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

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