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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 : parrello 1.42 You can specify a different default trace level by setting C<$options->{trace}>
279 :     prior to calling this method.
280 :    
281 : parrello 1.31 An example at this point would help. Consider, for example, the command-line utility
282 :     C<TransactFeatures>. It accepts a list of positional parameters plus the options
283 :     C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
284 :     the following code.
285 :    
286 :     my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
287 : parrello 1.36 { safe => [0, "use database transactions"],
288 :     noAlias => [0, "do not expect aliases in CHANGE transactions"],
289 :     start => [' ', "start with this genome"],
290 :     tblFiles => [0, "output TBL files containing the corrected IDs"] },
291 :     "command transactionDirectory IDfile",
292 :     @ARGV);
293 : parrello 1.31
294 :    
295 :     The call to C<ParseCommand> specifies the default values for the options and
296 :     stores the actual options in a hash that is returned as C<$options>. The
297 :     positional parameters are returned in C<@parameters>.
298 :    
299 :     The following is a sample command line for C<TransactFeatures>.
300 :    
301 :     TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
302 :    
303 :     In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
304 :     parameters, and would find themselves in I<@parameters> after executing the
305 :     above code fragment. The tracing would be set to level 2, and the categories
306 :     would be C<FIG>, C<Tracer>, and <DocUtils>. C<FIG> and C<Tracer> are standard,
307 :     and C<DocUtils> was included because it came in within the first parameter
308 :     to this method. The I<$options> hash would be
309 :    
310 :     { trace => 2, sql => 0, safe => 0,
311 :     noAlias => 1, start => ' ', tblFiles => 0 }
312 :    
313 :     Use of C<StandardSetup> in this way provides a simple way of performing
314 :     standard tracing setup and command-line parsing. Note that the caller is
315 :     not even aware of the command-line switches C<-trace> and C<-sql>, which
316 :     are used by this method to control the tracing. If additional tracing features
317 :     need to be added in the future, they can be processed by this method without
318 :     upsetting the command-line utilities.
319 :    
320 : parrello 1.42 If the C<background> option is specified on the command line, then the
321 :     standard and error outputs will be directed to files in the temporary
322 :     directory, using the same suffix as the trace file. So, if the command
323 :     line specified
324 :    
325 :     -user=Bruce -background
326 :    
327 :     then the trace output would go to C<traceBruce.log>, the standard output to
328 :     C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
329 :     simplify starting a command in the background.
330 :    
331 : parrello 1.36 Finally, if the special option C<-h> is specified, the option names will
332 :     be traced at level 0 and the program will exit without processing.
333 :     This provides a limited help capability. For example, if the user enters
334 :    
335 :     TransactFeatures -h
336 :    
337 :     he would see the following output.
338 :    
339 :     TransactFeatures [options] command transactionDirectory IDfile
340 :     -trace tracing level (default 2)
341 :     -sql trace SQL commands
342 :     -safe use database transactions
343 :     -noAlias do not expect aliases in CHANGE transactions
344 :     -start start with this genome
345 :     -tblFiles output TBL files containing the corrected IDs
346 :    
347 : parrello 1.31 The parameters to this method are as follows.
348 :    
349 :     =over 4
350 :    
351 :     =item categories
352 :    
353 :     Reference to a list of tracing category names. These should be names of
354 :     packages whose internal workings will need to be debugged to get the
355 :     command working.
356 :    
357 :     =item options
358 :    
359 :     Reference to a hash containing the legal options for the current command mapped
360 : parrello 1.36 to their default values and descriptions. The user can override the defaults
361 :     by specifying the options as command-line switches prefixed by a hyphen.
362 :     Tracing-related options may be added to this hash. If the C<-h> option is
363 :     specified on the command line, the option descriptions will be used to
364 :     explain the options.
365 :    
366 :     =item parmHelp
367 :    
368 :     A string that vaguely describes the positional parameters. This is used
369 :     if the user specifies the C<-h> option.
370 : parrello 1.31
371 :     =item ARGV
372 :    
373 :     List of command line parameters, including the option switches, which must
374 :     precede the positional parameters and be prefixed by a hyphen.
375 :    
376 :     =item RETURN
377 :    
378 :     Returns a list. The first element of the list is the reference to a hash that
379 :     maps the command-line option switches to their values. These will either be the
380 :     default values or overrides specified on the command line. The remaining
381 :     elements of the list are the position parameters, in order.
382 :    
383 :     =back
384 :    
385 :     =cut
386 :    
387 :     sub StandardSetup {
388 :     # Get the parameters.
389 : parrello 1.36 my ($categories, $options, $parmHelp, @argv) = @_;
390 : parrello 1.31 # Add the tracing options.
391 : parrello 1.41 if (! exists $options->{trace}) {
392 :     $options->{trace} = [2, "tracing level"];
393 :     }
394 : parrello 1.36 $options->{sql} = [0, "turn on SQL tracing"];
395 :     $options->{h} = [0, "display command-line options"];
396 : parrello 1.38 $options->{user} = [$$, "trace log file name suffix"];
397 : parrello 1.42 $options->{background} = [0, "spool standard and error output"];
398 : parrello 1.36 # Create a parsing hash from the options hash. The parsing hash
399 :     # contains the default values rather than the default value
400 :     # and the description. While we're at it, we'll memorize the
401 :     # length of the longest option name.
402 :     my $longestName = 0;
403 :     my %parseOptions = ();
404 :     for my $key (keys %{$options}) {
405 :     if (length $key > $longestName) {
406 :     $longestName = length $key;
407 :     }
408 :     $parseOptions{$key} = $options->{$key}->[0];
409 :     }
410 : parrello 1.31 # Parse the command line.
411 : parrello 1.36 my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
412 : parrello 1.42 # Get the logfile suffix.
413 :     my $suffix = $retOptions->{user};
414 :     # Check for background mode.
415 :     if ($retOptions->{background}) {
416 :     my $outFileName = "$FIG_Config::temp/out$suffix.log";
417 :     my $errFileName = "$FIG_Config::temp/err$suffix.log";
418 :     open STDOUT, ">$outFileName";
419 :     open STDERR, ">$errFileName";
420 :     }
421 : parrello 1.31 # Now we want to set up tracing. First, we need to know if SQL is to
422 :     # be traced.
423 :     my @cats = @{$categories};
424 :     if ($retOptions->{sql}) {
425 :     push @cats, "SQL";
426 :     }
427 :     # Add the default categories.
428 :     push @cats, "Tracer", "FIG";
429 :     # Next, we create the category string by prefixing the trace level
430 :     # and joining the categories.
431 : parrello 1.36 my $cats = join(" ", $parseOptions{trace}, @cats);
432 : parrello 1.40 # Verify that we can open a file in the temporary directory.
433 :     my $traceMode = "TEXT";
434 :     my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
435 :     if (open TESTTRACE, ">$traceFileName") {
436 :     $traceMode = "+>$traceFileName";
437 :     close TESTTRACE;
438 :     }
439 : parrello 1.31 # Now set up the tracing.
440 : parrello 1.40 TSetup($cats, $traceMode);
441 : parrello 1.36 # Check for the "h" option. If it is specified, dump the command-line
442 :     # options and exit the program.
443 :     if ($retOptions->{h}) {
444 :     $0 =~ m#[/\\](\w+)(\.pl)?$#i;
445 :     Trace("$1 [options] $parmHelp") if T(0);
446 :     for my $key (sort keys %{$options}) {
447 :     my $name = Pad($key, $longestName, 0, ' ');
448 :     my $desc = $options->{$key}->[1];
449 :     if ($options->{$key}->[0]) {
450 :     $desc .= " (default " . $options->{$key}->[0] . ")";
451 :     }
452 :     Trace(" $name $desc") if T(0);
453 :     }
454 :     exit(0);
455 :     }
456 : parrello 1.31 # Return the parsed parameters.
457 :     return ($retOptions, @retParameters);
458 :     }
459 :    
460 : parrello 1.11 =head3 Setups
461 :    
462 :     C<< my $count = Tracer::Setups(); >>
463 :    
464 :     Return the number of times L</TSetup> has been called.
465 :    
466 :     This method allows for the creation of conditional tracing setups where, for example, we
467 :     may want to set up tracing if nobody else has done it before us.
468 :    
469 :     =cut
470 :    
471 :     sub Setups {
472 : parrello 1.12 return $SetupCount;
473 : olson 1.1 }
474 :    
475 : parrello 1.10 =head3 Open
476 :    
477 :     C<< my $handle = Open($fileHandle, $fileSpec, $message); >>
478 :    
479 : parrello 1.11 Open a file.
480 : parrello 1.10
481 :     The I<$fileSpec> is essentially the second argument of the PERL C<open>
482 :     function. The mode is specified using Unix-like shell information. So, for
483 :     example,
484 :    
485 : parrello 1.12 Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
486 : parrello 1.10
487 :     would open for output appended to the specified file, and
488 :    
489 : parrello 1.12 Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
490 : parrello 1.10
491 :     would open a pipe that sorts the records written and removes duplicates. Note
492 : parrello 1.11 the use of file handle syntax in the Open call. To use anonymous file handles,
493 :     code as follows.
494 : parrello 1.10
495 : parrello 1.12 my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
496 : parrello 1.10
497 : parrello 1.11 The I<$message> parameter is used if the open fails. If it is set to C<0>, then
498 :     the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
499 :     failed open will throw an exception and the third parameter will be used to construct
500 :     an error message. If the parameter is omitted, a standard message is constructed
501 :     using the file spec.
502 : parrello 1.10
503 : parrello 1.12 Could not open "/usr/spool/news/twitlog"
504 : parrello 1.10
505 :     Note that the mode characters are automatically cleaned from the file name.
506 :     The actual error message from the file system will be captured and appended to the
507 :     message in any case.
508 :    
509 : parrello 1.12 Could not open "/usr/spool/news/twitlog": file not found.
510 : parrello 1.10
511 :     In some versions of PERL the only error message we get is a number, which
512 :     corresponds to the C++ C<errno> value.
513 :    
514 : parrello 1.12 Could not open "/usr/spool/news/twitlog": 6.
515 : parrello 1.10
516 :     =over 4
517 :    
518 :     =item fileHandle
519 :    
520 :     File handle. If this parameter is C<undef>, a file handle will be generated
521 :     and returned as the value of this method.
522 :    
523 :     =item fileSpec
524 :    
525 :     File name and mode, as per the PERL C<open> function.
526 :    
527 :     =item message (optional)
528 :    
529 :     Error message to use if the open fails. If omitted, a standard error message
530 :     will be generated. In either case, the error information from the file system
531 : parrello 1.11 is appended to the message. To specify a conditional open that does not throw
532 :     an error if it fails, use C<0>.
533 : parrello 1.10
534 :     =item RETURN
535 :    
536 : parrello 1.11 Returns the name of the file handle assigned to the file, or C<undef> if the
537 :     open failed.
538 : parrello 1.10
539 :     =back
540 :    
541 :     =cut
542 :    
543 :     sub Open {
544 : parrello 1.12 # Get the parameters.
545 :     my ($fileHandle, $fileSpec, $message) = @_;
546 :     # Attempt to open the file.
547 :     my $rv = open $fileHandle, $fileSpec;
548 :     # If the open failed, generate an error message.
549 :     if (! $rv) {
550 :     # Save the system error message.
551 :     my $sysMessage = $!;
552 :     # See if we need a default message.
553 :     if (!$message) {
554 :     # Clean any obvious mode characters and leading spaces from the
555 :     # filename.
556 :     my ($fileName) = FindNamePart($fileSpec);
557 :     $message = "Could not open \"$fileName\"";
558 :     }
559 :     # Terminate with an error using the supplied message and the
560 :     # error message from the file system.
561 :     Confess("$message: $!");
562 :     }
563 :     # Return the file handle.
564 :     return $fileHandle;
565 : parrello 1.10 }
566 :    
567 : parrello 1.11 =head3 FindNamePart
568 :    
569 :     C<< my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec); >>
570 :    
571 :     Extract the portion of a file specification that contains the file name.
572 :    
573 :     A file specification is the string passed to an C<open> call. It specifies the file
574 :     mode and name. In a truly complex situation, it can specify a pipe sequence. This
575 :     method assumes that the file name is whatever follows the first angle bracket
576 :     sequence. So, for example, in the following strings the file name is
577 :     C</usr/fig/myfile.txt>.
578 :    
579 :     >>/usr/fig/myfile.txt
580 :     </usr/fig/myfile.txt
581 :     | sort -u > /usr/fig/myfile.txt
582 :    
583 :     If the method cannot find a file name using its normal methods, it will return the
584 :     whole incoming string.
585 :    
586 :     =over 4
587 :    
588 :     =item fileSpec
589 :    
590 :     File specification string from which the file name is to be extracted.
591 :    
592 :     =item RETURN
593 :    
594 :     Returns a three-element list. The first element contains the file name portion of
595 :     the specified string, or the whole string if a file name cannot be found via normal
596 :     methods. The second element contains the start position of the file name portion and
597 :     the third element contains the length.
598 :    
599 :     =back
600 :    
601 :     =cut
602 :     #: Return Type $;
603 :     sub FindNamePart {
604 :     # Get the parameters.
605 :     my ($fileSpec) = @_;
606 : parrello 1.12 # Default to the whole input string.
607 :     my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
608 : parrello 1.11 # Parse out the file name if we can.
609 : parrello 1.12 if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
610 :     $retVal = $2;
611 :     $len = length $retVal;
612 :     $pos = (length $fileSpec) - (length $3) - $len;
613 :     }
614 : parrello 1.11 # Return the result.
615 :     return ($retVal, $pos, $len);
616 :     }
617 :    
618 :     =head3 OpenDir
619 :    
620 : parrello 1.31 C<< my @files = OpenDir($dirName, $filtered, $flag); >>
621 : parrello 1.11
622 :     Open a directory and return all the file names. This function essentially performs
623 :     the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
624 : parrello 1.31 set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
625 : parrello 1.33 or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
626 :     filtered out of the return list. If the directory does not open and I<$flag> is not
627 :     set, an exception is thrown. So, for example,
628 : parrello 1.11
629 : parrello 1.12 my @files = OpenDir("/Volumes/fig/contigs", 1);
630 : parrello 1.29
631 : parrello 1.11 is effectively the same as
632 :    
633 : parrello 1.12 opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
634 : parrello 1.33 my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
635 : parrello 1.11
636 :     Similarly, the following code
637 :    
638 : parrello 1.31 my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
639 : parrello 1.29
640 : parrello 1.11 Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
641 : parrello 1.31 automatically returns an empty list if the directory fails to open.
642 : parrello 1.11
643 :     =over 4
644 :    
645 :     =item dirName
646 :    
647 :     Name of the directory to open.
648 :    
649 :     =item filtered
650 :    
651 :     TRUE if files whose names begin with a period (C<.>) should be automatically removed
652 :     from the list, else FALSE.
653 :    
654 : parrello 1.31 =item flag
655 :    
656 :     TRUE if a failure to open is okay, else FALSE
657 :    
658 : parrello 1.11 =back
659 :    
660 :     =cut
661 :     #: Return Type @;
662 :     sub OpenDir {
663 :     # Get the parameters.
664 : parrello 1.31 my ($dirName, $filtered, $flag) = @_;
665 : parrello 1.11 # Declare the return variable.
666 : parrello 1.31 my @retVal = ();
667 : parrello 1.12 # Open the directory.
668 :     if (opendir(my $dirHandle, $dirName)) {
669 :     # The directory opened successfully. Get the appropriate list according to the
670 :     # strictures of the filter parameter.
671 :     if ($filtered) {
672 : parrello 1.33 @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
673 : parrello 1.12 } else {
674 :     @retVal = readdir $dirHandle;
675 :     }
676 : parrello 1.31 } elsif (! $flag) {
677 :     # Here the directory would not open and it's considered an error.
678 : parrello 1.12 Confess("Could not open directory $dirName.");
679 :     }
680 : parrello 1.11 # Return the result.
681 :     return @retVal;
682 :     }
683 :    
684 : parrello 1.6 =head3 SetLevel
685 :    
686 :     C<< Tracer::SetLevel($newLevel); >>
687 :    
688 :     Modify the trace level. A higher trace level will cause more messages to appear.
689 :    
690 :     =over 4
691 :    
692 :     =item newLevel
693 :    
694 :     Proposed new trace level.
695 :    
696 :     =back
697 :    
698 :     =cut
699 :    
700 :     sub SetLevel {
701 :     $TraceLevel = $_[0];
702 :     }
703 :    
704 : olson 1.1 =head3 Now
705 :    
706 :     C<< my $string = Tracer::Now(); >>
707 :    
708 :     Return a displayable time stamp containing the local time.
709 :    
710 :     =cut
711 :    
712 :     sub Now {
713 : parrello 1.12 my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
714 :     my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
715 :     _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
716 :     return $retVal;
717 : olson 1.1 }
718 :    
719 :     # Pad a number to 2 digits.
720 :     sub _p2 {
721 : parrello 1.12 my ($value) = @_;
722 :     $value = "0$value" if ($value < 10);
723 :     return $value;
724 : olson 1.1 }
725 :    
726 :     =head3 LogErrors
727 :    
728 :     C<< Tracer::LogErrors($fileName); >>
729 :    
730 :     Route the standard error output to a log file.
731 :    
732 :     =over 4
733 :    
734 :     =item fileName
735 :    
736 :     Name of the file to receive the error output.
737 :    
738 :     =back
739 :    
740 :     =cut
741 :    
742 :     sub LogErrors {
743 : parrello 1.12 # Get the file name.
744 :     my ($fileName) = @_;
745 :     # Open the file as the standard error output.
746 :     open STDERR, '>', $fileName;
747 : olson 1.1 }
748 :    
749 : parrello 1.5 =head3 ReadOptions
750 :    
751 :     C<< my %options = Tracer::ReadOptions($fileName); >>
752 :    
753 :     Read a set of options from a file. Each option is encoded in a line of text that has the
754 :     format
755 :    
756 :     I<optionName>C<=>I<optionValue>C<; >I<comment>
757 :    
758 :     The option name must consist entirely of letters, digits, and the punctuation characters
759 : parrello 1.9 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
760 :     character is a semi-colon will be ignored. The return hash will map each option name to
761 : parrello 1.5 the corresponding option value.
762 :    
763 :     =over 4
764 :    
765 :     =item fileName
766 :    
767 :     Name of the file containing the option data.
768 :    
769 :     =item RETURN
770 :    
771 :     Returns a hash mapping the option names specified in the file to their corresponding option
772 :     value.
773 :    
774 :     =back
775 :    
776 :     =cut
777 :    
778 :     sub ReadOptions {
779 : parrello 1.12 # Get the parameters.
780 :     my ($fileName) = @_;
781 :     # Open the file.
782 :     (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
783 :     # Count the number of records read.
784 :     my ($records, $comments) = 0;
785 :     # Create the return hash.
786 :     my %retVal = ();
787 :     # Loop through the file, accumulating key-value pairs.
788 :     while (my $line = <CONFIGFILE>) {
789 :     # Denote we've read a line.
790 :     $records++;
791 :     # Determine the line type.
792 :     if ($line =~ /^\s*[\n\r]/) {
793 :     # A blank line is a comment.
794 :     $comments++;
795 :     } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
796 :     # Here we have an option assignment.
797 :     retVal{$1} = $2;
798 :     } elsif ($line =~ /^\s*;/) {
799 :     # Here we have a text comment.
800 :     $comments++;
801 :     } else {
802 :     # Here we have an invalid line.
803 :     Trace("Invalid option statement in record $records.") if T(0);
804 :     }
805 :     }
806 :     # Return the hash created.
807 :     return %retVal;
808 : parrello 1.5 }
809 :    
810 : olson 1.1 =head3 GetOptions
811 :    
812 :     C<< Tracer::GetOptions(\%defaults, \%options); >>
813 :    
814 :     Merge a specified set of options into a table of defaults. This method takes two hash references
815 :     as input and uses the data from the second to update the first. If the second does not exist,
816 :     there will be no effect. An error will be thrown if one of the entries in the second hash does not
817 :     exist in the first.
818 :    
819 :     Consider the following example.
820 :    
821 :     C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>
822 :    
823 :     In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
824 :     B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
825 :     B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
826 :     the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
827 :     will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
828 :    
829 :     C<< {databaseType => 'Oracle'} >>
830 :    
831 :     an error will occur because the B<databaseType> option does not exist.
832 :    
833 :     =over 4
834 :    
835 :     =item defaults
836 :    
837 :     Table of default option values.
838 :    
839 :     =item options
840 :    
841 :     Table of overrides, if any.
842 :    
843 :     =item RETURN
844 :    
845 :     Returns a reference to the default table passed in as the first parameter.
846 :    
847 :     =back
848 :    
849 :     =cut
850 :    
851 :     sub GetOptions {
852 : parrello 1.12 # Get the parameters.
853 :     my ($defaults, $options) = @_;
854 :     # Check for overrides.
855 :     if ($options) {
856 :     # Loop through the overrides.
857 :     while (my ($option, $setting) = each %{$options}) {
858 :     # Insure this override exists.
859 :     if (!exists $defaults->{$option}) {
860 :     croak "Unrecognized option $option encountered.";
861 :     } else {
862 :     # Apply the override.
863 :     $defaults->{$option} = $setting;
864 :     }
865 :     }
866 :     }
867 :     # Return the merged table.
868 :     return $defaults;
869 : olson 1.1 }
870 :    
871 :     =head3 MergeOptions
872 :    
873 :     C<< Tracer::MergeOptions(\%table, \%defaults); >>
874 :    
875 :     Merge default values into a hash table. This method looks at the key-value pairs in the
876 :     second (default) hash, and if a matching key is not found in the first hash, the default
877 :     pair is copied in. The process is similar to L</GetOptions>, but there is no error-
878 :     checking and no return value.
879 :    
880 :     =over 4
881 :    
882 :     =item table
883 :    
884 :     Hash table to be updated with the default values.
885 :    
886 :     =item defaults
887 :    
888 :     Default values to be merged into the first hash table if they are not already present.
889 :    
890 :     =back
891 :    
892 :     =cut
893 :    
894 :     sub MergeOptions {
895 : parrello 1.12 # Get the parameters.
896 :     my ($table, $defaults) = @_;
897 :     # Loop through the defaults.
898 :     while (my ($key, $value) = each %{$defaults}) {
899 :     if (!exists $table->{$key}) {
900 :     $table->{$key} = $value;
901 :     }
902 :     }
903 : olson 1.1 }
904 :    
905 :     =head3 Trace
906 :    
907 :     C<< Trace($message); >>
908 :    
909 :     Write a trace message to the target location specified in L</TSetup>. If there has not been
910 :     any prior call to B<TSetup>.
911 :    
912 :     =over 4
913 :    
914 :     =item message
915 :    
916 :     Message to write.
917 :    
918 :     =back
919 :    
920 :     =cut
921 :    
922 :     sub Trace {
923 : parrello 1.12 # Get the parameters.
924 :     my ($message) = @_;
925 :     # Get the timestamp.
926 :     my $timeStamp = Now();
927 :     # Format the message. Note we strip off any line terminators at the end.
928 :     my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);
929 :     # Process according to the destination.
930 :     if ($Destination eq "TEXT") {
931 :     # Write the message to the standard output.
932 :     print "$formatted\n";
933 :     } elsif ($Destination eq "ERROR") {
934 :     # Write the message to the error output.
935 :     print STDERR "$formatted\n";
936 :     } elsif ($Destination eq "QUEUE") {
937 :     # Push the message into the queue.
938 :     push @Queue, "$formatted";
939 :     } elsif ($Destination eq "HTML") {
940 :     # Convert the message to HTML and write it to the standard output.
941 :     my $escapedMessage = CGI::escapeHTML($message);
942 :     print "<p>$formatted</p>\n";
943 : parrello 1.4 } elsif ($Destination eq "WARN") {
944 :     # Emit the message as a warning.
945 :     warn $message;
946 : parrello 1.12 } elsif ($Destination =~ m/^>>/) {
947 :     # Write the trace message to an output file.
948 : parrello 1.14 (open TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
949 : parrello 1.12 print TRACING "$formatted\n";
950 :     close TRACING;
951 :     # If the Tee flag is on, echo it to the standard output.
952 :     if ($TeeFlag) {
953 :     print "$formatted\n";
954 :     }
955 :     }
956 : olson 1.1 }
957 :    
958 :     =head3 T
959 :    
960 : parrello 1.2 C<< my $switch = T($category, $traceLevel); >>
961 : olson 1.1
962 : parrello 1.12 or
963 : parrello 1.2
964 : olson 1.1 C<< my $switch = T($traceLevel); >>
965 :    
966 :     Return TRUE if the trace level is at or above a specified value and the specified category
967 :     is active, else FALSE. If no category is specified, the caller's package name is used.
968 :    
969 :     =over 4
970 :    
971 :     =item category
972 :    
973 :     Category to which the message belongs. If not specified, the caller's package name is
974 :     used.
975 :    
976 :     =item traceLevel
977 :    
978 :     Relevant tracing level.
979 :    
980 :     =item RETURN
981 :    
982 :     TRUE if a message at the specified trace level would appear in the trace, else FALSE.
983 :    
984 :     =back
985 :    
986 :     =cut
987 :    
988 :     sub T {
989 : parrello 1.12 # Declare the return variable.
990 :     my $retVal = 0;
991 :     # Only proceed if tracing is turned on.
992 :     if ($Destination ne "NONE") {
993 :     # Get the parameters.
994 :     my ($category, $traceLevel) = @_;
995 :     if (!defined $traceLevel) {
996 :     # Here we have no category, so we need to get the calling package.
997 :     # The calling package is normally the first parameter. If it is
998 :     # omitted, the first parameter will be the tracelevel. So, the
999 :     # first thing we do is shift the so-called category into the
1000 :     # $traceLevel variable where it belongs.
1001 :     $traceLevel = $category;
1002 :     my ($package, $fileName, $line) = caller;
1003 : parrello 1.3 # If there is no calling package, we default to "main".
1004 : parrello 1.12 if (!$package) {
1005 : parrello 1.3 $category = "main";
1006 : parrello 1.12 } else {
1007 :     $category = $package;
1008 :     }
1009 :     }
1010 : parrello 1.7 # Save the category name.
1011 :     $LastCategory = $category;
1012 : parrello 1.13 # Convert it to lower case before we hash it.
1013 :     $category = lc $category;
1014 : parrello 1.12 # Use the category and tracelevel to compute the result.
1015 : parrello 1.36 if (ref $traceLevel) {
1016 :     Confess("Bad trace level.");
1017 :     } elsif (ref $TraceLevel) {
1018 :     Confess("Bad trace config.");
1019 :     }
1020 : parrello 1.12 $retVal = ($traceLevel <= $TraceLevel && ($AllTrace || exists $Categories{$category}));
1021 : parrello 1.3 }
1022 : parrello 1.12 # Return the computed result.
1023 : parrello 1.3 return $retVal;
1024 : olson 1.1 }
1025 :    
1026 :     =head3 ParseCommand
1027 :    
1028 :     C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>
1029 :    
1030 :     Parse a command line consisting of a list of parameters. The initial parameters may be option
1031 : parrello 1.2 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
1032 :     off and merged into a table of default options. The remainder of the command line is
1033 : olson 1.1 returned as a list of positional arguments. For example, consider the following invocation.
1034 :    
1035 :     C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>
1036 :    
1037 :     In this case, the list @words will be treated as a command line. There are two options available,
1038 :     B<errors> and B<logFile>. If @words has the following format
1039 :    
1040 :     C<< -logFile=error.log apple orange rutabaga >>
1041 :    
1042 :     then at the end of the invocation, C<$options> will be
1043 :    
1044 :     C<< { errors => 0, logFile => 'error.log' } >>
1045 :    
1046 :     and C<@arguments> will contain
1047 :    
1048 :     C<< apple orange rutabaga >>
1049 :    
1050 : parrello 1.2 The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
1051 : olson 1.1 support for quote characters.
1052 :    
1053 :     =over 4
1054 :    
1055 :     =item optionTable
1056 :    
1057 :     Table of default options.
1058 :    
1059 :     =item inputList
1060 :    
1061 :     List of words on the command line.
1062 :    
1063 :     =item RETURN
1064 :    
1065 :     Returns a reference to the option table and a list of the positional arguments.
1066 :    
1067 :     =back
1068 :    
1069 :     =cut
1070 :    
1071 :     sub ParseCommand {
1072 : parrello 1.12 # Get the parameters.
1073 :     my ($optionTable, @inputList) = @_;
1074 :     # Process any options in the input list.
1075 :     my %overrides = ();
1076 :     while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {
1077 :     # Get the current option.
1078 :     my $arg = shift @inputList;
1079 :     # Pull out the option name.
1080 :     $arg =~ /^-([^=]*)/g;
1081 :     my $name = $1;
1082 :     # Check for an option value.
1083 :     if ($arg =~ /\G=(.*)$/g) {
1084 :     # Here we have a value for the option.
1085 :     $overrides{$name} = UnEscape($1);
1086 :     } else {
1087 :     # Here there is no value, so we use 1.
1088 :     $overrides{$name} = 1;
1089 :     }
1090 :     }
1091 :     # Merge the options into the defaults.
1092 :     GetOptions($optionTable, \%overrides);
1093 :     # Translate the remaining parameters.
1094 :     my @retVal = ();
1095 :     for my $inputParm (@inputList) {
1096 :     push @retVal, UnEscape($inputParm);
1097 :     }
1098 :     # Return the results.
1099 :     return ($optionTable, @retVal);
1100 : olson 1.1 }
1101 :    
1102 : parrello 1.9 =head3 Escape
1103 :    
1104 :     C<< my $codedString = Tracer::Escape($realString); >>
1105 :    
1106 : parrello 1.25 Escape a string for use in a command length. Tabs will be replaced by C<\t>, new-lines
1107 : parrello 1.28 replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
1108 :     result is to reverse the effect of L</UnEscape>.
1109 : parrello 1.9
1110 :     =over 4
1111 :    
1112 :     =item realString
1113 :    
1114 :     String to escape.
1115 :    
1116 :     =item RETURN
1117 :    
1118 :     Escaped equivalent of the real string.
1119 :    
1120 :     =back
1121 :    
1122 :     =cut
1123 :    
1124 :     sub Escape {
1125 : parrello 1.12 # Get the parameter.
1126 :     my ($realString) = @_;
1127 :     # Initialize the return variable.
1128 :     my $retVal = "";
1129 :     # Loop through the parameter string, looking for sequences to escape.
1130 :     while (length $realString > 0) {
1131 :     # Look for the first sequence to escape.
1132 : parrello 1.27 if ($realString =~ /^(.*?)([\n\t\r\\])/) {
1133 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1134 :     # itself is in $2. First, move the clear text to the return variable.
1135 :     $retVal .= $1;
1136 : parrello 1.14 # Strip the processed section off the real string.
1137 :     $realString = substr $realString, (length $2) + (length $1);
1138 : parrello 1.28 # Get the matched character.
1139 : parrello 1.12 my $char = $2;
1140 : parrello 1.28 # If we have a CR, we are done.
1141 :     if ($char ne "\r") {
1142 :     # It's not a CR, so encode the escape sequence.
1143 :     $char =~ tr/\t\n/tn/;
1144 :     $retVal .= "\\" . $char;
1145 :     }
1146 : parrello 1.12 } else {
1147 :     # Here there are no more escape sequences. The rest of the string is
1148 :     # transferred unmodified.
1149 :     $retVal .= $realString;
1150 :     $realString = "";
1151 :     }
1152 :     }
1153 :     # Return the result.
1154 :     return $retVal;
1155 : parrello 1.9 }
1156 :    
1157 : olson 1.1 =head3 UnEscape
1158 :    
1159 :     C<< my $realString = Tracer::UnEscape($codedString); >>
1160 :    
1161 : parrello 1.25 Replace escape sequences with their actual equivalents. C<\t> will be replaced by
1162 : parrello 1.28 a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
1163 :     be deleted.
1164 : olson 1.1
1165 :     =over 4
1166 :    
1167 :     =item codedString
1168 :    
1169 :     String to un-escape.
1170 :    
1171 :     =item RETURN
1172 :    
1173 :     Returns a copy of the original string with the escape sequences converted to their actual
1174 :     values.
1175 :    
1176 :     =back
1177 :    
1178 :     =cut
1179 :    
1180 :     sub UnEscape {
1181 : parrello 1.12 # Get the parameter.
1182 :     my ($codedString) = @_;
1183 :     # Initialize the return variable.
1184 :     my $retVal = "";
1185 :     # Only proceed if the incoming string is nonempty.
1186 :     if (defined $codedString) {
1187 :     # Loop through the parameter string, looking for escape sequences. We can't do
1188 : parrello 1.25 # translating because it causes problems with the escaped slash. ("\\t" becomes
1189 :     # "\<tab>" no matter what we do.)
1190 : parrello 1.12 while (length $codedString > 0) {
1191 :     # Look for the first escape sequence.
1192 : parrello 1.27 if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
1193 : parrello 1.12 # Here we found it. The text preceding the sequence is in $1. The sequence
1194 :     # itself is in $2. First, move the clear text to the return variable.
1195 :     $retVal .= $1;
1196 :     $codedString = substr $codedString, (2 + length $1);
1197 : parrello 1.28 # Get the escape value.
1198 : parrello 1.12 my $char = $2;
1199 : parrello 1.28 # If we have a "\r", we are done.
1200 :     if ($char ne 'r') {
1201 :     # Here it's not an 'r', so we convert it.
1202 :     $char =~ tr/\\tn/\\\t\n/;
1203 :     $retVal .= $char;
1204 :     }
1205 : parrello 1.12 } else {
1206 :     # Here there are no more escape sequences. The rest of the string is
1207 :     # transferred unmodified.
1208 :     $retVal .= $codedString;
1209 :     $codedString = "";
1210 :     }
1211 :     }
1212 :     }
1213 :     # Return the result.
1214 :     return $retVal;
1215 : olson 1.1 }
1216 :    
1217 :     =head3 ParseRecord
1218 :    
1219 :     C<< my @fields = Tracer::ParseRecord($line); >>
1220 :    
1221 :     Parse a tab-delimited data line. The data line is split into field values. Embedded tab
1222 :     and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
1223 :     These will automatically be converted.
1224 :    
1225 :     =over 4
1226 :    
1227 :     =item line
1228 :    
1229 :     Line of data containing the tab-delimited fields.
1230 :    
1231 :     =item RETURN
1232 :    
1233 :     Returns a list of the fields found in the data line.
1234 :    
1235 :     =back
1236 :    
1237 :     =cut
1238 :    
1239 :     sub ParseRecord {
1240 : parrello 1.12 # Get the parameter.
1241 :     my ($line) = @_;
1242 :     # Remove the trailing new-line, if any.
1243 :     chomp $line;
1244 :     # Split the line read into pieces using the tab character.
1245 :     my @retVal = split /\t/, $line;
1246 :     # Trim and fix the escapes in each piece.
1247 :     for my $value (@retVal) {
1248 :     # Trim leading whitespace.
1249 :     $value =~ s/^\s+//;
1250 :     # Trim trailing whitespace.
1251 :     $value =~ s/\s+$//;
1252 :     # Delete the carriage returns.
1253 :     $value =~ s/\r//g;
1254 :     # Convert the escapes into their real values.
1255 :     $value =~ s/\\t/"\t"/ge;
1256 :     $value =~ s/\\n/"\n"/ge;
1257 :     }
1258 :     # Return the result.
1259 :     return @retVal;
1260 : olson 1.1 }
1261 :    
1262 :     =head3 Merge
1263 :    
1264 :     C<< my @mergedList = Tracer::Merge(@inputList); >>
1265 :    
1266 :     Sort a list of strings and remove duplicates.
1267 :    
1268 :     =over 4
1269 :    
1270 :     =item inputList
1271 :    
1272 :     List of scalars to sort and merge.
1273 :    
1274 :     =item RETURN
1275 :    
1276 :     Returns a list containing the same elements sorted in ascending order with duplicates
1277 :     removed.
1278 :    
1279 :     =back
1280 :    
1281 :     =cut
1282 :    
1283 :     sub Merge {
1284 : parrello 1.12 # Get the input list in sort order.
1285 :     my @inputList = sort @_;
1286 :     # Only proceed if the list has at least two elements.
1287 :     if (@inputList > 1) {
1288 :     # Now we want to move through the list splicing out duplicates.
1289 :     my $i = 0;
1290 :     while ($i < @inputList) {
1291 :     # Get the current entry.
1292 :     my $thisEntry = $inputList[$i];
1293 :     # Find out how many elements duplicate the current entry.
1294 :     my $j = $i + 1;
1295 :     my $dup1 = $i + 1;
1296 :     while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
1297 :     # If the number is nonzero, splice out the duplicates found.
1298 :     if ($j > $dup1) {
1299 :     splice @inputList, $dup1, $j - $dup1;
1300 :     }
1301 :     # Now the element at position $dup1 is different from the element before it
1302 :     # at position $i. We push $i forward one position and start again.
1303 :     $i++;
1304 :     }
1305 :     }
1306 :     # Return the merged list.
1307 :     return @inputList;
1308 : olson 1.1 }
1309 :    
1310 :     =head3 GetFile
1311 :    
1312 : parrello 1.6 C<< my @fileContents = Tracer::GetFile($fileName); >>
1313 : olson 1.1
1314 : parrello 1.35 or
1315 :    
1316 :     C<< my $fileContents = Tracer::GetFile($fileName); >>
1317 :    
1318 :     Return the entire contents of a file. In list context, line-ends are removed and
1319 :     each line is a list element. In scalar context, line-ends are replaced by C<\n>.
1320 : olson 1.1
1321 :     =over 4
1322 :    
1323 :     =item fileName
1324 :    
1325 :     Name of the file to read.
1326 :    
1327 :     =item RETURN
1328 :    
1329 : parrello 1.6 In a list context, returns the entire file as a list with the line terminators removed.
1330 : parrello 1.39 In a scalar context, returns the entire file as a string. If an error occurs opening
1331 :     the file, an empty list will be returned.
1332 : olson 1.1
1333 :     =back
1334 :    
1335 :     =cut
1336 :    
1337 :     sub GetFile {
1338 : parrello 1.12 # Get the parameters.
1339 :     my ($fileName) = @_;
1340 :     # Declare the return variable.
1341 :     my @retVal = ();
1342 :     # Open the file for input.
1343 :     my $ok = open INPUTFILE, "<$fileName";
1344 :     if (!$ok) {
1345 :     # If we had an error, trace it. We will automatically return a null value.
1346 : parrello 1.16 Trace("Could not open \"$fileName\" for input: $!") if T(0);
1347 : parrello 1.12 } else {
1348 :     # Read the whole file into the return variable, stripping off any terminator
1349 : parrello 1.6 # characters.
1350 :     my $lineCount = 0;
1351 : parrello 1.12 while (my $line = <INPUTFILE>) {
1352 : parrello 1.6 $lineCount++;
1353 : parrello 1.9 $line = Strip($line);
1354 : parrello 1.12 push @retVal, $line;
1355 :     }
1356 :     # Close it.
1357 :     close INPUTFILE;
1358 : parrello 1.6 my $actualLines = @retVal;
1359 : parrello 1.12 }
1360 :     # Return the file's contents in the desired format.
1361 : parrello 1.9 if (wantarray) {
1362 : parrello 1.12 return @retVal;
1363 : parrello 1.6 } else {
1364 :     return join "\n", @retVal;
1365 :     }
1366 : olson 1.1 }
1367 :    
1368 :     =head3 QTrace
1369 :    
1370 :     C<< my $data = QTrace($format); >>
1371 :    
1372 :     Return the queued trace data in the specified format.
1373 :    
1374 :     =over 4
1375 :    
1376 :     =item format
1377 :    
1378 :     C<html> to format the data as an HTML list, C<text> to format it as straight text.
1379 :    
1380 :     =back
1381 :    
1382 :     =cut
1383 :    
1384 :     sub QTrace {
1385 : parrello 1.12 # Get the parameter.
1386 :     my ($format) = @_;
1387 :     # Create the return variable.
1388 :     my $retVal = "";
1389 : parrello 1.14 # Only proceed if there is an actual queue.
1390 :     if (@Queue) {
1391 :     # Process according to the format.
1392 :     if ($format =~ m/^HTML$/i) {
1393 :     # Convert the queue into an HTML list.
1394 :     $retVal = "<ul>\n";
1395 :     for my $line (@Queue) {
1396 :     my $escapedLine = CGI::escapeHTML($line);
1397 :     $retVal .= "<li>$escapedLine</li>\n";
1398 :     }
1399 :     $retVal .= "</ul>\n";
1400 :     } elsif ($format =~ m/^TEXT$/i) {
1401 :     # Convert the queue into a list of text lines.
1402 :     $retVal = join("\n", @Queue) . "\n";
1403 :     }
1404 :     # Clear the queue.
1405 :     @Queue = ();
1406 : parrello 1.12 }
1407 :     # Return the formatted list.
1408 :     return $retVal;
1409 : olson 1.1 }
1410 :    
1411 :     =head3 Confess
1412 :    
1413 :     C<< Confess($message); >>
1414 :    
1415 : parrello 1.22 Trace the call stack and abort the program with the specified message. When used with
1416 : parrello 1.9 the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
1417 : parrello 1.6 So, for example
1418 : olson 1.1
1419 : parrello 1.6 C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1420 : olson 1.1
1421 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1422 :    
1423 :     =over 4
1424 :    
1425 :     =item message
1426 :    
1427 :     Message to include in the trace.
1428 :    
1429 :     =back
1430 :    
1431 :     =cut
1432 :    
1433 :     sub Confess {
1434 : parrello 1.12 # Get the parameters.
1435 :     my ($message) = @_;
1436 :     # Trace the call stack.
1437 : parrello 1.22 Cluck($message);
1438 : parrello 1.12 # Abort the program.
1439 :     croak(">>> $message");
1440 : olson 1.1 }
1441 :    
1442 : parrello 1.6 =head3 Assert
1443 :    
1444 :     C<< Assert($condition1, $condition2, ... $conditionN); >>
1445 :    
1446 :     Return TRUE if all the conditions are true. This method can be used in conjunction with
1447 : parrello 1.29 the OR operator and the L</Confess> method as a debugging assert.
1448 : parrello 1.6 So, for example
1449 :    
1450 :     C<< Assert($recNum >= 0) || Confess("Invalid record number $recNum."); >>
1451 :    
1452 :     Will abort the program with a stack trace if the value of C<$recNum> is negative.
1453 :    
1454 :     =cut
1455 :     sub Assert {
1456 :     my $retVal = 1;
1457 :     LOOP: for my $condition (@_) {
1458 :     if (! $condition) {
1459 :     $retVal = 0;
1460 :     last LOOP;
1461 :     }
1462 :     }
1463 :     return $retVal;
1464 :     }
1465 :    
1466 : olson 1.1 =head3 Cluck
1467 :    
1468 :     C<< Cluck($message); >>
1469 :    
1470 :     Trace the call stack. Note that for best results, you should qualify the call with a
1471 :     trace condition. For example,
1472 :    
1473 :     C<< Cluck("Starting record parse.") if T(3); >>
1474 :    
1475 :     will only trace the stack if the trace level for the package is 3 or more.
1476 :    
1477 :     =over 4
1478 :    
1479 :     =item message
1480 :    
1481 :     Message to include in the trace.
1482 :    
1483 :     =back
1484 :    
1485 :     =cut
1486 :    
1487 :     sub Cluck {
1488 : parrello 1.12 # Get the parameters.
1489 :     my ($message) = @_;
1490 : parrello 1.5 # Trace what's happening.
1491 :     Trace("Stack trace for event: $message");
1492 : parrello 1.12 my $confession = longmess($message);
1493 :     # Convert the confession to a series of trace messages. Note we skip any
1494 : parrello 1.5 # messages relating to calls into Tracer.
1495 : parrello 1.12 for my $line (split /\s*\n/, $confession) {
1496 :     Trace($line) if ($line !~ /Tracer\.pm/);
1497 :     }
1498 : olson 1.1 }
1499 :    
1500 : parrello 1.5 =head3 Min
1501 :    
1502 :     C<< my $min = Min($value1, $value2, ... $valueN); >>
1503 :    
1504 :     Return the minimum argument. The arguments are treated as numbers.
1505 :    
1506 :     =over 4
1507 :    
1508 :     =item $value1, $value2, ... $valueN
1509 :    
1510 :     List of numbers to compare.
1511 :    
1512 :     =item RETURN
1513 :    
1514 :     Returns the lowest number in the list.
1515 :    
1516 :     =back
1517 :    
1518 :     =cut
1519 :    
1520 :     sub Min {
1521 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1522 :     my ($retVal, @values) = @_;
1523 :     # Loop through the remaining parameters, looking for the lowest.
1524 :     for my $value (@values) {
1525 :     if ($value < $retVal) {
1526 :     $retVal = $value;
1527 :     }
1528 :     }
1529 :     # Return the minimum found.
1530 :     return $retVal;
1531 : parrello 1.5 }
1532 :    
1533 :     =head3 Max
1534 :    
1535 :     C<< my $max = Max($value1, $value2, ... $valueN); >>
1536 :    
1537 :     Return the maximum argument. The arguments are treated as numbers.
1538 :    
1539 :     =over 4
1540 :    
1541 :     =item $value1, $value2, ... $valueN
1542 :    
1543 :     List of numbers to compare.
1544 :    
1545 :     =item RETURN
1546 :    
1547 :     Returns the highest number in the list.
1548 :    
1549 :     =back
1550 :    
1551 :     =cut
1552 :    
1553 :     sub Max {
1554 : parrello 1.12 # Get the parameters. Note that we prime the return value with the first parameter.
1555 :     my ($retVal, @values) = @_;
1556 :     # Loop through the remaining parameters, looking for the highest.
1557 :     for my $value (@values) {
1558 :     if ($value > $retVal) {
1559 :     $retVal = $value;
1560 :     }
1561 :     }
1562 :     # Return the maximum found.
1563 :     return $retVal;
1564 : parrello 1.5 }
1565 :    
1566 :     =head3 AddToListMap
1567 :    
1568 :     C<< Tracer::AddToListMap(\%hash, $key, $value); >>
1569 :    
1570 :     Add a key-value pair to a hash of lists. If no value exists for the key, a singleton list
1571 :     is created for the key. Otherwise, the new value is pushed onto the list.
1572 :    
1573 :     =over 4
1574 :    
1575 :     =item hash
1576 :    
1577 :     Reference to the target hash.
1578 :    
1579 :     =item key
1580 :    
1581 :     Key for which the value is to be added.
1582 :    
1583 :     =item value
1584 :    
1585 :     Value to add to the key's value list.
1586 :    
1587 :     =back
1588 :    
1589 :     =cut
1590 :    
1591 :     sub AddToListMap {
1592 :     # Get the parameters.
1593 :     my ($hash, $key, $value) = @_;
1594 :     # Process according to whether or not the key already has a value.
1595 :     if (! exists $hash->{$key}) {
1596 :     $hash->{$key} = [$value];
1597 :     } else {
1598 :     push @{$hash->{$key}}, $value;
1599 :     }
1600 :     }
1601 : olson 1.1
1602 : parrello 1.7 =head3 DebugMode
1603 :    
1604 :     C<< if (Tracer::DebugMode) { ...code... } >>
1605 :    
1606 : parrello 1.22 Return TRUE if debug mode has been turned on, else output an error
1607 :     page and return FALSE.
1608 : parrello 1.7
1609 :     Certain CGI scripts are too dangerous to exist in the production
1610 :     environment. This method provides a simple way to prevent them
1611 : parrello 1.21 from working unless they are explicitly turned on by creating a password
1612 :     cookie via the B<SetPassword> script. If debugging mode
1613 : parrello 1.22 is not turned on, an error web page will be output directing the
1614 :     user to enter in the correct password.
1615 : parrello 1.7
1616 :     =cut
1617 :    
1618 :     sub DebugMode {
1619 : parrello 1.12 # Declare the return variable.
1620 : parrello 1.21 my $retVal = 0;
1621 : parrello 1.12 # Check the debug configuration.
1622 : parrello 1.21 my $password = CGI::cookie("DebugMode");
1623 :     my $encrypted = Digest::MD5::md5_hex($password);
1624 :     if ($encrypted eq "252dec43280e0c0d6a75ffcec486e61d") {
1625 : parrello 1.12 $retVal = 1;
1626 :     } else {
1627 :     # Here debug mode is off, so we generate an error page.
1628 : parrello 1.9 my $pageString = PageBuilder::Build("<Html/ErrorPage.html", {}, "Html");
1629 : parrello 1.12 print $pageString;
1630 :     }
1631 :     # Return the determination indicator.
1632 : parrello 1.18 return $retVal;
1633 : parrello 1.9 }
1634 :    
1635 :     =head3 Strip
1636 :    
1637 :     C<< my $string = Tracer::Strip($line); >>
1638 :    
1639 :     Strip all line terminators off a string. This is necessary when dealing with files
1640 :     that may have been transferred back and forth several times among different
1641 :     operating environments.
1642 :    
1643 :     =over 4
1644 :    
1645 :     =item line
1646 :    
1647 :     Line of text to be stripped.
1648 :    
1649 :     =item RETURN
1650 :    
1651 :     The same line of text with all the line-ending characters chopped from the end.
1652 :    
1653 :     =back
1654 :    
1655 :     =cut
1656 :    
1657 :     sub Strip {
1658 : parrello 1.12 # Get a copy of the parameter string.
1659 :     my ($string) = @_;
1660 : parrello 1.29 my $retVal = (defined $string ? $string : "");
1661 : parrello 1.9 # Strip the line terminator characters.
1662 :     $retVal =~ s/(\r|\n)+$//g;
1663 : parrello 1.12 # Return the result.
1664 :     return $retVal;
1665 : parrello 1.9 }
1666 :    
1667 :     =head3 Pad
1668 :    
1669 :     C<< my $paddedString = Tracer::Pad($string, $len, $left, $padChar); >>
1670 :    
1671 :     Pad a string to a specified length. The pad character will be a
1672 :     space, and the padding will be on the right side unless specified
1673 :     in the third parameter.
1674 :    
1675 :     =over 4
1676 :    
1677 :     =item string
1678 :    
1679 :     String to be padded.
1680 :    
1681 :     =item len
1682 :    
1683 :     Desired length of the padded string.
1684 :    
1685 :     =item left (optional)
1686 :    
1687 :     TRUE if the string is to be left-padded; otherwise it will be padded on the right.
1688 :    
1689 :     =item padChar (optional)
1690 :    
1691 : parrello 1.22 Character to use for padding. The default is a space.
1692 :    
1693 : parrello 1.9 =item RETURN
1694 :    
1695 : parrello 1.22 Returns a copy of the original string with the pad character added to the
1696 :     specified end so that it achieves the desired length.
1697 : parrello 1.9
1698 :     =back
1699 :    
1700 :     =cut
1701 :    
1702 :     sub Pad {
1703 : parrello 1.12 # Get the parameters.
1704 :     my ($string, $len, $left, $padChar) = @_;
1705 :     # Compute the padding character.
1706 :     if (! defined $padChar) {
1707 :     $padChar = " ";
1708 :     }
1709 :     # Compute the number of spaces needed.
1710 :     my $needed = $len - length $string;
1711 :     # Copy the string into the return variable.
1712 :     my $retVal = $string;
1713 :     # Only proceed if padding is needed.
1714 :     if ($needed > 0) {
1715 :     # Create the pad string.
1716 :     my $pad = $padChar x $needed;
1717 :     # Affix it to the return value.
1718 :     if ($left) {
1719 :     $retVal = $pad . $retVal;
1720 :     } else {
1721 :     $retVal .= $pad;
1722 :     }
1723 :     }
1724 :     # Return the result.
1725 :     return $retVal;
1726 : parrello 1.7 }
1727 :    
1728 : parrello 1.29 =head3 EOF
1729 :    
1730 :     This is a constant that is lexically greater than any useful string.
1731 :    
1732 :     =cut
1733 :    
1734 :     sub EOF {
1735 :     return "\xFF\xFF\xFF\xFF\xFF";
1736 :     }
1737 :    
1738 : parrello 1.15 =head3 TICK
1739 :    
1740 :     C<< my @results = TICK($commandString); >>
1741 :    
1742 :     Perform a back-tick operation on a command. If this is a Windows environment, any leading
1743 :     dot-slash (C<./> will be removed. So, for example, if you were doing
1744 :    
1745 :     `./protein.cgi`
1746 :    
1747 :     from inside a CGI script, it would work fine in Unix, but would issue an error message
1748 :     in Windows complaining that C<'.'> is not a valid command. If instead you code
1749 :    
1750 :     TICK("./protein.cgi")
1751 :    
1752 :     it will work correctly in both environments.
1753 :    
1754 :     =over 4
1755 :    
1756 :     =item commandString
1757 :    
1758 :     The command string to pass to the system.
1759 :    
1760 :     =item RETURN
1761 :    
1762 :     Returns the standard output from the specified command, as a list.
1763 :    
1764 :     =back
1765 :    
1766 :     =cut
1767 :     #: Return Type @;
1768 :     sub TICK {
1769 :     # Get the parameters.
1770 :     my ($commandString) = @_;
1771 :     # Chop off the dot-slash if this is Windows.
1772 :     if ($FIG_Config::win_mode) {
1773 :     $commandString =~ s!^\./!!;
1774 :     }
1775 :     # Activate the command and return the result.
1776 :     return `$commandString`;
1777 :     }
1778 :    
1779 : parrello 1.35 =head3 ScriptSetup
1780 :    
1781 :     C<< my ($query, $varHash) = ScriptSetup(); >>
1782 :    
1783 :     Perform standard tracing and debugging setup for scripts. The value returned is
1784 :     the CGI object followed by a pre-built variable hash.
1785 :    
1786 :     The C<Trace> query parameter is used to determine whether or not tracing is active and
1787 :     which trace modules (other than C<Tracer> and C<FIG>) should be turned on. Specifying
1788 :     the C<CGI> trace module will trace parameter and environment information. Parameters are
1789 :     traced at level 3 and environment variables at level 4. At the end of the script, the
1790 :     client should call L</ScriptFinish> to output the web page.
1791 :    
1792 :     =cut
1793 :    
1794 :     sub ScriptSetup {
1795 :     # Get the CGI query object.
1796 :     my $query = CGI->new();
1797 :     # Check for tracing. Set it up if the user asked for it.
1798 :     if ($query->param('Trace')) {
1799 :     # Set up tracing to be queued for display at the bottom of the web page.
1800 :     TSetup($query->param('Trace') . " FIG Tracer", "QUEUE");
1801 :     # Trace the parameter and environment data.
1802 :     if (T(CGI => 3)) {
1803 :     # Here we want to trace the parameter data.
1804 :     my @names = $query->param;
1805 :     for my $parmName (sort @names) {
1806 :     # Note we skip "Trace", which is for our use only.
1807 :     if ($parmName ne 'Trace') {
1808 :     my @values = $query->param($parmName);
1809 :     Trace("CGI: $parmName = " . join(", ", @values));
1810 :     }
1811 :     }
1812 :     }
1813 :     if (T(CGI => 4)) {
1814 :     # Here we want the environment data too.
1815 :     for my $envName (sort keys %ENV) {
1816 :     Trace("ENV: $envName = $ENV{$envName}");
1817 :     }
1818 :     }
1819 :     } else {
1820 :     # Here tracing is to be turned off. All we allow is errors traced into the
1821 :     # error log.
1822 :     TSetup("0", "WARN");
1823 :     }
1824 :     # Create the variable hash.
1825 :     my $varHash = { DebugData => '' };
1826 :     # If we're in DEBUG mode, set up the debug mode data for forms.
1827 :     if (Tracer::DebugMode) {
1828 :     $varHash->{DebugData} = GetFile("Html/DebugFragment.html");
1829 :     }
1830 :     # Return the query object and variable hash.
1831 :     return ($query, $varHash);
1832 :     }
1833 :    
1834 :     =head3 ScriptFinish
1835 :    
1836 :     C<< ScriptFinish($webData, $varHash); >>
1837 :    
1838 :     Output a web page at the end of a script. Either the string to be output or the
1839 :     name of a template file can be specified. If the second parameter is omitted,
1840 :     it is assumed we have a string to be output; otherwise, it is assumed we have the
1841 :     name of a template file. The template should have the variable C<DebugData>
1842 :     specified in any form that invokes a standard script. If debugging mode is turned
1843 :     on, a form field will be put in that allows the user to enter tracing data.
1844 :     Trace messages will be placed immediately before the terminal C<BODY> tag in
1845 :     the output, formatted as a list.
1846 :    
1847 :     A typical standard script would loook like the following.
1848 :    
1849 :     BEGIN {
1850 :     # Print the HTML header.
1851 :     print "CONTENT-TYPE: text/html\n\n";
1852 :     }
1853 :     use Tracer;
1854 :     use CGI;
1855 :     use FIG;
1856 :     # ... more uses ...
1857 :    
1858 :     my ($query, $varHash) = ScriptSetup();
1859 :     eval {
1860 :     # ... get data from $query, put it in $varHash ...
1861 :     };
1862 :     if ($@) {
1863 :     Trace("Script Error: $@") if T(0);
1864 :     }
1865 :     ScriptFinish("Html/MyTemplate.html", $varHash);
1866 :    
1867 :     The idea here is that even if the script fails, you'll see trace messages and
1868 :     useful output.
1869 :    
1870 :     =over 4
1871 :    
1872 :     =item webData
1873 :    
1874 :     A string containing either the full web page to be written to the output or the
1875 :     name of a template file from which the page is to be constructed. If the name
1876 :     of a template file is specified, then the second parameter must be present;
1877 :     otherwise, it must be absent.
1878 :    
1879 :     =item varHash (optional)
1880 :    
1881 :     If specified, then a reference to a hash mapping variable names for a template
1882 :     to their values. The template file will be read into memory, and variable markers
1883 :     will be replaced by data in this hash reference.
1884 :    
1885 : parrello 1.37 =back
1886 :    
1887 : parrello 1.35 =cut
1888 :    
1889 :     sub ScriptFinish {
1890 :     # Get the parameters.
1891 :     my ($webData, $varHash) = @_;
1892 :     # Check for a template file situation.
1893 :     my $outputString;
1894 :     if (defined $varHash) {
1895 :     # Here we have a template file. We need to apply the variables to the template.
1896 :     $outputString = PageBuilder::Build("<$webData", $varHash, "Html");
1897 :     } else {
1898 :     # Here the user gave us a raw string.
1899 :     $outputString = $webData;
1900 :     }
1901 :     # Check for trace messages.
1902 :     if ($Destination eq "QUEUE") {
1903 :     # We have trace messages, so we want to put them at the end of the body. This
1904 :     # is either at the end of the whole string or at the beginning of the BODY
1905 :     # end-tag.
1906 :     my $pos = length $outputString;
1907 :     if ($outputString =~ m#</body>#gi) {
1908 :     $pos = (pos $outputString) - 7;
1909 :     }
1910 :     substr $outputString, $pos, 0, QTrace('Html');
1911 :     }
1912 :     # Write the output string.
1913 :     print $outputString;
1914 :     }
1915 :    
1916 : parrello 1.37 =head3 Insure
1917 :    
1918 :     C<< Insure($dirName); >>
1919 :    
1920 :     Insure a directory is present.
1921 :    
1922 :     =over 4
1923 :    
1924 :     =item dirName
1925 :    
1926 :     Name of the directory to check. If it does not exist, it will be created.
1927 :    
1928 :     =back
1929 :    
1930 :     =cut
1931 :    
1932 :     sub Insure {
1933 :     my ($dirName) = @_;
1934 :     if (! -d $dirName) {
1935 :     Trace("Creating $dirName directory.") if T(2);
1936 :     mkpath $dirName;
1937 :     }
1938 :     }
1939 :    
1940 : redwards 1.8 1;

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