escape sequences converted to their actual
1142 :     values.
1143 :    
1144 :     =back
1145 :    
1146 :     =cut
1147 :    
1148 :     sub UnEscape {
1149 : parrello 1.12 # Get the parameter.
1150 :     my ($codedString) = @_;
1151 :     # Initialize the return variable.
1152 :     my $retVal = "";
1153 :     # Only proceed if the incoming string is nonempty.
1154 :     if (defined $codedString) {
1155 :     # Loop through the parameter string, looking for escape sequences. We can't do
1156 : parrello 1.25 # translating because it causes problems with the escaped slash. ("\\t" becomes
1157 :     # "\<tab>" no matter what we do.)
1158 : parrello 1.12 while (length $codedString > 0) {
1159 :     # Look for the first escape sequence.
1160 : parrello 1.27 if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1161 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1162 :     # itself is in $2. First, move the clear text to the return variable.
1163 :     $retVal .= $1;
1164 :     $codedString = substr $codedString, (2 + length $1);
1165 : parrello 1.28 # Get the escape value.
1166 : parrello 1.12 my $char = $2;
1167 : parrello 1.28 # If we have a "\r", we are done.
1168 :     if ($char ne 'r') {
1169 :     # Here it's not an 'r', so we convert it.
1170 :     $char =~ tr/\\tn/\\\t\n/;
1171 :     $retVal .= $char;
1172 :     }
1173 : parrello 1.12 } else {
1174 :     # Here there are no more escape sequences. The rest of the string is
1175 :     # transferred unmodified.
1176 :     $retVal .= $codedString;
1177 :     $codedString = "";
1178 :     }
1179 :     }
1180 :     }
1181 :     # Return the result.
1182 :     return $retVal;
1183 : olson 1.1 }
1184 :    
1185 :     =head3 ParseRecord
1186 :    
1187 :     C<< my @fields = Tracer::ParseRecord($line); >>
1188 :    
1189 :     Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1190 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1191 :     These will automatically be converted.
1192 :    
1193 :     =over 4
1194 :    
1195 :     =item line
1196 :    
1197 :     Line of data containing the tab-delimited fields.
1198 :    
1199 :     =item RETURN
1200 :    
1201 :     Returns a list of the fields found in the data line.
1202 :    
1203 :     =back
1204 :    
1205 :     =cut
1206 :    
1207 :     sub ParseRecord {
1208 : parrello 1.12 # Get the parameter.
1209 :     my ($line) = @_;
1210 :     # Remove the trailing new-line, if any.
1211 :     chomp $line;
1212 :     # Split the line read into pieces using the tab character.
1213 :     my @retVal = split /\t/, $line;
1214 :     # Trim and fix the escapes in each piece.
1215 :     for my $value (@retVal) {
1216 :     # Trim leading whitespace.
1217 :     $value =~ s/^\s+//;
1218 :     # Trim trailing whitespace.
1219 :     $value =~ s/\s+$//;
1220 :     # Delete the carriage returns.
1221 :     $value =~ s/\r//g;
1222 :     # Convert the escapes into their real values.
1223 :     $value =~ s/\\t/"\t"/ge;
1224 :     $value =~ s/\\n/"\n"/ge;
1225 :     }
1226 :     # Return the result.
1227 :     return @retVal;
1228 : olson 1.1 }
1229 :    
1230 :     =head3 Merge
1231 :    
1232 :     C<< my @mergedList = Tracer::Merge(@inputList); >>
1233 :    
1234 :     Sort a list of strings and remove duplicates.
1235 :    
1236 :     =over 4
1237 :    
1238 :     =item inputList
1239 :    
1240 :     List of scalars to sort and merge.
1241 :    
1242 :     =item RETURN
1243 :    
1244 :     Returns a list containing the same elements sorted in ascending order with duplicates
1245 :     removed.
1246 :    
1247 :     =back
1248 :    
1249 :     =cut
1250 :    
1251 :     sub Merge {
1252 : parrello 1.12 # Get the input list in sort order.
1253 :     my @inputList = sort @_;
1254 :     # Only proceed if the list has at least two elements.
1255 :     if (@inputList > 1) {
1256 :     # Now we want to move through the list splicing out duplicates.
1257 :     my $i = 0;
1258 :     while ($i < @inputList) {
1259 :     # Get the current entry.
1260 :     my $thisEntry = $inputList[$i];
1261 :     # Find out how many elements duplicate the current entry.
1262 :     my $j = $i + 1;
1263 :     my $dup1 = $i + 1;
1264 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1265 :     # If the number is nonzero, splice out the duplicates found.
1266 :     if ($j > $dup1) {
1267 :     splice @inputList, $dup1, $j - $dup1;
1268 :     }
1269 :     # Now the element at position $dup1 is different from the element before it
1270 :     # at position $i. We push $i forward one position and start again.
1271 :     $i++;
1272 :     }
1273 :     }
1274 :     # Return the merged list.
1275 :     return @inputList;
1276 : olson 1.1 }
1277 :    
1278 :     =head3 GetFile
1279 :    
1280 : parrello 1.6 C<< my @fileContents = Tracer::GetFile($fileName); >>
1281 : olson 1.1
1282 : parrello 1.35 or
1283 :    
1284 :     C<< my $fileContents = Tracer::GetFile($fileName); >>
1285 :    
1286 :     Return the entire contents of a file. In list context, line-ends are removed and
1287 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1288 : olson 1.1
1289 :     =over 4
1290 :    
1291 :     =item fileName
1292 :    
1293 :     Name of the file to read.
1294 :    
1295 :     =item RETURN
1296 :    
1297 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1298 :     In a scalar context, returns the entire file as a string.
1299 : olson 1.1
1300 :     =back
1301 :    
1302 :     =cut
1303 :    
1304 :     sub GetFile {
1305 : parrello 1.12 # Get the parameters.
1306 :     my ($fileName) = @_;
1307 :     # Declare the return variable.
1308 :     my @retVal = ();
1309 :     # Open the file for input.
1310 :     my $ok = open INPUTFILE, "<$fileName";
1311 :     if (!$ok) {
1312 :     # If we had an error, trace it. We will automatically return a null value.
1313 : parrello 1.16 Trace("Could not open \"$fileName\" for input: $!") if T(0);
1314 : parrello 1.12 } else {
1315 :     # Read the whole file into the return variable, stripping off any terminator
1316 : parrello 1.6 # characters.
1317 :     my $lineCount = 0;
1318 : parrello 1.12 while (my $line = <INPUTFILE>) {
1319 : parrello 1.6 $lineCount++;
1320 : parrello 1.9 $line = Strip($line);
1321 : parrello 1.12 push @retVal, $line;
1322 :     }
1323 :     # Close it.
1324 :     close INPUTFILE;
1325 : parrello 1.6 my $actualLines = @retVal;
1326 : parrello 1.12 }
1327 :     # Return the file's contents in the desired format.
1328 : parrello 1.9 if (wantarray) {
1329 : parrello 1.12 return @retVal;
1330 : parrello 1.6 } else {
1331 :     return join "\n", @retVal;
1332 :     }
1333 : olson 1.1 }
1334 :    
1335 :     =head3 QTrace
1336 :    
1337 :     C<< my $data = QTrace($format); >>
1338 :    
1339 :     Return the queued trace data in the specified format.
1340 :    
1341 :     =over 4
1342 :    
1343 :     =item format
1344 :    
1345 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
1346 :    
1347 :     =back
1348 :    
1349 :     =cut
1350 :    
1351 :     sub QTrace {
1352 : parrello 1.12 # Get the parameter.
1353 :     my ($format) = @_;
1354 :     # Create the return variable.
1355 :     my $retVal = "";
1356 : parrello 1.14 # Only proceed if there is an actual queue.
1357 :     if (@Queue) {
1358 :     # Process according to the format.
1359 :     if ($format =~ m/^HTML$/i) {
1360 :     # Convert the queue into an HTML list.
1361 :     $retVal = "<ul>\n";
1362 :     for my $line (@Queue) {
1363 :     my $escapedLine = CGI::escapeHTML($line);
1364 :     $retVal .= "<li>$escapedLine</li>\n";
1365 :     }
1366 :     $retVal .= "</ul>\n";
1367 :     } elsif ($format =~ m/^TEXT$/i) {
1368 :     # Convert the queue into a list of text lines.
1369 :     $retVal = join("\n", @Queue) . "\n";
1370 :     }
1371 :     # Clear the queue.
1372 :     @Queue = ();
1373 : parrello 1.12 }
1374 :     # Return the formatted list.
1375 :     return $retVal;
1376 : olson 1.1 }
1377 :    
1378 :     =head3 Confess
1379 :    
1380 :     C<< Confess($message); >>
1381 :    
1382 : parrello 1.22 Trace the call stack and abort the program with the specified message. When used with
1383 : parrello 1.9 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1384 : parrello 1.6 So, for example
1385 : olson 1.1
1386 : parrello 1.6 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1387 : olson 1.1
1388 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1389 :    
1390 :     =over 4
1391 :    
1392 :     =item message
1393 :    
1394 :     Message to include in the trace.
1395 :    
1396 :     =back
1397 :    
1398 :     =cut
1399 :    
1400 :     sub Confess {
1401 : parrello 1.12 # Get the parameters.
1402 :     my ($message) = @_;
1403 :     # Trace the call stack.
1404 : parrello 1.22 Cluck($message);
1405 : parrello 1.12 # Abort the program.
1406 :     croak(">>> $message");
1407 : olson 1.1 }
1408 :    
1409 : parrello 1.6 =head3 Assert
1410 :    
1411 :     C<< Assert($condition1, $condition2, ... $conditionN); >>
1412 :    
1413 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
1414 : parrello 1.29 the OR operator and the L</Confess> method as a debugging assert.
1415 : parrello 1.6 So, for example
1416 :    
1417 :     C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1418 :    
1419 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1420 :    
1421 :     =cut
1422 :     sub Assert {
1423 :     my $retVal = 1;
1424 :     LOOP: for my $condition (@_) {
1425 :     if (! $condition) {
1426 :     $retVal = 0;
1427 :     last LOOP;
1428 :     }
1429 :     }
1430 :     return $retVal;
1431 :     }
1432 :    
1433 : olson 1.1 =head3 Cluck
1434 :    
1435 :     C<< Cluck($message); >>
1436 :    
1437 :     Trace the call stack. Note that for best results, you should qualify the call with a
1438 :     trace condition. For example,
1439 :    
1440 :     C<< Cluck("Starting record parse.") if T(3); >>
1441 :    
1442 :     will only trace the stack if the trace level for the package is 3 or more.
1443 :    
1444 :     =over 4
1445 :    
1446 :     =item message
1447 :    
1448 :     Message to include in the trace.
1449 :    
1450 :     =back
1451 :    
1452 :     =cut
1453 :    
1454 :     sub Cluck {
1455 : parrello 1.12 # Get the parameters.
1456 :     my ($message) = @_;
1457 : parrello 1.5 # Trace what's happening.
1458 :     Trace("Stack trace for event: $message");
1459 : parrello 1.12 my $confession = longmess($message);
1460 :     # Convert the confession to a series of trace messages. Note we skip any
1461 : parrello 1.5 # messages relating to calls into Tracer.
1462 : parrello 1.12 for my $line (split /\s*\n/, $confession) {
1463 :     Trace($line) if ($line !~ /Tracer\.pm/);
1464 :     }
1465 : olson 1.1 }
1466 :    
1467 : parrello 1.5 =head3 Min
1468 :    
1469 :     C<< my $min = Min($value1, $value2, ... $valueN); >>
1470 :    
1471 :     Return the minimum argument. The arguments are treated as numbers.
1472 :    
1473 :     =over 4
1474 :    
1475 :     =item $value1, $value2, ... $valueN
1476 :    
1477 :     List of numbers to compare.
1478 :    
1479 :     =item RETURN
1480 :    
1481 :     Returns the lowest number in the list.
1482 :    
1483 :     =back
1484 :    
1485 :     =cut
1486 :    
1487 :     sub Min {
1488 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1489 :     my ($retVal, @values) = @_;
1490 :     # Loop through the remaining parameters, looking for the lowest.
1491 :     for my $value (@values) {
1492 :     if ($value < $retVal) {
1493 :     $retVal = $value;
1494 :     }
1495 :     }
1496 :     # Return the minimum found.
1497 :     return $retVal;
1498 : parrello 1.5 }
1499 :    
1500 :     =head3 Max
1501 :    
1502 :     C<< my $max = Max($value1, $value2, ... $valueN); >>
1503 :    
1504 :     Return the maximum argument. The arguments are treated as numbers.
1505 :    
1506 :     =over 4
1507 :    
1508 :     =item $value1, $value2, ... $valueN
1509 :    
1510 :     List of numbers to compare.
1511 :    
1512 :     =item RETURN
1513 :    
1514 :     Returns the highest number in the list.
1515 :    
1516 :     =back
1517 :    
1518 :     =cut
1519 :    
1520 :     sub Max {
1521 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1522 :     my ($retVal, @values) = @_;
1523 :     # Loop through the remaining parameters, looking for the highest.
1524 :     for my $value (@values) {
1525 :     if ($value > $retVal) {
1526 :     $retVal = $value;
1527 :     }
1528 :     }
1529 :     # Return the maximum found.
1530 :     return $retVal;
1531 : parrello 1.5 }
1532 :    
1533 :     =head3 AddToListMap
1534 :    
1535 :     C<< Tracer::AddToListMap(\%hash, $key, $value); >>
1536 :    
1537 :     Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1538 :     is created for the key. Otherwise, the new value is pushed onto the list.
1539 :    
1540 :     =over 4
1541 :    
1542 :     =item hash
1543 :    
1544 :     Reference to the target hash.
1545 :    
1546 :     =item key
1547 :    
1548 :     Key for which the value is to be added.
1549 :    
1550 :     =item value
1551 :    
1552 :     Value to add to the key's value list.
1553 :    
1554 :     =back
1555 :    
1556 :     =cut
1557 :    
1558 :     sub AddToListMap {
1559 :     # Get the parameters.
1560 :     my ($hash, $key, $value) = @_;
1561 :     # Process according to whether or not the key already has a value.
1562 :     if (! exists $hash->{$key}) {
1563 :     $hash->{$key} = [$value];
1564 :     } else {
1565 :     push @{$hash->{$key}}, $value;
1566 :     }
1567 :     }
1568 : olson 1.1
1569 : parrello 1.7 =head3 DebugMode
1570 :    
1571 :     C<< if (Tracer::DebugMode) { ...code... } >>
1572 :    
1573 : parrello 1.22 Return TRUE if debug mode has been turned on, else output an error
1574 :     page and return FALSE.
1575 : parrello 1.7
1576 :     Certain CGI scripts are too dangerous to exist in the production
1577 :     environment. This method provides a simple way to prevent them
1578 : parrello 1.21 from working unless they are explicitly turned on by creating a password
1579 :     cookie via the B<SetPassword> script. If debugging mode
1580 : parrello 1.22 is not turned on, an error web page will be output directing the
1581 :     user to enter in the correct password.
1582 : parrello 1.7
1583 :     =cut
1584 :    
1585 :     sub DebugMode {
1586 : parrello 1.12 # Declare the return variable.
1587 : parrello 1.21 my $retVal = 0;
1588 : parrello 1.12 # Check the debug configuration.
1589 : parrello 1.21 my $password = CGI::cookie("DebugMode");
1590 :     my $encrypted = Digest::MD5::md5_hex($password);
1591 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1592 : parrello 1.12 $retVal = 1;
1593 :     } else {
1594 :     # Here debug mode is off, so we generate an error page.
1595 : parrello 1.9 my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");
1596 : parrello 1.12 print $pageString;
1597 :     }
1598 :     # Return the determination indicator.
1599 : parrello 1.18 return $retVal;
1600 : parrello 1.9 }
1601 :    
1602 :     =head3 Strip
1603 :    
1604 :     C<< my $string = Tracer::Strip($line); >>
1605 :    
1606 :     Strip all line terminators off a string. This is necessary when dealing with files
1607 :     that may have been transferred back and forth several times among different
1608 :     operating environments.
1609 :    
1610 :     =over 4
1611 :    
1612 :     =item line
1613 :    
1614 :     Line of text to be stripped.
1615 :    
1616 :     =item RETURN
1617 :    
1618 :     The same line of text with all the line-ending characters chopped from the end.
1619 :    
1620 :     =back
1621 :    
1622 :     =cut
1623 :    
1624 :     sub Strip {
1625 : parrello 1.12 # Get a copy of the parameter string.
1626 :     my ($string) = @_;
1627 : parrello 1.29 my $retVal = (defined $string ? $string : "");
1628 : parrello 1.9 # Strip the line terminator characters.
1629 :     $retVal =~ s/(\r|\n)+$//g;
1630 : parrello 1.12 # Return the result.
1631 :     return $retVal;
1632 : parrello 1.9 }
1633 :    
1634 :     =head3 Pad
1635 :    
1636 :     C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1637 :    
1638 :     Pad a string to a specified length. The pad character will be a
1639 :     space, and the padding will be on the right side unless specified
1640 :     in the third parameter.
1641 :    
1642 :     =over 4
1643 :    
1644 :     =item string
1645 :    
1646 :     String to be padded.
1647 :    
1648 :     =item len
1649 :    
1650 :     Desired length of the padded string.
1651 :    
1652 :     =item left (optional)
1653 :    
1654 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1655 :    
1656 :     =item padChar (optional)
1657 :    
1658 : parrello 1.22 Character to use for padding. The default is a space.
1659 :    
1660 : parrello 1.9 =item RETURN
1661 :    
1662 : parrello 1.22 Returns a copy of the original string with the pad character added to the
1663 :     specified end so that it achieves the desired length.
1664 : parrello 1.9
1665 :     =back
1666 :    
1667 :     =cut
1668 :    
1669 :     sub Pad {
1670 : parrello 1.12 # Get the parameters.
1671 :     my ($string, $len, $left, $padChar) = @_;
1672 :     # Compute the padding character.
1673 :     if (! defined $padChar) {
1674 :     $padChar = " ";
1675 :     }
1676 :     # Compute the number of spaces needed.
1677 :     my $needed = $len - length $string;
1678 :     # Copy the string into the return variable.
1679 :     my $retVal = $string;
1680 :     # Only proceed if padding is needed.
1681 :     if ($needed > 0) {
1682 :     # Create the pad string.
1683 :     my $pad = $padChar x $needed;
1684 :     # Affix it to the return value.
1685 :     if ($left) {
1686 :     $retVal = $pad . $retVal;
1687 :     } else {
1688 :     $retVal .= $pad;
1689 :     }
1690 :     }
1691 :     # Return the result.
1692 :     return $retVal;
1693 : parrello 1.7 }
1694 :    
1695 : parrello 1.29 =head3 EOF
1696 :    
1697 :     This is a constant that is lexically greater than any useful string.
1698 :    
1699 :     =cut
1700 :    
1701 :     sub EOF {
1702 :     return "\xFF\xFF\xFF\xFF\xFF";
1703 :     }
1704 :    
1705 : parrello 1.15 =head3 TICK
1706 :    
1707 :     C<< my @results = TICK($commandString); >>
1708 :    
1709 :     Perform a back-tick operation on a command. If this is a Windows environment, any leading
1710 :     dot-slash (C<./> will be removed. So, for example, if you were doing
1711 :    
1712 :     `./protein.cgi`
1713 :    
1714 :     from inside a CGI script, it would work fine in Unix, but would issue an error message
1715 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
1716 :    
1717 :     TICK("./protein.cgi")
1718 :    
1719 :     it will work correctly in both environments.
1720 :    
1721 :     =over 4
1722 :    
1723 :     =item commandString
1724 :    
1725 :     The command string to pass to the system.
1726 :    
1727 :     =item RETURN
1728 :    
1729 :     Returns the standard output from the specified command, as a list.
1730 :    
1731 :     =back
1732 :    
1733 :     =cut
1734 :     #: Return Type @;
1735 :     sub TICK {
1736 :     # Get the parameters.
1737 :     my ($commandString) = @_;
1738 :     # Chop off the dot-slash if this is Windows.
1739 :     if ($FIG_Config::win_mode) {
1740 :     $commandString =~ s!^\./!!;
1741 :     }
1742 :     # Activate the command and return the result.
1743 :     return `$commandString`;
1744 :     }
1745 :    
1746 : parrello 1.35 =head3 ScriptSetup
1747 :    
1748 :     C<< my ($query, $varHash) = ScriptSetup(); >>
1749 :    
1750 :     Perform standard tracing and debugging setup for scripts. The value returned is
1751 :     the CGI object followed by a pre-built variable hash.
1752 :    
1753 :     The C<Trace> query parameter is used to determine whether or not tracing is active and
1754 :     which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1755 :     the C<CGI> trace module will trace parameter and environment information. Parameters are
1756 :     traced at level 3 and environment variables at level 4. At the end of the script, the
1757 :     client should call L</ScriptFinish> to output the web page.
1758 :    
1759 :     =cut
1760 :    
1761 :     sub ScriptSetup {
1762 :     # Get the CGI query object.
1763 :     my $query = CGI->new();
1764 :     # Check for tracing. Set it up if the user asked for it.
1765 :     if ($query->param('Trace')) {
1766 :     # Set up tracing to be queued for display at the bottom of the web page.
1767 :     TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1768 :     # Trace the parameter and environment data.
1769 :     if (T(CGI => 3)) {
1770 :     # Here we want to trace the parameter data.
1771 :     my @names = $query->param;
1772 :     for my $parmName (sort @names) {
1773 :     # Note we skip "Trace", which is for our use only.
1774 :     if ($parmName ne 'Trace') {
1775 :     my @values = $query->param($parmName);
1776 :     Trace("CGI: $parmName = " . join(", ", @values));
1777 :     }
1778 :     }
1779 :     }
1780 :     if (T(CGI => 4)) {
1781 :     # Here we want the environment data too.
1782 :     for my $envName (sort keys %ENV) {
1783 :     Trace("ENV: $envName = $ENV{$envName}");
1784 :     }
1785 :     }
1786 :     } else {
1787 :     # Here tracing is to be turned off. All we allow is errors traced into the
1788 :     # error log.
1789 :     TSetup("0", "WARN");
1790 :     }
1791 :     # Create the variable hash.
1792 :     my $varHash = { DebugData => '' };
1793 :     # If we're in DEBUG mode, set up the debug mode data for forms.
1794 :     if (Tracer::DebugMode) {
1795 :     $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1796 :     }
1797 :     # Return the query object and variable hash.
1798 :     return ($query, $varHash);
1799 :     }
1800 :    
1801 :     =head3 ScriptFinish
1802 :    
1803 :     C<< ScriptFinish($webData, $varHash); >>
1804 :    
1805 :     Output a web page at the end of a script. Either the string to be output or the
1806 :     name of a template file can be specified. If the second parameter is omitted,
1807 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1808 :     name of a template file. The template should have the variable C<DebugData>
1809 :     specified in any form that invokes a standard script. If debugging mode is turned
1810 :     on, a form field will be put in that allows the user to enter tracing data.
1811 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1812 :     the output, formatted as a list.
1813 :    
1814 :     A typical standard script would loook like the following.
1815 :    
1816 :     BEGIN {
1817 :     # Print the HTML header.
1818 :     print "CONTENT-TYPE: text/html\n\n";
1819 :     }
1820 :     use Tracer;
1821 :     use CGI;
1822 :     use FIG;
1823 :     # ... more uses ...
1824 :    
1825 :     my ($query, $varHash) = ScriptSetup();
1826 :     eval {
1827 :     # ... get data from $query, put it in $varHash ...
1828 :     };
1829 :     if ($@) {
1830 :     Trace("Script Error: $@") if T(0);
1831 :     }
1832 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1833 :    
1834 :     The idea here is that even if the script fails, you'll see trace messages and
1835 :     useful output.
1836 :    
1837 :     =over 4
1838 :    
1839 :     =item webData
1840 :    
1841 :     A string containing either the full web page to be written to the output or the
1842 :     name of a template file from which the page is to be constructed. If the name
1843 :     of a template file is specified, then the second parameter must be present;
1844 :     otherwise, it must be absent.
1845 :    
1846 :     =item varHash (optional)
1847 :    
1848 :     If specified, then a reference to a hash mapping variable names for a template
1849 :     to their values. The template file will be read into memory, and variable markers
1850 :     will be replaced by data in this hash reference.
1851 :    
1852 : parrello 1.37 =back
1853 :    
1854 : parrello 1.35 =cut
1855 :    
1856 :     sub ScriptFinish {
1857 :     # Get the parameters.
1858 :     my ($webData, $varHash) = @_;
1859 :     # Check for a template file situation.
1860 :     my $outputString;
1861 :     if (defined $varHash) {
1862 :     # Here we have a template file. We need to apply the variables to the template.
1863 :     $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1864 :     } else {
1865 :     # Here the user gave us a raw string.
1866 :     $outputString = $webData;
1867 :     }
1868 :     # Check for trace messages.
1869 :     if ($Destination eq "QUEUE") {
1870 :     # We have trace messages, so we want to put them at the end of the body. This
1871 :     # is either at the end of the whole string or at the beginning of the BODY
1872 :     # end-tag.
1873 :     my $pos = length $outputString;
1874 :     if ($outputString =~ m#</body>#gi) {
1875 :     $pos = (pos $outputString) - 7;
1876 :     }
1877 :     substr $outputString, $pos, 0, QTrace('Html');
1878 :     }
1879 :     # Write the output string.
1880 :     print $outputString;
1881 :     }
1882 :    
1883 : parrello 1.37 =head3 Insure
1884 :    
1885 :     C<< Insure($dirName); >>
1886 :    
1887 :     Insure a directory is present.
1888 :    
1889 :     =over 4
1890 :    
1891 :     =item dirName
1892 :    
1893 :     Name of the directory to check. If it does not exist, it will be created.
1894 :    
1895 :     =back
1896 :    
1897 :     =cut
1898 :    
1899 :     sub Insure {
1900 :     my ($dirName) = @_;
1901 :     if (! -d $dirName) {
1902 :     Trace("Creating $dirName directory.") if T(2);
1903 :     mkpath $dirName;
1904 :     }
1905 :     }
1906 :    
1907 : redwards 1.8 1;

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